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.

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.

Proteolysis Targeting Chimeras (PROTACs) describe compounds that bind to and induce degradation of a target by simultaneously binding to a ubiquitin ligase. More generally referred to as bifunctional degraders, PROTACs have led the way in the field of targeted protein degradation (TPD) with several compounds currently undergoing clinical testing. Alongside bifunctional degraders, single-moiety compounds, or molecular glue degraders (MGDs), are increasingly being considered as a viable approach for development of therapeutics, driven by advances in rational discovery approaches. This review focusses on drug discovery with respect to bifunctional and molecular glue degraders within the ubiquitin proteasome system, including analysis of mechanistic concepts and discovery approaches, with an overview of current clinical and pre-clinical degrader status in oncology, neurodegenerative and inflammatory disease.

This study introduces a novel computational approach for testing conditional independence (BB CI test) within causal Directed Acyclic Graphs (DAGs), leveraging Bayesian non-parametric bootstrap and machine learning techniques. Our method offers an alternative for validating the assumptions underpinning causal DAGs. Through simulation studies and an industrial case analysis, we demonstrate the test procedure in accurately assessing conditional independence, comparing it with the Generalized Covariance Measure (GCM) test. Our findings suggest that the BB CI test is advantageous in scenarios where existing methods may falter due to violations of model assumptions. This research contributes to the causal inference literature by providing a computational tool for researchers and practitioners to validate causal models.

In this study, the causal-effect between carbon dioxide emissions and forestry production and trade was investigated in Ghana by employing a data spanning from 1961 to 2014 by using the VECM and ARDL model. Evidence of the long-run equilibrium relationship in the VECM shows that, a 1% increase in veneer sheet production reduces carbon dioxide emissions by 1.47% in the long-run. There was evidence of a bidirectional causality between carbon dioxide emissions and veneer sheet production, carbon dioxide emissions and wood charcoal production, and a unidirectional causality running from carbon dioxide emissions to wood fuel production and plywood production to carbon dioxide emissions. Evidence from the long-run equilibrium relationship in the ARDL model shows that; a 1% increase in plywood production will increase carbon dioxide emissions by 0.17% in the long-run, a 1% increase in sawnwood production will increase carbon dioxide emissions by 0.17% in the long-run, a 1% increase in wood charcoal production will increase carbon dioxide emissions by 0.36% in the long-run and a 1% increase in wood fuel production will increase carbon dioxide emissions by 0.37% in the long-run.

The conventional explanation of delayed-choice experiments seems to violate our causal intuition. This apparent violation is caused by a misinterpretation of the conventional formulation of quantum mechanics. I reanalyze these experiments using advanced and time-symmetric formulations of quantum mechanics. All three formulations give the same experimental predictions, but the advanced and time-symmetric formulations violate our causal intuition that effects only happen after causes. I explore reasons why our causal intuition may be wrong at the quantum level. I also suggest how conventional causation might be recovered in the classical limit, and speculate on cosmological boundary conditions.

Based on screening in computational biology and biological in vitro assays, five natural products isolated from extracts of the herbal medicine toad skin, such as cinobufagin (CBFi), bufalin (BFi), arenobufagin (ABFi), telocinobufagin (TBFi), bufotalin (BFTi), were subjected to molecular docking calculations with the use of SARS-CoV-2 main protease (PDB 6LU7 and 7BTF) and top-scoring ligand-receptor complexes were obtained. The results showed that the binding energy of ABFi to the 3CL protein was -17.044kcal/mol, which was higher than CBFi and TBFi. However, the binding energy of ABFi to the RdRp protease was -23.250 kcal/mol, which was much lower than that of CBFi and TBFi, EVEN lower than that of ABFi to the 3CL protein. ABFi also has polar interactions with amino acids such as Glu811, Ser814, Ser681 and Thr680 of RdRp enzyme. The results revealed that ABFi had a moderate inhibitory effect on the cell proliferation of SARS-CoV-2 in vitro, with an inhibition rate of 61.12%, even weaker than Remdesivir. This new discovery provides us with new ideas for in-depth studies on the development of natural products with this class of structural generalizations as inhibitors of SARS-CoV-2, and provides an experimental basis for the next step of mechanistic studies.

Molecularly imprinted polymers (MIPs) were synthesized and applied for the selective extraction of oblongifolin C (OC) from fruit extracts of Garcinia yunnanensis Hu. A series of experiments and computational approaches were employed to improve the efficiency of screening for optimal MIP systems in the study. The molar ratio (1:4) was chosen at last based on the comparison of the binding energy of the complexes between the template (OC) and functional monomers using density functional theory (DFT) at the RI-PBE-D3-gCP/def2-TZVP level of theory. The binding characterization and the molecular recognition mechanism of MIPs were further explained using the molecular modeling method and NMR and IR spectra data. The reusability of this approach was demonstrated in over 20 batch rebinding experiments. 140.5 mg of OC (>95% purity) was obtained from the 5 g extracts with 2 g of MIPs with the best binding properties through gradient elution program from 35% to 70% methanol-water solution. At the same time, another structural analog, 46.5 mg of guttiferone K (GK) (>88% purity), was also obtained by the gradient elution procedure. Our results showed that the structural analogs could be separated from the crude extracts by the molecularly imprinted solid-phase extraction (MISPE) using a gradient elution procedure for the first time.

Lead optimization in drug discovery is a crucial phase where initial hits are refined into compounds with improved pharmacological properties. While traditional methods rely on manual experimentation and modifications, AI-driven techniques have revolutionized this process by leveraging big data and predictive modeling. This review explores how AI-driven approaches accelerate lead optimization, showcasing examples like deep neural networks and reinforcement learning. Integration of multi-omic data and experimental validation further enhances AI-driven strategies. The future lies in refining these AI methods, democratizing tools, and interdisciplinary collaboration to streamline drug discovery and address medical needs efficiently.

Artificial intelligence (AI) systems are poised to become deeply integrated into society. If developed responsibly, AI has potential to benefit humanity immensely. However, it also poses a range of risks, including risks of catastrophic accidents. It is crucial that we develop oversight mechanisms that prevent harm. This article outlines a framework for evaluating and auditing AI to provide assurance of responsible development and deployment, focusing on catastrophic risks. We argue that responsible AI development requires comprehensive auditing that is proportional to AI systems’ capabilities and available affordances. This framework offers recommendations toward that goal and may be useful in the design of AI auditing and governance regimes.

This article presents a state-of-the-art system to extract and synthesize causal statements from company reports into a directed causal graph. The extracted information is organized by the relevance to different stakeholder groups’ benefits (customers, employees, investors, and the community/environment). The presented method of synthesizing extracted data into a knowledge graph comprises a framework that can be used for similar tasks in other domains, e.g. medical information. The current work addresses the problem of finding, organizing, and synthesizing a view of the cause-and-effect relationships based textual data, in order to inform and even prescribe the best actions that may affect target business outcomes related to different stakeholders’ benefits (customers, employees, investors, and the community/environment).

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.

We propose a novel interpretation of consciousness and an enlarged definition of locality, which provide a solution to the problem of the consistency of measurements in quantum mechanics: consciousness is a characteristics of the Universe as a whole. Besides its physical conse- quences, this interpretation has also moral implications: individuality comes out naturally to be just an accident functional to evolution which shaped past and present history through competition, and re- alizing this fact should enforce cooperation.

Wilms tumor (WT), the most prevalent type of renal cancer in children, exhibits overall survival rates exceeding 90%. However, chemotherapy resistance, which occurs in approximately 10% of WT cases, is a major challenge for the treatment of WT, particularly for advanced-stage patients. In this study, we aimed to discover potential mutation markers and drug targets associated with chemotherapy resistance in advanced stage WT. We performed exome sequencing to detect somatic mutations and molecular targets in 43 WT samples, comprising 26 advanced stage WTs, of which 7 cases are chemotherapy-resistant. Our analysis revealed four genes (ALPK2, C16orf96, PRKDC, and SVIL) that correlated with chemotherapy resistance and reduced disease-free survival in ad-vanced-stage WT. Additionally, we identified driver mutations in 55 genes within the chemo-therapy-resistant group, including 14 druggable cancer driver genes. Based on the mutation profile of the resistant WT samples, we propose potential therapeutic strategies involving platinum-based agents, PARP inhibitors, and antibiotic/antineoplastic agents. Our findings provide insights into the genetic landscape of WT and offer potential avenues for targeted treatment, particularly for patients with chemotherapy resistance.

Recent research has highlighted associations between sleep and microbial taxa and pathways. However, the causal effect of these associations remains unknown. To investigate this, we performed a two-sample bidirectional Mendelian randomization (MR) analysis using summary statistics of genome-wide association studies (GWAS) from 412 gut microbiome traits (N = 7,738) and GWAS studies from seven sleep-associated traits (N = 345,552 to 386577). We employed multiple MR methods to assess causality, with Inverse Variance Weighted (IVW) as the primary method. We further applied Cochran’s Q statistical analysis, MR-Egger intercept, and MR-PRESSO for heterogeneity and pleiotropy assessment, alongside a Bonferroni correction ((P

We propose a partial information decomposition based on the newly introduced framework of causal tensors, i.e., multilinear stochastic maps that transform source data into destination data. The innovation that causal tensors introduce is that the framework allows for an exact expression of an indirect association in terms of the constituting, direct associations. This is not possible when expressing associations only in measures like mutual information or transfer entropy. Instead of a priori expressing associations in terms of mutual information or transfer entropy, the a posteriori expression of associations in these terms results in an intuitive definition of a nonnegative and left monotonic redundancy, which also meets the identity property. Our proposed redundancy satisfies the three axioms introduced by Williams and Beer. Symmetry and self-redundancy axioms follow directly from our definition. The data processing inequality ensures that the monotonicity axiom is satisfied. Because causal tensors can describe both mutual information as transfer entropy, the partial information decomposition applies to both measures. Results show that the decomposition closely resembles the decomposition of other another approach that expresses associations in terms of mutual information a posteriori. A negative synergistic term could indicate that there is an unobserved common cause.

Subseasonal-to-seasonal (S2S) weather forecasting has improved in recent years, thanks partly to better representation of physical variables in models. For instance, realistic initializations of snow and soil moisture in models yield enhanced predictability on S2S time scales. Snow depth and soil moisture also mediate month-to-month persistence of near-surface air temperature. Here the role of snow depth as predictor of temperature one month ahead in the Northern Hemisphere is probed via two causal pathways. Through the first pathway, snow depth anomalies in month 1 cause snow depth anomalies in month 2, which then cause temperature anomalies in month 2. This pathway represents the snow–albedo feedback, as well as cooling due to insulation, emissivity and heat loss. It is active from fall to summer, and its effect peaks in March/April in the midlatitudes and in May/June at high latitudes. A complementary second pathway, where snow depth anomalies in month 1 cause soil moisture anomalies in month 2, which then cause temperature anomalies in month 2 through soil moisture–temperature feedbacks, is only active in spring and summer. Its effect peaks later in the warm season than the effect of the first pathway. Geographically, snow depth mediates north of, and soil moisture south of, the areas with the highest temperature predictability from snow depth. These results indicate that the two pathways describe complementary physical mechanisms. The first pathway embodies month-to-month persistence of snow depth, and the second pathway represents melting of snow from one month to the next.

β-Lactams are pharmacologically important compounds because of their various biological uses, including antibiotic and so on. β-Lactams were synthesized from benzylidene-inden derivatives and acetoxyacetyl chloride. The inhibitory effect of these compounds was also examined for human carbonic anhydrase I and II (hCA I, and II) and acetylcholinesterase (AChE). The results reveal that β-lactams are inhibitors of hCA I, II and AChE. The K_i values of β-lactams (2a-k) were 0.44-6.29 nM against hCA I, 0.93-8.34 nM against hCA II, and 0.25-1.13 nM against AChE. Our findings indicate that β-lactams (2a-k) inhibit both CA isoenzymes and AChE at low nanomolar concentrations.

Latest evidence revealed a possible association between Parkinson’s disease (PD) and periodontitis. We explored the causal relationship of this association through two-sample Mendelian randomization (MR) in European ancestry populations. To this end, we used openly accessible data of genome-wide association studies (GWAS) on PD and periodontitis. As instrumental variables for periodontitis, seventeen single-nucleotide polymorphisms (SNPs) from a GWAS of periodontitis (1817 periodontitis cases vs. 2215 controls) and forty-five SNPs from a GWAS of PD (20,184 cases and 397,324 controls). Eight non-overlapping SNPs of periodontitis from an additional GWAS assisted in the validation of association being studied. Multiple approaches of MR were carried-out. There was no evidence of genetic liability of periodontitis being associated with a higher risk of PD (B= -0.0003, Standard Error [SE] 0.0003, P = 0.26). The eight independent SNPs (B= -0.0000, SE 0.0001, P = 0.99) validated this outcome. We found no association of genetically primed PD towards periodontitis (B= -0.0001, SE 0.0001, P = 0.19). This MR study found no conclusive evidence to support a bidirectional causal genetic liability between PD and periodontitis. Further GWAS studies are needed to confirm the consistency of these results.

Candidiasis is considered an emerging public health concern because of the occurrence of drug-resistant Candida strains and the lack of available structurally diverse antifungal drug armamentariums. The indole alkaloid globospiramine from the anticandidal Philippine medicinal plant Voacanga globosa exhibits a variety of biological activities; however, its antifungal properties remain to be explored. In this study, we report the in vitro antifungal activities of globospiramine against Candida albicans and Candida tropicalis and explore its possible target proteins using in silico methods. The colony-forming unit (CFU) viability assay revealed time- and concentration-dependent anticandidal effects of the alkaloid by decreasing almost 50% of the viable CFUs 60 min after treatment. Results of the MIC and MFC assays indicated inhibitory and fungicidal effects of globospiramine against C. albicans (MIC = 8 µg/mL; MFC = 4 µg/mL) and potential fungistatic effects against C. tropicalis at lower concentrations (MIC = 4 µg/mL; MFC > 64 µg/mL). The FAM-FLICA poly-caspase assay showed metacaspase activation in C. albicans cells at concentrations of 16 and 8 µg/mL, which agreed with the MIC and MFC values. Molecular docking and molecular dynamics simulation experiments indicated stable, strong binding of globospiramine with the target proteins 1,3-β-glucan synthase and Als3 adhesin enzymes, which are indirectly involved in apoptotic-driven candidal inhibition.

Background: Circulating rare cells participate in breast cancer evolution as systemic components of the disease and thus, are a source of theranostic information. Exploration of cancer-associated rare cells is in its infancy. We determined the validity of a rare-cell detection platform and demonstrated the usefulness of a certain rare cell subset as a novel approach to characterize the breast cancer system. Methods: Linearity of the Rarmax® platform was established using a spike-in approach. The platform includes red blood cell lysis, leukocyte depletion and high-resolution fluorescence image recording. Rare cell analysis was conducted on 28 samples (before and after surgery) from 14 patients with breast cancer, 20 healthy volunteers and 9 non-cancer control volunteers. In-depth identification of rare cells, including circulating tumor cells, endothelial-like cells, erythroblasts and inflammation-associated cells, was performed using a phenotype and morphology-based classification system. Results: The platform performed linearly over a range of 5-950 spiked cells, with an average recovery of 84.6%. Circulating epithelial and endothelial-like cell subsets have been demonstrated to be associated with or independent of cancer with tumor presence. Furthermore, certain cell patterns may be associated with treatment-related adverse effects. The sensitivity in detecting tumor-presence and cancer-associated abnormality before surgery was 50% and 85.7%, respectively and the specificity was 100% and 96.6%, respectively. Conclusion: The present study supports the idea of a cancer-associated rare cell abnormality to represent tumor entities as well as systemic cancer. The latter is independent of the apparent clinical cancer.

The integration of bioinformatics in drug discovery has revolutionized the field of pharmaceutical research. The use of computational tools and techniques has enabled researchers to analyze vast amounts of data, identify potential drug targets, and design new drugs with greater precision and efficiency. The integration of bioinformatics has also facilitated the development of personalized medicine, where drugs can be tailored to individual patients based on their genetic makeup. However, there are still challenges that need to be addressed, such as the need for more accurate predictive models and the ethical considerations surrounding the use of patient data. Overall, the integration of bioinformatics in drug discovery holds great promise for improving human health and advancing our understanding of disease mechanisms. In this mini-review, we discuss how Bioinformatics plays a crucial role in each step of drug discovery by providing tools and techniques to analyze large amounts of data generated from various sources, as well as the challenges and the opportunities offered by bioinformatics.

Rapid urbanization, increasing population and increased industrialization to cater to demands of the growing population has imposed upon us a huge environmental cost. The significantly deteriorated air quality across the globe is associated with a direct and indirect impact on public health. While associated disorders such as chronic obstructive pulmonary diseases, heart failures are well documented, less is known about the biological basis of the process. We hypothesize that the worsening air quality may likely impact common systemic inflammatory processes, thus driving communicable and non-communicable diseases alike.Receptor mediated entry of particulate matter (PM2.5) results in activation of signaling cascades which culminate in production of inflammatory chemokine and cytokine responses, traversing through the blood mediating impacting not only on other organs but also dysbiosis of microflora. For the purpose of the review we choose tuberculosis (TB) as a model for communicable infectious disease and type 2 diabetes mellitus (T2DM) as a marker for non-communicable disorder. The increasing prevalence of these co-morbidities and the burdening of public health systems justifies this example. However the hypothesis may be applicable to other inflammation driven disorders also.

Medical insurance claims are becoming increasingly common data sources to answer a variety of questions in biomedical research. Although comprehensive in terms of longitudinal characterization of disease development and progression for a potentially large number of patients, population-based studies using these datasets require thoughtful modification to sample selection and analytic strategies, relative to other types of studies. Along with complex selection bias and missing data issues, claims-based studies are purely observational, which limits effective understanding and characterization of the treatment differences between groups being compared. All these issues contribute to a crisis in reproducibility and replication of comparative findings. This paper offers some practical guidance to the full analytical process, demonstrates methods for estimating causal treatment effects on several types of outcomes common to such studies, such as binary, count, time to event and longitudinally varying repeated measures outcomes, and aims to increase transparency and reproducibility. We provide an online version of the paper with readily implementable code for the entire analysis pipeline to serve as a guided tutorial for practitioners. The online version can be accessed at https://rydaro.github.io/. The analytic pipeline is illustrated using a sub-cohort of patients with advanced prostate cancer from the large Clinformatics TM Data Mart Database (OptumInsight, Eden Prairie, Minnesota), consisting of 73 million distinct private payer insurees from 2001-2016.

A large variety of molecular interactions occurs between biomolecular components in cells. When one or a cascade of molecular interactions results in a regulatory effect, by one component onto a downstream component, a so-called ‘causal interaction’ takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g., gene regulation) need to be described with a careful appreciation of molecular interactions that occur between entities. A proper description of this information enables archiving, sharing, and reuse by humans and for computational science. Various representations of causal relationships between biological components are currently used in a variety of resources. Here, we propose a checklist that accommodates current representations, and call it the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while assuring uniformity and interoperability of the data across resources.

Mosquitoes conveying Plasmodium store parasites into the skin of the mammalian host. Parasites make a trip through the circulation system to the liver, where they cross a few hepatocytes prior to building up a disease. Inside the last hepatocyte the parasite goes through morphogenesis and afterward abiogenetically partitions to become more than 20,000 blood-infective parasites, called merozoites. On account of P. vivax, P. ovale, and P. cynomolgi, the parasites can stay lethargic in the liver in structures called hypnozoites. The merozoites are delivered once again into the circulation system, where they start the repetitive blood stage. Inside erythrocytes, a little division of parasites separate into male or female gametocytes. These gametocytes are ingested by the mosquito during blood taking care of, where they will duplicate explicitly, in the long run prompting the arrangement of sporozoites

Epilepsy is one of the most prevalent and serious brain disorders, affecting 70 million people worldwide. Antiseizure medications (ASMs) though relieve symptoms and prevent the occurrence of future seizures in epileptic patients have limited effect on epileptogenesis. Addressing the multifaceted nature of epileptogenesis and its association with Nod-like receptor family pyrin domain containing 3 (NLRP3) inflammasome-mediated neuroinflammation requires a comprehensive understanding of the underlying mechanisms for development of targeted therapeutic strategies beyond conventional antiseizure treatments. Several types of NLRP3 inhibitors have been developed and their effect has been validated both in vitro and in vivo models of epileptogenesis. In this review, we discuss the advances in understanding the regulatory mechanisms of NLRP3 activation as well as progress made and challenges facing in the development of NLRP3 inhibitors for the treatment of epilepsy.

Saccharomyces cerevisiae (S. cerevisiae) ethanol fermentation has left an indelible trace in human history. It is regarded as the original beverage synthesis, and has developed into an essential energy supply for mankind today. However, the history of ethanol synthesis using S. cerevisiae, including the mechanism analysis process, has not been carefully and succinctly reported. In this paper, we review the history of ethanol synthesis using S. cerevisiae. In addition, we also review the substrates that drive S. cerevisiae ethanol synthesis, including the utilization of glucose, sucrose, starch and molasses, in order to summarize the current development status and to contribute to the further improvement of this field.

Continuous discovery and update of applications or their boundaries running in cloud environments in an automatic way is a highly required function of modern data center ops solutions. Prior attempts to address this problem within various products or projects were/are applying rule-driven approaches or machine learning techniques on specific types of data − network traffic as well as property/configuration data of infrastructure objects, which all have their drawbacks in effectively identifying roles of those resources. The current proposal (ADLog) leverages log data of sources, which contain incomparably richer contextual information, and native constructs of VMware Aria Operations for Logs in terms of Event Types and their distributions to group those entities, potentially automatically enrich with indicative tags, and recommend for further management tasks and policies. Our methods discriminate not only diverse kinds of applications, but also their specific deployments thus providing hierarchical representation of the applications in time and topology. For several applications under Aria Ops management in our experimental test bed, we discover those in terms of similarity behavior of their components with a high accuracy. The validation of the proposal paves the path for an AI-driven solution in the cloud management scenarios.

Background: With continuous advances in next-generation sequencing (NGS), novel hepadnaviruses have been discovered in many species over the last 10 years. Methods: In this study, the cloud search and analysis of NGS data published in Nature by Edgar et al. was used as a basis to re-mine and reanalyze public NGS data for new hepadnaviruses. Results: Ultimately, at least 41 new species of hepadnaviruses were identified, including hepadnaviruses from the model animals hamster and mouse, frog hepadnavirus with pan-species infectivity, and diverse African cichlid hepadnaviruses that circulate within populations. Conclusions: The discovery of the new species of hepadnaviruses not only provides new clues for the study of the origin and evolution of hepadnaviruses, but also can be used to construct new hepadnavirus animal infection models, which will be helpful for the research of eradicative drugs for hepatitis B virus (HBV).

Process model discovery covers different methodologies to mine a process model from traces of process executions, and is gaining an important role in Artificial Intelligence research. Current approaches in the area, with few exceptions, focus on determining a model of the flow of actions only. However, in several contexts, (i) restricting the attention to actions is quite limitative, since the effects of such actions have to be analysed, too, and (ii) traces provide additional pieces of information, in the form of states (i.e., values of parameters possibly affected by the actions): for instance, in several medical domains traces include both actions and measurements of patients’ parameters. In this paper, we propose AS-SIM (Action-State SIM), the first approach able to mine a process model which comprehends two distinct classes of nodes, to capture both actions and states.

A wide variety of bacteria, fungi and plants can produce bioactive secondary metabolites, which are often referred to as natural products. With the rapid development of DNA sequencing technology and bioinformatics, a large number of putative biosynthetic gene clusters have been reported. However, only a few natural products can be detected when isolated species are grown under conventional laboratory conditions, as most biosynthetic gene clusters are not expressed or are expressed at extremely low levels at these conditions. With the rapid development of synthetic biology, advanced genome mining and modification strategies have been reported, and they provide new opportunities for discovery of natural products. This review discusses advances in recent years that can accelerate the design, build, test, and learn (DBTL) cycle of natural product discovery, and prospects trends and key challenges for future research directions.

After screening nearly 1000 synthetic peptides, a synthetic peptide termed JAL-AK22 (KYEGHWYPEKPYKGSGFRCIHI) derived from the BoxA domain in Tob1 protein was found to activate both unfolded and folded proMMP-7. In addition, JAL-AK22 showed auto-proteolytic activity. Interestingly, the smaller derivative of JAL-AK22 termed JAL-TA9 (YKGSGFRMI) also possessed auto-proteolytic activity and cleaved 2 fragment peptides (MMP18-33 and MMP18-40) derived from the prodomain of proMMP-7 under physiological conditions. These proteolytic activities were inhibited by AEBSF, a serine protease inhibitor. Our results demonstrate that a small synthetic peptide consisting of only 9 amino acids has serine protease-like activity and activates proMMP-7 by cleaving the prodomain region. We thus propose calling small peptides possessing with protease-like activity Catalytides (catalytic peptides). We expect that our findings will stimulate the development of novel Catalytides and related applications.

Deep learning heavily relies on statistical correlations to drive artificial intelligence (AI) innovations, particularly in computer vision applications like autonomous driving and robotics. However, despite providing a solid foundation for deep learning, these statistical correlations can be vulnerable to unforeseen and uncontrolled factors. The lack of prior knowledge guidance can result in spurious correlations, introducing confounding factors and affecting the model's robustness. To address this challenge, recent research efforts have focused on integrating causal theory into deep learning methodologies. By modelling the inherent and unbiased causal structure, causal theory can potentially mitigate the impact of spurious correlations effectively. Hence, this paper explores the basics of causal methodologies in image classification.

To accurately identify high-quality functional wood with superior mechanical properties and enhance its durability, it is imperative to understand the relationships between the physical and mechanical attributes of diverse wood types. Presently, there exist issues related to accuracy, efficiency, and differentiation in studying these performance correlations. The Liang Kleeman (L-K) information flow theory, a causative analytical approach rooted in fundamental physics principles, offers swift computational capabilities. Furthermore, the coefficient of variation in L-K information flow quantitatively gauges the intensity of causal effects. Therefore, this article adopts a causal artificial intelligence perspective and introduces a wood performance analysis method based on L-K information flow.This study focuses on four Chinese fir varieties, including fast-growing Chinese fir (YKS), red heart Chinese fir (CSH, XXH), and iron heart Chinese fir (XXT). By computing and comparing variation coefficients of L-K information flow for various physical properties and their impact on mechanical properties, causal relationships between these properties are elucidated. These findings are then applied to predict wood mechanical properties, achieving a remarkable maximum accuracy of 90%.In the future, these findings will prove invaluable for the selection of high-quality wood and for improving the manufacturing process to prolong the service life of functionalized wood.

Measurements of systems taken along a continuous functional dimension, such as time or space, are ubiquitous in many fields, from the physical and biological sciences to economics and engineering. Such measurements can be viewed as realisations of an underlying smooth process sampled over the continuum. However, traditional methods for independence testing and causal learning are not directly applicable to such data, as they do not take into account the dependence along the functional dimension. By using specifically designed kernels, we introduce statistical tests for bivariate, joint, and conditional independence for functional variables. Our method not only extends the applicability to functional data of the Hilbert-Schmidt independence criterion (HSIC) and its d-variate version (d-HSIC), but also allows us to introduce a test for conditional independence by defining a novel statistic for the conditional permutation test (CPT) based on the Hilbert-Schmidt conditional independence criterion (HSCIC), with optimised regularisation strength estimated through an evaluation rejection rate. Our empirical results of the size and power of these tests on synthetic functional data show good performance, and we then exemplify their application to several constraint- and regression-based causal structure learning problems, including both synthetic examples and real socio-economic data.

The study focuses on the crucial aspect of lossless compression for FAST pulsar search data. The deep generative model PixelCNN, stacking multiple masked convolutional layers, achieves neural network autoregressive modeling, making it one of the most excellent image density estimators. However, the local nature of convolutional networks causes PixelCNN to concentrate only on nearby information, neglecting important information at greater distances. Although deepening the network can broaden the receptive field, excessive depth can compromise model stability, leading to issues like gradient degradation. To address these challenges, the study combines causal attention modules with residual connections, proposing the Causal Residual Attention Module to enhance the PixelCNN model. This innovation not only resolves convergence problems arising from network deepening but also widens the receptive field. It effectively utilizes global features, particularly capturing vertically correlated features prominently present in subgraphs of candidates. This significantly enhances its capability to model pulsar data.In the experiments, the model is trained and validated using the HTRU1 dataset. The study compares the average negative log-likelihood score with baseline models like GMM, STM, and PixelCNN. The results demonstrate the superior performance of the our model over other models. Finally, the study introduces the practical compression encoding process by combining the proposed model with arithmetic coding.

Molecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments, and can be used for connecting biological molecules into regulatory computational models that represent biological systems. However, including a molecular causal interaction into a model requires assessing its relevance to that model, based on detailed knowledge about the biomolecules, interaction type, and biological context. In order to standardize the representation of this knowledge in ‘causal statements’, we recently developed the MI2CAST guidelines. Here we introduce causalBuilder: an intuitive web-based curation interface for the annotation of molecular causal interactions that comply with the MI2CAST standard. The causalBuilder prototype essentially embeds the MI2CAST curation guidelines in its interface, and makes its rules easy to follow by a curator. In addition, causalBuilder serves as an original application of the VSM general-purpose curation technology, and provides both curators and tool developers with an interface that can be fully configured to allow focusing on selected MI2CAST concepts to annotate. After information is entered, the causalBuilder prototype produces genuine causal statements that can be exported in different formats.

Phytochemicals have a long and successful history in drug discovery. With recent advancements in analytical techniques and methodologies, discovering bioactive leads from natural compounds has become easier. Computational techniques like molecular docking, QSAR modelling and machine learning, and network pharmacology are among the most promising new tools that allow researchers to make predictions concerning natural products' potential targets, thereby guiding experimental validation efforts. Additionally, approaches like LC-MS or LC-NMR speed up compound identification by streamlining analytical processes. Integrating structural and computational biology aids in lead identification, thus providing invaluable information to understand how phytochemicals interact with potential targets in the body. Emerging computational approach is machine learning involving QSAR modelling and deep neural networks that interrelate phytochemical properties with diverse physiological activities such as antimicrobial or anticancer effects.

In the dynamic landscape of drug discovery, Computer-rAided Drug Design (CADD) emerges as a transformative force, bridging the realms of biology and technology. This paper overviews CADD's historical evolution, categorization into structure-based and ligand-based approaches, and its crucial role in rationalizing and expediting drug discovery. As CADD advances, incorporating diverse biological data and ensuring data privacy become paramount. Challenges persist, demanding the optimization of algorithms and robust ethical frameworks. Integrating Machine Learning and Artificial Intelligence amplifies CADD's predictive capabilities, yet ethical considerations and scalability challenges linger. Collaborative efforts and global initiatives, exemplified by platforms like Open Source Malaria, underscore the democratization of drug discovery. The convergence of CADD with personalized medicine offers tailored therapeutic solutions, though ethical dilemmas and accessibility concerns must be navigated. Emerging technologies like quantum computing, immersive technologies, and green chemistry promise to redefine the future of CADD. The trajectory of CADD, marked by rapid advancements, anticipates challenges in ensuring accuracy, addressing biases in AI, and incorporating sustainability metrics. The paper concludes by highlighting the need for proactive measures in navigating the ethical, technological, and educational frontiers of CADD to shape a healthier, brighter future in drug discovery.

Despite significant strides in prevention, diagnosis, and treatment, cardiovascular diseases remain the number one cause of mortality in the United States, with rates climbing at an alarming rate in the developing world. Targeted delivery of therapeutics to the heart has been a lofty goal to achieve with strategies ranging from direct intra-cardiac or intra-pericardial delivery, intra-coronary infusion, to adeno-associated viral vectors which have preference, if not complete cardio-selectivity, for cardiac tissue. Cell penetrating peptides (CPP) are 5-30 amino acid long peptides that are able to breach cell membrane barriers while carrying cargoes up to several times their size, in an intact functional form. Identified nearly three decades ago, the first of these CPPs came from the HIV coat protein transactivator of transcription. Although a highly efficient CPP, its clinical utility is limited by its robust ability to cross any cell membrane barrier, including crossing the blood-brain barrier and transducing neuronal tissue non-specifically. Several strategies have been utilized to identify cell or tissue specific CPPs, one of which is phage display. Using this latter technique, we identified a cardiomyocyte targeting peptide (CTP) more than a decade ago, a finding that has been corroborated by several independent labs across the world that have utilized CTP for myriad different purposes in pre-clinical animal models. The goal of this publication is to provide a comprehensive review of the identification, validation, and application of CTP, and outlining its potential in diagnostic and therapeutic applications especially in the field of targeted RNA interference.

Mycobacterium tuberculosis (Mtb) is the etiological agent of tuberculosis (TB), a disease that alt-hough preventable and curable, remains a global epidemic due to the emergence of resistance and a latent form responsible for a long period of treatment. Drug discovery in TB is a challenging task due to the heterogeneity of the disease, the emergence of resistance and an uncomplete knowledge of the pathophysiology of the disease. The limited permeability of the cell wall and the presence of multiple efflux pumps remain a major barrier to achieve effective intracellular drug accumulation. While the complete genome sequence of Mtb has been determined and several potential protein targets have been validated, the lack of adequate models for in vitro and in vivo studies is a limit-ing factor in TB drug discovery programs. In current therapeutic regimens, less than 0.5% of bac-terial proteins are targeted being the biosynthesis of the cell wall and the energetic metabolism two of the most important processes exploited for TB chemotherapeutics. This review provides an overview on the current challenges in TB drug discovery and emerging Mtb druggable proteins, and how chemical probes for protein profiling enabled the identification of new targets and bi-omarkers, paving the way to disruptive therapeutic regimens and diagnostic tools.

Background：Increasingly, epidemiological surveys and experimental research findings indicate the involvement of immune cells in the onset and progression of prostate cancer. However, it remains unclear whether the relationship between specific immune cell types and prostate cancer is causal or influenced by bias. Through a two-sample Mendelian randomization design, our study aims to uncover the association between different immune cells and the risk of prostate cancer.Methods：A comprehensive study was conducted to investigate the association between immunophenotypes and prostate cancer risk. The study included a total of 731 immunophenotypes as potential exposure factors and analyzed data from 182,625 individuals of European ancestry from the UK Biobank. A screening of 12,097,504 single nucleotide polymorphisms (SNPs) was performed. The main analysis utilized the two-sample Mendelian randomization method with inverse variance weighting (IVW). Additionally, multiple analysis methods were combined, and various tests were conducted to assess heterogeneity and pleiotropy.Results：The resulting study showed a causal relationship between a total of 34 immune phenotypes and prostate cancer. Among them, the four immune phenotypes of CD62L- DC AC, CD19 on sw mem, FSC-A on plasmacytoid DC and HLA DR on monocyte simultaneously meet three or more statistical methods, suggesting a significant causal relationship with prostate cancer. Additionally, among the 34 immunophenotypes, CD28-CD8dim AC was shown to be positive in reverse Mendelian randomization. Most of these cell phenotypes have been reported to be potentially associated with prostate cancer.Conclusions：Our study demonstrates a causal link between immune cells and prostate cancer risk. Filled in the possible roles of all current immune cell pathways in the development and progression of prostate cancer. The next step is to verify the content and influencing mechanism of these immune phenotypes in cancer cells and adjacent cells through experiments, so as to provide new ideas and methods for the prevention and treatment of prostate cancer.

In this paper, we introduce an innovative approach to distinguish Gliosarcoma (GSM) from Glioblastoma (GBM). Our method combines causal fuzzy logic rules with the Big Bird architecture, a Transformer-based Deep Learning algorithm. Unlike prior research, which often relied on statistical models to reduce dataset dimensions before causal analysis, our approach harnesses the complete dataset in tandem with our causal fuzzy Big Bird architecture. Additionally, we benchmark our results not only against previous Gliosarcoma/Glioblastoma studies but also against GPT-2 for a comprehensive evaluation.

In complex systems constrained by multiple factors, it is of great significance to accurately identify the key influencing factors for mastering the evolution and development law of the system and obtaining scientific decision-making suggestions or schemes. At present, the method based on experimental simulation is limited by the difficulty of system model construction; the method based on decision trial and Evaluation laboratory (DEMATEL) involves a wide range of subjects and is greatly influenced by subjective factors. In view of this, we propose a novel model based on heuristic causal inference. The model uses the FCI algorithm with prior knowledge to learn the global causal network among multiple factors of the complex system. The causal effect among variables in the causal network is calculated by using heuristic causal inference method. Specifically, the causal path contribution degree of cause variable to target variable is calculated to replace the causal effect of each cause variable to target variable. The key influencing factors in the system are screened out according to the contribution degree of causal pathways. Based on the dataset generated in the production process of a semiconductor manufacturing system, we carried out simulation experiments, identified several factors that have a key impact on product quality, and proved the feasibility and effectiveness of the proposed model.

Genome-wide association studies have revealed a locus at 8p12 that is associated with breast cancer risk. Fine-mapping of this locus identified 16 candidate causal variants (CCVs). However, as these variants are intergenic, their function is unclear. To map chromatin looping from this risk locus to a previously identified candidate target gene, DUSP4, we performed chromatin conformation capture analyses in normal and tumoral breast cell lines. We identified putative regulatory elements, containing CCVs, that loop to the DUSP4 promoter region. Using reporter gene assays, we found that the risk allele of CCV rs7461885 reduced the activity of a DUSP4 enhancer element, consistent with the function of DUSP4 as a tumor suppressor gene. Furthermore, the risk allele of CCV rs12155535, located in another DUSP4 enhancer element, was negatively correlated with looping of this element to the DUSP4 promoter region, suggesting that this allele would be associated with reduced expression. These findings provide the first evidence that CCV risk alleles downregulate DUSP4 expression, suggesting that this gene is a regulatory target of the 8p12 breast cancer risk locus.

Introduction: The combination of Virtual Screening (VS) techniques with in vivo screening in the zebrafish model is currently being used in tandem for drug development in a faster and more efficient way. Areas covered: We review the different virtual screening techniques, the use of zebrafish as a vertebrate model for drug discovery and the synergy that exists between them. Expert opinion: We highlight the advantages of combining virtual and zebrafish larvae screening for drug discovery. On the one hand, VS is a faster and cheaper tool for searching active compounds and possible candidates for therapy than in vivo screening when processing large compound libraries. On the other hand, zebrafish larvae form a vertebrate model which allows in vivo screening of large amounts of the compounds. Importantly physiology and chemical response are mostly conserved between zebrafish and mammals. The availability of the transgenic and mutant zebrafish lines allows an analysis of a specific phenotype upon treatment along with toxicity, off-target effect, side effects, and dosage. Advantages of VS, in vivo whole animal approach screening, and the screening combinations are also reviewed.

Microbiome research has gained considerable interest due to the emerging evidence of its impact on human and animal health. Similar to higher organisms, the gut-associated microbiota of mosquitoes affect host fitness and other phenotypes. It is now well established that microbes can alter pathogen transmission in mosquitoes, either positively or negatively, and avenues are being explored to exploit microbes for vector control. However, less attention has been paid to how microbiota affect phenotypes that impact vectorial capacity. Several mosquito and pathogen components, such as vector density, biting rate, survival, vector competence and pathogen extrinsic incubation period all influence pathogen transmission. Interestingly, the mosquito gut-associated microbes can impact each of these components, and therefore ultimately modulate vectorial capacity. Promisingly, this expands the options available to exploit microbes for vector control by also targeting parameters that affect vectorial capacity. However, there are still many knowledge gaps in the biology of the mosquito – microbe symbiosis that need to be addressed in order to understand these interactions more thoroughly and exploit them efficiently. Here, we review current evidence of the impacts of the microbiome on aspects of vectorial capacity highlighting opportunities for novel vector control strategies and areas where further studies are required.

Induced pluripotent stem cells (iPSC) are derived from reprogrammed adult somatic cells. These adult cells are manipulated in vitro to express genes and factors essential for acquiring and maintaining embryonic stem cell (ESC) properties. This technology is widely applied in many fields, and there has been much attention to developing iPSC-based disease models to validate drug discovery platforms and study pathophysiological molecular processes underlying disease onset. Especially in neurological diseases, there is a great need for iPSC-based technological research, as these cells can be obtained from each patient and carry the individual’s bulk of genetic mutations and properties. Moreover, iPSC can differentiate into multiple cell types. These are essential characteristics since the study of neurological diseases is affected by limited access to injured sites, in vitro models composed of various cell types, the complexity of reproducing the brain’s anatomy, ethical issues, and the fact that post-mortem cell culture is challenging. Neurodegenerative diseases enormously impact global health due to their high incidence, symptoms severity, and usually lack of effective therapies. Recently, analyses using disease-specific iPSC-based models confirmed their efficacy for testing multiple drugs. This review summarizes the advances in iPSC technology used in disease modeling and drug testing with a primary focus on neurodegenerative diseases, including Parkinson’s and Alzheimer’s diseases.

In an era of unparalleled technical advancement, the pharmaceutical industry is struggling to transform data into increased research and development efficiency, and as a corollary, new drugs for patients. Here, we briefly review some of the commonly discussed issues around this counterintuitive innovation crisis. Looking at both industry and science related factors, we posit that traditional preclinical research is front-loading the development pipeline with data and drug candidates that are unlikely to succeed in patients. Applying a first principles analysis, we highlight the critical culprits and provide suggestions as to how these issues can be rectified through pursuit of a Human Data-driven Discovery (HD3) paradigm. Consistent with other examples of disruptive innovation, we propose that new levels of success are not dependent on new inventions, but rather the strategic integration of existing data and technology assets. In support of these suggestions, we highlight the power of HD3, through recently published proof-of-concept applications in the areas of drug safety analysis and prediction, drug repositioning, rational design of combination therapies and the global response to the Covid19 pandemic. We conclude that innovators must play a key role in expediting the path to a largely human focused, systems-based approach to drug discovery and research.

Meprin α is a zinc metalloproteinase (metzincin) that has been implicated in multiple diseases, including fibrosis and cancers. It has proven difficult to find small molecules that are capable of selectively inhibiting meprin α, or its close relative meprin β, over numerous other metzincins which, if inhibited, would elicit unwanted effects. We recently identified possible molecular starting points for meprin α-specific inhibition through an HTS effort (see part I, preceding paper). In part II we report the optimization of a potent and selective hydroxamic acid meprin α inhibitor probe which may help define the therapeutic potential for small molecule meprin α inhibition and spur further drug discovery efforts in the area of zinc metalloproteinase inhibition.

Meprin α and β are zinc-dependent proteinases implicated in multiple diseases including cancers, fibrosis, and Alzheimer’s. However, until recently, only a few inhibitors of either meprin were reported and no inhibitors are in pre-clinical development. Moreover, inhibitors of other metzincins developed in previous years are not effective in inhibiting meprins suggesting the need for de novo discovery effort. To address the paucity of tractable meprin inhibitors we developed ultra-high throughput assays and conducted parallel screening of >650,000 compounds against each meprin. As a result of this effort, we identified 5 selective meprin α hits belonging to three different chemotypes (triazole-hydroxyacetamides, sulfonamide-hydroxypropanamides, and phenoxy-hydroxyacetamides). These hits demonstrated a nanomolar to micromolar inhibitory activity against meprin α with low cytotoxicity and >30-fold selectivity against meprin β and other related metzincincs. These are the most selective inhibitors of meprin α to date.

The world faces two seemingly unrelated challenges—a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery.

Viral diseases are one of the leading causes of morbidity and mortality in the world. Virus-specific vaccines and antiviral drugs are the most powerful tools to combat viral diseases. However, broad-spectrum antiviral agents (BSAAs, i.e. compounds targeting viruses belonging to two or more viral families) could provide additional protection of general population from emerging and re-emerging viral diseases reinforcing the arsenal of available antiviral options. Here, we reviewed discovery and development of BSAAs and summarized the information on 120 safe-in-man agents in freely accessible database (https://drugvirus.info/). Future and ongoing pre-clinical and clinical studies will increase the number of BSAAs, expand spectrum of their indications, and identify drug combinations for treatment of emerging and re-emerging viral infections as well as co-infections.

The discovery and settlement of the tiny and remote Easter Island (Rapa Nui) has been a classical controversy for decades. Present-day aboriginal people and their culture are undoubtedly of Polynesian origin but it has been debated whether Native Americans discovered the island before the Polynesian settlement. Until recently, the paradigm was that Easter Island was discovered and settled just once by Polynesians in their millennial-scale eastward migration across the Pacific. However, the evidence for cultivation and consumption of an American plant, the sweet potato (Ipomoea batatas), on the island before the European contact (1722 CE), even prior to the Europe-America contact (1492 CE), revived the controversy. This paper reviews the classical archaeological, ethnological and paleoecological literature on the subject and summarizes the information into four main hypotheses to explain the sweet potato enigma: the long-distance-dispersal hypothesis, the back-and-forth hypothesis, the Heyerdahl hypothesis and the newcomer’s hypothesis. These hypotheses are evaluated in light of the more recent evidence (last decade), including molecular DNA phylogeny and phylogeography of humans and associated plants and animals, physical anthropology (craniometry, dietary analysis) and new paleoecological findings. It is concluded that, with the available evidence, none of the former hypotheses may be rejected and, therefore, all possibilities remain open. For future work, it is recommended to use the multiple-working-hypothesis framework and the strong inference method of hypothesis testing, rather than the ruling theory approach, very common in Easter Island’s research.

The storm 'Daniel' has caused the most severe flood phenomenon that Greece has ever experienced, with thousands of hectares of farmland submerged for days. This led to sediment deposition in the inundated areas, which significantly altered the chemical properties of the soil, as revealed by extensive soil sampling and laboratory analysis. Causal relationships between soil chemical properties and sediment deposition were extracted using the DirectLiNGAM algorithm. Results of causality analysis showed that the sediment deposition affected the CaCO3 concentration in the soil. Also, causal relationships were identified between CaCO3 and available phosphorus (P-Olsen), as well as between sediment deposit depth and available manganese. The quantified relationships between the soil variables were then used to generate data using a Multiple Linear Perceptron (MLP) regressor for various levels of deposit depth (0, 5, 10, 15, 20, 25 and 30 cm). Then linear regression equations were fitted across the different levels of deposit depth to determine the effect of deposit depth on CaCO3, P, and Mn. The results show that there is a linear slope of 0.12, -0.16, and 0.13, for CaCO3, P, and Mn with deposit depth, respectively. Statistical analysis indicates that corn growing in soils with sediment over 10 cm requires a 31.8% increase in P rate to prevent yield decline. Additional notifications regarding cropping strategies in the near future are also discussed.

Prediabetes, a pivotal phase in glucose metabolism between normalcy and diabetes, exerts a profound influence on the aging process and the risk of age-related diseases. This comprehensive review delves into the intricate web of blood-based biomarkers that collectively expedite senescence, marking the transition from a state of health to age-related complications. Key findings underscore the significance of diverse biomarkers, such as telomere length, p16INK4a, senescence-associated secretory phenotype (SASP) factors, DNA methylation clocks, advanced glycation end products (AGEs), inflammatory and oxidative stress markers, circulating hormones, and additional factors like folate, B12, osteocalcin, and more. Not only do these biomarkers serve as indicators of senescence, but they actively fuel chronic inflammation, oxidative stress, and metabolic dysregulation, all of which contribute to accelerated aging. The implications of this understanding are profound, as prediabetes emerges as a critical period in an individual's life, influencing various physiological systems, including the vascular and neural systems, metabolic functions, hormonal regulation, and bone health. Recognizing the profound influence of prediabetes on senescence provides a foundation for personalized intervention strategies to mitigate age-related complications and promote healthy aging. Future research directions call for a more diverse array of biomarkers, in-depth exploration of their roles, and the development of tailored precision medicine strategies to ensure a holistic understanding and effective management of prediabetes-induced senescence and its implications for aging. This knowledge has far-reaching implications for public health and clinical practice, emphasizing the need for early detection and intervention in prediabetic individuals to enhance the quality of life in an aging population with diverse needs.

The causal effects of chondroitin, glucosamine, and vitamin/mineral supplement intake on kidney function remain unknown, despite being commonly used. We conducted a two-sample summary-level Mendelian randomization (MR) analysis to test for causal associations between regular dietary supplement intake and kidney function. Genetic instruments for chondroitin, glucosamine, and vitamin/mineral supplement intake were obtained from genome-wide association study of European ancestry. Summary statistics for the log-transformed estimated glomerular filtration rate (log-eGFR) were provided by the CKDGen consortium. The multiplicative random-effects inverse variance-weighted method showed that genetically predicted chondroitin and glucosamine intake was causally associated with a lower eGFR (chondroitin, eGFR change beta = -0.113 %, standard error (SE) = 0.03 %, P-value = 2E-04; glucosamine, eGFR change beta = -0.240 %, SE = 0.035 %, P-value = 6E-12). However, a genetically predicted vitamin/mineral supplement intake was associated with a higher eGFR (eGFR change beta = 1.426 %, SE = 0.136 %, P-value = 1E-25). Validation analyses and pleiotropy-robust MR results for chondroitin and vitamin/mineral supplement intake supported the main results. Our MR study suggests a potential causal effect of chondroitin and glucosamine intake on kidney function. Therefore, clinicians should carefully monitor their long-term effects.

Non-systemic oral drugs, which do not get absorbed through the gastrointestinal membrane, are an important group of compounds for targeting diseases residing within the gastrointestinal lumen. However, they require a set of design principles not sufficiently covered by traditional druglikeness metrics, such as Lipinski’s Rule of 5. These druglikeness metrics fail to accurately identify true negative outcomes; such is the requirement for novel cheminformatic based approaches for the discovery of non-systemic small molecules. One such example of these newer metrics is the fraction of SP3-hybridised carbon atoms (fSP3) which has shown promising application as an identifier of poor oral-bioavailability. Herein, we discuss the application of fSP3 in the drug discovery process in a number of case studies, including our own work discovering non-systemic fructose scavengers for the treatment of fructose malabsorption.

Electroencephalography (EEG) is a brain imaging technique in which electrodes are placed on the scalp. EEG signals are commonly decomposed into frequency bands called delta, theta, alpha, and beta.While these bands have been shown to be useful for characterizing various brain states, their utility as a one-size-fits-all analysis tool remains unclear. We present a two-part data-driven methodology for objectively determining the best EEG bands for a given dataset in this paper. First, a decision tree is used to estimate the optimal frequency band boundaries for reproducing the signal’s power spectrum for a predetermined number of bands. The optimal number of bands is then determined using an Akaike Information Criterion (AIC)-inspired quality score that balances goodness-of-fit with a small band count. Data-driven EEG band discovery may aid in objectively capturing key signal components and uncovering new indices of brain activity.

Ebola Virus Disease (EVD) is one of the most lethal transmissible infections characterized by a high fatality rate, and caused by members of the Filoviridae family. The recent large outbreak of EVD in West Africa (2013-2016), highlighted the worldwide danger of this disease and its impact on global public health and economy. The development of highly needed anti-Filoviridae antivirals has been so far hampered by the shortage of tools to study their life cycle in vitro, and therefore screen for potential active compounds outside a biosafety level-4 (BSL-4) containment. Importantly, the development of surrogate models to in vitro study of Filoviridae entry in a BSL-2 setting, such as viral pseudotypes and Ebola virus like particles, tremendously boosted both our knowledge on viral life cycle and the identification of promising anti-Filoviridae compounds interfering with viral entry. In this context, the combination of such surrogate systems with large-scale small molecule compounds and haploid genetic screenings, as well as rational drug design and drug repurposing approaches will prove priceless in our quest for the development of a treatment for EVD.

Cone snails (genus Conus) are venomous marine snails that inject prey with a lethal cocktail of conotoxins, small, secreted, cysteine-rich peptides. Given the diversity and often high affinity for their molecular targets, consisting of ion channels, receptors or transporters, many conotoxins have become invaluable pharmacological probes, drug leads and therapeutics. Transcriptome sequencing of Conus venom glands followed by de novo assembly and homology-based toxin identification and annotation is currently the state-of-the-art for discovery of new conotoxins. However, homology-based search techniques, by definition, can only detect novel toxins that are homologous to previously reported conotoxins. To overcome these obstacles for discovery we have created ConusPipe, a machine learning tool that utilizes prominent chemical characters of conotoxins to predict whether a certain transcript in a Conus transcriptome, which has no otherwise detectable homologs in current reference databases, is a putative conotoxin. By using ConusPipe on RNASeq data of 10 species, we report 5,230 new putative conotoxin transcripts that have no homologues in current reference databases. 893 of these were identified by at least 3 out of 4 models used. These data significantly expand current publicly available conotoxin datasets and our approach provides a new computational avenue for the discovery of novel toxin families.

The Western ‘discovery’ of Japanese cinema in the 1950s prompted scholars to articulate essentialist visions understanding its singularities as a result of its isolation from the rest of the World and its close links to local aesthetic and philosophical traditions. Recent approaches however, have evidenced the limitations of this paradigm of ‘national cinema’. Higson (1989) opened a critical discussion on the existing consumption, text andproduction-based approaches to this concept. This article draws on Higson´s contribution and calls into question traditional theorising of Japanese film as a national cinema. Contradictions are illustrated by assessing the other side of the ‘discovery’ of Japanese cinema: certain gendaigeki works that succeeded at the domestic box office while jidaigeki burst into European film festivals. The Taiyōzoku and subsequent Mukokuseki Action created a new postwar iconography by adapting codes of representation from Hollywood youth and western films. This article does not attempt to deny the uniqueness of this film culture, but rather seeks to highlight the need to reformulate the paradigm of national cinema in the Japanese case, and illustrate the sense in which it was created from outside, failing to recognise its reach transnational intertextuality.

Mental health issues can have significant impacts on individuals and communities and hence on social sustainability. There are several challenges facing mental health treatment, however, more important is to remove the root causes of mental illnesses because doing so can help prevent mental health problems from occurring or recurring. This requires a holistic approach to understanding mental health issues that are missing from the existing research. Mental health should be understood in the context of social and environmental factors. More research and awareness are needed, as well as interventions to address root causes. The effectiveness and risks of medications should also be studied. This paper proposes a big data and machine learning-based approach for the automatic discovery of parameters related to mental health from Twitter data. The parameters are discovered from three different perspectives, Drugs & Treatments, Causes & Effects, and Drug Abuse. We used Twitter to gather 1,048,575 tweets in Arabic about psychological health in Saudi Arabia. We built a big data machine learning software tool for this work. A total of 52 parameters were discovered for all three perspectives. We defined 6 macro-parameters (Diseases & Disorders, Individual Factors, Social & Economic Factors, Treatment Options, Treatment Limitations, and Drug Abuse) to aggregate related parameters. We provide a comprehensive account of mental health, causes, medicines and treatments, mental health and drug effects, and drug abuse, as seen on Twitter, discussed by the public and health professionals. Moreover, we identify their associations with different drugs. The work will open new directions for social media-based identification of drug use and abuse for mental health, as well as other micro and macro factors related to mental health. The methodology can be extended to other diseases and provides a potential for discovering evidence for forensics toxicology from social and digital media.

Background: Immunoglobulin A nephropathy (IgAN) is a complex autoimmune disease, and the exact pathogenesis remains to be elucidated. Methods: We conducted summary data-based Mendelian randomization (SMR) analysis and performed functional mapping and annotation using FUMA to explore genetic loci that are po-tentially involved in the pathogenies of IgAN. Both analyses used summarized data of a recent genome-wide association study (GWAS) on IgANs, which included 477,784 Europeans (15,587 cases and 462,197 controls) and 175,359 East Asians (71 cases and 175,288 controls). We performed separate SMR analysis using CAGE and GTEx eQTL data. Results: Using the CAGE eQTL data, our SMR analysis identified 32 probes tagging 25 unique genes that were pleiotropically/potentially causally associated with IgAN, with the top three probes being ILMN_2150787 (tagging HLA-C, PSMR=2.10×10-18), ILMN_1682717 (tagging IER3, PSMR=1.07×10-16) and ILMN_1661439 (tagging FLOT1, PSMR=1.16×10-14). Using GTEx eQTL data, our SMR analysis identified 24 probes tagging 24 unique genes, with the top three probes being ENSG00000271581.1 (tagging XXbac-BPG248L24.12, PSMR=1.44×10-10), ENSG00000186470.9 (tagging BTN3A2, PSMR=2.28×10-10), and ENSG00000224389.4 (tagging C4B, PSMR=1.23×10-9). FUMA analysis identified 3 independent, significant and lead SNPs, 2 genomic risk loci and 39 genes. Conclusion: We identified many genetic variants/loci that are potentially involved in the patho-genesis of IgAN.

Since the first published genome sequence of Trypanosoma cruzi in 2005, there has been tremendous technological advance in genomics, reverse genetics, and assay development for this elusive pathogen. However, there is still an unmet need for new and better drugs to treat Chagas disease. Here we introduce a T. cruzi assay strain that is useful for drug research as well as basic studies in host-pathogen interaction. Trypanosoma cruzi STIB980 is a strain of discrete typing unit TcI that grows well in culture as axenic epimastigotes or intracellular amastigotes. We have evaluated the optimal parameters for genetic transfection and constructed derivatives of T. cruzi STIB980 that express reporter genes for fluorescence- or bioluminescence-based drug efficacy testing, as well as a Cas9-expressing line for CRISPR/Cas9-mediated gene editing. The genome of T. cruzi STIB980 was sequenced by combining short-read Illumina with long-read Oxford Nanopore technologies. The latter served for the primary assembly, the former to correct mistakes and fill the gaps. This resulted in a high-quality nuclear haplotype assembly of 28 Mb in 400 contigs, containing 10,043 open-reading frames with a median length of 1077 bp. We believe that T. cruzi STIB980 is a useful addition to the antichagasic toolbox, and propose that it can serve as a DTU TcI reference strain for drug efficacy testing.

Lemonomycin (1) was first isolated from the fermentation broth of Streptomyces candidus in 1964. The complete chemical structure was not elucidated until 2000 with extensive spectroscopic analysis. Lemonomycin is currently known as the only glycosylated tetrahydroisoquinoline antibiotic. Its potent antibacterial activity against Staphylococcus aureus and Bacillus subtilis and complex architecture make it an ideal target for total synthesis. In this short review, we summarize the research status of lemonomycin for biological activity, biosynthesis and chemical synthesis. The unique deoxy aminosugar-lemonose was proposed to play a crucial role in biological activity, as shown in other antibiotics, such as arimetamycin A, nocathiacin I, glycothiohexide α, and thiazamycins. Given the self-resistance of the original bacterial host, the integration of biosynthesis and chemical synthesis to pursue efficient synthesis and further derivatization is in high demand for the development of novel antibiotics to combat antibiotic-resistant infections.

The purpose of this paper is to analyze market reflexivity in agricultural futures contracts with different maturities. To this end, we apply a four-dimensional Hawkes model to storable and non-storable agricultural commodities. We find market reflexivity for both storable and non-storable commodities. Reflexivity accounts for about 50 to 70 percent of the total trading activity. Differences between nearby and deferred contracts are less pronounced for non-storable than for storable commodities. We conclude that the co-existence of exogenous and endogenous price dynamics does not change qualitative characteristics of the price discovery process that have been observed earlier without consideration of market reflexivity.

(1) Background: Violence against each other via social media has increased and caused cyberbullying that can happen anytime through electronic communication tools that everyone can access easily. So, this study aims to investigate causal factors contributing to youth cyberbullying in Thailand's three Southern border provinces. (2) Methods: The subject group consisted of 340 youths and the data were analyzed with structural equation modeling (SEM). (3) Results: The study found that the model of the causal factors resulting in youth cyberbullying in the three Southern border provinces was consistent with the empirical data (the relative chi-square (χ2/df) was 1.77. The goodness-of-fit index (GFI) was 0.95. The root-mean-square-error of approximate (RMSEA) was 0.049). Cyberbullying was positively influenced directly and indirectly by negative upbringing, the influence of personal violence, and the influence of media violence at a statistically significant level of 0.001, with total effect sizes of 1.13, 0.74, and 0.64, respectively. Additionally, cyberbullying was positively influenced directly by negative mental traits with a statistically significant level of 0.05 and a total effect size of 0.17. (4) Conclusions: The study results could be beneficial in concretely forming policies and strategies to prevent and mitigate the problem of youth cyberbullying.

The COVID-19 pandemic has severely affected the food supply chain, including producers, retailers, wholesalers, and customers. To minimize the impacts caused by pandemics and epidemics on food supply chains, it is fundamental to implement effective policies that ensure continuity in the provision, affordability, and distribution of basic food items. This research aims to identify the main impacts of pandemics and epidemics on food supply chains and policies that can minimize these impacts. Based on a systematic literature review (SLR), 174 documents are analysed to propose a taxonomy of impacts on four supply chain links: demand-side, supply-side, logistics and infrastructure, and management and operation. The taxonomy presents the main impacts, as well as the respective mitigation policies simultaneously. In addition, the literature review leads to the development of a comprehensive causal loop diagram (CLD) with the identification of main variables and their relationship with food supply chains. Finally, a specific research agenda is proposed by identifying main research gaps. These findings provide a structured method for evaluating policies that ensure the functioning of food supply chains, particularly in disruptions such epidemics and pandemics.

Many causal factors to marine traffic accidents (MTA) influence each other and have associated effects. It is necessary to quantify the correlation path mode of these factors to improve accident prevention measures and their effects. In the application of human factors to the accident mechanisms, the complex structural chains on causes to MTA systems were analyzed combining the Human Failure Analysis and Classification System (HFACS) with theoretical Structural Equation Modeling (SEM). First, the accident causation model was established as a human error analysis classification in sight of MTA, and the constituent elements of the causes of accident was conducted. Second, a hypothetical model of Human factors classification was proposed applying the practice of the structural model. Third, with the data resource from ship accident cases, this hypothetical model was discussed and simulated, and as a result the relationship path dependency mode between the latent independent variable of the accident was quantitatively analyzed based on the observed dependent variable of human behaviors. Application examples show that relationships in HFACS are verified and in line with the path developing mode, and resource management factors have a pronounced influence and a strong relevance to the causal chain of the accidents. Appropriate algorithms for the theoretical model can be used to numerically understand the safety performance of marine traffic systems under different parameters through mathematical analysis. Hierarchical assumptions in the HFACS model are quantitatively verified.

Background: As the most invasive breast cancer (BrCa), triple-negative BrCa (TNBC) has the worst survival. The use of dexmedetomidine potentially affected BrCa surgery and dexmedetomidine was reported to have direct effects on TNBC cells. The objective of this study is to explore the mechanisms underlying the effect of dexmedetomidine on TNBC. Methods: Dexmedetomidine targets were predicted using The Cancer Genome Atlas data SwissTargetPrediction. Cell lines MDA-MB-231, MCF7, and MCF10A were used to validate the targets in TNBC with both clinical samples and cell lines. Cancer cell lines and normal breast cell lines were grouped in cancer and normal groups respectively. Both groups were exposed to dexmedetomidine treatment. Cell Counting Kit-8 was used to determine the effect of dexmedetomidine on cells with target silencing. The binding model of the candidate targets was docked and critical amino acids were mutated to validate the binding model. Results: Dexmedetomidine selectively inhibits cancer cells. Catalytic subunit of the DNA-dependent protein kinase (PRKDC), indoleamine 2,3-dioxygenase 1 (IDO1), opioid receptor kappa 1 (OPRK1), glutaminyl-peptide cyclotransferase (QPCT), macrophage migration inhibitory factor (MIF), potassium voltage-gated channel, subfamily H (Eag-related), member 2 (KCNH2), cholinergic receptor, muscarinic 3 (CHRM3), and potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 (KCNN4) were identified as dexmedetomidine targets in TNBC. The expression levels of PRKDC, IDO1, MIF, KCNH2, CHRM3, and KCNN4 were found to be upregulated in TNBC tissues compared to non-TNBC tissues(p<0.05). Silencing of these genes was found to reduce the sensitivity of TNBC cells to dexmedetomidine(p<0.05). This effect was counteracted when the silenced genes were overexpressed, resulting in an increase in the sensitivity of cells to dexmedetomidine (p<0.05). Furthermore, a direct interaction between dexmedetomidine and IDO1 and CHRM3 was observed, which regulated the sensitivity of cells to dexmedetomidine(p<0.05).Conclusion: IDO1 and CHRM3 are direct targets of dexmedetomidine in TNBC.

Inhibition of amyloid fibril formation could benefit patients with systemic amyloidosis. In this group of diseases, deposition of amyloid fibrils derived from normally soluble proteins leads to progressive tissue damage and organ failure. Although many small molecules have been proposed as inhibitors of amyloid formation, few have been successful in clinical trials. Amyloid formation is complex and several individual steps could be targeted by small molecules. However, the exact mechanism of action for a molecule is often not known, which impedes medicinal chemistry efforts to develop more potent molecules. Furthermore, commonly used assays are prone to artifacts that must be controlled for. Here, potential mechanisms by which small molecules could inhibit aggregation of immunoglobulin light chain dimers, the precursor proteins for AL amyloidosis are studied in assays that recapitulate different aspects of amyloidogenesis in vitro. One molecule reduced unfolding-coupled proteolysis of light chains, but no molecules inhibited aggregation of light chains or disrupted pre-formed amyloid fibrils. This work demonstrates the challenges associated with drug development for amyloidosis, but also highlights the potential to combine therapies that target different aspects of amyloidogenesis.

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.

G protein-coupled receptors (GPCRs) are critical drug targets. GPCRs convey signals from the extracellular to the intracellular environment through G proteins. There is evidence that some ligands that bind to the GPCRs activate different downstream signaling pathways. G protein activation or -arrestin biased signaling involves ligands binding to receptors and stabilizing conformations that trigger a specific pathway. Molecular dynamics (MD) simulations are especially valuable for obtaining detailed mechanistic information, including identification of allosteric sites and understanding modulators' interactions between receptors and ligands. Here, we highlight recent simulation studies and methods used to study biased G protein-coupled receptor signaling and their conformational dynamics. We also highlight applications of MD simulations to drug discovery.

Background: Ongoing molecular profiling studies enabled by advances in biomedical technologies are producing vast amounts of ‘omic’ data for early detection, monitoring, and prognosis of diverse diseases. A major common limitation is the scarcity of biological samples, necessitating integrative modeling frameworks that can make optimal use of available data for disease classification tasks. Related data sets are often available from different studies, but may have been generated using different technology platforms. Thus, there is a critical need for flexible modeling methods that can handle data from diverse sources to facilitate the discovery of robust biomarkers that underlie disease regulatory processes. Results: In this paper, we introduce a novel framework called Knowledge Augmented Rule Learning (KARL), which incorporates two sources of knowledge, domain, and data, for pattern discovery from small and high-dimensional datasets, such as transcriptomic data. We propose KARL as a transfer rule learning framework in which knowledge of the domain is transferred to the learning process on data in order to 1) improve the reliability of the discovered patterns, and 2) study the knowledge of the domain when used along with data for modeling. In this work, we generated KARL models on gene expression datasets for five types of cancer, including brain, breast, colon, lung, and prostate. As our knowledge of the domain, we used the Ingenuity Knowledge Base (IKB) to extract genes related to hallmarks of cancer and annotated these prior relationships before learning classifiers from these datasets. Conclusions: Our results show that KARL produces, on average, rule models that are more robust classifiers than the baseline without such background knowledge, for our tasks of cancer prediction using 25 publicly available gene expression datasets. Moreover, KARL helped us learn insights about previously known relationships in these gene expression datasets, along with new relationships not input as known, to enable informed biomarker discovery for cancer prediction tasks. KARL can be applied to modeling similar data from any other domain and classification task. Future work would involve extensions to KARL to handle hierarchical knowledge to derive more general hypotheses to drive biomedicine.

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.

This study aims to investigate the causal relationship between Levo-carnitine (LC) and its derivatives and schizophrenia (SZ) using a Two-sample Mendelian randomization (MR) method. Forward MR analysis was conducted using LC and its derivatives as exposure and SZ as the outcome. Candidate data were obtained from the openGWAS server. Instrumental variables (IVs) were identified as single nucleotide polymorphisms (SNPs) closely associated with exposure, and were harmonized with the outcome data after removing confounders and outliers. Hence, MR analysis was performed using inverse variance weighting (IVW) as the primary approach, and sensitivity analysis was conducted to assess the reliability and robustness of the MR results. Finally, a reverse MR analysis was carried out using the same analytical procedures as the forward one. The MR results indicate a significant negative causal relationship between isovalery-LC and SZ (P &lt; 0.05), but in no other groups (P&gt;0.05). Additionally, the reverse MR analysis did not identify any causal relationship between SZ and LC related exposures (P&gt;0.05). Sensitivity analyses, including pleiotropy and heterogeneity analysis, did not reveal any potential bias on the MR results (P&gt;0.05). The results implied that elevated levels of isovalery-LC may potentially mitigate the risk of developing SZ, thereby highlighting the prospective therapeutic and preventive implications of isovalery-LC in the clinical management of SZ.Keywords: schizophrenia; levo-carnitine; carnitine; mendelian randomization

This essay is a personal insight based on my own experience in the Iberian Pyrenees, which addresses three situations common in paleoecological research, such as the verification of previously devised hypotheses (anticipation), the finding on unknown events in unstudied sites (discovery) and the finding of unexpected outputs in already known areas (serendipity). The account is concentrated on the value of the coring sites by themselves as generators of paleoecological knowledge, rather than on the actual findings, which are presented and discussed in the corresponding data papers. The main aim is to show that there is still much room for new findings, even in areas that have been surveyed for long time and are supposed to be well known, from a paleoecological perspective. Finally, some general lessons are derived and conceptualized.

In this review we summarize existing trends of flow control used to improve the aerodynamic efficiency of wings. We first discuss active methods to control turbulence, starting with flat-plate geometries and building towards the more complicated flow around wings. Then, we discuss active approaches to control separation, a crucial aspect towards achieving high aerodynamic efficiency. Furthermore, we highlight methods relying on turbulence simulation, and discuss various levels of modelling. Finally, we thoroughly revise data-driven methods, their application to flow control, and focus on deep reinforcement learning (DRL). We conclude that this methodology has the potential to discover novel control strategies in complex turbulent flows of aerodynamic relevance.

Biological systems are highly regulated. They are also highly resistant to sudden perturbations enabling them to maintain the dynamic equilibrium essential for sustenance of life. This robustness is conferred by regulatory mechanisms that influence the activity of enzymes/proteins within their cellular context, to adapt to changing environmental conditions. However, the initial rules governing the study of enzyme kinetics were tested and implemented for mostly cytosolic enzyme systems that were easy to isolate and/or recombinantly express. Moreover, these enzymes lacked complex regulatory modalities. Now, with academic labs and pharmaceutical companies turning their attention to more complex systems (for instance, multi-protein complexes, oligomeric assemblies, membrane proteins and post-translationally modified proteins), the initial axioms defined by Michaelis-Menten (MM) kinetics are rendered inadequate and the development of a new kind of kinetic analysis to study these systems is required. The current review strives to present an overview of enzyme kinetic mechanisms that are atypical and, oftentimes, do not conform to the classical MM kinetics. Further, it presents initial ideas on the design and analysis of experiments in early drug-discovery for such systems, to enable effective screening and characterisation of small-molecule inhibitors with desirable physiological outcomes.

Curcumin and trans-cinnamaldehyde are acrolein-based Michael acceptor compounds that are commonly found in domestic condiments, and known to cause cancer cell death via redox mechanisms. Based on the structural features of these compounds we designed and synthesized several 2-cinnamamido-N-substituted-cinnamamide (bis-cinnamamide) compounds. One of the derivatives, (Z)-2-[(E)-cinnamamido]-3-phenyl-N-propylacrylamide 1512 showed a moderate antiproliferative potency (HCT-116 cell line inhibition of 32.0 µM), good selectivity profile (no inhibition of normal cell lines), and proven cellular activities leading to apoptosis. SAR studies led to more than 10-fold increase in activity. Our most promising compound, [(Z)-3-(1H-indol-3-yl)-N-propyl-2-[(E)-3-(thien-2-yl)propenamido)propenamide] 4112 killed colon cancer cells at IC50 = 0.89 µM (Caco-2), 2.85 µM (HCT-116) and 1.65 µM (HT-29), while exhibiting much weaker potency on C-166 and BHK normal cell lines (IC50 = 71 µM and 77.6 µM, respectively). Cellular studies towards identifying the compounds mechanism of cytotoxic activities revealed that apoptotic induction occurs in part as a result of oxidative stress. Importantly, the compounds showed inhibition of cancer stem cells that are critical for maintaining the potential for self-renewal and stemness. The results presented here show discovery of covalently-acting Michael addition compounds that potently kill cancer cells by a defined mechanism, with minimal effect on normal noncancerous cell.

Celtis sinensis is an adaptable species that is widely grown in southern China. In June 2022, a leaf blotch disease of C. sinensis was observed in Nanjing, Jiangsu, China. Based on morphological characterization, three isolates were identified as Alternaria species. Phylogenetic analysis of combined ITS, GAPDH, TEF1-α, RPB2 and Alt a 1 sequences identified the three isolates we obtained as Alternaria alternata and Alternaria koreana. Koch’s postulates were fulfilled in the greenhouse, and the pathogenicity of A. alternata and A. koreana was determined by leaf inoculation tests on C. sinensis seedlings. The symptoms of indoor inoculation were consistent with those in the field. A. alternata and A. koreana can grow at 15-35 °C, with an optimal growth temperature of 25 °C. The results of fungicide sensitivity experiments indicated that A. alternata and A. koreana were the most sensitive to prochloraz, which may be a useful strategy for the future prevention and control management of A. alternata and A. koreana. This study provides the first step for further research on A. alternata and A. koreana as pathogens of C. sinensis and provides a theoretical basis for future control strategies.

Corynebacterium pseudotuberculosis is a Gram-positive bacterium that causes caseous lymphadenitis, a disease that predominantly affects sheep, goat, cattle, buffalo, and horses, but has also been recognized in other animals. This bacterium generates a severe economic impact on countries producing meat. Gene expression studies using RNA-seq is one of the most commonly used techniques to perform transcriptional experiments. Computational analysis on such data through reverse-engineering algorithms leads to a better understanding of the genome-wide complexity of gene interactomes, enabling the identification of genes having the most significant functions inferred by the activated stress response pathways. In this study, we identified the influential or causal genes from four RNA-seq data-sets from different stress conditions (high iron, low iron, acid, osmosis, and PH) in C. pseudotuberculosis, using a consensus-based network inference algorithm called miRsig and identified the causal genes in the network using the miRinfluence tool, which is based on the influence diffusion model. We found that over 50\% of the genes identified as influential have some essential cellular functions in the genomes. In the strains analyzed, most of the causal genes have crucial roles or participate in processes associated with response to extracellular stresses, pathogenicity, membrane components, and essential genes. This research brings new insight into the understanding of virulence and infection by C. pseudotuberculosis.

Background: Numerous investigations have shed light on the intriguing interplay between gut microbiota(GM) and psoriasis (Ps) as well as psoriatic arthritis (PsA). However, the precise nature of the causal relationship between them remains an area of active investigation. Methods: For the purpose of our investigation, we meticulously curated a collection of genetic variants (P < 1 × 10−5) associated with GM (n = 18,340) derived from the MiBioGen study. To explore the intricate relationship between GM and Ps as well as PsA, we harnessed the comprehensive resources of the FinnGen database, encompassing a vast cohort of individuals, including 4,510 Ps cases and 212,242 controls, and 1,637 PsA cases and 212,242 controls. Even complementary MR methods were implemented, including an inverse variance weighting method, followed by a sensitivity analysis to verify the robustness of the results. Results: In this study, we found that certain bacterial taxa, such as Lactococcus, Ruminiclostridium 5, and Eubacterium fissicatena, were identified as risk factors. Conversely, Alloprevotella and Odoribacter demonstrated a protective effect against Ps. In the case of PsA, our results revealed a distinct set of risk factors and protective factors among the gut bacterial taxa. Lactococcus, Verrucomicrobiales, Akkermansia, Coprococcus 1, Lachnospiraceae, and Verrucomicrobiaceae were identified as risk factors for PsA. On the other hand, Odoribacter, Rikenellaceae, Clostridium innocuum, and Marvinbryantia exhibited a protective effect against the development of PsA. Conclusion: Our findings shed light on the distinctive disease characteristics and onset features between Ps and PsA. Notably, certain intestinal flora were implicated in the pathogenesis of PsA, suggesting their potential role as early diagnostic indicators. Furthermore, we identified several bacterial flora that exhibit a potential protective effect against the occurrence of Ps and PsA. These discoveries lay a solid foundation for future endeavors in the prevention and treatment of these conditions.

Atrial fibrillation (AF), the most prevalent type of sustained cardiac dysrhythmia globally, confers strikingly enhanced risks for cognitive dysfunction, stroke, chronic cardiac failure, and sudden cardiovascular demise. Aggregating studies underscore the crucial roles of inherited determinants in the occurrence and perpetuation of AF. However, due to conspicuous genetic heterogeneity, the inherited defects accounting for AF remain largely indefinite. Here, via the whole-genome genotyping with genetic markers and linkage assay in a family suffering AF, a new AF-causative locus was located at human chromosome 7p14.2-p14.3, a ~4.89-cM (~4.43-Mb) interval between the markers D7S526 and D7S2250. Exome-wide sequencing assay unveiled that at the defined locus, solely the mutation in the TBX20 gene, NM_001077653.2: c.695A&gt;G; p.(His232Arg), co-segregated with AF in the family. Additionally, Sanger sequencing assay of TBX20 in another family suffering AF uncovered a novel mutation, NM_001077653.2: c.862G&gt;C; p.(Asp288His). Neither of the two mutations was observed in 600 unrelated control individuals. Functional investigations demonstrated that the two mutations both significantly reduced the transactivation of the target gene KCNH2 (a well-established AF-causing gene) and the ability to bind the promoter of KCNH2, while without effect on the nuclear distribution of TBX20. Conclusively, these findings reveal a new AF-causative locus at human chromosome 7p14.2-p14.3 and strongly indicate TBX20 as a novel AF-causative gene, shedding light on the mechanism underlying AF and suggesting clinical significance for allele-specific treatment of AF patients.

Attention Deficit/Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder that affects attention and behavioral control, characterized by constant presence of inattention and hyperactivity. This article describes a study that used a database with results from tests of voluntary and automatic attentional orientation activity in a complex network of ADHD patients, in order to understand the characteristics of the elements and attentional variability of patients. Centrality metrics and the Louvain method were applied to obtain the network communities. The most important elements of the network were identified and differences in reaction times of the activities were observed in the identified communities. The study provides useful information to understand of deficit hyperactivity disorder spectrum in patients with ADHD.

Topic discovery is finding the main idea of large amounts of textual data. It indicates the recurring topics in the documents, allowing an overview of the texts. Current topic discovery models receive the texts, with or without pre-processing of Natural Language Processing. The processing consists of stopwords removal, text cleaning and normalization (lowercase conversion). A topic discovery model that receives texts with or without processing generates general topics since the input data is many uncategorized texts. The general topics do not offer a detailed overview of the input texts, and manual text categorization is a time-consuming and tedious task. Accordingly, it is necessary to integrate an automatic text classification task in the topic discovery process to obtain specific topics with their top words that contain relevant relationships based on belonging to a class. Text classification performs a word analysis that makes up a document to decide what class or category is being identified; then, integrating the text classification before a topic discovery process will provide latent topics depicted by top words with a high coherence in each topic based on the previously obtained classes. Therefore, this paper exposes a approach that integrates text classification into topic discovery from large amounts of English textual data, such as 20-Newsgroup and Reuters corpora. The text classification is accomplished with a Convolutional Neural Network(CNN) incorporating three embedding models based on semantic relationships. The topic discovery over categorized texts is realized with Latent Dirichlet Analysis(LDA), Probabilistic Latent Semantic Analysis(PLSA), and Latent Semantic Analysis(LSA) algorithms. An evaluation process was performed based on the normalized topic coherence metric. The 20-Newsgroup corpus was classified, and twenty topics with ten top words were discovered for each class, obtaining 0.1723 normalized topic coherence when applying LDA, 0.1622 with LSA, and 0.1716 with PLSA. The Reuters corpus was also classified, obtaining 0.1441 normalized topic coherence when applying the LDA algorithm to obtain 20 topics for each class.

The worldwide outbreak of SARS-CoV-2 in early 2020 caused numer- ous deaths and unprecedented measures to control its spread. We employed our Computational Analysis of Novel Drug Opportunities (CANDO) multiscale therapeutic discovery, repurposing, and design platform to identify small molecule inhibitors of the virus to treat its resulting indication, COVID-19. Initially, few experimental studies existed on SARS-CoV-2, so we optimized our drug candidate prediction pipelines using results from two independent high-throughput screens against prevalent human coronaviruses. Ranked lists of candidate drugs were generated using our open source cando.py software based on viral protein inhibition and proteomic interaction similarity. For the former viral protein inhibition pipeline, we computed interaction scores between all compounds in the corresponding candidate library and eighteen SARS-CoV proteins using an interaction scoring protocol with extensive parameter optimization which was then applied to the SARS-CoV-2 proteome for prediction. For the latter similarity based pipeline, we computed interaction scores between all compounds and human protein structures in our libraries then used a consensus scoring approach to identify candidates with highly similar proteomic interaction signatures to multiple known anti-coronavirus actives. We published our ranked candidate lists at the very beginning of the COVID-19 pandemic. Since then, 51 of our 276 predictions have demonstrated anti-SARS-CoV-2 activity in published clinical and experimental studies. These results illustrate the ability our platform to rapidly respond to emergent pathogens and provide greater evidence that treating compounds in a multitarget context more accurately describes their behavior in biological systems.

The field of biobanking human biospecimens has evolved significantly, transitioning from the basic, often poorly documented collection of clinical leftovers kept privately to well-organized and extensively documented collections overseen by both commercial and non-profit platforms. The increasing demand for high-quality and clinically annotated biospecimens is propelled by unprecedented levels of health research activities. Meeting this growing demand presents both new opportunities and challenges, particularly in developing strategies to establish international biospecimen sourcing (IBS) platforms. These platforms aim to facilitate collaboration among biobanks to address future biospecimen needs. In this manuscript, we delve into the advantages and challenges of establishing IBS platforms to provide high-quality and cost-effective biospecimens to drive drug discovery research, ultimately leading to improved health and quality of life for everyone.

Toxoplasma gondii, a protozoan parasite with the ability to infect various warm-blooded vertebrates, including humans, is the causative agent of toxoplasmosis. This infection poses significant risks, leading to severe complications in immunocompromised individuals and potentially affecting the fetus through congenital transmission. A comprehensive understanding of the intricate molecular interactions between T. gondii and its host is pivotal for the development of effective therapeutic strategies. This review emphasizes the crucial role of proteomics in T. gondii research, with a specific focus on host-parasite interactions, post-translational modifications (PTMs), PTM crosstalk, and ongoing efforts in drug discovery. Additionally, we provide an overview of recent advancements in proteomics techniques, encompassing interactome sample preparation methods such as BioID, APEX, and Y2H, as well as various proteomics approaches, including single-cell analysis, DIA, targeted, top-down, and plasma proteomics. Furthermore, we discuss the integration of proteomics with other omics technologies, highlighting its potential in unraveling the intricate mechanisms of T. gondii pathogenesis and identifying novel therapeutic targets.

The Global natural and manmade events are exposing the fragility of the tourism industry and its impact on the global economy. Prior to the COVID-19 pandemic, tourism contributed 10.3% to the global GDP and employed 333 million people but saw a significant decline due to the pandemic. Sustainable and smart tourism requires collaboration from all stakeholders and a comprehensive understanding of global and local issues to drive responsible and innovative growth in the sector. This paper presents an approach for leveraging big data and deep learning to dis-cover holistic, multi-perspective (e.g., local, cultural, national, and international) and objective information on a subject. Specifically, we develop a machine learning pipeline to extract parameters from academic literature and public opinions on Twitter, providing a unique and comprehensive view of the industry from both academic and public perspectives. The academic-view dataset was created from the Scopus database and contains 156,759 research articles from 2000 to 2022, which were modelled to identify 33 distinct parameters in 4 categories: Tourism Types, Planning, Challenges, and Media &amp; Technologies. A Twitter dataset of 485,813 tweets was collected over 18 months starting March 2021 to August 2022 to showcase public perception of tourism in Saudi Arabia, which was modelled to reveal 13 parameters categorized into two broader sets: Tourist Attractions and Tourism Services. Discovering system parameters are re-quired to embed autonomous capabilities in systems and for decision-making and problem-solving during system design and operations. The proposed approach improves AI-based information discovery by extending the use of scientific literature, Twitter, and other sources for autonomous, dynamic optimizations of systems, promoting novel research in the tourism sector and contributing to the development of smart and sustainable societies. The paper also presents a comprehensive knowledge structure and literature review of the tourism sector based on over 250 research articles.

Myxobacteria feature unique biological characteristics including their capability to glide on surface, undergo different multicellular developmental stages and produce structurally unique natural products such as the catecholate-type siderophores myxochelin A and B. Herein, we report the isolation, structure elucidation and biosynthesis of the new congener myxochelin B-succinate from the terrestrial myxobacterial strain MSr12020, featuring a succinyl decoration at its primary amine group. Myxochelin-B-succinate exhibited antifungal growth inhibition and moderate cytotoxic activity against selected human cancer cell lines. This unique chemical modification of myxochelin B might provide interesting insights for future microbiological studies to understand the biological function and biosynthesis of secondary metabolite succinylation.

Small molecule inhibitors of adipocyte fatty-acid binding protein 4 (FABP4) have got interest following the recent publication of their pharmacologically beneficial effects. Recently it comes out that FABP4 is an attractive molecular target for the treatment of type 2 diabetes, other metabolic diseases, and some type of cancers. In the past years, hundreds of effective FABP4 inhibitors have been synthesized and discovered but, unfortunately, none of them is in the clinical research phase. The field of computer-aided drug design seems to be promising and useful for the identification of FABP4 inhibitors; hence, different structure- and ligand-based computational approaches were already performed for their identification. In this paper, we searched for new potentially active FABP4 ligands in the Marine Natural Products (MNP) database. 14,492 compounds were retrieved from this database and filtered through a statistical and computational filter. Seven compounds were suggested by our methodology to possess a potential inhibitory activity upon FABP4 in the range of 79–245 nM. ADMET properties prediction were performed to validate the hypothesis of the interaction with the intended target and to assess the drug-likeness of these derivatives; from these analyses, three molecules resulted as excellent candidates for becoming new drugs.

The levels of informatization, automation, and intelligence are continuously improving; however, the risks due to the increased design and operational complexity of ship systems are increasing. Large-scale ship accidents occur for various reasons. Existing accident analysis methods that examine marine accidents from the perspective of causal one-to-one correspondence have limitations in systematically analyzing complex marine risks when identifying their causes for the prevention of similar accidents. This study focuses on a systematic causality analysis of the factors related to human errors in marine accidents that may occur during the arrival and departure of mega container ships. In particular, a representative case of the Milano Bridge crane contact accident at Busan New Port is considered. To explore the complex organizational–technical, human–technical, and organizational–human relationships relevant to this case, human factors (seafarer, pilot, etc) that are closely related to the linked causes were analyzed using the functional resonance analysis method. This study aims to reduce human error and prevent marine accidents including pilotage.

Fracture is a global public health disease. Bone health and fracture risk have become the focus of public and scientific attention. Observational studies have reported that tea consumption is associated with fracture risk, but the results are inconsistent. The present study was conducted to evaluate whether tea consumption was causally associated with the risk of bone fracture through two-sample Mendelian Randomization (MR) analysis. We included a large genome-wide association study (GWAS) associated with tea consumption of 447,485 individuals and analyzed the effects of genetic instruments on fractures using fracture cases from the UK Biobank dataset (n=361,194). Inverse variance weighted (IVW) indicated no causal effects of tea consumption on fractures of the skull and face, shoulder and upper arm, hand and wrist, femur, calf, and ankle (odds ratio=1.000, P=0.881; OR=1.000, P=0.857; OR=1.002, P=0.339; OR=0.997, P=0.054; OR=0.998, P=0.569, respectively). Consistent results were also found in MR-Egger, weighted median, and weighted mode. Our research provided evidence that tea consumption is unlikely to affect the incidence of fractures.

Emerging RNA virus infections are a growing concern among domestic bird and poultry industries due to the severe impact it can have on the flock health and economic livelihoods. Avian paramyxoviruses (APMV) are pathogenic, negative sense RNA viruses that cause serious infections in the respiratory and central nervous system. APMV was detected in multiple avian species during the 2017 migration season in Ukraine, and studied using PCR, virus isolation, and sequencing. Of the 4090 wild bird samples, eleven swabs were isolated in chicken embryos and identified for APMV serotype by hemagglutinin inhibition test: APMV-1, APMV-4, APMV-6, APMV-7. At a variety of sites in Ukraine we characterized the virulence of the virus and further analyzed and predicted the potential risks of spillover to immunologically naïve populations. RNA was extracted and amplified using a multiplex-tiling primer approach to encompass full cDNA genomes. Full-length APMV-1 (n=5) and APMV-6 (n=2) genomes were sequenced on an Oxford Nanopore MinION device in Ukraine. All APMV-1 and APMV-6 fusion (F) proteins possessed a monobasic cleavage site, suggesting these APMV were likely low virulence, annually circulating strains. Utilization of this low-cost method will identify gaps in viral evolution and circulation in this understudied but important critical region for Eurasia.

Project complexity is usually considered as one of main causes of cost overruns, resulting in poor performance and thus project failure. However, empirical studies focused on evaluating its effects on project cost remain lacking. Given this circumstance, this study attempts to develop the relationships between project cost and the multidimensional project complexity elements. We establish complexity as a multidimensional factor including the task, organization, market, legal, and environment complexities. This study uses an empirical evidence-based structural model to account for the relationships between project cost and project complexity. By doing so, a quantitative assessment of multi-dimensional project complexity has been developed. The findings suggest that task and organization complexities have direct effects on project cost, while market, legal and external environment complexities have indirect effects on project cost. The practical contribution is that the findings can improve the understanding of which dimension of complexity significantly influence project cost, and the need to focus efforts on strategically addressing that complexities.

Alzheimer’s disease (AD) is one of the most widespread neurodegenerative diseases affecting people averaging over 65 years. It manifests with severe cognitive damage, loss of memory, impairment in performing activities, ventricular expansion and final dementia. AD is associated with the deposit of amyloid β protein (Aβ) plaques, intracellular neurofibrillary tangles (NFTs), progressive inflammation and impairment of synaptic transmission and of mitochondrial function. Due to the poor diagnostic tools for the early stages of the disease, proteomics biomarkers have gained a paramount role because they can monitor the prodromal variations of the disease-linked molecular changes. Further, proteome biomarkers can help the follow up of AD progression over time and aid in setting personalized medical care, before the catastrophic consequences of dementia occurs. Research has focused on the identification of proteome biomarkers in cerebrospinal fluid (CSF) and plasma, which are discussed in the present review, but also in other matrices, as saliva and urine, revealing the high potentiality of proteomics approach and, at the same time, the difficulty to identify, for the different stages of the disease, sensitive and specific biomarkers clinically available.

We review the topological gauge theory description of Josephson junction arrays (JJA), fabricated systems which exhibit the superconductor to insulator transition (SIT). This description revealed the topological nature of the phases appearing at the SIT and lead to the discovery of a new state of matter, the superinsulator, characterized by an infinite resistance, even at finite temperature, due to linear confinement of electric charges. This discovery is particularly relevant for the physics of superconducting films with emergent granularity, which are modeled by JJA, and share the same phase diagram.