Transfer RNA fragments (tRFs) have gene silencing effects similarly to miRNAs, can be sorted into extracellular vesicles (EVs) and are emerging as potential circulating biomarkers for cancer diagnosis. We aimed at analyzing the expression of tRFs in gastric cancer (GC) and understanding their potential as biomarkers. We explored miRNA datasets from gastric tumors and normal adjacent tissues (NAT) from TCGA repository, and proprietary 3D-cultured GC cell lines and corresponding EVs, in order to identify differentially represented tRFs using MINTmap and R/Bioconductor packages. Selected tRFs were validated in patient-derived EVs. We found 613 Differentially Expressed (DE)-tRFs in the TCGA dataset, of which 19 were concomitantly upregulated in TCGA gastric tumors and present in 3D-cells and EVs, but barely expressed in NAT. Moreover, 20 tRFs were expressed in 3D-cells and EVs and downregulated in TCGA gastric tumors. Of these 39 DE-tRFs, 9 tRFs were also detected in patient-derived EVs. Interestingly, the targets of these 9 tRFs affect neutrophil activation and degranulation, cadherin binding, focal adhesion and cell-substrate junction, highlighting these pathways as major targets of EV-mediated crosstalk with the tumor microenvironment. Furthermore, as they are present in four distinct GC datasets and can be detected even in low quality patient-EV derived samples, they hold promise as GC biomarkers. By repurposing already available NGS data, we could identify and cross-validate a set of tRFs holding potential as GC diagnosis biomarkers.

Next-generation sequencing (NGS) has been a widely-used technology in biomedical research for understanding the role of molecular genetics of cells in health and disease. A variety of computational tools have been developed to analyse the vastly growing NGS data, which often require bioinformatics skills, tedious work and significant amount of time. To facilitate data processing steps minding the gap between biologists and bioinformaticians, we developed CSI NGS Portal, an online platform which gathers established bioinformatics pipelines to provide fully automated NGS data analysis and sharing in a user-friendly website. The portal currently provides 16 standard pipelines for analysing data from DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, Bisulfite and scRNA sequencing, and is flexible to expand with new pipelines. The users can upload raw data in fastq format and submit jobs in a few clicks, and the results will be self-accessible via the portal to view/download/share in real-time. The output can be readily used as the final report or as input for other tools depending on the pipeline. Overall, CSI NGS Portal helps researchers rapidly analyse their NGS data and share results with colleagues without the aid of a bioinformatician. The portal is freely available at: https://csibioinfo.nus.edu.sg/csingsportal

Segment Anything Model 2 (SAM 2) is a state-of-the-art development by Meta AI Research, designed to address the limitations of its predecessor, SAM, particularly in the realm of video segmentation. SAM 2 employs a transformer-based architecture enhanced with streaming memory, enabling real-time processing for both images and videos. This advancement is important given the exponential growth of multimedia content and the subsequent demand for efficient video analysis. Utilizing the SA-V dataset, SAM 2 excels in handling the intricate spatio-temporal dynamics inherent in video data, ensuring accurate and efficient segmentation. Key features of SAM 2 include its ability to provide real-time segmentation with minimal user interaction, maintaining robust performance even in dynamic and cluttered visual environments. This study provides a comprehensive overview of SAM 2, detailing its architecture, functionality, and diverse applications. It further explores the model's potential in improving practical implementations across various domains, emphasizing its significance in advancing real-time video analysis.

Laser-targeted weeding methods further enhance the sustainable development of green agriculture, with one key technology being the improvement of weed localization accuracy. Here, we propose an improved YOLOv8 instance segmentation based on bidirectional feature fusion and deformable convolution (BFFDC-YOLOv8-seg) to address the challenges of insufficient weed localization accuracy in complex environments with resource-limited laser weeding devices. Initially, by training on extensive datasets of plant images, the most appropriate model scale and training weights are determined, facilitating the development of a lightweight network. Subsequently, the introduction of the Bidirectional Feature Pyramid Network (BiFPN) during feature fusion effectively prevents the omission of weeds. Lastly, the use of Dynamic Snake Convolution (DSConv) to replace some convolutional kernels enhances flexibility, benefiting the segmentation of weeds with elongated stems and irregular edges. Experimental results indicate that the BFFDC-YOLOv8-seg model achieves a 4.9% increase in precision, an 8.1% increase in recall rate, and a 2.8% increase in mAP50 value to 98.8% on a vegetable weed dataset compared to the original model. It also shows improved mAP50 over other typical segmentation models such as Mask R-CNN, YOLOv5-seg, and YOLOv7-seg by 10.8%, 13.4%, and 1.8%, respectively. Furthermore, the model achieves a detection speed of 24.8 FPS on the Jetson Orin nano standalone device, with a model size of 6.8MB that balances between size and accuracy. The model meets the requirements for real-time precise weed segmentation, suitable for complex vegetable field environments and resource-limited laser weeding devices.

Selecting road networks in cartographic generalization has consistently posed formidable challenges, driving research towards the application of intelligent models. Despite previous efforts, the accuracy and connectivity preservation in these studies, particularly when dealing with road types of similar sample sizes, still warrant improvement. To address these shortcomings, we introduce a Heterogeneous Graph Attention Network (HAN) for road selection, where feature masking method is initially utilized to assess the significance of road features. Concentrating on the most relevant features, two meta-paths are introduced within the HAN framework: one for aggregating features of the same road type within the first-order neighborhood, emphasizing local connectivity, and another extending this aggregation to the second-order neighborhood, capturing a broader spatial context. For a comprehensive evaluation, we introduce a set of metrics considering both quantitative and qualitative aspects of the road network. Compared to traditional neural networks, our HAN model demonstrates superior accuracy and F1-score, particularly for road types with comparable samples. Additionally, it enhances the overall connectivity of the selected network. In summary, our HAN-based method provides an advanced solution for road network selection, surpassing previous approaches in terms of accuracy and connectivity preservation.

Next-generation sequencing is now a mature technology, allowing partial animal genomes to be produced for many clades. Though many software exist for genome assembly and annotation, a simple pipeline that allows researchers to input raw sequencing reads in fastq format and allow the retrieval of a completely assembled and annotated mitochondrial genome is still missing. mitoMaker 1.0 is a pipeline developed in python that implements (i) recursive de novo assembly of mitochondrial genomes using a set of increasing k-mers; (ii) search for the best matching result to a target mitogenome and; (iii) performs iterative reference-based strategies to optimize the assembly. After (iv) checking for circularization and (v) positioning tRNA-Phe at the beginning, (vi) geneChecker.py module performs a complete annotation of the mitochondrial genome and provides a GenBank formatted file as output.

The key links of face recognition are digital image preprocessing, facial feature extraction and pattern recognition, this article aimed at the current problem of slow speed and low recognition accuracy of face recognition , from the above three key links, on the basic of analyzing the therories of Fractional Differential Masks Operator (FDMO), Principal Component Analysis (PCA) and Support Vector Machine (SVM), design a kind of FDMO+PVA+SVM coupling algorithm that applies to face recognition to improve the speed and accuracy of it. To realize FDMO+PCA+SVM coupling algorithm, first, we should apply FDMO to face image processing binary marginalization, the purpose is getting face contour; Then, we apply PCA to get the feature of face image which is disposed by binary marainalization. At last, we can apply One-Against All of the SVM classifier and LibSVM software package to realize face recognition. Beside, the article with nine different coupling algorithm design four groups of experimental reaults on the ORL face database verified by comparative analysic FDMO+PCA+SVM coupling algorithm in the superiority of face recognition accuracy and speed.

The emerging working mode of coordinated trucks and drones has demonstrated significant practical potential in various fields, including logistics and delivery, intelligence surveillance reconnaissance, area monitoring, and patrol. The seamless collaboration between trucks and drones is garnering widespread attention in academia and has emerged as a key technology for achieving efficient and secure transportation. This paper provides a comprehensive and in-depth review of the research status on the routing problem for coordinated trucks and drones, covering aspects such as application background, cooperative modes, configurations, issues have been taken into consideration, and solution methodologies.

Users with Autism Spectrum Disorder may find human-computer interaction (HCI) challenging due to a number of symptoms experienced, one of which is difficulty coping with change. Through capturing, comparing and statistically analysing the reactions of autistic and neurotypical users to seven individual design changes, it has been possible to identify the changes that cause significant difficulty in autistic users. These difficulty points were then used to form heuristics that can followed by HCI practitioners in the industry to reduce the negative impact of software interface design change on autistic users, hence making software updates more accessible.

Private Set Intersection (PSI) is a cryptographic method in secure multi-party computation that allows entities to identify common elements in their datasets without revealing their private data. Traditional approaches assume similar-sized datasets and equal computational power, overlooking practical imbalances. In real-world applications, dataset sizes and computational capacities often vary, particularly in the Internet of Things and mobile scenarios where device limitations restrict computational types. Traditional PSI protocols are inefficient here, as computational and communication complexities correlate with the size of larger datasets. Thus, adapting PSI protocols to these imbalances is crucial. This paper explores unbalanced PSI scenarios where one party (the receiver) has a relatively small dataset and limited computational power, while the other party (the sender) has a large amount of data and strong computational capabilities. It introduces three innovative solutions for unbalanced PSI: unbalanced PSI protocol based on Cuckoo filters, unbalanced PSI protocol based on single cloud assistance, and unbalanced PSI protocol based on dual cloud assistance, each addressing the shortcomings of the previous solution. These protocols primarily optimize database computational load, storage capacity, protocol execution time, and security. Depending on performance and security needs, different protocols can be employed for applications such as private contact discovery.

Functional genomics, a multidisciplinary subject, investigates the functions of genes and their products in biological systems to better understand diseases and find new drugs. Drug repurposing is an economically efficient approach that entails discovering novel therapeutic applications for already-available medications. Genomics enables the identification of illness and therapeutic molecular characteristics and interactions, which in turn facilitates the process of drug repurposing. Techniques like gene expression profiling and Mendelian randomization are helpful in identifying possible medication candidates. Progress in computer science allows for the investigation and modelling of gene expression networks that involve large amounts of data. The integration of data from DNA, RNA, and protein activities has resemblance to pharmacogenomics, which is of utmost importance in the development of cancer drugs. Functional genomics in drug discovery, particularly for cancer, is still not thoroughly investigated, despite the existence of a significant amount of literature on the subject. Next-generation sequencing and proteomics present highly intriguing opportunities. Publicly available databases and mining techniques facilitate the development of cancer treatments based on functional genomics. Expanding the study and application of functional genomics has great promise to advance the process of discovering and repurposing drugs, especially in the field of oncology.

The outbreak of novel Coronavirus (SARS-COV-2 ) disease (COVID-19) in Wuhan has attracted worldwide attention. SARS-COV-2 known to share a similar clinical manifestation that includes various symptoms such as pneumonia, fever, breathing difficulty, and in particular, SARS-COV-2 also causes a severe in ammation state that leads to death. Consequently, massive and rapid research growth has been observed across the globe to elucidate the mechanisms of infections and disease progression in genotype and phenotype scale. Data Science is playing a pivotal role in in-silico analysis to draw hidden and novel insights about the SARS-COV-2 origin, pathogenesis, COVID-19 outbreak forecasting, medical diagnosis, and drug discovery. With the availability of multi-omics, radiological, biomolecular, and medical data urges to develop novel exploratory and predictive models or customise exiting learning models to t the current problem domain. The presence of many approaches generates the need for the systematic surveys to guide both data scientists and medical practitioners. We perform an elaborate study on the state-of-the-art data science method ologies in action to tackle the current pandemic scenario. We consider various active COVID-19 data analytics domains such as phylogeny analysis, SARS-COV-2 genome identication, protein structure prediction, host-viral protein interactomics, clinical imaging, epidemiological analysis, and most importantly (existing) drug discovery. We highlight types of data, their generation pipeline, and the data science models in use. We believe that the current study will give a detailed sketch of the road map towards handling COVID-19 like situation by leveraging data science in the future. We summarise our review focusing on prime challenges and possible future research directions .

The Chikungunya virus (CHIKV) poses a significant global public health concern, especially in Africa. Since its first isolation in Tanzania in 1953, CHIKV has caused recurrent outbreaks, challenging healthcare systems in low-resource settings. Recent outbreaks in Africa highlight the dynamic nature of CHIKV transmission and the challenges of underreporting and underdiagnosis. Here, we review literature and analyze publicly available cases, outbreaks, and genomic data providing insights into the epidemiology, genetic diversity, and transmission dynamics of CHIKV in Africa. Our analyses reveal the circulation of geographically distinct CHIKV genotypes, with certain regions experiencing a disproportionate burden of disease. Phylogenetic analysis of sporadic outbreaks in West Africa suggests repeated emergence of the virus through enzootic spillover, which is markedly different from inferred transmission dynamics in East Africa, where the virus is often introduced from Asian outbreaks, including the recent reintroduction of the Indian Ocean lineage from the Indian subcontinent to east Africa. Furthermore, there is limited evidence of viral movement between these two regions. Understanding the history and transmission dynamics of outbreaks is crucial for public health planning. Despite advances in surveillance and research, diagnostic and surveillance challenges persist. This review and secondary analysis highlight the importance of ongoing surveillance, research, and collaboration to mitigate the burden of CHIKV in Africa and improve public health outcomes.

Tackling the intricacies of network dismantling in complex systems poses significant challenges. This task has relevance across various practical domains, yet traditional approaches focus primarily on singular metrics, such as the number of nodes in the Giant Connected Component (GCC) or average pairwise connectivity. In contrast, we propose a unique metric that concurrently targets nodes with the highest degree and reduces the GCC size. Given the NP-hard nature of optimizing this metric, we introduce MaxShot, an innovative end-to-end solution that leverages graph representation learning and reinforcement learning. Through comprehensive evaluations on both synthetic and real-world datasets, our method consistently outperforms leading benchmarks in accuracy and efficiency. These results highlight MaxShot’s potential as a superior approach to address the network dismantling problem effectively.

Large Language Models (LLMs) have demonstrated promising capabilities to solve complex tasks in critical sectors such as healthcare. However, LLMs are limited by their training data which is often outdated, the tendency to generate inaccurate ("hallucinated") content and a lack of transparency in the content they generate. To address these limitations, retrieval augmented generation (RAG) grounds the responses of LLMs by exposing them to external knowledge sources. However, in the healthcare domain there is currently a lack of systematic understanding of which datasets, RAG methodologies and evaluation frameworks are available. This review aims to bridge this gap by assessing RAG-based approaches employed by LLMs in healthcare, focusing on the different steps of retrieval, augmentation and generation. Additionally, we identify the limitations, strengths and gaps in the existing literature. Our synthesis shows that proprietary models such as GPT-3.5/4 are the most used for RAG applications in healthcare. Also, there is a lack of standardized evaluation frameworks for RAG-based applications. In addition, the majority of the studies do not assess or address ethical considerations related to RAG in healthcare. It is important to account for ethical challenges that are inherent when AI systems are implemented in the clinical setting. Lastly, we highlight the need for further research and development to ensure responsible and effective adoption of RAG in the medical domain.

Over the past decade and a half, dynamic functional imaging has revolutionized the neuroimaging field. Since 2009, it has revealed low dimensional brain connectivity measures, has identified potential common human spatial connectivity states, has tracked the transition patterns of these states, and has demonstrated meaningful alterations in these transition and spatial patterns in neurological disorders, psychiatric disorders, and over the course of development. Recently, researchers have begun to analyze this data from the perspective of dynamic system and information theory in the hopes of understanding how these dynamics support less easily quantified processes, such as information processing, cortical hierarchy, and consciousness. Consciousness, in particular, appears to be strongly linked to entropy production in the brain. Little attention has been paid to the effects of psychiatric disease on entropy production in the human brain, however. Even disorders characterized by substantial changes in conscious experience have not been widely analyzed from this perspective. We begin to rectify this by examining the complexity of subject trajectories in state space through the lens of information theory. Specifically, we identify a basis for the dynamic functional connectivity state space and track subject trajectories through this space over the course of the scan. The dynamic complexity of these trajectories is assessed along each dimension of the proposed basis space. Using these estimates, we demonstrate that schizophrenia patients display substantially simpler trajectories than demographically matched healthy controls, and that this drop in complexity concentrates along specific dimensions. We also demonstrate that entropy generation in at least one of these dimensions is linked to cognitive performance. Overall, results suggest great value in applying dynamic systems theory to problems of neuroimaging and reveal a substantial drop in the complexity of schizophrenia patients’ brain function.

This research introduces a hybrid feature extraction approach that combines Linear Discriminant Analysis (LDA) and Multilayer Perceptron (MLP) methods to address the challenges of reducing feature vector dimensionality and accurately classifying smartphone-based human activities. Moreover, to refine activity classification accuracy, Support Vector Machine (SVM) optimization with Stochastic Gradient Descent (SGD) is employed. LDA, a statistical tool, is leveraged to derive a new feature space for data projection, enhancing class separation and test feature label prediction. The proposed approach, named LMSS, was evaluated using the UCI-HAR dataset and compared with state-of-the-art models. The results demonstrate that the proposed approach outperformed the best-performing method over this dataset. It achieved an accuracy rate of 99.52%, precision of 99.55%, recall of 99.53%, and an F1-score of 99.54%, highlighting the effectiveness of the proposed method in accurately classifying the data.

In this paper, we first discuss the research status and application progress of the finite element method and the smoothed particle method. By analyzing the advantages of the smoothed particle method and the finite element method, a new coupling algorithm, namely FEM-SPH algorithm, is proposed. By the method of comparison, it shows that finite element method and SPH method in the simulation of large deformation problems each have advantages and disadvantages, the finite element method smoothed particle coupling algorithm is effective to achieve the performance of high computational efficiency and can naturally simulate large deformation problems across. In the process of calculation, the large deformation unit can be freely into an algorithm to facilitate the calculation accuracy and efficiency of three methods of numerical simulation. Through the study found, FEM-SPH algorithm not only overcome the defect of smooth particle tensile instability, but also overcomes the problem of low efficiency of finite element computation. To further test the FEM-SPH algorithm has advantages in the practical engineering, we have carried out the actual test to the example of the super high speed collision, concluded that, since the target of most of the computational domain is always finite element, smoothed particle focused only in contact with the projectile and target of local area, particle number is not much, the whole calculation process just ten minutes, computational efficiency has been greatly improved, at the same time in the simulation of large deformation, the advantage is very obvious .This provides a criterion for the actual project, depending on the specific material deformation mode and choose a more appropriate conversion algorithm.

As previous study in many countries shown that stroke patient onsets are not distributed randomly, but associate with meteorological factors. However, the relationship between stroke occurence and meteorological factors remain unknown in mountain area in Guizhou China. This paper firstly introduces multi-source fusion data which is integrated by the mountain meteorological factor, geographic mapping elevation information data and stroke population monitoring of Guizhou province. Mainly elaborates from a few aspects, which concludes data collection, data sorting, data extraction, data cleaning and data production in detail. A completed and detailed meteorological stroke data set was successfully established and multi-source data fusion was realized by the use of Gbase and unified data service interface of Guizhou meteorological big data cloud platform. And we report the impact of meteorological variables in Guizhou mountain area climate on stroke. In this study, we performed a statistical fusion data between January 2017 and December 2020 about stroke incidence rate and meteorological factors respectively, for instance, concerning the mean (Mean), maximum (Max), minimum (Min), median (Median), standard deviation (Std) . We calculated stroke rates (date stroke occurence)/(year stroke occurence) and we investigated the distribution of days included in the label. Results: the distribution of the incidence rate basically conforms to the normal distribution with the label Max 0.007399, label Min 0.000204, label Mean 0.002738, label Median 0.002643, label Std 0.00076. We observed a positive significant correlation of stroke incidence rate directly proportional to the daily temperature difference (between 0 and 20 degrees Celsius), as the value of this factor exhibits variation larger, the incidence rate is gradually increasing. And we investigated from the Pearson correlation coefficients that stroke incidence increasing when meteorological factors at low humidity (less than 40% (RH 80%), temperature higher than 31℃); the 24-hour daily temperature difference varies between 6 and 10℃ (6

The ASEAN Community-based Tourism (CBT) Standard has been adopted by 10 ASEAN member states in 2016 in order to collectively promote ASEAN as a competitive community-based tourism destination. Among the ASEAN member states, Lao PDR (Laos), has a unique CBT development experience through collaboration with various international development agencies. Such history has brought about issues when ASEAN CBT Standard was implemented at to provincial and district levels in Laos, including concerns of related communities on the Standard being not easily applicable considering the state of tourism development. While the application of the regional standard is a significant issue to the tourism industries in the Member States, however, there has been a lack of studies regarding the dynamics of implementation of regional tourism standards at the national level. In order to fill the research gap, this study utilized in-depth interviews with seven executives with significant experiences from the government, international development agency, international organization, and the private sector. Interviewees projected a diversity of perspectives on enabling factors and challenges in implementing ASEAN Community-based Tourism Standard at the national level focusing on Laos, which showed the complexity of CBT dynamics. The results also revealed how regional standards can be further recognized and promoted to the key stakeholders of Laos, better accepted and utilized by end users, and possibly better customized according to the local circumstances. Findings of this study evidence that collaboration among key stakeholders and the expected role of these stakeholders are critical when implementing ASEAN CBT Standard.

Accurate diagnosis for the 400 million people with rare diseases is critical for healthcare decisions, prognosis, understanding disease mechanisms, and identification of treatments. Despite advances in genome sequencing, barriers such as high interpretation costs, diagnostic expertise, throughput associated delays, and uncertain variant classifications persist, with demand exceeding capacity. Many variant classification methods focus narrowly on specific consequences, leading to the use of complex integrative pipelines that often overlook transcript variability and lack prediction transparency. To overcome these limitations, we introduce DITTO. This transparent, transcript-aware machine-learning method demonstrates superior overall performance in accuracy, recall, and precision when compared to existing tools. DITTO is publicly available at https://github.com/uab-cgds-worthey/DITTO

Timely and accurate information on tree species is crucial for the sustainable management of natural resources, forest inventory, biodiversity detection, and carbon stock calculation. The advancement of remote sensing technology and artificial intelligence has facilitated the acquisition and analysis of remote sensing data, resulting in more precise and effective classification of tree species. Multimodal remote sensing data and deep learning seem to be the current tree species classification research mainstream, whether or not. The current review on the remote sensing data and deep learning tree species classification methods perspectives to analyze the unimodal and multimodal remote sensing data and classification methods in this realm is missing. To bridge the gap, we search for major trends in the remote sensing data and tree species classification methods, provide a detailed overview of classic deep learning-based methods for tree species classification, and discuss the limitations.

Increasing efforts have been devoted to promoting sustainable demolition waste management (DWM) from a life cycle-thinking perspective. To this end, facilitating sustainability-oriented de-cision-making for DWM planning requires a sustainability assessment framework for assessing multifaceted criteria. This study develops a BIM-based DWM sustainability assessment ap-proach to facilitate the life cycle assessment (LCA) and decision-making by coupling the enriched IFC model with hybrid Multi-Criteria Decision-Aiding (MCDA) methods using Dynamo visual scripting. To streamline the data-intensive LCA process, this study enriched the BIM properties and accommodated them into the LCA data template to enhance data interoperability, thus achieving seamless data transfer. Moreover, hybrid MCDA methods are integrated into the deci-sion-making workflow for DWM scenario ranking. A pilot study is employed to verify the ap-plicability of the decision-aiding framework. The results unveil that the sustainability score ascended with the recycling rate. The optimal DWM alternative with the highest recycling rate yields the highest sustainability score at 91.63. Conversely, a DWM alternative reflecting the ‘status quo’ in China’s recycling industry has the lowest score at 8.37, significantly lower than the baseline scenario with a 50% recycling rate. It is worth noting that the ‘growth curve’ of the sustainability score continuously flattens as the target recycling rate escalates. The increment in recycling rate from the “Australian standard” scenario to the optimal scenario is 18.4%, while the sustainability score merely increases by 2.3%, signal-ling that the former scenario arrived at an optimum point for maximising the cost-efficiency of DWM under the predefined framework and contexts.

Gene regulation is vital for cellular function and homeostasis, involving diverse mechanisms controlling specific gene products and contributing to tissue-specific gene expression. Dysregulation leads to diseases, emphasizing the need for understanding these mechanisms. Non-coding regions, notably enhancers and super-enhancers (SEs), act as crucial gene regulators, orchestrating transcriptional activity via transcription factors (TFs). SEs, with high activity, are pivotal in cell identity and disease progression. Current computational approaches focus on individual regulators like TFs and miRNAs, neglecting SE interactions. We emphasize incorporating SEs into models to enhance understanding. Experimental studies have recently linked miRNAs and TFs to SEs. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) provides valuable SE information. In this review, we categorize computational methods leveraging TF and miRNA data into three areas and explore challenges integrating enhancers/SEs. These include unraveling indirect regulatory networks, identifying network motifs, and enriching pathway identification by dissecting gene regulators, including SEs. We hypothesize that addressing these challenges will enhance our understanding of gene regulation, aiding in identifying therapeutic targets and disease biomarkers. We believe that understanding the role of ChIP-Seq data in predicting the effect of miRNA on gene regulation is crucial to construct statistical/computational model that would tackle these challenges.

The rapid development of specific-purpose Large Language Models (LLMs), such as Med-PaLM, MEDITRON-70B, and Med-Gemini, has significantly impacted healthcare, offering unprecedented capabilities in clinical decision support, diagnostics, and personalized health monitoring. This paper reviews the advancements in medicine-specific LLMs, the integration of Retrieval-Augmented Generation (RAG) and prompt engineering, and their applications in improving diagnostic accuracy and educational utility. Despite the potential, these technologies present challenges, including bias, hallucinations, and the need for robust safety protocols. The paper also discusses the regulatory and ethical considerations necessary for integrating these models into mainstream healthcare. By examining current studies and developments, this paper aims to provide a comprehensive overview of the state of LLMs in medicine and highlight the future directions for research and application. The study concludes that while LLMs hold immense potential, their safe and effective integration into clinical practice requires rigorous testing, ongoing evaluation, and continuous collaboration among stakeholders.

The raw material purchasing (RMP) problem is to determine the purchasing quantities of raw materials in given periods or cycles. Raw material purchasing optimization is crucial for large-scale steel plants because it is closely related to the supply of raw materials and cost savings. The raw material purchasing of large-scale steel enterprises is characterized by many varieties, large quantities, and high costs. The RMP objective is to minimize the total purchasing cost consisting of the price of raw materials, purchasing set-up costs, and inventory costs and meet product demand. We present a mixed integer linear programming (MILP) model and a column generation (CG) solution for the resulting optimization problem. The column generation algorithm is the generalization of the branch & bound algorithm with solving the linear programming (LP) relaxation of MILP using column generation (CG), and its advantage is to handle large-sized MILPs. Experimental results show the effectiveness and efficiency of the solution.

With increasing air and sea temperatures, the thermodynamic environments over the oceans become more favourable for the development of intense tropical cyclones (TCs) with rapid intensification (RI). In fact, the number of TCs undergoing RI is rising (Zhao, et al., 2018; Bhatia, et al., 2019; Song, et al., 2020; Hong & Wu, 2021; Liu, et al., 2022). RI over coastal sea areas before landfalling is particularly impactful and threatening to coastal lives and properties. There have been studies showing that offshore areas within 400 km of the coastline have experienced a significant increase in RI events with the count tripling from 1980 to 2020 (Li et al., 2023). The south China coastal region consists of highly densely populated cities especially the Pearl River Delta (PRD) region. Intense TCs maintaining its strength or RI of TCs close to the coastal region presents substantial forecasting challenges. This study investigates the effect of sea surface and subsurface temperature and salinity on the intensification of five TCs, namely Super Typhoons Hato in 2017 and Mangkhut in 2018, Typhoon Talim, Super Typhoon Saola and Severe Typhoon Koinu in 2023, which significantly affected the south China coastal region and triggered high TC warning signals in Hong Kong. The analysis utilized the Hong Kong Observatory (HKO) TC track and intensity data, along with the sea temperature and salinity profiles generated using the China Ocean ReAnalysis version 2 (CORA2) of the National Marine Data and Information Service (NMDIS) of China. While high sea surface temperature (SST) of 30°C or above, low surface sea surface salinity (SSS) of 34 psu or below, and strong salinity stratification of at least 0.8 psu per 100 m depth may offer useful hints for predicting RI, they are part of a broader set of contributing factors. This study represents the initial documentation of sub-surface salinity's impact on intense TCs over the South China Sea (SCS) in recent years and will encourage further research to refine forecasting RI of TCs before making landfall near PRD taking into account the effect of freshwater from the Pearl River.

Cloud computing refers to applications delivered as services over the Internet. Cloud systems employ policies that are inherently dynamic in nature and that depend on temporal conditions defined in terms of external events, such as the measurement of bandwidth, use of hosts, intrusion detection or specific time events. In this paper, we investigate an optimized resource management scheme named v-Mapper. The basic premise of v-Mapper is to exploit application-awareness concepts using software-defined networking (SDN) features. This paper makes three key contributions to the field: (1) We propose a virtual machine (VM) placement scheme that can effectively mitigate the VM placement issues for data-intensive applications; (2) We propose a validation scheme that will ensure that a service is entertained only if there are sufficient resources available for its execution and (3) We present a scheduling policy that aims to eliminate network load constraints. An evaluation was carried out with various benchmarks and demonstrated that v-Mapper shows improved performance over other state-of-the-art approaches in terms of average task completion time, service delay time and bandwidth utilization. Given the growing importance of supporting large-scale data processing and analysis in datacentres, the v-Mapper system has the potential to make a positive impact in improving datacentre performance in the future.

RaTG13 (a bat derived SARS-like CoV) is the closest relative sequence of SARS-CoV-2 reported till date. The sample from which RaTG13 was sequenced was a bat fecal swab collected in 2013 from Tongguan, Mojiang, Yunnan province, China. The Illumina based sequence of RaTG13, MN996532.1, was deposited on 27^th Jan 2020 and the raw data (Illumina), https://www.ncbi.nlm.nih.gov/sra/SRX7724752[accn]. There are discrepancies in dates about when the metagenome sequencing of RaTG13 sample was done (2018 or 2020), both stated by the same corresponding author. Comparison of the RNA Seq data of RaTG13 fecal swab to the corresponding data from the bat fecal swabs deposited by the same working group using the same methods indicated that the RaTG13 raw data seemed to be different in various aspects. The fecal swab sample showed abnormally less read of bacterial reads in the swab was exceptionally low, i.e. 0.7%, compared to the 20-90% abundance in other fecal swabs from bats processed by similar methods. Also, another raw data in the form of amplicon sequences was deposited in May 2020; however, the dates mentioned on the files of the sequenced amplicons were older (2017, 2018). The genome assembly of RaTG13 could not be done de-novo and the average coverage of the genome ~8%. Also, literature indicates that RaTG13 RBD cannot bind to Rhinolophus ACE-2 receptors. Collectively, the anomalies in the raw data of RaTG13 and other issues pose an important question about the overall authenticity of the RaTG13 genome sequence.

Methicillin-resistant Staphylococcus aureus (MRSA) infections, in particular biofilm-organized bacteria, remain a clinical challenge and a serious health problem. Rifabutin (RFB), an antibiotic of the rifamycins class, has shown in previous work excellent anti-staphylococcal activity. Here, we proposed to load RFB in liposomes aiming to promote the accumulation of RFB at infected sites and consequently enhancing the therapeutic potency. Two clinical isolates of MRSA, MRSA-C1 and MRSA-C2, were used to test the developed formulations, as well as the positive control, vancomycin (VCM). RFB in free and liposomal forms displayed high antibacterial activity, with minimal inhibitory concentrations (MIC) ranging from 0.009-0.013 μg/mL and MBIC50 values ranging from 0.008-0.012 μg/mL, in planktonic and biofilm bacteria, respectively. Confocal microscopy studies demonstrated the rapid internalization of unloaded and RFB-loaded liposomes in the bacterial biofilm matrix. In murine models of systemic MRSA-C1 infection, Balb/c mice were treated with RFB formulations and VCM at 20 and 40 mg/kg of body weight, respectively. Obtained data proved the superior therapeutic effectiveness of RFB formulations compared to Control and VCM groups even using a two-fold lower therapeutic dose as demonstrated by significantly reduced bacterial burden and growth index values in major organs. In addition, RFB formulations were the only formulations associated with 100% survival. Globally, this study emphasizes the potential of RFB nanoformulations as an effective and safe approach against MRSA infections.

Next-generation sequencing (NGS) has actualized human papillomavirus (HPV) virome profiling for in-depth investigation of viral evolution and pathogenesis. However, viral computational analysis remains a bottleneck due to semantic discrepancies between computational tools and curated reference genomes. To address this, we developed and tested automated workflows for HPV taxonomic profiling and visualization using a customized Papillomavirus database in CLC Microbial Genomics Module. HPV genomes from Papilloma Virus Episteme were customized and incorporated into CLC “ready-to-use” workflows for stepwise data processing to include: 1) Taxonomic Analysis, 2) Estimate Alpha/Beta Diversities, and 3) Map Reads to Reference. Low-grade (n = 95) and high-grade (n = 60) Pap smears were tested with ensuing collective runtimes: Taxonomic Analysis (36 min); Alpha/Beta Diversities (5 sec); Map Reads (45 min). Tabular output conversion to visualizations entailed 1-2 keystrokes. Biodiversity analysis between low- (LSIL) and high-grade squamous intraepithelial lesions (HSIL) revealed loss of species richness and gain of dominance by HPV-16 in HSIL. Integrating clinically relevant, taxonomized HPV reference genomes within automated workflows proved to be an ultra-fast method of virome profiling. The entire process named “HPV DeepSeq” provides a simple, accurate and practical means of NGS data analysis for a broad range of applications in viral research.

Accurate power curve modelling is essential to continuously evaluate the performance of a wind turbine (WT). In this work, we characterize the wind power curves using SCADA data acquired at a frequency of 5 minutes in a wind farm (WF) consisting of 5 WTs. Regarding the non-parametric methods, we select artificial neural networks (ANNs) to make curve estimations. Given that, we have the curves provided by the manufacturer of the WTs given by some very precisely measured pair of wind speed and power points. We can evaluate the difference between the manufacturer characterization and the ones estimated with the data provided by the SCADA system. Before the estimation, we propose a method of filtering the anomalies based on the characteristics provided by the manufacturer. We use three-quarters of the available data for curve estimation and one-quarter for the test. One WT suffered a break in the test part, so we can check how the test estimates reflect this problem in its wind-power curve compared to the estimations obtained in the WTs that worked adequately.

This study explores fault-tolerant consensus in leader-following heterogeneous multi-agent systems, focusing on actuator failures in uncrewed aerial vehicles (UAVs) and uncrewed ground vehicles (UGVs). An optimization-based fault-tolerant consensus algorithm is proposed. The algorithm utilizes the Euler-Lagrange formula to ensure system consistency under actuator failures, with the Lyapunov stability theory proving the asymptotic stability of the consistency error. The algorithm is applied to heterogeneous multi-agent systems of UAVs and UGVs to derive optimal fault-tolerant consensus control laws for each vehicle type. Simulation experiments give evidence for the feasibility of the proposed control strategy.

Intrinsically Disordered Proteins (IDPs) play crucial roles in signal transduction, cell differentiation, and transcriptional regulation. Many disrupted genes associated with mental disorders are identified as IDPs, and emerging evidence suggests the functional role of IDPs in neuropsychiatric disorders. However, few studies comprehensively explore the functional association between protein disorder properties and different mental diseases. To address this gap, we collected disrupted gene sets for seven mental diseases (MDD, SCZ, BP, ID, AD, ADHD, ASD) and a control gene set from normal brains using DisGeNET and GeneCards databases. The state-of-the-art predictor IUPred2A was then utilized to calculate the disorder properties , followed by a thorough comparison between the disordered proteins in mental diseases and healthy controls. Functional enrichment analysis and protein-protein interaction networks were conducted to investigate the IDPs’ functional roles in psychiatric diseases. Additionally, we demonstrated the role of IDPs in protein binding formations through a case study of alpha-synuclein using protein docking. Our findings reveal that differentially expressed proteins in mental disorders, especially in ASD and ADHD, exhibit more IDPs than those in healthy controls. IDPs in psychiatric disorders are significantly enriched in neurodevelopmental pathways and play an important role in in gene expression regulation. Our results indicate distinct functional patterns of disorder proteins among mental diseases and healthy controls. When comparing the IDPs between ASD and ADHD, we observed that IDPs in ADHD are more likely linked to the synaptic signaling and regulation, while IDPs in ASD are more tendentiously related to diverse and complex biological processes. Our work offers valuable insights into the important functions of IDPs in psychiatric disorders, enhancing our understanding of the molecular mechanisms involved in psychiatric disorders.

Since its emergence in March 2020, the SARS-CoV-2 global pandemic has produced more than 65 million cases and one point five million deaths worldwide. Despite the enormous efforts carried out by the scientific community, no effective treatments have been developed to date. We created a novel computational pipeline aimed to speed up the process of repurposable candidate drug identification. Compared with current drug repurposing methodologies, our strategy is centered on filtering the best candidate among all selected targets focused on the introduction of a mathematical formalism motivated by recent advances in the fields of algebraic topology and topological data analysis (TDA). This formalism allows us to compare three-dimensional protein structures. Its use in conjunction with two in silico validation strategies (molecular docking and transcriptomic analyses) allowed us to identify a set of potential drug repurposing candidates targeting three viral proteins (3CL viral protease, NSP15 endoribonuclease, and NSP12 RNA-dependent RNA polymerase), which included rutin, dexamethasone, and vemurafenib among others. To our knowledge, it is the first time that a TDA based strategy has been used to compare a massive amount of protein structures with the final objective of performing drug repurposing

Sex differences are essential factors in disease etiology and manifestation in many diseases such as cardiovascular disease, cancer, and neurodegeneration (1). The biological influence of sex differences (including genomic, epigenetic, hormonal, immunological, and metabolic differences between males and females) and the lack of biomedical studies considering sex differences in their study design has led to several policies. For example, the National Institute of Health’s (NIH) sex as a biological variable (SABV) and Sex and Gender Equity in Research (SAGER)) policies to motivate researchers to consider sex differences (2). However, drug repurposing, a promising alternative to traditional drug discovery by identifying novel uses for FDA-approved drugs, lacks sex-aware methods that can improve the identification of drugs that have sex-specific responses (1,3–5). Sex-aware drug repurposing methods either select drug candidates that are more efficacious in one sex or deprioritize drug candidates based on if they are predicted to cause a sex-bias adverse event (SBAE), unintended therapeutic effects that are more likely to occur in one sex. Computational drug repurposing methods are encouraging approaches to develop for sex-aware drug repurposing because they can prioritize sex-specific drug candidates or SBAEs at lower cost and time than traditional drug discovery. Sex-aware methods currently exist for clinical, genomic, and transcriptomic information (3,6,7). They have not expanded to other data types, such as DNA variation, which has been beneficial in other drug repurposing methods that do not consider sex (8). Additionally, some sex-aware methods suffer from poorer performance because a disproportionate number of male and female samples are available to train computational methods (3). However, there is development potential for several different categories (i.e., data mining, ligand binding predictions, molecular associations, and networks). Low-dimensional representations of molecular association and network approaches are also especially promising candidates for future sex-aware drug repurposing methodologies because they reduce the multiple hypothesis testing burden and capture sex-specific variation better than the other methods (9,10). Here we review how sex influences drug response, the current state of drug repurposing including with respect to sex-bias drug response, and how model organism study design choices influence drug repurposing validation.

Northern Nigeria has had historically low antenatal care (ANC) utilization rates with poor health outcomes. Group antenatal care (gANC) improves ANC behavior and pregnancy outcomes. The gANC has been adopted in Kaduna and Kano states, Nigeria. This paper presents baseline findings from the evaluation of the implementation of the gANC program to support scaling in real-world setting. Baseline data were collected from a cohort of 1,269 and 1,200 pregnant women enrolled in gANC at health facilities in Kaduna and Kano states respectively from March to April 2024. Analyses of socio-demographic and pregnancy behavior data were done. Participants were mostly between ages 19-31 years, married or living with a partner, with over 50% having their own businesses. Over 62% and 34% had completed secondary or higher-level education with 60% and 80% living in urban areas in Kaduna and Kano States, respectively. In Kano State, >60% of the women had their last delivery at home with 41.6% not assisted by a skilled birth attendant. In Kaduna, >63% delivered in the hospital and >50% had skilled attendance during labor. Almost half had not used contraceptives previously. Subsequent longitudinal data will examine the impact of gANC utilization on perinatal outcomes.

For the purpose of improve the sustainability of products sold in the EU, Digital Product Passports is a mandatory solution. These passports would systematically gather information about products, such as detailing the materials involved to aid recycling and remanufacturing efforts, or recording the emissions produced throughout the manufacturing process. The overall goal is the establishment of a circular economy in the EU. Current research on Digital Product Passports is focused on collating content for sector-specific applications. However, achieving sustainability goals through Digital Product Passports will require new methods and technical solutions for digital collaboration between supply chain participants, especially in the manufacturing sector. Collaborative work on Digital Product Passports requires trust and traceability in data and access management to ensure privacy over the data contained. One way to enable this securely and confidentially is through the use of blockchain technology, in which stored data cannot be concealed, which is key to the traceability of digital product data documentation. This paper therefore presents a concept for the implementation of generically applicable cross-industry blockchain-based digital product passports. To this end, generic supply chain processes have been abstracted and condensed into the architecture of smart contracts. Great attention is paid to the establishment of traceability as well as privacy through the selection of the blockchain technology Secret Network in combination with Gaia-X functionalities. An illustrative use case for digital product passports in manufacturing is used to demonstrate the applicability of the presented concept. In this use case information about the digital nameplate and carbon footprint is exchanged securely and confidentially in a multi-tenant supply chain network based on the Industry 4.0 infomation model of the Asset Administration Shell.

Sentiment analysis has become an important tool for understanding public opinion across languages and domains. Recently, there has been an increase in the number of studies on sentiment analysis in low-resource languages such as Kazakh. This is important to ensure that modern text analysis technologies are accessible to all users, regardless of their language background. The aim of the study is to create a sentiment analysis model for analyzing texts in Kazakh. As part of this work, we aim to use fine-tuning techniques on our own dataset for already existing models, thus improving their accuracy and efficiency for analyzing Kazakh language texts. This paper presents a manually collected dataset "KazIntTelCom" from the city information service 2GIS, consisting of user reviews, manually annotated by the authors taking into account the polarity of sentiment (i.e. negative positive or neutral). This dataset was used to fine-tune two pre-trained multi-lingual Transformer-based sentiment analysis models taken from the HuggingFace platform. The distillBERT and XLM-RoBERTa models were used for tuning. Also, the models were tested on the dataset "KazSAnDRA". The results show that accurate tuning even on a relatively small dataset gives a significant increase in performance, which is confirmed by an increase in the accuracy index by 20%-30%. In addition, false misses and false detections are analyzed, which allows us to identify directions for further improvement of the models. The contribution of this work, in addition to the dataset, is the analysis of model errors, which will help future developers to make more accurate settings of hyperparameters of training for sentiment analysis in Kazakh. These results are important for natural language processing and their adaptation to low-resource languages, promoting more inclusive and equitable access to modern analytical tools. Thus, this study demonstrates the effectiveness of the Transformers architecture for sentiment analysis in Kazakh and opens new opportunities for further model improvement.

Precise monitoring of individual crop growth and health status is crucial for precision agriculture practices. However, traditional manual inspection methods are time-consuming, labor-intensive, and often lack the spatial resolution required for detailed analysis. This research addresses the need for efficient and high-resolution crop monitoring by leveraging Unmanned Aerial Vehicle (UAV) imagery and advanced computational techniques. The primary objective was to develop a methodology for precise identification, extraction, and monitoring of individual corn crops throughout their growth cycle. This was achieved by integrating UAV-derived data with image processing, computational geometry, and machine learning techniques. UAV imagery was ac-quired bi-weekly at altitudes of 40m and 70m, capturing the entire growth cycle of a corn crop from planting to harvest. A time-series Canopy Height Model (CHM) was generated by analyzing the differences between the Digital Terrain Model (DTM) and the Digital Surface Model (DSM) derived from the UAV data. Local spatial analysis and image processing techniques were em-ployed to determine the local maximum height of each crop. Subsequently, a Voronoi data model was developed to delineate individual crop canopies, successfully identifying 13,000 out of 13,050 corn crops in the study area. For enhanced accuracy in canopy size delineation, vegetation indices were incorporated into the Voronoi model segmentation, refining the initial canopy area esti-mates by eliminating interference from soil and shadows. The proposed methodology enables precise estimation and monitoring of crop canopy size, height, biomass reduction, lodging, and stunted growth over time, providing valuable insights for precision agriculture practices. This work contributes to the scientific community by demonstrating the potential of integrating UAV technology, computational geometry, and machine learning for accurate and efficient crop mon-itoring at the individual plant level.

(1) Background: Adolescent girls have increasingly faced mental health challenges. We examined prevalence trends and associated risk factors for depression among adolescent girls. (2) Methods: Data for girls aged 12 to 17 years (N=4346) from the 2021 cross-sectional National Survey on Drug Use and Health were analyzed. Factors associated with depression were examined using multiple regression analysis. (3) Results: Rates of severe depression were significantly higher (p<.001) in older girls (adjusted odds ratio [AOR]: 1.63, 1.61, those who did not have authoritative parents (AOR: 3.40), and those with negative school experiences (AOR: 4.03). Black and Asian/Native Hawaiian or other Pacific Islanders were less likely to report severe depression than white girls. As previously reported, non-White girls were significantly less likely to receive treatment for depression (p<.05). Parents’ characteristics and school experiences had no effect on the likelihood of receiving mental health treatment. (4) Conclusion: Depression has become increasingly common among American adolescent girls, who are now three times as likely as adolescent boys to have had recent experiences with depression. Our results show that family structure, parenting style, and negative school experiences significantly contribute to the rate of depression and that treatment disparities exist with regard to race and ethnicity. The results of our research could be valuable for policymakers, healthcare professionals, and educators in developing specific preventative initiatives and support networks that effectively address these unique challenges.

In the process of climate change mitigation and adaptation, the focus on climate risk driven by transition innovations has received widespread attention from governments, regulators, and investors. Based on the identification of low-carbon patents through the Green and Low-carbon Technology Inventory in China, this study constructs low-carbon innovation measurements of listed firms in China from 2015 to 2021. Then, an empirical model is used to investigate the impact and mechanism of climate transition innovations on the default risk. The baseline regression model shows that low-carbon innovations can mitigate the default risk of listed firms. Moreover, our findings are supported by instrumental variable regressions that use the time costs of innovation. Finally, the mediation effect demonstrates that investor attention, total factor productivity, and technology spillovers are paths through which transition innovations can affect the default risk. This study reveals that low-carbon technological advances have a positive effect on climate transition risks.

Diarrhea remains one of the leading causes of mortality worldwide, especially among children. Recent epidemiological studies conducted in developing countries identified Shigella species as the most predominant pathogenic bacteria responsible for diarrhea. Antimicrobial therapy is necessary for Shigella infections; however, the rapid emergence of resistance against existing antimicrobials in Shigella spp. poses a serious global health problem. To identify alternative antimicrobial compounds with activity against Shigella species, the pathogens responsible for bacterial diarrhea. In this study, we have applied antibacterial phenotypic screening to identify potent anti-Shigella compounds across a broad chemical diversity, including selected acetaminophen derivatives containing benzothiazoles backbone, and their combination with certain antibiotics. In continuation to our effort in searching potent antimicrobial compounds, we have found this time around that two acetaminophen derivatives containing benzothiazoles backbone (4a and 4b) could inhibit the growth of Shigella flexneri with common MIC value of 12.5 µg/ml. These compounds were established through a time-kill kinetics’ study to be bactericidal. Meanwhile, the 2-aminobenzothiazoles (1a and 1b) used for the synthesis of compounds 4 (a & b) were found to be poorly active (MIC: 100 µg/ml) against this pathogen. Combination studies of 4a and 4b with the least susceptible antibiotics (ceftriaxone and cotrimoxazole) demonstrated synergistic anti-Shigella activity. The present study demonstrates that the azobenzothiazole dyes 4 (a & b) can be repurposed as potential anti-Shigella compounds, which can serve as scaffolds for the development of new agents against infectious diarrhea caused by Shigella and other enteric pathogens, especially in developing countries.

Endometrial cancer (EC) is the most frequent gynaecological malignancy. The ESGO/ESTRO/ESP 2020 guidelines identify prognostic groups based on morpho-molecular characteristics. This study aims to evaluate the clinical applicability of NGS analysis to define an appropriate risk class and application for a better diagnostic and prognostic stratification of ECs. Cases of serous carcinoma (OHEC), high (HGEC) and low (LGEC) grade endometrioid carcinoma diagnosed with the morphological and immunohistochemical (IHC) protocols were considered. After a standardized pre-analytical phase, the tumor DNA was semi-automatically extracted and analyzed by NGS with a panel of 14 genes. A total of 63 cases were considered. NGS analysis was successful in 60 cases; all of these were classified according to the new diagnostic algorithm. The molecular risk classification showed a good correlation with the morphological (k=0.8). The study showed that the protocols of the pre-analytical and analytical phases used are robust and can lead to molecular results that fall within the standards required for use in clinical practice for a more precise diagnostic-therapeutic management of patients. The implementation of the classification is particularly relevant for better prognostic stratification of HGECs. In addition, the identification of a suspicious VUS in POLE questions the classification of truncating variants.

Increasing environmental distress is associated with a growing asthma incidence and, with no treatments available, montelukast (MTK) – an antagonist of the cysteinyl leukotrienes receptor 1 – is widely used in the management of symptoms among adults and children. Recently, new molecular targets have been identified and MTK has been proposed for repurposing in other therapeutic applications, with several ongoing clinical trials. The proposed applications include neuroinflammation control, which could be explored in some neurodegenerative disorders, such as Alzheimer’s and Parkinson’s diseases (AD and PD). However, this drug has been associated with an increasing number of reported neuropsychiatric adverse drug reactions. Besides, and despite being on the market since 1998, MTK metabolism is still poorly understood and the mechanisms underlying neuropsychiatric ADRs remain unknown. We review the role of MTK as modulator of leukotriene pathways and systematize the knowledge about MTK metabolism. Known toxic effects of MTK are discussed, and repurposing applications are presented comprehensively, with a focus on AD and PD.

Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world's most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and validation by PCR and RT-PCR were used. Single and mixed infections with Tomato mosaic virus (ToMV), Tomato golden mosaic virus (ToGMoV), and Pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3' UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3' UTR of Mexican ToMV isolates suggest the need to evaluate known resistance genes against these viral variants. The precise identification and characterization of viruses that naturally infect tomato germplasm could be used as a strategy for selecting the appropriate disease management and guiding breeding efforts.

Causal language can be a powerful tool for media outlets to subtly influence public perception and reinforce specific narratives. Therefore, identifying these linguistic patterns can be helpful in assessing the level of bias present in media content. In this paper, we directly compare the prevalence of causal language in headlines pertaining to the coverage of the Israel-Palestine conflict and the Russia-Ukraine war. We specifically look at the BBC and AlJazeera headlines covering the assault on Gaza since October 7, 2023. We use UniCausal, a model for causal text mining, in order to automatically extract the cause and effect of each headline. Our findings reveal that BBC headlines tend to avoid directly attributing causality to Israel for the violence in Gaza, whereas Al Jazeera headlines explicitly identify Israel as the responsible party. This differential use of causal language suggests a potential bias in media reporting.

In higher education, the cultivation of research competency is pivotal for students’ critical thinking development and their subsequent transition into the professional workforce. While statistics plays a fundamental role in supporting the completion of a research project, it is often perceived as challenging, particularly by students in majors outside mathematics or statistics. The connection between students’ statistical proficiency and their research competency remains unexplored despite its significance. To address this gap, we utilized the supervised machine learning approach to predict students’ research competency, as represented by their performance in a research methods class, with predictors of students’ proficiency in statistical topics. Predictors relating to students’ learning behavior in a statistics course such as assignment completion and academic dishonesty are also included as auxiliary variables. Results indicate that the three primary categories of statistical skills—namely, understanding of statistical concepts, proficiency in selecting appropriate statistical methods, and statistics interpretation skills— can be used to predict students’ research competency, as demonstrated by their final course scores and letter grades. This study advocates for strategic emphasis on the identified influential topics to enhance efficiency in developing students’ research competency. Findings could inform instructors in adopting a strategic approach to teaching the statistical component of research for enhanced efficiency.

Parkinson's disease (PD) is the second most common neurodegenerative disorder, entailing several motor-related symptoms that contribute to a reduced quality of life in affected subjects. Recent advances in wearable technologies and computing resources have shown great potential for the assessment of PD-related symptoms. However, the potential applications (e.g., early diagnosis, prognosis and monitoring) and key features of digital biomarkers for motor symptoms of PD (DB-MS-PD) have not been comprehensively studied. This study aims to provide a state-of-the-art review of current digital biomarker definitions for PD, focusing on the use of wearable devices. This review systematically examines research articles from 2012 to 2024, focusing on key features and recent technologies in PD research. A total of 22 studies were included and thoroughly analyzed. Results indicate that DB-MS-PD can accurately distinguish patients with PD (PwPD) from healthy controls (HC), assess disease severity or treatment response, and detect motor symptoms. Large sample sizes, proper validation, non-invasive devices, and ecological monitoring make DB-MS-PD promising for improving PD management. Challenges include sample and method heterogeneity and lack of public datasets. Future studies can leverage evidence of the current literature to provide more effective and ready-to-use digital tools for monitoring PD.

This article systematically studied the A-optimal designs of a high-order mixture central polynomial model, which is an advancement of the research results for the A-optimal design of the most recent third-order mixture central polynomial model and a more accurate response surface model. This article is based on the simplex center design, obtaining measurement values at various design points, and verifying them through the A-optimal equivalence theorem. We also compare the A-efficiency of designs through examples, which can be applied to the A-optimal precise design of the fourth-order mixture model.

This review highlights the potential and limitations of mRNA vaccines with a particular focus on mucosal delivery as an alternative to parenteral administration. The strengths of mRNA vaccines are: a) Versatility: they can be adapted to target a wide range of pathogens; b) Faster development: designed and produced more quickly than traditional vaccines; c) High efficacy: effective in preventing severe disease, as demonstrated during the COVID-19 pandemic. Current challenges: a) Delivery: current methods (mainly intramuscular injection) may not be optimal for inducing mucosal immunity; b) Stability: mRNA is fragile and needs to be protected from degradation; c) Safety: potential side effects, including myocarditis, blood clotting, allergic reactions need further investigation. Mucosal delivery could be more effective in preventing the transmission of pathogens and is generally better accepted by the population. Pros: offers the potential to induce local immunity at the site of pathogen entry, potentially providing broader protection; Cons: developing effective delivery systems and adjuvants for mucosal delivery is difficult. Extracellular vesicles as a mucosal delivery system are promising and offer a potentially safe, scalable, and needle-free approach. Future directions: a) Optimizing mRNA constructs: strategies like codon optimization and self-amplifying RNA can improve stability and translation efficiency; b) Rigorous pre-clinical studies are essential before human trials.

Several tumor types have been efficiently treated with PARPis, which are now approved for the treatment of ovarian, breast, prostate, and pancreatic cancer. The BRCA1/2 genes and mutations in many additional genes involved in the HR pathway may be responsible for the HRD phenomenon. In the present study, an NGS assay was used to analyze 513 genes associated with targeted and immuno-oncology therapies in 406 samples. In addition, the %gLOH values of 24 samples were also calculated using the Affymetrix technology to compare the results obtained by the two methodologies. HR variations occurred in 20.93% of the malignancies, while BRCA1/2 gene alterations in 5.17%. %LOH was highly correlated with alterations in the BRCA1/2 genes since 76.19% (16/21) of the BRCA1/2 positive tumors had a high %LOH value (p=0.007). Moreover, the LOH status was highly correlated with the TP53 and KRAS statuses, but there was no association with the TMB value. Lin's Concordance Correlation Coefficient for the 24 evaluable samples simultaneously examined by both assays was 0.87, indicating a nearly perfect agreement. In conclusion, the addition of gLOH analysis could assist the detection of additional patients eligible for PARPis

In this work, we explore the ability to dynamically group the Wind Turbine (WT) of a Wind Farm (WF) based on the behaviour of some of their Supervisory Control And Data Acquisition (SCADA) signals to detect the turbines that exhibit abnormal behaviour. We centre this study on a small WF of five WTs. We use the fact that the same signals from different turbines in the same WF coherently evolve temporally in a time domain, describing very similar waveforms. In this contribution, we use averaged signals from the SCADA system and omit maximums, minimums and standard deviations, focusing mainly on velocities and other slowly varying signals. For the temporal analysis, sliding windows of different temporal durations and overlapings are explored. The capability to automatically identify WTs whose signals differ from the group’s behaviour can alert and program preventive maintenance operations on such WTs before a major breakdown occurs.

NF-κB is a central mediator of inflammation, response to DNA damage and oxidative stress. As a result of its central role in so many important cellular processes, NF-κB dysregulation has been implicated in the pathology of important human diseases. NF-κB activation causes inappropriate inflammatory responses in diseases including rheumatoid arthritis (RA) and multiple sclerosis (MS). Thus, modulation of NF-κB signaling is being widely investigated as an approach to treat chronic inflammatory diseases, autoimmunity and cancer. The emergence of COVID-19 in late 2019, the subsequent pandemic and the huge clinical burden of patients with life-threatening SARS-CoV-2 pneumonia led to a massive scramble to repurpose existing medicines to treat lung inflammation in a wide range of healthcare systems. These efforts continue and these efforts continue to be con-troversial. Drug repurposing strategies are a promising alternative to de-novo drug development, as they minimize drug development timelines and reduce the risk of failure due to unexpected side effects. Different experimental approaches have been applied to identify existing medicines which inhibit NF-κB that could be repurposed as anti-inflammatory drugs.

Session-based recommendations which aim to predict subsequent user-item interaction based on historical user behavior during anonymous sessions can be challenging tasks. Two main challenges need to be addressed and improved: (1) How to analyze these sessions to accurately and completely capture users’ preferences, and (2) how to identify and eliminate any interference caused by noisy behavior. Existing methods have not adequately addressed these issues since they either neglected the valuable insight that can be gained from analyzing consecutive groups of items or failed to take these noisy data in sessions seriously and handled them properly, which can jointly impede recommendation systems from capturing users’ real intentions. To address these two problems, we designed a multi-order semantic denoising (MSD) model for session-based recommendations. Specifically, we grouped items of different lengths as varying multi-order semantic units to mine the user’s primary intention from multiple dimensions. Meanwhile, a novel denoising network was designed to alleviate the interference of noisy behavior and provide a more precise session representation. The result of extensive experiments on three real-world datasets demonstrated that the proposed MSD model exhibited improved performance compared with existing state-of-the-art methods in session-based recommendation.

Analysis of immediate effects of the COVID-19 pandemic on SMEs in Rwanda aims to assess and quantify the economic and financial impacts of the pandemic during the lockdown and presents options adopted by SMEs to reopen their business opera-tions. It also seeks to recommend options for sustainable and resilient economic recovery from the scars of COVID-19. This analysis used data collected from nearly 220 SMEs located across the country and applied an Exploratory Data Analysis (EDA) and multivariate linear regression models to measure the pandemic effects. The study revealed that firms downsized employment by 36.4 per cent, but data depict significant deviation within SMEs by their size. The COVID-19 pandemic has had a greater magni-tude of negative effects on sales levels among small businesses. Tax amounts were reduced amidst the crisis however, data do not show any significant variations among SMEs. Additionally, SMEs owners applied various coping mechanisms during re-opening. The study used firm-level data, providing detailed and reliable effects of the shocks on business performance. This analysis recommends establishing the medium-term financing and technical support for SMEs to ensure steady and sustainable recovery from pandemic effects as well as strengthening their resilience to any other socio-economics shocks.

The morbidity and mortality caused by invasive fungal infections is increasing across the globe due to developments in transplant surgery, the use of immunosuppressive agents, and the emergence of drug-resistant fungal strains, which has led to a challenge in terms of treatment due to the limitations of three classes of drugs. Hence, it is imperative to establish effective strategies to identify and design new antifungal drugs. Drug repurposing is an effective way of expanding the application of existing drugs. In the last years, various existing drugs have been shown to be useful in the prevention and treatment of the invasive fungi. In this review, we summarize the currently used antifungal agents. In addition, the most up to date information on the effectiveness of existing drugs with antifungal activity is discussed. Moreover, the antifungal mechanisms of existing drugs are highlighted. These data will provide valuable knowledge to stimulate further investigation and clinical application in this field.

Drug repurposing, rebranding an existing drug for a new therapeutic indication, is deemed a beneficial approach for a quick and cost-effective drug discovery process by skipping preclinical, Phase 1 trials and pharmacokinetic studies. Several psychotropic drugs including selective serotonin reuptake inhibitors (SSRIs) and tricyclic antide-pressants (TCAs) were studied for their potential application in different diseases es-pecially in cancer therapy. Fluoxetine (FLX) is one of the most prescribed psychotropic agents from SSRIs class for the treatment of several neuropsychiatric disorders with a favourable safety profile. FLX exhibited different oncolytic effects via mechanisms dis-tinct from its main serotonergic activity. Taking advantage of its ability to rapidly pen-etrate the blood-brain barrier, FLX could be particularly useful in brain tumors. This was proved by different in vitro and in vivo experiments using FLX as a monotherapy or combination with temozolomide (TMZ) or radiotherapy. In this review of literature, we summarize the potential pleiotropic oncolytic roles of FLX against different cancers highlighting the multifaceted activities of FLX and its ability to interrupt cancer prolif-eration via several molecular mechanisms and even surmount multidrug resistance (MDR). We elaborated on the successful synergistic combinations such as FXR/temozolomide and FXR/raloxifene for the treatment of glioblastoma and breast cancer, respectively. We showcased beneficial pharmaceutical trials to load FLX on car-riers to enhance its safety and efficacy on cancer cells. This is the first review article ex-tensively summarizing all previous FLX repurposing studies for the management of cancer.

Pepper leaf segmentation plays a crucial role in monitoring pepper leaf diseases in various backgrounds and ensuring the healthy growth of peppers. However, existing transformer-based segmentation methods suffer from computational inefficiency, excessive parameterization, and limited utilization of edge information. To tackle these challenges, we propose an adaptive multi-scale MLP framework, named AMS-MLP, which combines the multi-path aggregation module (MPAM) and the multi-scale context relation mask module (MCRD) to refine the object boundaries in pepper leaf segmentation. AMS-MLP consists of an encoder-based network, an adaptive multi-scale MLP (AM-MLP) module, and a decoder network. In the encoder network, the MPAM module effectively fuses five-scale features to generate a single-channel mask, improving the accuracy of pepper leaf boundary extraction. The AM-MLP module divides the input features into two branches: the global multi-scale MLP branch captures long-range dependencies between image information, while the local multi-scale MLP branch focuses on extracting local feature maps. Adaptive attention mechanism is designed to dynamically adjust the weights of global and local features. The decoder network incorporates the MCRD module into the convolutional layer, enhancing the extraction of boundary features. To verify the performance of the proposed method, we conducted extensive experiments on three pepper leaf datasets with different backgrounds. The results demonstrate mIoU scores of 97.39%, 96.91%, and 97.91%, as well as F1 scores of 98.29%, 97.86%, and 98.51%, respectively. Comparative analysis with U-Net and state-of-the-art models reveals that the proposed method dramatically improves the accuracy and efficiency of pepper leaf image segmentation.

This study aims to propose a method for constructing basic digital twin data in South Korea by adhering to international standards and utilizing publicly available data. Specifically, the study focuses on designing and proposing a digital twin data model for buildings, which are the most applicable among the basic digital twin data. To achieve this, the first section provides essential background information, introduces concepts and requirements related to digital twin basic data, and offers a brief overview of CityGML. The second section explains the methodology and data used in this study. The third section presents the main findings: the selection of public data (buildings) for constructing digital twin basic data, the mapping process using CityGML, and the creation of UML diagrams. The fourth section discusses these findings. Finally, the conclusion and suggestions for future research are provided. This approach enhances the accuracy of building-related digital twin data and supports the use of digital twin services in both public and private sectors by enabling various spatial analyses.

Since the beginning of the internet era, there has been an explosion of growth in structured data (such as numbers, symbols, and labels) as well as unstructured data (including images, videos, and text). Efficient and accurate mixed query of these two types of data is a key technology to achieve high-quality information retrieval, and it is also a major challenge that needs to be solved urgently in the industry. In this study, we employ an advanced Transformer model that combines strategies and fine-tuning techniques for multi-task learning. Specifically, the model is first pre-trained on a large-scale, general-purpose dataset to learn different types of data representations and basic language comprehension skills. After that, we fine-tuned the parameters of the model to better suit these specific data processing tasks for specific application scenarios, such as image annotation, video content analysis, and structured data query. At the heart of the model is the self-attention mechanism, which allows the model to automatically emphasize the important parts and ignore irrelevant information when processing the input data. In addition, we have introduced task-specific adaptation layers that are designed to add additional processing power to the original Transformer architecture, such as a semantic analysis layer for unstructured text data and a relational extraction layer for structured data. This combination of general pre-training and task-specific fine-tuning allows the model to flexibly process and integrate information from different data sources, improving processing efficiency and accuracy. Experimental results show that the model performs well in a variety of data processing tasks, significantly improves the accuracy and efficiency of information retrieval, and verifies the strong potential and adaptability of large language models in processing mixed data types.

This research project aimed to address the growing concern about methane emissions from seaweed by developing a Convolutional Neural Network (CNN) model capable of accurately predicting these emissions. The study used PANDAS to read and analyze the dataset, incorporating statistical measures like mean, median, and standard deviation to understand the dataset. The CNN model was trained using the ReLU activation function and mean absolute error as the loss function. Model performance was evaluated through MAPE graphs, comparing the mean absolute percentage error (MAPE) between training and validation sets and between true and predicted emissions, and analyzing trends in yearly greenhouse gas emissions. The results demonstrated that the CNN model achieved a high level of accuracy in predicting methane emissions, with a low MAPE between the expected and actual values. This approach should enhance our understanding of methane emissions from Sargassum, contributing to more accurate environmental impact assessments and effective mitigation strategies.

Background: Alzheimer's disease (AD) is a leading cause of dementia, significantly influenced by the Apolipoprotein E4 (APOE4) gene and gender. This study aims to use machine learning (ML) algorithms to predict brain age and assess AD risk by considering the effects of APOE4 genotype and gender. Methods: We collected brain volumetric MRI data and medical records from 1100 cognitively unimpaired individuals and 602 AD patients. We applied three ML regression models—XGBoost, Random Forest (RF), and Linear Regression (LR)—to predict brain age. Additionally, we introduced two novel metrics, Brain Age Difference (BAD) and Integrated Difference (ID), to evaluate model performance and analyze the influence of APOE4 genotype and gender on brain aging. Results: AD patients displayed significantly older brain ages compared to their chronological ages, with BADs ranging from 6.5 to 10 years. The RF model outperformed both XGBoost and LR in terms of accuracy, delivering higher ID values and more precise predictions. Comparing APOE4 carriers with non-carriers, the models showed enhanced ID values and consistent brain age predictions, improving overall performance. Gender-specific analyses indicated slight enhancements, with models performing equally well on both genders. It indicates that APOE4 may be a more robust predictor of brain age than gender. Conclusion: Robust ML models for brain age prediction can be pivotal in the early detection of AD risk via MRI brain structural imaging, especially for APOE4 carriers. Such early identification may facilitate timely preventive interventions for AD.

Portugal’s EPAC silo network, initially planned in the 1930s but constructed and utilized primarily in the 1970s, consisted of 31 silos with a total capacity of 841,100 t. The network’s usage declined, however, due to market liberalization and Portugal’s accession to the European Economic Community in 1985. This study focuses on adapting a methodology to inventory and analyse the 31 silos in the EPAC network considering their general features, construction, technological facilities, and socioeconomic aspects. The silos are situated in 30 cities and towns, predominantly in the country’s key grain-growing regions, particularly the Alentejo region. While there are variations in design and construction, most EPAC silos contain two or three rows of circular reinforced-concrete cells and use the spaces between cells for storage. Their capacities range from 6,000 to 35,000 t. Some are inland grain reception and storage silos, while others are larger-capacity port silos designed to unload grain rapidly onto ships using mechanical or pneumatic unloaders. These structures are a significant part of Portugal’s agro-industrial heritage and have in some cases been repurposed as museums or event venues. Compared to other agro-industrial buildings, silos pose unique conversion challenges due to their height and design complexities. Examples of successful reuse in countries like Spain and Italy may provide insights for potential silo projects in Portugal. However, analysis suggests that such proposals and similar initiatives may be viable only in the more highly populated towns.

Artificial intelligence AI or machine learning has proven to be a potential activity in the health and biomedical sciences. Previous research it has found that AI can learn new data and transform it into the useful knowledge. In the field of pharmacology, the aim is to design more efficient and novel vaccines using this method which are also cost effective. The underlying fact is to predict the molecular mechanism and structure for increased likelihood of developing new drugs. Clinical, electronic and high resolution imaging datasets can be used as inputs to aid the drug development niche. Moreover, the use of comprehensive target activity has been performed for repurposing a drug molecule by extending target profiles of drugs which also include off targets with therapeutic potential providing a new indication.

Stalk rot caused by Fusarium fungi is one of the most widespread and devastating diseases of maize, and the introduction of resistant genotypes is one of the most effective strategies for controlling the disease. Breeding genotypes with genetically determined resistance will also allow less use of crop protection products. The aim of the research was to identify molecular markers and associated candidate genes determining maize plant resistance to Fusarium stalk rot. The plant material for the study consisted of 122 maize hybrids, which were sown in plots of 10 m2, in a complete randomized block design, in three repetitions, at two locations (Smolice: 51 42’ 58.904’’ N, 17 13’ 29.13’’ E and Kobierzyce: 50 58’ 19.411’’ N, 16 55’ 47.323’’ E). The analyzed genotypes were simultaneously subjected to next-generation sequencing using the Illumina platform. The results of the observation of the degree of infection and sequencing were used for association mapping, which ultimately resulted in the selection of 10 molecular markers important at both places. Among the identified markers, two SNP markers that are located inside candidate genes play an important role. Marker 4772836 is located inside the serine/threonine-protein kinase bsk3 gene, while marker 4765764 is located inside the histidine kinase 1 gene. Both genes can be associated with plant resistance to Fusarium stalk rot, and these genes can also be used in breeding programs to select resistant varieties.

Atypical Polypoid Adenomyoma (APA) is a benign uterine lesion that occurs in women of reproductive age. The histological pattern is characterized by irregular epithelial proliferation and muscular stroma. Our work consists of a systematic review of the literature, including the description and analysis of a case study, and assesses the main immunohistochemical and molecular markers that contribute to making a differential diagnosis against endometrial adenocarcinoma. This allows offering patients conservative treatment compared to the radical management required for endometrial cancer, due to the significant physical and psychological consequences that one procedure or another can have on women's health. The goal of this research is to carry out an adequate diagnosis of APA by providing the necessary information to guide clinical management, establish patient prognosis, and minimize the emotional impact associated with the disease, all in combination with clinical and histopathological findings and complementary imaging tests. In conclusion, an appropriate immunohistochemical and molecular approach, along with the presumptive histological diagnosis, determine the correct classification of the lesion as APA and not as other malignant pathologies, which allows establishing a treatment protocol adjusted to the biological reality of this pathology.

Next generation sequencing (NGS) from SARS-CoV-2-positive swabs collected during the last months of 2022 revealed a large deletion between ORF7b and ORF8 (426 nt) in six patients infected with the BA.5.1 Omicron variant. This extensive genome loss removed a large part of these two genes, maintaining in frame the first 22 aminoacids of ORF7b and the last 3 aminoacids of ORF8. Interestingly, the deleted region was flanked by 2 small repeats, likely involved in the formation of a hairpin structure. Similar rearrangements, comparable in size and location to the deletion, were also identified in 15 sequences in the NCBI database. In this group, 7 out of 15 cases from the USA and Switzerland presented both the BA.5.1 variant and the same 426 nuclotides deletion. It is noteworthy that 3 out of 6 cases were detected in patients with immunodeficiency and is conceivable that this clinical condition could promote the replication and selection of these mutations.

Evaluation ecosystem service value (ESV) is critical for “lucid waters and lush mountains are invaluable assets”. However, the ESV estimation and spatial-temporal analysis for mountainous soil erosion area is rare, e.g., Changting county, China. In this study, we developed a remote sensing driven mountainous equivalent factor (RS-MEF) method to estimate the ESV of soil erosion area in subtropical mountain. It is a hybrid of a conventional equivalent factor framework and the remote sensing techniques for mountains, and achieves several highlights of spatial adjustment using carbon sink with vegetation canopy, improvement spatial resolution, and removal topographic effect. Using the RS-MEF method, we estimated that the ESV of Changting county was about 15.80 billion CNY in 2010 and 34.83 billion CNY in 2022. Specifically, the ESV per unit area of major soil erosion area (MSEA) in the county was less than that of non-major soil erosion area (n-MSEA), however, the ESV growth rate of MSEA from 2010 to 2022 was faster than that of n-MSEA. Therefore, the ESV gap between two areas was shortened from 28.99% in 2010 to 15.83% in 2022. Topographic gradient effect analysis illustrates that the area with high elevation and small slope is one control focus in the next step. Our study indicates that the ecological restoration in the county has made great achievements in the ESV perspective, with low ESV area shrank evidently in MSEA; and the achieved knowledge of the ESV growth and inherent factors is valuable and instructive for the next soil and water conservation.

As cancer remains resistant to several modes of treatment, novel therapeutics are still under active investigation to overcome treatment inefficacy in cancer. Given the high attrition rate of de novo drug discovery, drug screening, and drug repurposing have offered time- and cost-effective alternative strategies for the identification of potentially effective therapeutics. In contrast to large-scale drug screens, computational approaches for drug repurposing leverage the increasing amounts of biomedical data to predict candidate therapeutic agents prior to testing in biological models. Current studies in drug repurposing for cancer therapy prediction have increasingly focused on the prediction of combination therapies, as combination therapies have numerous advantages over monotherapies. These include increased effect from synergistic interactions, reduced toxicity from lowered drug doses, and a reduced risk of resistance due to multiple non-overlapping mechanisms of action. This review provides a summary of several classes of computational methods used for drug combination therapy prediction in cancer research, including networks, regression-based machine learning, classifier machine learning models, and deep learning approaches, with the goal of presenting current progress in the field, particularly to non-computational cancer biologists. We conclude by discussing the need for further advancements in technologies that incorporate disease mechanisms, drug characteristics, multi-omics data, and clinical considerations to generate effective patient-specific drug combinations, as holistic data integration will inevitably result in optimal targeted therapeutics for cancer.

Increasing concerns on animal welfare in commercial pig industry include aggression between pigs as it affects their health and growth. Early detection of aggressive behaviors is essential for optimizing their living environment. A major challenge for detection is that these behaviors are observed occasionally in normal conditions. Under this circumstance, a limited amount of aggressive behavior data will lead to class imbalance issue, making it difficult to develop an effective classification model for the detection of aggressive behaviors. To overcome this problem, we approach the aggressive behavior detection problem as a case of anomaly detection rather than classification and propose a model based on anomaly detection, which can better handle unbalanced class distribution and effectively detect the infrequent, aggressive episodes of pigs. The model consists of a convolutional neural network (CNN) and a variational long short-term memory (LSTM) autoencoder. Additionally, we adopted a training method similar to weakly supervised anomaly detection and included a few aggressive behavior data in the training set for prior learning. To effectively utilize the aggressive behavior data, we created Reconstruction Loss Inversion, a novel objective function, to train the autoencoder-based model to increase the reconstruction error of aggressive behaviors by inverting the loss function. Our anomaly detection approach significantly outperforms traditional classification-based methods, effectively identifying aggressive behaviors in a natural farming environment. This method offers a robust solution for detecting aggressive animal behaviors and contributes to improving their welfare.

The silos built in the 1930s for Italy’s ammasso (obligatory grain stockpile) stood as powerful symbols of the country’s fascist era. Many of them were destroyed in World War II; only a few remain today, and recent demolitions underscore the urgency of their preservation. This study adapts a methodology developed for inventorying Spanish silos based on their general features, construction, technological facilities, and socioeconomic aspects and applies it to the 30 remaining ammasso silos. These silos are located in grain-producing areas near communication routes and are mostly owned by agricultural consortia. Over half of them are disused and in disrepair. All of them have machinery for receiving, storing, and dispatching grain, and most have equipment for cleaning, sorting, weighing, and packaging if needed. These structures are part of Italy’s agro-industrial heritage and should be protected. Some have been made over into commercial spaces, leisure areas, museums, and even homes. Vertical-cell silos are challenging to convert, unlike horizontally-oriented silos and other open-plan agro-industrial buildings. Examples of silo reuse in other countries, such as Spain and Portugal, can offer useful insights for the ammasso silos. However, socio-economic indicators suggest that such projects are most viable in large population centres.

This paper discusses the application and advantages of artificial intelligence technology in digital media interactive product design. Firstly, the development background of artificial intelligence technology and its promoting effect on design innovation is introduced, and the application of new technologies, such as generative adversarial networks in art creation and design personalization, is definitely analyzed. It then explores in detail the ability of AI to break traditional constraints in interactive design, innovate design, and optimize user experience, especially in digital media. Finally, the case study of Microsoft Cortana shows the method of classifying and processing user queries by machine learning system and its experimental results. The research of this paper provides the theoretical basis and empirical support for the application of artificial intelligence technology in the future interactive design of digital media and has important academic and practical significance.

In this paper we describe a method which combines sentiment analysis with machine learning techniques and/or multivariate statistical analysis. By applying this methodology it is possible to classify a collection of texts into two or more groups or clusters. On the basis of a number of previously defined clusters, the novelty of the outlined approach is the use of the sentiment analysis results as input to the machine learning model or multivariate statistical analysis. Once the classifier has been obtained, we can assign a given text into one of the pre-established clusters. The groups or clusters can represent different time periods, classes of texts transcribed from different conversations, etc. The method is illustrated through an example taken from one of the two studies in which we have applied this methodology. In one of the studies, the method was used to classify press news of a volcanic eruption, while in the other study it was used to classify the conversations recorded between a chatbot with different kinds of speakers (humans or chatbots). This last study was the seminal work in which we introduced this methodology.

(1) Background: the NGS based mutational study of hereditary cancer genes is crucial to design tailored prevention strategies in subjects with different hereditary cancer risk. The ease of amplicon-based NGS library construction protocols contrasts with the greater uniformity of enrichment provided by capture-based protocols and so with greater chances for detecting larger genomic rearrangements and copy-number variations. Capture-based protocols, however, are characterized by a higher level of complexity of sample handling, extremely susceptible to human bias. Robotics platforms may definitely help dealing with these limits, reducing hands-on time, limiting random errors and guaranteeing process standardization. (2) Methods: We implemented and validated the complete automation of the SOPHiA GENETICS’ CE-IVD Hereditary Cancer Solution™ (HCS) libraries preparation workflow on the Hamilton’s STARlet platform. (3) Results: We demonstrate that this automated workflow, used for more than 1000 samples achieved the same performances of manual setup in terms of coverages and reads uniformity, with extremely lower variability of reads mapping rate onto the regions of interest. (4) Conclusions: This automated solution offers same reliable and affordable NGS data, but with the essential advantages of a flexible, automated and integrated framework, minimizing possible human errors and depicting a laboratory’s walk-away scenario.

The COVID-2019 disease caused by the SARS-CoV-2 virus (aka 2019-nCoV) has raised significant health concerns in China and worldwide. While novel drug discovery and vaccine studies are long, repurposing old drugs against the COVID-2019 epidemic can help identify treatments, with known preclinical, pharmacokinetic, pharmacodynamic, and toxicity profiles, which can rapidly enter Phase 3 or 4 or can be used directly in clinical settings. In this study, we presented a novel network based drug repurposing platform to identify potential drugs for the treatment of COVID-2019. We first analysed the genome sequence of SARS-CoV-2 and identified SARS as the closest disease, based on genome similarity between both causal viruses, followed by MERS and other human coronavirus diseases. Using our AutoSeed pipeline (text mining and database searches), we obtained 34 COVID-2019-related genes. Taking those genes as seeds, we automatically built a molecular network for which our module detection and drug prioritization algorithms identified 24 disease-related human pathways, five modules and finally suggested 78 drugs to repurpose. Following manual filtering based on clinical knowledge, we re-prioritized 30 potential repurposable drugs against COVID-2019 (including pseudoephedrine, andrographolide, chloroquine, abacavir, and thalidomide) . We hope that this data can provide critical insights into SARS-CoV-2 biology and help design rapid clinical trials of treatments against COVID-2019.

Japanese encephalitis is a zoonotic disease caused by Japanese encephalitis virus (JEV). It is mainly epidemic in Asia with an estimated 69,000 cases occurring per year. However, no approved agents are available for the treatment of JEV infection, and existing vaccines cannot resist various types of JEV strains. Drug repurposing is a new concept for finding new indication of existing drugs, and recently, it has been used to discover new antiviral agents. Identifying host proteins involved in the progress of JEV infection and using these proteins as targets are the center of drug repurposing for JEV infection. In this study, based on the gene expression data of JEV infection and the phenome-wide association study (PheWAS) data, we identified 286 genes participating in the progress of JEV infection using the systems biology methods. The enrichment analysis of these genes suggested that the genes identified by our methods were predominantly related to viral infection pathways and immune response-related pathways. We found that bortezomib which can target these genes may have potential effect on the treatment of JEV infection. Subsequently, we evaluated the antiviral activity of bortezomib using the JEV-infected mice model. The results showed that bortezomib can lower JEV-induced lethality in mice, alleviate suffering in JEV-infected mice and reduce the damage in brains caused by JEV infection. This work provides a new method for the development of antiviral agents.

The main contribution of this paper is to develop a graphical tool to evaluate the suitability of a candidate parametric model to fit a data set. The practical motivation is to check the adequacy of the so called SAINT model proposed in Jarner and Kryger (2011). This model has been implemented in practice by an important European pension fund concerned with setting annuity reserves for all current or former employees of Denmark. So, one particular relevant question is whether this mortality model is actually fitting old-age. Our graphical test can be described as follows. First we transform the data by means of the parametric model which is being evaluated. Should the model be correct, the transformed data will be in accordance with an Exponential distribution with rate 1. Then we construct a family of local linear hazard estimates based on the data on the transformed scale. Finally we use the statistical tool SiZer to assess the goodness-of-fit of the Exponential distribution to the data on the transformed scale. If the model is correct the SiZer map should not reveal any significant feature in the family of kernel estimates. Our method allow us to establish a diagnostic regarding the validity of the SAINT model when describing mortality patterns in four different countries.

(1) Background: Emotional resilience is defined as the capacity of individuals to cultivate positive emotions and effectively navigate through negative emotions in terms of stress or adversity. Recent research has focused on the significant impact of adolescents’ negative emotions, as opposed to positive emotions, on mental health. The examination of positive emotion provides a distinct viewpoint on the relationship between emotional resilience and mental health in adolescents. Consequently, the current research conducted two separate investigations to examine the impact of adolescent emotional resilience on mental health, as well as the mediating influence of positive emotion. (2) Methods: Study 1 comprised a cross-sectional analysis of 3086 Chinese adolescents, while Study 2 involved a longitudinal examination of 266 Chinese adolescents. (3) Results: Results indicated that emotional resilience was associated with enhanced levels of life satisfaction, self-esteem, and overall mental health, while also demonstrating a negative correlation with symptoms of depression and anxiety. Positive emotions were found to have a partial mediating effect on the relationship between emotional resilience and mental health. These results indicate that emotional resilience not only has a direct impact on mental health but also influences mental health indirectly through positive emotions. (4) Conclusions: The findings highlighted the role of emotional resilience in mitigating psychological problems and enhancing mental health in Chinese adolescents. The implications and limitations were discussed.

Device to Device (D2D) is a pivotal technology in the next generation of communication, allowing for direct task offloading between mobile devices (MDs) to improve the efficient utilization of idle resources. This paper proposes a novel algorithm for dynamic task offloading between active MDs and idle MDs in the D2D-MEC (Mobile Edge Computing) system by deploying multi-agent deep reinforcement learning (DRL) to minimize the long-term average delay of delay-sensitive tasks under deadline constraints. Our core innovation is a dynamic partitioning scheme for idle and active devices in the D2D-MEC system, accounting for stochastic task arrivals and multi-time-slot task execution, which has been insufficiently addressed in existing literature. We adopt a queue-based system to formulate a dynamic task offloading optimization problem. To address the challenges of large action space and coupling of actions across time slots, we model the problem as a Markov Decision Process (MDP) and perform the multi-agent DRL through Multi-Agent Proximal Policy Optimization (MAPPO). We employ a centralized training with decentralized execution (CTDE) framework to enable each MD to make offloading decisions solely based on its local system state. Extensive simulations demonstrate the efficiency and fast convergence of our algorithm. In comparison with the existing sub-optimal results deploying single-agent DRL, our algorithm reduces the average task completion delay by 11.0% and the ratio of dropped tasks by 17.0%.

The “circular bioeconomy” offers numerous opportunities for the health, cosmetic, and nutrition sectors through the potential reuse of Castanea sativa by-products. This abundant and sustainable resource provides valuable bioactive secondary metabolites with antioxidants and anti-inflammatory properties. The transformation of these by-products into high-value products for human health can contribute to sustainable economic growth and reduce the environmental impact of traditional waste disposal practices, thus creating added value from previously underutilized resources. In the present study, we investigated the antioxidant capacity, phytochemical composition and in vitro antioxidant and anti-inflammatory activity of C. sativa burrs (CSB) aqueous extract. The spectrophotometric study yielded optimal total phenolic content (TPC) values, along with significant antioxidant and anti-radical properties. The utilization of UPLC-MS-MS techniques for phytochemical investigation resulted in the identification of a total of 56 metabolites, providing confirmation of the presence of phenolic compounds in CSB. In addition, CSB significantly downregulated pro-inflammatory mediators in LPS-stimulated RAW 264.7 macrophage cells without significant cell toxicity.

Repurposing previously approved drugs may fast track the route to clinic for potential senotherapeutics and improves the inefficiency of the clinical drug development pipeline. We carried out a repurposing screen of 240 clinically approved molecules in human primary dermal fibroblasts for effects on CDKN2A expression. Molecules demonstrating effects on CDKN2A expression underwent secondary screening for senescence-associated beta galactosidase (SAB) activity, based on effect size, direction and/or molecule identity. Selected molecules then underwent a more detailed assessment of senescence phenotypes including proliferation, apoptosis, DNA damage, senescence-associated secretory phenotype (SASP) expression and regulators of alternative splicing. A selection of the molecules demonstrating effects on senescence were then used in a new bioinformatic structure-function screen to identify common structural motifs. 90 molecules displayed altered CDKN2A expression at one or other dose, of which 15 also displayed effects on SAB positivity in primary human dermal fibroblasts. Of these, three were associated with increased SAB activity, and 11 with reduced activity. The female synthetic sex hormones; diethylstilboestrol, ethynyl estradiol and levonorgestrel; were all associated with a reduction in aspects of the senescence phenotype in male cells, with no effects visible in female cells. Finally, we identified that the 30 compounds that decreased CDKN2A activity the most had a common substructure linked to this function. Our results suggest that several drugs licenced for other indications may warrant exploration as future senotherapies, but that different donors and potentially different sexes may respond differently to senotherapeutic compounds. This underlines the importance of consideration of donor-related characteristics when designing drug screening platforms.

Drug repurposing, the practice of utilizing existing drugs for novel clinical indications, has tremendous potential for improving human health outcomes and increasing therapeutic development efficiency. The goal of multidisease multitarget drug repurposing, also known as shotgun drug repurposing, is to develop platforms that assess the therapeutic potential of each existing drug for every clinical indication. Our Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget repurposing implements several pipelines via large scale modelling and simulation of interactions between comprehensive libraries of drugs/compounds and protein structures. In these pipelines, each drug is described by an interaction signature that is then compared to all other signatures that are then sorted and ranked based on similarity. Pipelines within the platform are benchmarked based on their ability to recover known drugs for all indications in our library, and predictions are generated based on the hypothesis that (novel) drugs with similar signatures may be repurposed for the same indication(s). The drug-protein interactions in the platform used to create the drug-proteome signatures may be determined by any screening or docking method but the primary approach used thus far has been an in house similarity docking protocol. In this study, we calculated drug-proteome interaction signatures using the publicly available molecular docking method Autodock Vina and created hybrid decision tree pipelines that combined our original bio- and cheminformatic approach with the goal of assessing and benchmarking their drug repurposing capabilities and performance. The hybrid decision tree pipeline outperformed the corresponding two docking-based pipelines it was synthesized from, yielding an average indication accuracy of 13.3% at the top10 cutoff (the most stringent), relative to 10.9% and 7.1% for its constituent pipelines, and a random control accuracy of 2.2%. We demonstrate that docking based virtual screening pipelines have unique performance characteristics and that the CANDO shotgun repurposing paradigm is not dependent on a specific docking method. Our results also provide further evidence that multiple CANDO pipelines can be synthesized to enhance drug repurposing predictive capability relative to their constituent pipelines. Overall, this study indicates that pipelines consisting of varied docking based signature generation methods can capture unique and useful signal for accurate comparison of drug-proteome interaction signatures, leading to improvements in the benchmarking and predictive performance of the CANDO shotgun drug repurposing platform.

Multimodal remote sensing data classification can enhance the model’s ability to distinguish land features through multimodal data fusion. In this context, how to help models understand the relationship between multimodal data and target tasks is the focus of researchers. Inspired by human feedback learning mechanisms, causal reasoning mechanisms, and knowledge induction mechanisms, this paper integrates causal learning, reinforcement learning, and meta learning into a unified remote sensing data classification framework and proposed the causal meta-reinforcement learning (CMRL). First, based on feedback learning mechanisms, we have overcome the limitations of traditional implicit optimization of fusion features and customized a reinforcement learning environment for multimodal remote sensing data classification tasks. Through feedback interactive learning between agents and the environment, we help them understand the complex relationships between multimodal data and labels, thereby achieving full mining of multimodal complementary information. Second, based on the causal inference mechanism we designed causal distribution prediction action, classification reward, and causal intervention reward, capturing pure causal factors in multimodal data and cutting off false statistical associations between non-causal factors and class labels. Finally, based on the knowledge induction mechanism, we designed a bi-layer optimization mechanism based on meta-learning. By constructing a meta training task and meta validation task simulation model in the generalization scenario of unseen data, we helped the model induce cross-task shared knowledge, thereby improving its generalization ability for unseen multimodal data. The experimental results on multiple sets of multimodal datasets show that the proposed method achieved state-of-the-art performance in multimodal remote sensing data classification tasks.

The essence of cross-modal generation and retrieval modeling for image-text interactions lies in semantic consistency. Among these, cross-modal representation alignment serves as the foundational requirement for achieving cross-modal semantic consistency. The crux of our proposed method entails the collaborative training of an image captioning model(referred to as the ’captioner’) and a pair of contrastive encoders for image-text matching(referred to as the ’concoder’). This synergistic approach yields concurrent enhancements in concoder’s performance, captioner’s proficiency, and cross-modal semantic coherence. We coin the proposed method as ‘ReCap’. To begin, we initialize the concoder through knowledge distillation from a pre-trained model. During the training process, we use the output of the initialized concoder as input to a residual attention network, jointly training it with the captioner to achieve semantic consistency. Subsequently, we iteratively update the concoder during the image-text momentum encoding phase using the residual attention network, creating a closed-loop for semantic consistency resolution. Upon completion of training, the concoder and captioner modules can be used independently to perform tasks related to cross-modal retrieval and cross-modal generation of text and images. In order to substantiate the efficacy of our proposed method, we initially conducted empirical experiments encompassing image-text retrieval and image captioning tasks, employing a widely recognized benchmark dataset, MSCOCO. Subsequently, we assessed the fine-grained cross-modal alignment performance of the concoder through an image classification task on the iNaturalist 2018 dataset. The achieved performance metrics notably surpassed those achieved by several incumbent state-of-the-art models, thus validating the proficiency of our method. Finally, motivated by the practical requirements of handling the nature conservation image data, we performed caption annotation for the iNaturalist 2018 dataset. Subsequently, we trained the ReCap on this annotated data. Experimental results demonstrate that our proposed method can maintain semantic consistency between cross-modal retrieval and image caption generation for species with similar visual features but distinct semantics. This achievement signifies a meaningful exploration in the field of cross-modal semantic consistency representation, holding significant practical value in the domain of biological research.

Quantum computing (QC) has opened the door to advancements in machine learning (ML) tasks that are currently implemented in the classical domain. Convolutional neural networks (CNNs) are classical ML architectures that exploit data locality and possess a simpler structure than fully-connected multi-layer perceptrons (MLPs) without compromising the accuracy of classification. However, the concept of preserving data locality is usually overlooked in the existing quantum counterparts of CNNs, particularly for extracting multi-features in multidimensional data. In this paper, we present a multidimensional quantum convolutional classifier (MQCC) that performs multidimensional and multi-feature quantum convolution with average and Euclidean pooling and thus adapting the CNN structure to a variational quantum algorithm (VQA). Average pooling is based on the quantum Haar transform (QHT) and Euclidean pooling is based on partial quantum measurement. The experimental work was conducted using multidimensional data to validate the correctness and demonstrate the scalability of the proposed method utilizing both noisy and noise-free quantum simulations. We evaluated the MQCC model with reference to reported work on state-of-the-art quantum simulators from IBM Quantum and Xanadu using a variety of standard ML datasets. The experimental results showed favorable characteristics of our proposed techniques compared to existing work with respect to a number of quantitative metrics such as the number of training parameters, cross-entropy loss, classification accuracy, circuit depth, and quantum gate count.

(1)Background: Fascioliasis is considered a neglected tropical disease affecting an estimated 17 million people in more than 70 countries worldwide. The highest prevalence of human fascioliasis is found in regions where livestock farming and consumption of raw or undercooked freshwater plants are common, such as parts of Africa, Asia, Europe, and Latin America. It is responsible for over 90,000 disability-adjusted years of life due to associated abdominal complications. We conducted a study to investigate the prevalence of human fascioliasis through a systematic review and meta-analysis of all available literature in Sun-Saharan Africa.(2). Methods: We screened a total of 126 publications using pubmed online search engine databases; Web of Science and CAB for articles published within a 20-year period between 2000 and 2022. We used a comprehensive search method using a combination of terms, parasite and disease names. The initial search resulted in a screening of articles by title, abstracts and full texts. The relevant information on the prevalence of human fascioliasis in Africa was extracted. Of the 126 publications, 33 articles were selected for meta-analysis. The essential information required was extracted from these documents and determined through statistical analysis in Microsoft Excel for calculating the prevalence of human fascioliasis in sub-Saharan Africa. The variance of each study was assessed using a bimodal distribution and heterogeneity assessment using a I2 index. Analysis was performed using random effects models.(3)Results: A total of 271 articles were searched through the database search and 33 articles were eligible studies that provided qualitative information on the prevalence of human fascioliasis in Africa. These make up 12.17% (n=33). The pooled prevalence estimates for human fascioliasis are 0.032% (IVhet PPE: 0.032% (95%CI 1.4-6.53). The highest prevalence rate was observed in Egypt with a prevalence of 100%. The prevalence of human fascioliasis is very high in some sub-Saharan countries, partly due to neglect of diagnostics, demonstrating the bias of available information for decision-making in human fascioliasis across Africa, given the spatial presence, scarcity and incompleteness are region.(4)Conclusions: The prevalence of Human fascioliasis is very high in some Sub-Saharan Countries partly due to neglect in diagnostics. This presents how highly focal with spatial occurrences, scarcity and patchy the available information for decision making is on Human fascioliasis across the Sub-Saharan African region.

The present grievous situation of the tuberculosis disease can be improved by efficient case management and timely follow-up evaluations. With the advent of digital technology this can be achieved by quick summarization of the patient-centric data. The aim of our study was to assess the effectiveness of the ODK Scan paper-to-digital system during testing period of three months. A sequential, explanatory mixed-method research approach was employed to elucidate technology use. Training, smartphones, application and 3G enabled SIMs were provided to the four field workers. At the beginning, baseline measures of the data management aspects were recorded and compared with endline measures to see the impact of ODK Scan. Additionally, at the end, users’ feedback was collected regarding app usability, user interface design and workflow changes. 122 patients’ records were retrieved from the server and analysed for quality. It was found that ODK Scan recognized 99.2% of multiple choice bubble responses and 79.4% of numerical digit responses correctly. However, the overall quality of the digital data was decreased in comparison to manually entered data. Using ODK Scan, a significant time reduction is observed in data aggregation and data transfer activities, however, data verification and form filling activities took more time. Interviews revealed that field workers saw value in using ODK Scan, however, they were more concerned about the time consuming aspects of the use of ODK Scan. Therefore, it is concluded that minimal disturbance in the existing workflow, continuous feedback and value additions are the important considerations for the implementing organization to ensure technology adoption and workflow improvements.

Viral integration within the host genome plays a pivotal role in carcinogenesis. Various disruptive mechanisms are involved, leading to genomic instability, mutations, and DNA damage. With next-generation sequencing (NGS), we can now precisely identify viral and host genomic breakpoints and chimeric sequences, which are useful for integration site analysis. In this study, we evaluated a commercial hybrid-capture NGS panel specifically designed for detecting three key viruses: HPV, HBV, and HIV-1. We also tested workflows for Viral Hybrid Capture (VHC) and Viral Integration Site (VIS) analysis, leveraging customized viral databases in CLC Microbial Ge-nomics. By analyzing sequenced data from virally infected cancer cell lines (including SiHa, HeLa, CaSki, C-33A, DoTc2, 2A3, SCC154 for HPV; 3B2, SNU-182 for HBV; and ACH-2 for HIV-1), we precisely pinpointed viral integration sites. The workflow also highlighted disrupted and neigh-boring human genes that may play a crucial role in tumor development. Our results included in-formative virus-host read mappings, genomic breakpoints, and integration circular plots. These visual representations enhance our understanding of the integration process. In conclusion, our seamless end-to-end workflow bridges the gap in understanding viral contributions to cancer development, paving the way for improved diagnostics and treatment strategies.

Coronavirus-infected diseases have posed great threats to human health. In past years, highly infectious coronavirus-induced diseases, including COVID-19, SARS, and MERS, have resulted in world-wide severe infections. Our literature annotations identified 110 chemical drugs and 26 antibodies effective against at least one human coronavirus infection in vitro or in vivo. Many of these drugs inhibit viral entry to cells and viral replication inside cells or modulate host immune responses. Many antimicrobial drugs, including antimalarial (e.g., chloroquine and mefloquine) and antifungal (e.g., terconazole and rapamycin) drugs as well as antibiotics (e.g., teicoplanin and azithromycin) were associated with anti-coronavirus activity. A few drugs, including remdesivir, chloroquine, favipiravir, and tocilizumab, have already been reported to be effective against SARS-CoV-2 infection in vitro or in vivo. After mapping our identified drugs to three ontologies ChEBI, NDF-RT, and DrON, many features such as roles and mechanisms of action (MoAs) of these drugs were identified and categorized. For example, out of 57 drugs with MoA annotations in NDF-RT, 47 have MoAs of different types of inhibitors and antagonists. A total of 29 anticoronaviral drugs are anticancer drugs with the antineoplastic role. Two clustering analyses, one based on ChEBI-based semantic similarity, the other based on drug chemical similarity, were performed to cluster 110 drugs to new categories. Moreover, differences in physicochemical properties among the drugs were found between those inhibiting viral entry and viral replication. A total of 163 host genes were identified as the known targets of 68 anti-coronavirus drugs, resulting in a network of 428 interactions among these drugs and targets. Chlorpromazine, dasatinib, and anisomycin are the hubs of the drug-target network with the highest number of connected target proteins. Many enriched pathways such as calcium signaling and neuroactive ligand-receptor interaction pathways were identified. These findings may be used to facilitate drug repurposing against COVID-19.

In a dynamic production processes, mechanical degradation poses a significant challenge, impacting product quality and process efficiency. This paper explores a novel approach for monitoring degradation in the context of viscose fiber production, a highly dynamic manufacturing process. Using causal discovery techniques, our method allows domain experts to incorporate background knowledge into the creation of causal graphs. Further, it enhances the interpretability and increases the ability to identify potential problems via changes in causal relations over time. The case study employs a comprehensive analysis of the viscose fiber production process within a prominent textile industry, emphasizing the advantages of causal discovery for monitoring degradation. The results are compared with state-of-the-art methods, which are not considered to be interpretable, specifically LSTM-based autoencoders, showcasing the alignment and validation of our approach. This paper provides valuable information on degradation monitoring strategies, demonstrating the efficacy of causal discovery in dynamic manufacturing environments. The findings contribute to the evolving landscape of process optimization and quality control.

Aims: To date, precision medicine plays a pivotal role in the clinical administration of solid tumor patients. In this scenario, a rapidly increasing number of predictive biomarkers have been approved in diagnostic practice or are currently investigated in clinical trials. A pitfall in the molecular tests is the diagnostic routine sample available to analyze predictive biomarkers; scant tissue sample often represents the only diagnostical source of nucleic acids to assess molecular analysis. At the sight of these critical issues, Next Generation Sequencing (NGS) platforms emerged as referral testing strategy for molecular analysis of predictive biomarkers in routine practice but high-skilled personnel, extensive working-time drastically impact on the widespread diffusion of this technology in diagnostic setting. Here, we technically validate a fully integrated NGS platform on diagnostic routine tissue samples previously tested with NGS based diagnostic workflow by a referral institution. Methods: A retrospective series of n=64 samples (n=32 DNA, n=32 RNA samples), previously tested using a customized NGS assay (SiRe™ and SiRe fusion) were retrieved from internal archive of University of Naples Federico II. Each sample was tested by adopting Oncomine Precision Assay (OPA), able to detect 2769 molecular actionable alterations [hot spot mutations, copy number variations (CNV) and gene fusions on fully integrated NGS platform (Genexus, Thermofisher Scientifics. (26,27) Concordance rate between these technical approaches was carried out. Results: Genexus system successfully carried out molecular analysis in all instances. A concordance rate of 96.9% (31 out of 32) was observed between OPA and SiRe™ panel both for DNA and RNA based analysis. A negative predictive value of 100% and a positive predictive value of 96.9% (62 out of 64) was assessed. Conclusions: Fully automatized Genexus system combined with OPA (Thermofisher Scientifics) may be considered a technically valuable, saving time sequencing platform to test predictive biomarkers in diagnostic routine practice.

Background: Advancements in the next-generation sequencing (NGS) techniques have allowed for efficient genetic variant detection at reduced costs. Methods: We describe an ad hoc NGS-based custom designed resequencing gene panel to identify genetic variants in 8 patients with dementing disorders. Results: We found variants of TREM2 and APP genes in three patients; these have been previously identified as pathogenic or likely pathogenic and, therefore, considered as “Disease Causing”. In the remaining subjects, the pathogenicity was evaluated on the in silico analysis, according to the guidelines of the American College of Medical Genetics. In one patient, the p.R205W variant was causative of the disease, thus considered as “Possibly Disease Causing”. The variants found from the other four subjects in the CSF1R, SERPINI1, GRN, and APP genes revealed discordant in silico results and, therefore, it was not possible to assign a definitive pathogenicity. Conclusions: Notwithstanding the limitations of a customized panel, we detected some rare genetic variants with a probable disease association. The future application of NGS techniques and the further replication of these experimental data will replace the so-called “gene by gene” approach with a “panel of genes” strategy, that offers promising perspectives in the diagnosis and management of neurodegenerative disorders.

The abstract should be a total of about 250 words and structured to contain the following headings: Background/Objectives, Methods, Results, Conclusions. Background/Objectives: Place the question addressed in a broad context and highlight the purpose of the study; Methods: Describe briefly the main methods or treatments applied. Include any relevant preregistration numbers, and species and strains of any animals used; Results: Summarize the article’s main findings; Conclusions: Indicate the main conclusions or interpretations. The abstract should be an objective representation of the article: it must not contain results which are not presented and substantiated in the main text and should not exaggerate the main conclusions. Clinical trial abstracts should include items that the CONSORT group has identified as essential.

Beginning in 2022, the Mpox outbreak, formerly known as monkeypox, has since spread to more than 100 countries and is now a global public health concern. This disease, caused by the Mpox virus, is usually mild, and most infected individuals recover within a few weeks without treatment. However, severe cases have been seen especially in children, pregnant women, or immunocompromised individuals. Antiviral medications such as brincidofovir, tecovirimat, and cidofovir were recently approved for Mpox; but these drugs are expensive and not easily obtainable. Therefore, identifying effective and low-cost drugs against Mpox and testing these through clinical trials remains a priority for global health. Drug repurposing is a well-known strategy for redeploying existing licensed drugs for newer indications, allowing for the shortest possible transition from bench to bedside. Recent in silico studies have determined the efficacy of minocycline, oleanolic acid, ursolic acid, and glycyrrhizinic acid against Mpox virus. Notably, oleanolic acid, ursolic acid, and glycyrrhizinic acid are some of the components of Japanese Kampo medicines, which are low-cost medicines prescribed daily in Japan. Thus, minocycline and Japanese Kampo medicines could potentially be used to treat Mpox.

The open data market is growing, driven by laws requiring governments to make data publicly available. However, the true value of this market lies in the products and services derived from open data. In Slovenia, the open data market has been growing since 2015, especially in the field of mobility. Platforms such as Avtolog.si facilitate the retrieval of vehicle data via vehicle identification numbers, while tocen.si, ojpp.si, and brezavta.si aggregate mobility data, focusing on sustainable and micromobile public transportation services. These platforms use open government data and private sector open data, and are freely accessible. This study examines the use of open data in the Slovenian mobility applications and similar solutions developed in other countries. By mapping these applications, we gain valuable insights into potential advances in the field, and provide a useful resource for future developers worldwide. By focusing on the socio-economic impact of these innovations, the study identifies methods for evaluating such applications. This approach highlights how transforming open data into user-friendly products and services can deepen our understanding of their broader societal and economic benefits. While open data is valuable in its own right, its full transformative potential is realized through innovative products that support sustainable lifestyles and promote environmentally conscious behavior.

Amidst the escalating demands for efficient Intelligent Transportation Systems (ITS) management, the significance of accurate Origin-Destination (OD) data prediction has emerged as a paramount concern, given its indispensable role in the ITS domain. This paper introduces a groundbreaking integrated model, creatively fusing the unique strengths of Graph Convolutional Network (GCN), Residual Neural Network (ResNet), and Long Short-Term Memory Network (LSTM) into a single architecture, which we name GraphResLSTM, to exploit road segment average speed data for OD prediction. Compared with conventional road segment traffic volume data, average speed data is more readily available, significantly reducing the data accessibility barrier for OD prediction. We underscore the critical role of selection of key road segments and employs a combination of Entropy Weight Method and Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) to identify 41 representative road segments from the experimental road network. In the experimental phase, we simulate 86400000 seconds of traffic conditions, generating a total of 1440000 data records. Utilizing these simulated data, we design and conduct comparative experiments between models as well as data types. The results demonstrate that both the GraphResLSTM model and road segment average speed data outperform other models and data types notably in OD prediction tasks.

The increasing demand for large-scale, high-frequency environmental monitoring has driven the adoption of satellite-based technologies for effective forest management, especially in the context of climate change. This study explores the potential of SAR for estimating the mass of harvesting residues, a significant component of forest ecosystems that impacts nutrient cycling, fire risk, and bioenergy production. The research hypothesizes that while the spatial distribution of residues remains stable, changes in moisture content—reflected in variations in the dielectric properties of the woody material—can be detected through SAR techniques. Two models, generalized linear model (GLM) and random forest (RF), were used to predict the mass of residues using interfer-ometric variables (phase, amplitude and coherence) as well as the backscatter signal from several acquisition pairs. The models provided encouraging results (R2 of 0.48 for GLM and 0.13 for RF), with acceptable bias and RMSE. We concluded that SAR data are feasible to predict the mass of harvesting residues and the findings could lead to improved monitoring and management of forest residues, contributing to sustainable forestry practices and enhanced bioenergy resource utilization.

Background:Advanced heart failure is characterized by repeated hospital admissions due to recurring need for intravenous inotropes. Among the most commonly used medications used in this context, is milrinone, which increases the myocardial relaxation velocity, what is known as lusitropy. This effect is mediated by increasing cyclic AMP, which in turn switches on phospholamban activity, an enzyme promoting calcium reuptake by sarcoplasmic reticulum. The aim of this review is to shed light on oral medications that can play a similar role by alternative pathways. Main Body:Phospholamban can be as well stimulated by cGMP, the latter is known to be increased by medications which inhibit phosphodiesterase 5. Two well-established drugs can perform this action and are currently exclusively used as vasodilators, namely sildenafil and tadalafil. Another emerging hope is vericiguat, a medication that can directly stimulates guanylyl cyclase, leading to increase in cGMP. Conclusion:We speculate that the possible introduction of these oral medications is thought to replace the need for repeated hospital and intensive care admissions. This also might mean, delaying the necessity for mechanical support or transplantations, which can change the face of advanced or end-stage heart failure.

Respiratory transmission is the primary route of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. Angiotensin I converting enzyme 2 (ACE2) is the known receptor of SARS-CoV-2 surface spike glycoprotein for entry into human cells. A recent study reported absent to low expression of ACE2 in a variety of human lung epithelial cell samples. Three bioprojects (PRJEB4337, PRJNA270632 and PRJNA280600) invariably found abundant expression of ACE1 (a homolog of ACE2 and also known as ACE) in human lungs compared to very low expression of ACE2. In fact, ACE1 has a wider and more abundant tissue distribution compared to ACE2. Although it is not obvious from the primary sequence alignment of ACE1 and ACE2, comparison of X-ray crystallographic structures show striking similarities in the regions of the peptidase domains (PD) of these proteins, which is known (for ACE2) to interact with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Critical amino acids in ACE2 that mediate interaction with the viral spike protein are present and organized in the same order in the PD of ACE1. In silico analysis predicts comparable interaction of SARS-CoV-2 spike protein with ACE1 and ACE2. In addition, this study predicts from a list of 1263 already approved drugs that may interact with ACE2 and/or ACE1, potentially interfere with the entry of SARS-CoV-2 inside the host cells and alleviate the symptoms of Coronavirus disease (COVID-19).