Abiotic stress, especially drought stress poses a significant threat to the terrestrial plant growth, development, and productivity. Although mulberry have great genetic diversity and extensive stress tolerant traits in agroforestry systems, only a few reports offer preliminary insight into biochemical responses of mulberry leaves under drought conditions. In this study, we performed a comparative metabolomic and transcriptomic analysis on the “drooping mulberry” (Morus alba var. Pendula Dippel) under PEG-6000-simulated drought stress. Our research revealed that drought stress significantly enhanced flavonoid accumulation and up-regulated the expression of phenylpropanoid biosynthetic genes. Furthermore, the activities of superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) content were elevated. In vitro enzyme assays and fermentation tests indicated the involvement of flavonol synthase/flavanone 3-hydroxylase (XM_010098126.2) and anthocyanidin 3-O-glucosyltransferase 5 (XM_010101521.2) in the biosynthesis of flavonol aglycones and glycosides, respectively. The recombinant MaF3GT5 protein was found to recognize kaempferol, quercetin, and UDP-glucose as substrates, but not 3-/7-O-glucosylated flavonols and UDP-rhamnose. MaF3GT5 is capable of forming 3-O- and 7-O-monoglucoside, but not di-O-glucosides, form kaempferol. This implies its role as a flavonol 3, 7-O-glucosyltransferase. The findings from this study provided insights into the biosynthesis of flavonoids and could have substantial implications for the future diversified utilization of mulberry.

The landscape of clinical management for metastatic melanoma (MM) and other solid tumors has been modernized by the advent of immune checkpoint inhibitors (ICI), including programmed cell death-1 (PD-1), programmed cell death-ligand 1 (PD-L1), and cytotoxic T lymphocyte antigen 4 (CTLA-4) inhibitors. While these agents demonstrate efficacy in suppressing tumor growth, they also lead to immune-related adverse events (irAEs), resulting in exacerbation of autoimmune diseases such as Rheumatoid arthritis (RA), Ulcerative colitis (UC), and Crohn’s disease (CD). The immune checkpoint inhibitors offer promising advancements in the treatment of melanoma and other cancers, but they also present significant challenges related to irAEs and autoimmune diseases. Ongoing research is crucial to better understand these challenges and develop strategies for mitigating adverse effects while maximizing therapeutic benefits. In this manuscript, we addressed this challenge using network-based approaches by constructing and analyzing molecular and signaling networks associated with tumor-immune cross-talk.. Our analysis revealed that IL6 is the key regulator responsible for irAEs during ICI therapies. Furthermore, we conducted an integrative network and molecular-level analysis, including virtual screening, of drug libraries, such as the Collection of Open Natural Products (COCONUT) and the Zinc15 FDA-approved library, to identify potential IL-6 inhibitors.. Subsequently, the compound amprenavir was identified as the best molecule that may disrupt essential interactions between IL6 and IL6R responsible for initiating signaling cascades underlying irAEs in ICI therapies.

Bats are natural hosts for a wide variety of viruses and could therefore be the reservoir, source and spillover for several mammalian viruses, including adenoviruses. We examined faecal samples from 12 bats (five species of the family Vespertilionidae) from central Russia (Moscow Region) and found that two of them (16%) were positive for mastadenoviruses. One of the identified viruses was isolated from faeces of Nyctalis noctule and named BatAdV/MOW15-Nn19. The genome of the BatAdV/MOW15-Nn19 was 37,915 bp in length. Comparative studies have shown significant divergence of the nucleotide sequence of the BatAdV/MOW15-Nn19 genome from European mastadenoviruses, the highest genome sequence similarity was to isolate WA3301 from an Australian bat. Phylogenetic analysis, as well as a comparative analysis of the protein coding genes to homologous available from public database, showed evidence of novel species within Mastadenovirus genus (preliminary named «K»). Analysis of the short part of the DNA polymerase gene of BatAdV/MOW15-Nn19 reveals few NCBI records from Europe with high identity to the new virus, i.e. mastadenoviruses related to the new species are circulating in European bats. The partial genome of another mastadenovirus from Pipistrellus nathusii was identified, it represented bat adenovirus species B, which is widely distributed in European Vespertilionidae bats. New data on the genetic diversity of bat adenoviruses may help to better understand how they evolved in mammals and spread across Europe.

Graph databases (GDBs) are becoming increasingly popular across scientific disciplines, being highly suitable to store and connect complex heterogeneous data. In systems biology, they are used as a backend solution for biological data repositories, ontologies, networks, pathways, and knowledge graph (KG) databases. In this review, we analyse all publications using or mentioning graph databases retrieved from PubMed and PubMed Central full-text search, focusing on the top 16 available GDB technologies. Relevant publications are then categorised according to their domain and application. We detail different approaches and highlight advantages of outstanding resources, such as UniProtKB, Disease Ontology, and Reactome, which provide graph-based solutions. We discuss ongoing efforts of the systems biology community to standardise and harmonise KG creation and the maintenance of integrated resources. Outlining prospects, including the use of GDBs as a way of communication between biological data repositories, we conclude that efficient design, querying, and maintenance of GDBs will be key for knowledge generation in systems biology and other research fields with heterogeneous data.

Uterine pathologies pose a challenge to women’s health on a global scale. Despite extensive research, the causes and origin of some of these common disorders are not well defined yet. This study presents a comprehensive analysis of transcriptome data from diverse datasets encompassing relevant uterine pathologies such as endometriosis, endometrial cancer and uterine leiomyomas. Leveraging the Comparative Analysis of Shapley values (CASh) technique, we demonstrate its efficacy in improving the outcomes of classical differential expression analysis on transcriptomic data derived from microarray experiments. CASh integrates the Microarray game algorithm with Bootstrap resampling, offering a robust statistical framework to mitigate the impact of potential outliers in the expression data. Our findings unveil novel insights into the molecular signatures underlying these gynecological disorders, highlighting CASh as a valuable tool for enhancing the precision of transcriptomics analyses in complex biological contexts. This research contributes to a deeper understanding of gene expression patterns and potential biomarkers associated with these pathologies, offering implications for future diagnostic and therapeutic strategies.

Prochlorococcus, a cyanobacteria genus of the smallest and most abundant oceanic phototrophs, encompasses ecotype strains adapted to high-light (HL) and low-light (LL) niches. To elucidate the adaptive evolution of this genus, we analyzed 40 Prochlorococcus marinus ORFeomes, including two cornerstone strains, MED4 and NATL1A. Employing deep learning with robust statistical methods, we detected new protein family distributions in the strains and identified key genes differentiating HL and LL strains. HL strains harbor genes (ABC-2 transporters) related to stress resistance, such as DNA repair and RNA processing, while LL strains exhibit unique chlorophyll adaptations (ion transport proteins, HEAT repeats). We report variable, depth-dependent endogenous viral elements in the 40 strains. We constructed the ORFeomes of MED4 and NATL1A covering 99 % of the annotated protein-coding sequences of the two species, totaling 3976 cloned, sequence-verified ORFs. These comparative genomics analyses, paired with MED4 and NATL1A ORFeomes, will facilitate future genotype-to-phenotype mappings and systems biology exploration of Prochlorococcus ecology.

Visual exploration of complex data helps interpretation, especially in the case of omics data analysis in life sciences and clinical research. Generating and analysing omics data requires bioinformatic skills, while they are interpreted by domain experts, for whom parsing large and complex data structures may be challenging. However, outcomes of visual analytics are often difficult to quantify, which emphasises precision and reproducibility, especially for research on human diseases. Here, we propose a workflow combining a reproducible computational environment with a dedicated visualisation functionality for systems biology diagrams. By linking the Galaxy with the MINERVA Platform, we visualise and explore COVID-19 transcriptomic data to demonstrate the utility of our workflow. Visualised data recapitulate findings of the original publication and offer new insights about the COVID-19 pathology. Our results offer a blueprint for quick prototyping of computational workflows that facilitate communication and exploration of complex data in biomedical research.

Lung cancer, including both non-small cell lung cancer and small cell lung cancer, remains the leading cause of cancer-related mortality worldwide representing 18% of the total cancer deaths in 2020. Many patients are identified already at an advanced stage with metastatic disease and have a worsening prognosis. Recent advances in the genetic understanding of lung cancer have opened new avenues for personalized treatments and targeted therapies. This review examines the latest discoveries in the genetics of lung cancer, discusses key biomarkers, and analyzes current clinical therapies based on this genetic information. It will conclude with a discussion of future prospects and potential research directions.

Lung cancer (LC) continues to be an important public health problem being the most common form of cancer and a major cause of cancer deaths worldwide. Despite the great bulk of research to identify genetic susceptibility genes by genome-wide association studies, only few loci associated to nicotine dependence have been consistently replicated. Our previously published study in few phenotypically discordant sib-pairs identified a combination of germline truncating mutations in known cancer susceptibility genes in never smoker early-onset LC patient does not present in their healthy sib. These results firstly demonstrated the presence of an oligogenic combination of disrupted cancer predisposing genes in non-smokers patients, giving experimental support to a model of a “private genetic epidemiology”. Here, we used a combination of whole-exome and RNA sequencing coupled with a discordant sib’s model in a novel cohort of pairs of never-smokers early-onset LC patients and in their healthy sibs used as controls. We selected rare germline variants predicted as deleterious by CADD and SVM bio-informatics tools and absent in the healthy sib. Overall, we identified an average of 200 variants per patient, about 10 of which in cancer predisposing genes. In most of them, RNA sequencing data reinforced the pathogenic role of the identified variants showing: i) downregulation in LC tissue (indicating “second hit” in tumor suppressor genes); ii) upregulation in cancer tissue (likely oncogene); iii) downregulation in both normal and cancer tissue (indicating transcript instability). The combination of the two techniques demonstrates that each patient has an average of six (with a range from four to eight) private mutations with functional effect in tumor predisposing genes. The presence of a unique combination of disrupting events in the affected subjects may explain the absence of familial clustering of non-small cell lung cancer. In conclusion, these findings indicate that each patient has his/her own “predisposing signature” to cancer development and suggest the use of personalized therapeutic strategies in lung cancer.

The vast array of omics data in microbiology presents significant opportunities for studying bacterial pathogenesis and creating computational tools for predicting pathogenic potential. However, the field lacks a comprehensive, curated resource that catalogs bacterial strains and their ability to cause human infections. Current methods for identifying pathogenicity determinants often introduce biases and miss critical aspects of bacterial pathogenesis.In response to this gap, we introduce BacSPaD (Bacterial Strains’ Pathogenicity Database), a thoroughly curated database focusing on pathogenicity annotations for a wide range of high-quality, complete bacterial genomes. Our rule-based annotation workflow combines metadata from trusted sources with automated keyword matching, extensive manual curation, and detailed literature review. Our analysis classified 5,502 genomes as pathogenic to humans (HP) and 490 as non-pathogenic to humans (NHP), encompassing 532 species, 193 genera, and 96 families. Statistical analysis demonstrated a significant but moderate correlation between virulence factors and HP classification, highlighting the complexity of bacterial pathogenicity and the need for ongoing research. This resource is poised to enhance our understanding of bacterial pathogenicity mechanisms and aid in the development of predictive models. To improve accessibility and provide key visualization statistics, we developed a user-friendly web interface, accessible at https://bacspad.altrabio.com.

Summary: Studying biological systems generally relies on computational modeling and simulation, e.g., for model-driven discovery and hypothesis testing. Progress in standardization efforts led to the development of interrelated file formats to exchange and reuse models in systems biology, such as SBML, the Simulation Experiment Description Markup Language (SED-ML), or the Open Modeling EXchange format (OMEX). Conducting simulation experiments based on these formats requires efficient and reusable implementations to make them accessible to the broader scientific community and to ensure the reproducibility of the results. The Systems Biology Simulation Core Library (SBSCL) provides interpreters and solvers for these standards as a versatile open-source API in Java™. The library simulates even complex bio-models and supports deterministic Ordinary Differential Equations (ODEs); Stochastic Differential Equations (SDEs); constraint-based analyses; recent SBML and SED-ML versions; exchange of results, and visualization of in silico experiments; open modeling exchange formats (COMBINE archives); hierarchically structured models; and compatibility with standard testing systems, including the Systems Biology Test Suite and published models from the BioModels and BiGG databases. Availability and implementation: SBSCL is freely available at https://draeger-lab.github.io/SBSCL/.

Macrophages are well known for the involvement in the biocompatibility, as well as biodistribution, of nano(bio)materials. Although there are a number of rodent cell lines, they may not fully recapitulate primary cell responses; particularly for those of human cells. Isolation of tissue resident macrophages, from humans, is difficult and may result in insufficient cells with which to determine the possible interaction with nano(bio)materials. Isolation of primary human monocytes, and differentiation to monocyte-derived macrophages, may provide a useful tool with which to study, further, these interactions. To that end, we developed a standard operating procedure for this differentiation, as part of the REFINE project, and used it to measure the secretion of bioactive molecules from M1 and M2 differentiated monocytes in response to model nano(bio)materials, following an initial assessment of pyrogenic contamination which may confound, potential, observations. The SOP was deployed in two partner institutions with, broadly, similar results. The work presented here shows the utility of this assay but, highlights the relevance of donor variability in responses to nano(bio)materials. Whilst donor variability can provide some, logistical, challenges to application of such assays, this variability is much closer to the heterogeneous cells that are present in vivo, compared to homogeneous, non-human, cell lines.

This article develops a multi-perspective view on motivations and methods for tobamovirus purification through the ages, and presents a novel efficient, easy-to-use approach that can be well-adapted to different species of native and functionalized virions. We survey the various driving forces prompting researchers to enrich tobamoviruses: from the search for the causative agents of mosaic diseases in plants to their increasing recognition as versatile nanocarriers in biomedical and engineering applications. Best practice and also rarely applied options for the serial processing steps required for successful isolation of tobamoviruses are then reviewed. Adaptations for distinct particle species, pitfalls and 'forgotten' or underrepresented technologies are considered as well. The article is topped off with our own development of a method for virion preparation, rooted in historical protocols. It combines selective re-solubilization of polyethylene glycol (PEG) virion raw precipitates with density step gradient centrifugation in biocompatible iodixanol formulations, yielding ready-to-use particle suspensions. This newly established protocol and some considerations for perhaps worthwile further developments could serve as putative stepping stones towards preparation procedures appropriate for routine practical uses of the multivalent soft-matter nanorods.

Systems biology has been established for more than a decade in the post-genomic era. With the help of the computational and mathematical tools, systems biology reconstitutes the entire scenario of the cell, tissue and even organism from the pieces data generated in the past decades. However, the modern biology is mainly focusing on the structure and function of the biomolecule, cell, tissue or organ, which are far from the essence of the life because of missing thermodynamic information. It is doubtable that the current systems biology-based omics is no-how to fully understand the dynamic courses of the structure, function and information in life. For this reason, we promote a novel concept of aquamoleculomics, in which the biological structure and function as well as thermodynamic characteristics and bioinformation of the aquamolecule complexes are included in this theoretical model of systems biology. Water is mother of life, matter and matrix of organism. Indeed, the fundamental roles of H₂O molecules in biological processes might be dramatically underestimated. Extremely speaking, H₂O networks in the living system might be engaged in all the biological processes including building all the biological structures, the residential places of the motherhood molecules as the honeycombs of honeybees.

Alzheimer's disease (AD) is a multifaceted neurodegenerative disorder characterized by cognitive decline and neuronal loss, representing a most challenging health issue. We present a computational analysis of transcriptomic data of AD tissues vs. healthy controls, focused on elucidation of functional roles played by long non-coding RNAs (lncRNAs) throughout the AD progression. We first assembled our own lncRNA transcripts from the raw RNA-Seq data generated from 527 samples of dorsolateral prefrontal cortex, resulting in the identification of 31,574 novel lncRNA genes. Based on co-expression analyses between mRNAs and lncRNAs, a co-expression network is constructed. Maximal subnetworks with dense connections are identified as functional clusters. Pathway enrichment analyses are conducted over mRNAs and lncRNAs in each cluster, which serve as the basis for the inference of functional roles played by lncRNAs involved in each of the key steps in an AD development model that we have previously build based on transcriptomic data of protein-encoding genes. Detailed information is presented about the functional roles by lncRNAs in activities related to stress response, reprogrammed metabolism, cell-polarity, and development. Our analyses have also revealed that lncRNAs have discerning power in distinguishing between AD samples of each stage and healthy controls. This study represents the first of its kind.

The supply chain has incorporated products by putting them into hair scarfs. This study introduces the use of mini chips in health and beauty products and can reduce fatigue through enhanced sleep patterns. The mini chip could be placed in the scarf and used as a prototype. RFID technology provides the supply chain with specific information that is used to identify products and make communication easier. (Muhammad, et. al. 2013) This paper presents a new tool herein referred to as a scarf prototype which is developed to analyse EMG (electromyogram), ECG (electrocardiography), EEG (electroencephalogram), and EOG (electro-oculogram) signals that focuses in the area of sleep disorders. The mini chips used can be used to determine a solution for sleep disruption by using automated analytics. This could lead to improvement in our understanding of sleep disruption and overall sleep physiology. Automated technology allows repeated measurements, evaluation of sleep patterns, and provide suggestions to improve a person’s quality of sleep. This analysis compares the use of polysomnography and the scarf prototype. The analytics provide models and shows correlation between variables, such as EMG, ECG, EEG, and EOG. This study shows that the results from the scarf prototype is just as reliable as the original method, polysomnography.

The particulars of stimulus-response experiments done on dynamic biosystems clearly limit what one can learn and validate about their structural interconnectivity (topology), even when collected kinetic output data are perfect (noise-free). As always, available access ports and other data limitations rule. For linear systems, exponential modes, visible and hidden, play an important role in understanding data limitations, embodied in what we call dynamical signatures in the data. We show here how to circumscribe and analyze modal response data in compartmentalizing model structures – so that modal analysis can be used constructively in systems biology model building – for nonlinear (NL) as well as linear biosystems. We do this by developing and exploiting the modal basis for dynamical signatures in hypothetical (perfect) input-output data associated with a structural model – one that includes inputs and outputs explicitly – and for NL as well as linear biosystems. The methodology establishes model dimensionality (size, complexity) from particular data sets; helps select among multiple candidate models (model distinguishability); helps in designing new experiments to extract “hidden” structure; and helps to simplify (reduce) models to their essentials. For NL biosystems, results are not as comprehensive, similarly informative about their dominant dynamical properties, and unified with linear models on invariant 2-dimensional manifolds in phase space. Some automation of these highly technical aspects of biomodeling is also introduced.

(1) Background: Multiple alterations of cellular metabolism have been documented in experimental studies of autosomal dominant polycystic kidney disease (ADPKD) and are thought to contribute to its pathogenesis. (2) Methods: To elucidate the molecular pathways and transcriptional regulators associated with the metabolic changes of renal cysts in ADPKD, we compared global gene expression data from human PKD1 renal cysts, minimally cystic tissues (MCT) from the same patients, and healthy human kidney cortical tissue samples. (3) Results: We found PKD1 renal cysts displayed the Warburg effect with gene pathway changes favoring increased cellular glucose uptake and lactate production, instead of pyruvate oxidation. Additionally, mitochondrial energy metabolism was globally depressed, associated with downregulation of gene pathways related to fatty acid oxidation (FAO), branched-chain amino acid (BCAA) degradation, the Krebs cycle, and oxidative phosphorylation (OXPHOS) in renal cysts. Activation of mTORC1 and its two target proto-oncogenes, HIF-1α and MYC, was predicted to drive the expression of multiple genes involved in the observed metabolic reprogramming (e.g., GLUT3, HK1/HK2, ALDOA, ENO2, PKM, LDHA/LDHB, MCT4, PDHA1, PDK1/3, MPC1/2, CPT2, BCAT1, NAMPT); indeed, their predicted expression patterns were confirmed by our data. Conversely, we found AMPK inhibition was predicted in renal cysts. AMPK inhibition was associated with decreased expression of PGC-1α, a transcriptional coactivator for transcription factors PPARα, ERRα, and ERRγ, all of which play a critical role in regulating oxidative metabolism and mitochondrial biogenesis. (4) Conclusions: These data provide a comprehensive map of metabolic pathway reprogramming in ADPKD and highlight nodes of regulation that may serve as targets for therapeutic intervention.

Flexible wearable pressure sensors offer numerous benefits, including superior sensing capabilities, a lightweight and compact design, and exceptional conformal properties, making them highly sought after in various applications including medical monitoring, human-computer interaction, and electronic skin. Because of their excellent characteristics, such as simple fabrication, low power consumption, and short response time, capacitive pressure sensors have received widespread attention. As a flexible polymer material, polydimethylsiloxane (PDMS) is widely used in the preparation of dielectric layers for capacitive pressure sensors. The Young's modulus of the flexible polymer can be effectively decreased through the synergistic application of sacrificial template and laser ablation techniques, thereby improving the functionality of capacitive pressure sensors. In this study, a novel sensor was developed through a series of processes including sacrificial template method using NaCl microparticles, CO₂ laser ablation, and sandwiching a porous PDMS dielectric layer between two flexible electrodes to create a capacitive pressure sensor. The sensor demonstrates a sensitivity of 0.694 kPa-1 within the pressure range of 0-1 kPa, and can effectively detect pressures ranging from 3 Pa to 200 kPa. The sensor demonstrates stability for up to 500 cycles, with a rapid response time of 96ms and a recovery time of 118ms, coupled with a low hysteresis of 6.8%. Furthermore, our testing indicates that the sensor possesses limitless potential for use in detecting human physiological activities and signaling emergencies.

The Mining Industry has changed significantly in recent decades with the introduction of advanced technologies such as Artificial Intelligence (AI) and Machine Learning (ML). These innovations contribute to the creation of expert systems that help in optimizing processes, increasing the safety and sustainability of operations. This article is a literature review of modern AI and ML methods and technologies used in the Mining Industry. Discusses various intelligent and expert systems used to improve productivity, reduce operating costs, improve occupational safety, environmental sustainability, machine automation, predictive analytics, quality monitoring and control, and inventory and logistics management. The advantages and disadvantages of different approaches are analyzed, as well as their potential impact on the future of the Mining Industry. The review highlights the importance of integrating AI and ML into mining processes to achieve more efficient and safer solutions.

This article proposes a particular strategy to proceed with a progressive electrification of public transport systems in cities. Starting from a bus operation model, the possible electrification of two routes is analysed, one urban and another extra-urban in the city of Pisa. An estimate is made of the energy uses associated with certain operating modes. The maximum level of consumption is estimated at approximately 280 kWh per day per bus for the urban route and excluding some special days, less than 215 kWh per day for the extra-urban route, for which a hybrid bus is proposed. Starting from an estimate of the daily consumption for the management of the two routes, the sizing of a photovoltaic system distributed on some modular shelters which serves to power the same routes is carried out. The resulting system has a power of the order of 190-200 kW. The modular solution is also outlined, and an installation is proposed. The analyzed case lends itself to being easily replicated.

This dissertation is a rigorous study of ecology and macrocellular biology as a subfield of abstract algebra. We begin with the creation of an axiomatic paradigm, then move onto constructing a universal genetic code of biology. We use this to define increasingly complex algebraic structures (ecosystem, evolving populations, etc.). We prove a variety of theorems regarding to the members of the previous mathematical constructs, notably the following three: 1. There is one unique phenotypic representation of each organism. For example, if you subdivide any piece of genetic code into its phenotypic components, then two identical organisms have identical decomposed DNA 2. There are a finite number of indivisible phenotypic traits. 3. The three sophioid-definitions are equivalent: (a) dynamical evolutionary enlargement of the medial temporal lobe and frontal lobe, (b) reliance upon intelligence, (c) the existence of an intellectually- or socially-hierarchical society. Much has yet to be done on this work, but as a first draft, it stands as a jumping point for future exploits; I am working on an entirely revised second draft.

Significance: Cellular redox processes are highly interconnected, yet not in equilibrium, and governed by a wide range of biochemical parameters. Technological advances continue refining how specific redox processes are regulated, but broad understanding of the dynamic interconnectivity between cellular redox modules remains limited. Systems biology investigates multiple components in complex environments and can provide integrative insights into the multi-faceted cellular redox state. This review describes the state of the art in redox systems biology as well as provides an updated perspective and practical guide for harnessing thousands of cysteine sensors in the redoxome for multi-parameter characterization of cellular redox networks. Recent Advances: Redox systems biology has been applied to genome-scale models and large public datasets, challenged common conceptions and provided new insights that complement reductionist approaches. Advances in public knowledge and user-friendly tools for proteome-wide annotation of cysteine sentinels can now leverage cysteine redox proteomics datasets to provide spatial, functional, and protein structural information. Critical Issues: Careful consideration of the analytical approaches is needed to broadly characterize the systems level properties of redox signaling networks and be experimentally feasible. The cysteine redoxome is an informative focal point since it integrates many aspects of redox biology. The mechanisms and redox modules governing cysteine redox regulation, cysteine oxidation assays, proteome-wide annotation of the biophysical and biochemical properties of individual cysteines, and their clinical application are discussed. Future Directions: Investigating the cysteine redoxome at a systems level will uncover new insights into the mechanisms of selectivity and context-dependence of redox signaling networks.

For a long time, a company's Product Development Process (PDP) was seen as supporting the operations department, although PDP decisions and mistakes have a considerable impact on market performance. This is critical even in agriculture where bad habits and practices in the PDP can lead rural producers to great losses. Therefore, this research investigated the effect on the market performance of rural products (banana) in the southern region of Brazil, based on two analyses: (i) how sustainability practices support the PDP phases and (ii) how the phases of the Product Life Cycle Assessment (LCA) mediate sustainability practices and PDP phases. This study presents a quantitative analysis using Confirmatory Factor Analysis (CFA) and hierarchical ordinary least squares (OLS) regression of data obtained from a survey of 110 rural producers who directly participate in the banana production and planning process in southern Brazil. Our results shows that sustainability practices support the PDP, and we confirm that the product development and post-development phase has an effect on market performance. In addition, we identified that in the pre-development phase of the PDP, dealing with rural products (bananas), the maturity stage of the LCA mediates sustainability. In the PDP development phase, we concluded that rural families that develop economic and environmental practices with their products in the market growth phase may have reduced results. As for the post-development phase of the PDP, we conclude that when companies invest in environmental and social practices, there is a complete mediation of the effect, where these practices lose strength if the product is in the introduction and maturity phases in the market. As originality, our study contributed to demonstrate value on the product life cycle for the product development process in agriculture using sustainability practices through a systemic approach, filling the gap in the literature due to the lack of research on these areas seen in an integrated way.

Computational models of homologous protein groups are essential in sequence bioinformatics. Due to the diversity and rapid evolution of viruses, the grouping of protein sequences from virus genomes is particularly challenging. The low sequence similarities of homologous genes in viruses require specific approaches for sequence- and structure-based clustering. Furthermore, the annotation of virus genomes in public databases is not as consistent and up-to-date as for many cellular genomes. To tackle these problems, we have developed VOGDB, a database of Virus Orthologous Groups. VOGDB is a multi-layer database that progressively groups viral genes into groups connected by increasingly remote homology. The first layer is based on pair-wise sequence similarities, the second layer is based on the sequence profile alignments and the third layer uses predicted protein structures to find the most remote homology. VOGDB groups allow for more sensitive homology searches of novel genes and increase the chance of predicting annotations or inferring phylogeny. VOGDB uses all virus genomes from RefSeq and partially re-annotates them. VOGDB is updated with every RefSeq release. The unique feature of VOGDB is inclusion of both prokaryotic and eukaryotic viruses in the same clustering process which makes it possible to explore old evolutionary relationships of the two groups. VOGDB is freely available at https://vogdb.org under the CC BY 4.0 license.

Dynamic virtual testing by Hardware in the Loop (HIL) real time simulation systems is common to minimize physical tests to validate and verify control algorithms, logics and software, under normal and emergency conditions. The accurate but costly HIL models setup activities could have an extended use to simulate faulty conditions that are seldom observable in the real system, yet they must be detected in advance and recognized. Data driven diagnostic methods have reached a mature development, in various sectors, proving effective in early detecting slowly varying deviations from nominal patterns of signals, even without a priori knowledge of their nature and behavior. These methods rely on vast amount of data logged from real systems that are ever and ever richer of monitoring telemetries that are worth being exploited. However, due to the usually reliable and safe systems being managed, it is often difficult to collect enough data on anomalous situations to validate fault detection and isolation and limit false positives. HIL model-based simulations allow generating and observing operational domains or transients rarely observed in real operations. This allows identifying the signals that are most correlated to faults and that could be selected to setup data-based diagnostic models of parts or subsystems, which are more suitable than the whole HIL model for online diagnostics, as well as to identify the features and trends that are most symptomatic of anomalous conditions.

Infection with the Chikungunya virus (CHIKV) manifests as a febrile illness known as chikungunya fever (CHIKF). CHIKF is characterized by sudden-onset high fever, rash, polyarthritis, and polyarthralgia. Alt-hough the infection typically resolves within two weeks, many patients experience recurrent joint pain and inflammation that can outlast the other symptoms for many months. CHIKF has been previously linked to rheumatoid arthritis (RA) due to similar inflammatory processes. This study aimed to identify molecular markers in the blood of CHIKV-infected individuals associated with joint pain and chronicity of CHIKF. Sequencing of B and T cell receptors (BCR and TCR) revealed that CHIKV infection reduces CDR3 diver-sity. Lower BCR diversity was linked to increased expression of genes involved in osteoclast differentiation and activation through RANK/RANKL signaling. If osteoclast involvement in CHIKF pathogenesis is con-firmed, existing therapeutic approaches could be used as alternative treatments for CHIKF patients.

Obesity has increasingly become a worldwide epidemic, as demonstrated by epidemiological and clinical studies. Obesity may lead to development of a broad spectrum of cardiovascular diseases (CVDs), such as coronary heart disease (CHD), hypertension, heart failure (HF), cerebrovascular disease, atrial fibrillation (AF), ventricular arrhythmias, and sudden cardiac death (SCD). In addition to hypertension, there are other cardiometabolic risk factors (CRFs) such as visceral adiposity, dyslipidemia, insulin resistance, diabetes, elevated levels of fibrinogen, and C-reactive protein and others, all of which increase the risk of CVD events. Mechanisms involved between obesity and CVD mainly include insulin resistance, oxidative stress, inflammation, and adipokines dysregulation, which cause maladaptive structural and functional alterations of the heart, particularly left ventricular (LV) remodeling and diastolic dysfunction. Natural products of plants, provide a diversity of nutrients and different bioactive compounds, including phenolics, flavonoids, terpenoids, carotenoids, anthocyanins, vitamins, minerals, fibers, and others, which possess a wide range of biological activities including antihypertensive, antilipidemic, antidiabetic, and other activities, thus conferring cardiometabolic benefits. In this review, we discussed the main therapeutic interventions using extracts from herbs and plants in preclinical and clinical trials with protective properties targeting CRFs. Molecular mechanisms and therapeutic targets of herbs and plants extracts for the prevention and treatment of CRFs are also reviewed.

Many clinical research datasets have a large percentage of missing values that directly impacts their usefulness in yielding high accuracy classifiers when used for training in supervised machine learning. While missing value imputation methods have been shown to work well with smaller percentages of missing values, their ability to impute sparse clinical research data can be problem specific. We previously attempted to learn quantitative guidelines for ordering cardiac magnetic resonance imaging during the evaluation for pediatric cardiomyopathy, but missing data significantly reduced our usable sample size. In this work, we sought to determine if increasing the usable sample size through imputation would allow us to learn better guidelines. We first review several machine learning methods for estimating missing data. Then, we apply four popular methods (mean imputation, decision tree, k-nearest neighbors, and self-organizing maps) to a clinical research dataset of pediatric patients undergoing evaluation for cardiomyopathy. Using Bayesian Rule Learning (BRL) to learn ruleset models, we compared the performance of imputation-augmented models versus unaugmented models. We found that all four imputation-augmented models performed similarly to unaugmented models. While imputation did not improve performance, it did provide evidence for the robustness of our learned models.

Lung cancer accounts for the highest number of deaths among men and women worldwide. Although extensive therapies, either alone or in conjunction with some specific drugs, continue to be the principal regimen for evolving lung cancer, significant improvements are still needed to understand the inherent biology behind progressive inflammation and its detection. Unfortunately, despite every advancement in its treatment, lung cancer patients display different growth mechanisms and continue to die at significant rates. Autophagy, which is a physiological defense mechanism, serves to meet the energy demands of nutrient-deprived cancer cells and sustain the tumor cells under stressed conditions. In contrast, autophagy is believed to play a dual role during different stages of tumorigenesis. During early stages, it acts as a tumor suppressor, degrading oncogenic proteins; however, during later stages, autophagy supports tumor cell survival by minimizing stress in the tumor microenvironment. The pivotal role of the IL6-IL17-IL23 signaling axis has been observed to trigger autophagic events in lung cancer patients. Since the obvious roles of autophagy are a result of different immune signaling cascades, systems biology can be an effective tool to understand these interconnections and enhance cancer treatment and immunotherapy. In this review, we focus on how systems biology can be exploited to target autophagic processes that resolve inflammatory responses and contribute to better treatment for carcinogenesis.

Nowadays, cervical cancer (CC) is treated as the leading cancer among women throughout the world. Despite effective vaccination and improved surgery and treatment, CC remains its fatality rate about half of the infected populations globally. The major screening biomarkers and therapeutic target identification have now become a global concern. The present study, we have employed systems biology approaches to retrieve the potential biomarkers and pathways from the transcriptomic profiling. Initially, we have identified 76 of each up-regulated and down-regulated gene from a total of 4,643 differentially expressed genes. The up-regulatory genes are mainly concentrating on immune-inflammatory response and the down-regulatory genes are on receptor binding and gamma-glutamyltransferase. The involved pathways associated with these genes were also assessed through pathway enrichment and they were mainly focused on different cancer pathways, immunoresponse, and cell cycle pathways. After the subsequent enrichment of these genes, we have identified 12 hub genes, which play a crucial role in CC. Furthermore, the survival of the hub genes was also assessed, and among them, finally, CXCR4 has identified as one of the most potential differentially expressed gene that might play a vital role to the survival of CC patients. Thus CXCR4 could be used as a prognostic biomarker and development of a drug target for CC.

Myocardial infarction, more commonly known as heart attack, is a huge health problem around the world. It is a result of inadequate blood supply to certain parts of the heart and death of heart muscle cells in that region. Although it has been around for a long time, newer and newer ways of probing myocardial infarction is being followed. Bioinformatics and Systems Biology are relatively recent fields to try to give new insights into myocardial infarction. Following the footsteps of others, this in silico study has tried to chime in on the investigation into myocardial infarction. The study began with the gene expression omnibus dataset uploaded to the NCBI from a whole-genome gene expression analysis carried out at Mayo Clinic in Rochester, Minnesota. From the dataset, differentially expressed genes following first-time myocardial infarction were identified and classified into up-regulated and down-regulated ones. Gene Set Enrichment Analysis (GSEA) was carried out on the up-regulated genes which were statistically significant and corresponded with the NCBI generated annotations. Protein-Protein Interaction Network for these genes was constructed. GSEA revealed 5 transcription factors, 5 microRNAs and 3 pathways significantly associated with them. From the Protein-Protein Interaction Network, 6 key proteins (hub nodes) have been identified. These 6 proteins may open a new window of opportunity for the discovery/design of new drugs for mitigating the damage caused by myocardial infarction.

The dawn of quasispecies theory revolutionized our understanding of viral evolution and pathogenesis. This theory conceptualises viruses as dynamic populations of closely related but genetically diverse variants that constantly mutate and adapt to environmental pressures. Quasispecies dynamics govern key aspects of virus-host interactions, such as adaptive evolution, immune evasion, drug resistance, and host tropism. In this article, we discuss the fundamental role of quasispecies theory in elucidating viral fitness landscapes, shaping antiviral strategies, and predicting viral emergence and evolution. We provide a concise overview of the original quasispecies model and its latest advancements, which enable the study of the connection between viral dynamics and the significant genetic diversity exhibited by viruses. We then point out some key features of virus dynamics that need to be incorporated into quasispecies theory. We continue with examples of convergence between theory and real viruses by discussing theoretical results supported by RNA virus data and vice versa. Next, we discuss the need to extend the concept of sequence space beyond the classical hypercube towards more complex, multidimensional connected sequence spaces that we have called ultracubes. Finally, we highlight the necessity of developing multi-scale models to understand how viral evolutionary dynamics within a host can affect epidemiological patterns. We also examine the limitations of quasispecies theory in predicting virus evolution and emergence.

The early elongation events in transcription or translational control in the N-terminal of genes are assuming critical roles in their heterologous expression. The secretory expression of the alkaline pectin lyase APL in B. subtilis were studied to explore the effects of the N-terminal 5-7 amino acids sequences of different signal peptides on gene transcription and protein secretion in this study. The first 5 amino acid sequences of the N-terminal of the signal peptide LipA were identified to play an important role in promoting the expression of APL for the first time. Meanwhile, it also revealed that the signal peptide LipA could lead to higher secretory expression than other signal peptides not because of its sequence structure associated with secretion is stronger but because the N-terminal sequences showed greater advantages in gene transcription. At this basis, the recombinant strain structed in this work showed a new record for the highest extracellular yields (12 295 U/ml) of APL in B. subtilis which was 1.9 times higher than that expressed in the recombinant Escherichia coli strain we had reported before. The novel theories revealed in this study would assuming significance roles for improving expression of foreign proteins in or out of the cells.

Despite the growing capabilities of large language models, concerns exist about the biases they develop. In this paper, we propose a novel, automated mechanism for debiasing through specified dataset augmentation in the lens of bias producers that can be useful in a variety of industries, especially ones that are “restricted” and have limited data. We consider that bias can occur due to intrinsic model architecture and dataset quality. The two aspects are evaluated using two different metrics we created. We show that our dataset augmentation algorithm reduces bias as measured by our metrics.

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

In this paper, a new axial-type magnetic gear with auxiliary flux-enhancing structure (AFS-AMG) is proposed. Compared to conventional AFS-AMG, it has the higher torque density and higher permanent magnet (PM) utilization factor. Firstly, the design rules and operating principles of proposed AFS-AMG are elaborated. Then, the mapping relation between the radial-type magnetic gears (RMGs) and AMGs are elucidated. Compared to its counterpart in RMGs, AFS-AMGs achieve small size. Then, the geometrical parameters of AFS-AMGs are optimized to obtain the better electromagnetic performances, where the torque density per volume and per PM volume is adopted as the evaluation standard. Finally, three different AMG topologies are constructed in finite element analysis (FEA) software for comparison. It is proven that the AFS-AMG has the largest torque density per volume and per PM volume.

Estrogen receptor-positive (ER+) breast cancer is common among postmenopausal women and is frequently treated with Letrozole. Letrozole inhibits aromatase from synthesizing estrogen from androgens. Decreased estrogen slows the growth of tumors and can be an effective treatment. Letrozole resistance is increasingly being observed, which poses a unique problem for patients. We reanalyzed transcriptomic data comparing individuals who responded to Letrozole therapy (responders) to those who were resistant to treatment (non-responders). We identified SOX11 and S100A9 as two genes that significantly differed between these patients; with “PLK1 signaling events” being the most significant signaling pathway. We also identified PRDX4 and E2F8 as the top transcriptional biomarkers for ER+ treatment resistance. Many of the other significant gene products play a known role in ER+ breast cancer or other types of cancer, which partially validate our results. Several of the gene products we identified do not have a characterized role in ER+ breast cancer. Our analysis identified a set of genes that warrant further research to elucidate the molecular mechanism of Letrozole resistance in this patient population, as well as novel high-performing biomarkers. We anticipate that these findings could contribute to improved therapeutic outcomes in human patients.

In systems biology, biological phenomena are often modeled by ODE and distributed in the de facto standard file format SBML. The primary analyses performed with such models are dynamic simulation, steady-state analysis, and parameter estimation. These methodologies are mathematically formalized, and libraries for such analyses have been published. Several tools exist to create, simulate, or visualize models encoded in SBML. However, setting up and establishing analysis environments is a crucial hurdle for non-modelers. Therefore, easy access to perform fundamental analyses of ODE models is a significant challenge. We developed SBMLWebApp, a web-based service to execute SBML-based simulations, steady-state analysis, and parameter estimation directly in the browser without the need for any setup or prior knowledge to address this issue. SBMLWebApp visualizes the result and numerical table of each analysis and provides a download of the results. SBMLWebApp allows users to select and analyze SBML models directly from the BioModels Database. Taken together, SBMLWebApp provides barrier-free access to an SBML analysis environment for simulation, steady-state analysis, and parameter estimation for SBML models. SBMLWebApp is implemented in Java™ based on an Apache Tomcat® web server using COPASI, the SBSCL, and LibSBMLSim as simulation engines. SBMLWebApp is licensed under MIT with source code available from https://github.com/TakahiroYamada/SBMLWebApp. The program runs online at http://simulate-biology.org.

Bottom-up systems biology entails the construction of kinetic models of cellular pathways by collecting kinetic information on the pathway components (e.g. enzymes) and collating this into a kinetic model, based for example on ordinary differential equations. This requires integration and data transfer between a variety of tools, ranging from data acquisition in kinetics experiments, to fitting and parameter estimation, to model construction, evaluation and validation. Here, we present a workflow that uses the Python programming language, specifically the modules from the SciPy stack, to facilitate this task. Starting from raw kinetics data, acquired either from spectrophotometric assays with microtitre plates or from NMR spectroscopy time courses, we demonstrate the fitting and construction of a kinetic model using scientific Python tools. The analysis takes place in a Jupyter notebook, which keeps all information related to a particular experiment together in one place and thus serves as an e-labbook, enhancing reproducibility and traceability. The Python programming language serves as an ideal foundation for this framework because it is powerful yet relatively easy to learn for the non-programmer, has a large library of scientific routines and active user community, is open-source and extensible, and many computational systems biology software tools are written in Python or have a Python API. Our workflow thus enables investigators to focus on the scientific problem at hand rather than worrying about data integration between disparate platforms.

The current surge in the deployment of web applications underscores the need to consider users' individual preferences in order to enhance their experience. In response to this, an innovative approach is emerging that focuses on the detailed analysis of interaction data captured by web browsers. This data, which includes metrics such as the number of mouse clicks, keystrokes, and navigation patterns, offers insights into user behaviour and preferences. By leveraging this information, developers can achieve a higher degree of personalization in web applications, particularly in the context of interactive elements such as online games. This paper presents the WebTraceSense project, which aims to pioneer this approach by developing a framework that encompasses a backend and frontend, advanced visualization modules, a DevOps cycle, and the integration of AI and statistical methods. The backend of this framework will be responsible for securely collecting, storing, and processing vast amounts of interaction data from various websites. The frontend will provide a user-friendly interface that allows developers to easily access and utilize the platform’s capabilities. One of the key components of this framework is the visualization modules, which will enable developers to monitor, analyse, and interpret user interactions in real-time, facilitating more informed decisions about user interface design and functionality. Furthermore, the WebTraceSense framework incorporates a DevOps cycle to ensure continuous integration and delivery, thereby promoting agile development practices and enhancing the overall efficiency of the development process. Moreover, the integration of AI methods and statistical techniques will be a cornerstone of this framework. By applying machine learning algorithms and statistical analysis, the platform will not only personalize user experiences based on historical interaction data but also infer new user behaviours and predict future preferences. In order to validate the proposed components, a case study was conducted which demonstrated the usefulness of the WebTraceSense framework in the creation of visualizations based on an existing dataset.

In recent years, the research community has been interested in members of the Acinetobacter genus mainly because of their role as causative agents of nosocomial infections. However, this rich-in-species genus has been proven to play a significant role in different biotechnological processes, such as bioremediation and fermented foods production. To partially fill the lack of information on Acinetobacter’s dualistic nature, in this review, based on literature data, we attempt to summarize the available information on the different roles the members of the genus play by considering their genetic constitution and metabolic properties. We found pieces of evidence of genetic divergence between the pathogenic and non-pathogenic species and strains, which can be explained by their high adaptability to the different ecological niches. In turn, this adaptability could result from intrinsic genetic variability due to mechanisms of horizontal genetic transfer, as well as high mutability determined by the expression of error-prone DNA polymerases. Yet, further studies are needed, especially whole-genome sequencing of non-pathogenic isolates, which for the moment are relatively scarce.

Maintaining the optimal microclimate in broiler houses is crucial for bird productivity, yet enabling efficient temperature control remains a significant challenge. This study developed and validated a computational fluid dynamics (CFD) model to predict temporal changes in indoor air temperature in response to variable ventilation operations in a commercial broiler house. The model accurately simulated air velocity and airflow distribution for different numbers of tunnel fans in operation, with air-velocity errors ranging from -0.22 to 0.32 m s-1. The predicted airflow rates through inlets and cooling pads showed good agreement with measured values with an accuracy of up to 108.1%. Additionally, the CFD model effectively predicted temperature dynamics, accounting for chicken heat production and ventilation effect. The model successfully predicted the longitudinal temperature gradients and their variations during ventilation cycles, validating its reliability through comparison with experimental data. The study also explored different variable inlet configurations to mitigate the temperature gradient. The variable inlet adjustment showed the potential to relieve the high temperatures but may reduce overall ventilation efficiency or intensify temperature gradients, which confirms the importance of optimising ventilation strategies. This CFD model provides a valuable tool for evaluating and improving ventilation systems and contributes to enhanced indoor microclimates and productivity in poultry houses.

Hepatocellular carcinoma (HCC) development is associated with altered modifications in DNA methylation, changing transcriptional regulation. Emerging evidence indicates that DNA methyltransferase 1 (DNMT1) plays a key role in carcinogenesis process. This study aimed to investigate how pirfenidone (PFD) modifies this pathway and the effect generated by the association between c-Myc expression and DNMT1 activation. Rats F344 were used for HCC development using 50 mg/kg of diethylnitrosamine (DEN) and 25 mg/kg of 2-aminofluorene (2-AAF). HCC/PFD group received simultaneous doses of 300 mg/kg of PFD. All treatments lasted 12 weeks. On the other hand, HepG2 cells were used to evaluate the effects of PFD in restoring DNA methylation in the presence of the inhibitor 5-Aza. Histopathological, biochemical, immunohistochemical, and western blot analysis were carried out and our findings showed that PFD treatment reduced the amount and size of tumors along with decreased Glipican-3, β-catenin, and c-Myc expression in nuclear fractions. Also, this treatment improved lipid metabolism by modulating PPARγ and SREBP1 signaling. Interestingly, PFD augmented DNMT1 and DNMT3a protein expression, which restores global methylation, both in our in vivo and in vitro models. In conclusion, our results suggest that PFD could slow down HCC development by controlling DNA methylation.

Background: Ice formation on power transmission lines presents significant risks, including structural damage and power outages. Traditional methods for detecting ice on these lines have limitations, particularly in challenging environmental conditions. This study aims to enhance ice detection accuracy by introducing a novel image segmentation and edge detection methodology using improved multi-scale Retinex and advanced morphological operations. Method: The proposed method integrates multi-stage image processing techniques, including image enhancement, grayscale conversion, thresholding, segmentation, object isolation, and edge detection. High-resolution binocular cameras were used to capture images of ice formations on transmission lines. The effectiveness of the method was assessed through a series of metrics, including accuracy, sensitivity, specificity, and precision, and compared with existing methodologies. Results: The proposed method demonstrated superior performance in both ice detection and thickness measurement. The method effectively identified and isolated ice formations under various conditions with an average accuracy of 98.35%, sensitivity of 91.63%, specificity of 99.42%, and precision of 96.03%. Additionally, the analysis of ice thickness measurements further highlighted the method’s accuracy, with a notably low root mean squared error (RMSE) of 1.20 mm and mean absolute error (MAE) of 1.10 mm, along with a strong R-squared value of 0.95. These statistical metrics show that the proposed method not only outperforms previous methods in consistency and alignment with manual measurements but also stands out as the most reliable option for tasks requiring precise measurements, offering significant advancements in accuracy and reliability over existing methodologies. Conclusions: The enhanced image segmentation and edge detection approach provides a more accurate and reliable method for monitoring ice formations on power transmission lines.

This article presents an innovative approach to the design of a safe adaptive backstepping control system. Tailored specifically for underactuated marine robots, the system utilizes simple sensors for enhanced practicality and efficiency. Given their operation in diverse oceanic environments fraught with various sources of uncertainties, ensuring the system's safe and robust behavior holds paramount importance in the control literature. To address this concern, this paper introduces a control strategy designed to ensure robustness at both the kinematic and dynamic levels. By emphasizing the compensation for the system uncertainties, the design integrates a straightforward fuzzy system structure. To further ensure the system's safety, a funnel surface is defined, followed by the design of a suitable nonlinear sliding surface as a function of the funnel and tracking error. Specifically leveraging the Lyapunov function, the study formally establishes the Semi-globally Practically Finite-time Stability of the closed-loop system, validated through simulations conducted on underactuated marine robots.

The aim of this research work is to study the influence of temperature, solar irradiation and wind dust on the production of solar energy. In addition, it aims to study the assessment of water quality, in particular groundwater used for cooling and cleaning photovoltaic panels (quality analysis). it's an important source, stable and sustainable can be used entirely for cooling and cleaning PV modules from the sales dust, in order to improve their performance. To date, all research studies carried out in this context of cooling and cleaning using water have not taken account of the nature of this water. We have taken a sample of water from a well in a rural area in the Darra Tafilalet region of Morocco. This region has an arid and semi-arid climate, with very high temperatures and dust-laden winds, particularly in summer. These meteorological characteristics influence the efficiency of cells, particularly photovoltaic (PV) panels, reducing their performance. Next, the water sample was analysed in the laboratory. The results obtained show that the groundwater in this area is very sensitive to cooling and cleaning photovoltaic panels. Moreover, these results indicate that the temperature, solar irradiation and wind-blown dust have a significant influence on energy production.

Immortal-time bias (ITB) is known to be common in cohort studies and distorts the association estimates between treated and untreated groups. We used data from the last of two large studies in an Italian province on COVID-19 vaccines safety and effectiveness incurred this bias, and aligned the entire population on a single index date, to correct the ITB. We considered the "all-cause deaths" outcome to compare the survival curves between the unvaccinated group and the various vaccination statuses. The all-cause deaths Hazard Ratios in univariate analysis for unvaccinated (reference) versus vaccinated with 1, 2, 3/4 doses were 0.88 (CI95: 0.78 –1.00; p-value 0.044), 1.23 (1.16–1.32; p-value ≤0.001) and 1.21 (1.14–1.29; p-value ≤0.001), respectively. The multivariate values were 2.40 (2.00–2.88; p-value <0.0001), 1.98 (1.75–2.24; p-value <0.0001), 0.99 (0.90–1.09; ns). The possible explanations of the trend of the Hazard Ratios as vaccinations increase could be a harvesting effect; a calendar-time bias, accounting for seasonality and pandemic waves; a case-counting windows bias; a healthy-vaccinee bias; or some their combination. With two and even with 3/4 doses the calculated Restricted Mean Survival Time and Restricted Mean Time Lost have shown a small but significant downside for the vaccinated populations.

The Doppler band compensated by the keystone transform (KT) is limited. Therefore, it needs to be used in conjunction with the Doppler ambiguity compensation function to correct the range migration (RM) caused by maneuvering targets with Doppler ambiguity. However, the KT implemented by sinc interpolation suffers from significant performance loss at boundaries of compensation Doppler bands. Additionally, in a multi-target scenario, KT implementation methods occupy high complexity when the Doppler range of targets spans over two compensation Doppler bands. To address aforementioned issues, this study presents a variable Doppler starting point keystone transform (VDSPKT) method, where a new form of ambiguity compensation function is constructed, turning the Doppler starting point of the compensation band in KT variable. Firstly, the position of the compensation Doppler band is changed from fixed to adjustable as needed, enhancing the flexibility of KT. Crucially, the connection points of the compensation Doppler bands in sinc interpolation are reset, avoiding the performance loss at their boundaries. Also, the compensation band is adjusted to cover the narrow Doppler frequency range caused by targets, significantly improving the computational efficiency. Finally, the simulation results demonstrate that the proposed approach effectively addresses the performance degradation and high computational complexity of KT in the aforementioned scenarios, resulting in a computational load reduced by approximately 50% compared to traditional methods.

Pollution, urbanization and technological advancements have posed stress on the ecosystem and its matrices. Globally, pollutants are observed in all compartments of ecological communities which affect the integrity of the atmosphere, hydrosphere, lithosphere and biosphere. Xenobiotics bioaccumulate and biomagnify across trophic levels or webs. Heavy metals have been implicated in impacts towards biodiversity and environmental declination. In Nigeria, wastes issues are a cause of concern and landfilling or are waste disposal approaches that cause deleterious effects such as depauperation of diversity and species decline, prompting the non-invasive ecotoxicological hazard assessments. Feathers were used to assess concentration levels of 13 metals (Fe, Mn, Zn, Cu, Co, Cr, Cd, Pb, Ni, Al, B, Se and Hg) using fast atomic absorption spectrophotometer (FAAS), one-way ANOVA was used in comparing variations in mean concentrations across trophic levels, diversity indices and point count methods were used to estimate diversity and abundance. Four avian species were assessed Hirundo aethiopica (insectivore), Streptoptelia senegalensis (granivore), Turdus pelios (omnivore), and Anthus leucophrys. (insectivore). Observed concentrations of important metals like iron were high with the insectivores having the highest concentrations of iron (2.6985 ± 0.1975 ppm) and granivores having the lowest (2.0100 ± 0.3172 ppm). The insectivores had the highest concentrations for cadmium, cobalt and chromium (0.0005 ± 0.0005ppm), nickel (at 00.0012 ± 0.0017 ppm) and least was observed in the granivores (0.0003 ± 0.0006 ppm). Selenium concentrations were quite high in insectivores (0.0775 ± 0.0035 ppm) and lowest in granivores (0.0433 ± 0.0015 ppm) likewise mercury for insectivores (0.0280 ± 0.0010 ppm) and granivores (0.0213 ± 0.0015 ppm). From the study, it is apparent that landfills are sources of pollution and poor management of wastes can affect biota (causing effects such as asymmetry and bioaccumulation) and ecosystem balance. The observation of heavy metals in the feathers serve as good sentinels due to their trophic levels and could be signs for what could be yet to occur. The heavy metal concentrations were significantly different at p < 0.05.

System xc-, the cystine/glutamate exchanger, is a membrane transporter that plays a critical role in the antioxidant response of cells. Recent work has shown that System xc- localizes to the plasma membrane during oxidative stress, allowing for increased activity to support production of glutathione. In this study, we used site-directed mutagenesis to examine the role of C-terminal lysine residues (K422, K472, K473) of xCT (SLC7A11) in regulating System xc-. We observed that K473R exhibits loss of transporter activity and membrane localization and is 7.5 kD lower in molecular weight, suggesting that K473 regulates System xc- trafficking and is modified under basal conditions. After ruling out ubiquitination and neddylation, we demonstrated that unlike WT xCT, K473R lacks N- and O-glycosylation and is sequestered in the endoplasmic reticulum. Next we demonstrated that K473Q, a constitutively acetylated lysine mimic, also exhibits loss of transporter activity, decreased membrane expression, and a 4 kD decrease in molecular weight, however, it is N- and O-glycosylated and localized to the endoplasmic reticulum and Golgi. These results suggest that acetylation and deacetylation of K473 in the endoplasmic reticulum and Golgi, respectively, serves to regulate the progression of the transporter through the biosynthetic pathway.

The purpose of this paper is to explore the implementation of Retrieval-Augmented Gen- 14 eration (RAG) technology with open-source Large Language Models (LLMs). For this purpose, a 15 web-based application named PaSSER that integrates RAG with three models - Mistral:7b, 16 Llama2:7b: Orca2:7b, is developed. In its development various technologies are used, including 17 Blockchain for managing and storing assessment results of built-in testing modules. PaSSER em- 18 ploys a set of evaluation metrics for LLMs’ performance - METEOR, ROUGE, BLEU, Perplexity, 19 Cosine similarity, Pearson correlation, and F1 score. The specialized knowledge base is in the smart 20 agriculture domain. As an illustration, the paper presents results and analysis of two tests. First one 21 is assessing the performance of LLMs across different hardware configurations, the other is deter- 22 mining the model that delivers most accurate and contextually relevant responses within the RAG. 23 The paper also discusses the integration of blockchain technology with LLMs to manage and store 24 assessment results within a blockchain environment. The tests revealed that Mistral:7b demon- 25 strates the best results across most of the evaluated metrics. The discussion section comments on 26 technical and hardware considerations that affect the performance of LLMs. Future development 27 will focus in leveraging new larger pre-trained open-source LLMs, exploring different finetuning 28 approaches, and further integration with Blockchain and IPFS.

System-of-systems (SoS) evolution is a complex and unpredictable process. Although various principles to facilitate collaborative SoS evolution have been proposed, there is a lack of experimental data validating their effectiveness. To address these issues, we present an Agent-Based Model (ABM) for SoS evolution in the Internet of Vehicles (IoV) , serving as a quantitative analysis tool for SoS research. By integrating multiple complex and rational behaviors of individuals, we aim to simulate real-world scenarios as accurately as possible. To simulate the SoS evolution process, our model employs multiple agents with autonomous interactions and incorporates external environmental variables. Furthermore, we propose three evaluation metrics: evolutionary time, degree of variation, and evolutionary cost, to assess the performance of SoS evolution. Our study demonstrates that enhanced information transparency significantly improves the evolutionary performance of distributed SoS. Conversely, the adoption of uniform standards only brings limited performance enhancement to distributed SoSs. Although our proposed model has limitations, it stands out from other approaches that utilize Agent-Based Modeling to analyze SoS theories. Our model focuses on realistic problem contexts and simulates realistic interaction behaviors. This study enhances the comprehension of SoS evolution processes and provides valuable insights for the formulation of effective evolutionary strategies.

The majority of investigations on microbial communities from various environments are presently built on culture-independent methods. Many studies point to the pivotal, selective role of primers targeting hypervariable regions of 16S rRNA in the metabarcoding of bacteria, including cyanobacterial communities. The selectivity of primers designed to amplify targeted regions of the 16S rRNA gene, which has been highlighted by many authors, limited effective amplification. Moreover, the type and specificity of the studied material can also negatively influence the results of 16S metabarcoding. Most of the studies of cyanobacterial communities have been performed for planktonic microbial communities that are often represented by common, well-studied species. In this study, we present the results of 16S metabarcoding analysis using three primer pairs - two already well-known and a third designed in this study - that amplify divergent regions of the 16S rRNA gene (V3-V4, V4-V6, V6) for benthic, microbial mat-forming cyanobacteria communities. Such communities can be a source of toxigenic cyanobacterial taxa and should be monitored with adequate primers. The comparison of three primer pairs suggested that those designed within the present study describe the structure and composition of highly heterogeneous cyanobacterial mats’ communities better than the others

The number and size of computational models in biology have drastically increased over the past years and continue to grow. Modeled networks are becoming more complex, and reconstructing them from the beginning in an exchangeable and reproducible manner is challenging. Using precisely defined ontologies enables the encoding of field-specific knowledge and the association of disparate data types. In computational modeling, the medium for representing domain knowledge is the set of orthogonal structured controlled vocabularies named Systems Biology Ontology ( SBO). The SBO terms enable modelers to explicitly define and unambiguously describe model entities, including their roles and characteristics. Here, we present the first standalone tool that automatically assigns SBO terms to multiple entities of a given SBML model, named the SBOannotator. The main focus lies on the reactions, as the correct assignment of precise SBO annotations requires their extensive classification. Our implementation does not consider only top-level terms but examines the functionality of the underlying enzymes to allocate precise and highly specific ontology terms to biochemical reactions. Transport reactions are examined separately and are classified based on the mechanism of molecule transport. Pseudo-reactions that serve modeling purposes are given reasonable terms to distinguish between biomass production and the import or export of metabolites. Finally, other model entities, such as metabolites and genes, are annotated with appropriate terms. Including SBO annotations in the models will enhance the reproducibility, usability, and analysis of biochemical networks. Availability: The open-source project SBOannotator is freely available under the terms of LGPL version 3.0 from https://github.com/draeger-lab/SBOannotator/.

Ultrasound (US) scans of the inferior vena cava (IVC) provide useful information on the volume status of a patient. However, their investigation is user-dependent and prone to measurement errors. An important technical problem is the objective difficulty in studying a very compliant blood vessel like IVC, which makes large respirophasic movements and shows a complicated three dimensional geometry. Using bi-dimensional (2D) B-mode views either in long or short axis has improved the characterization of IVC dynamics compared to a measurement along a single direction (M-mode). However, specific movements of the IVC can challenge also the information provided by these 2D sections. Thus, these two orthogonal views, provided by an US system in X-plane, are here integrated by an innovative method. It is tested on simulated videos of the IVC performing complicated movements, that are compensated by the new method, overcoming the biased measurements provided by 2D scans. The method is then applied on example experimental data.

The continues evolution of coronaviruses has gained considerable attention prior to the outbreak of COVID 19. Although, COVID-19 is currently not recognized as a global pandemic, the virus's ability to evolve and cause disease outbreaks in both humans and animals necessitates ongoing research into its genetic and structural characteristics. Therefore, understanding the molecular origin, rapid evolution, as were as the immunogenicity of coronaviruses is a critical step towards preparing for and preventing future outbreaks. This study aimed to uncover the genetic diversity and evolutionary relationships among the main viral proteins of SARS-CoV-2 and other related coronaviruses. Amino acid sequences of structural viral proteins spike glycoprotein, nucleocapsid protein, membrane protein, and envelope protein were retrieved from the NCBI database for SARS-CoV-2 and 13 other coronaviruses. Here, we identified that SARS-CoV-2 is closely related to BatCoV RaTG13 and Pangolin-CoV, suggesting their potential role in the emergence of the virus. Additionally, we predicted novel epitopes, glycosylation sites, and cleavage sites, identifying three novel glycosylation sites (NATR, NXSN, and NGTK) and six new CTL epitopes (XSNQVAVLY, NSFTRGVYY, NATRFASVY, STQDLFLPF, NSASFSTFK, and ASFSTFKCY). Our comparative analysis revealed that BatCoV RaTG13 has the closest cleavage site to SARS-CoV-2, with significant similarities also observed with Pangolin-CoV. The study highlighted the unique features of SARS-CoV-2, including its furin cleavage site, which may account for its high infectivity during the pandemic. These findings contribute to the understanding of SARS-CoV-2 evolution and its relationship with other coronaviruses, providing critical insights for the development of broad-spectrum vaccines and antiviral therapies.

X-ray Fluorescence Computed Tomography (XFCT) is an emerging non-invasive imaging technique providing molecular-level data, gaining attention for high-resolution imaging. However, increased sensitivity with benchtop X-ray sources raises radiation exposure. Artificial Intelligence (AI), particularly deep learning (DL), has revolutionized medical imaging by delivering high-quality images in the presence of noise. In XFCT, traditional methods rely on complex algorithms for noise reduction, but AI holds promise in addressing high-dose concerns. We present an optimized SCUNet model for noise reduction in low-concentration XRF images. Compared to higher-dose images, our method’s effectiveness is evaluated. While various denoising techniques exist for X-ray and CT, few address to XFCT. The DL model is trained and assessed using the augmented data, focusing on background noise reduction. Image quality is measured using PSNR and SSIM, comparing outcomes with 100% X-ray dose images. Results show the proposed algorithm achieves high-quality images from low-dose and low-contrast agents, with a maximum PSNR of 39.05 and SSIM of 0.86. The model outperforms BM3D, NLM, DnCNN, and SCUNet in both visual inspection and quantitative analysis, particularly in high-noise scenarios. This indicates the potential of AI, specifically the SCUNet model, in significantly improving XFCT imaging by mitigating the trade-off between sensitivity and radiation exposure.

Nose mask is a fomite and its usage was mandatory during the COVID-19 outbreak. Its effectiveness has been established; however, as a fomite, it can harbor opportunistic respiratory pathogens such as Streptococcus spp., which could complicate COVID-19 infections. This study profiled Streptococcus species resident on nose masks obtained from consenting participants. Phenotypic assays and 16S rRNA sequencing were used to identify Streptococcus spp. resident on the interior and exterior of 100 nose masks analyzed. Antibiotic resistance (AMR) was determined with disc diffusion and broth microdilution assays. AMR and virulence makers were profiled with primer-specific PCR amplification. 23% of the analyzed samples had Streptococcus isolates. The isolates were highly resistant to the antimicrobials, including conventional, last-resort antibiotics, disinfectants and antiseptics. All the isolates are multidrug resistant with 80-100% levels of AMR to the 16 antibiotics tested with a Multiple-Antibiotic Resistance index greater than 0.2, indicative of potential pathogens. The isolates harbored tetB, ermB, pbp2B, pbp2b1 (resistance) and lytA, lytA1, ply1, cbpA, lytA, pavA (virulence) markers, which might constitute a serious public health risk. Overall, the study emphasizes the need to assess mask usage and the risks associated with opportunistic pathogens that are resident on frequently used nose masks in the COVID-19 era.

Neurologic disorders such as traumatic brain injury, multiple sclerosis, Alzheimer’s disease, and drug-resistant epilepsy have a high socioeconomic impact around the world. Current therapies for these disorders are often not effective. This creates a demand for the development of new therapeutic approaches to treat these disorders. Recent data suggest that autoreactive naturally occurring immunoglobulins produced by subsets of B cells called B1 B cells combined with complement are actively involved in the processes of restoration of neuronal functions during pathological conditions and remyelination. The focus of this review is to discuss the possibility of creating specific therapeutic antibodies that can activate and fix complement to enhance neuronal survival and promote central nervous system repair after injuries associated with many types of neurodegenerative diseases.

The rapid growth of the sharing economy has propelled shared mobility to the forefront of attention. The continuous advancement of autonomous driving technology also brings new opportunities and challenges to the shared mobility market. This study comprehensively analyzes the market potential concerning autonomous vehicles (AVs) to provide shared mobility services, utilizing SWOT analysis, PESTLE analysis, and Porter’s Five Forces. The findings reveal that AVs can provide improved shared mobility services by increasing transportation safety, reducing emissions, reducing costs, enhancing traffic efficiency, and increasing customer satisfaction and the profitability of shared mobility services. However, challenges such as technological and policy uncertainties, safety concerns, high initial costs, inadequate public communication infrastructure, and the absence of standardized regulations can hinder the widespread adoption of AVs. The benefits are also restricted with a low market penetration rate of AVs. To promote AVs in the shared mobility market, this study also provides implications for AV stakeholders tailored to the evolving shared mobility market dynamics.

Recent years have witnessed significant advances in reinforcement learning (RL), which has registered remarkable success in solving various sequential decision-making problems in machine learning. Most of the successful RL applications, e.g., the games of Go and Poker, robotics, and autonomous driving, involve the participation of more than one single agent, which naturally fall into the realm of multi-agent RL (MARL), a domain with a relatively long history, and has recently re-emerged due to advances in single-agent RL techniques. Although, typically, the communication protocol between agents is manually specified and not altered during training, recently, some papers have shown signs of trying to emerge a communication between agents on the one hand and, on the other hand, to understand what is exchanged between agents. So, there is a growing body of literature on this topic which includes qualitative and quantitative studies and the ones that apply mixed methods. This study presents the scoping review of the methodological strategies undertaken in a total of 16 research articles. The results present the critical appraisal of quantitative methods in terms of validity and reliability and for qualitative methods considering four trustworthiness factors. In the end, relevant insights are further explored with implications and reflections on how they can benefit one's research in the field.

Warsaw is among European cities with the worst atmospheric air quality, mainly due to very high pollution emitted by the residential sector and road traffic. This results in high concentrations of particulate matter and nitrogen oxides, often exceeding WHO standards. The paper discusses the current and expected effects of actions taken by the Warsaw authorities, to significantly improve air quality in the city. The Clean Air Program currently implemented mainly involves the reduction, and ultimately the total elimination, of coal combustion in all heat sources of the municipal sector, which is identified in numerous publications as the main source of air quality degradation in cities. The program's goal, which timeframe covers the years 2018-2029, is a definite reduction in particulate pollution. The second part of the remedial activities, covering the years 2024-2034, mainly concerns the reduction of nitrogen oxide pollution, the main source of which is urban road traffic. In the latter case, the expected effects of introducing Low-Emission Zone (launched July 2024) in the city center are considered. According to the project, the zone's implementation will consist of five two-year stages, in which the car emission limits will gradually tighten. The paper compares the effectiveness of two being considered versions, differing in size zones.

Rare Earth Elements (REE), also known as Lanthanides (Ln3+), are a group of 17 elements showing peculiar physical and chemical properties. Unlike technological applications, very little is known about the physiological role and toxicity of Ln3+ on biological systems, in particular on microorganisms (e.g., bacteria), which represent the most abundant domains on our planet. Up to now, very limited studies have been conducted due to Ln3+ precipitation with some anions commonly present in the culture media. Therefore, the development of a minimal medium is essential to allow the study of Ln3+-microbial interactions, limiting considerably the precipitation as insoluble salts. In this regard, a new minimal culture medium capable of solubilizing large amounts of Ln3+, and allowing the growth of different microbial taxa, was successfully developed. Assays have shown that the medium is capable of solubilizing Ln3+ up to 100 times more than other common culture media and allowed the growth of 63 bacteria and 5 fungi. The kinetic growth of one yeast and one gram-positive bacterium has been defined, proving to support superior growth and biomass compared to other commonly used minimal media. Moreover, the sensitivity and uptake/absorption of a Bacillus stratosphericus strain was tested, highlighting its capability to tolerate concentrations up to 10 mM of either Cerium, Gadolinium or Lanthanum and accumulate different quantities of the three.

In this review we aim to address the current status of phage therapy in the management of multidrug-resistant infections, from compassionate use cases to ongoing clinical trials, as well as the challenges this approach presents in the particular context of CF patients.

Image stitching is a crucial aspect of image processing. However, factors like perspective and environment often lead to irregular shapes in stitched images. Cropping or completion methods typically result in substantial loss of information. This paper proposes a method for rectifying irregularly images into rectangles using deformable meshes and residual networks. The method utilizes a convolutional neural network to quantify rigid structures of images. Choosing the most suitable mesh structure based on the extraction results, offering options such as triangular, rectangular, and hexagonal. Subsequently, the irregularly image, predefined mesh structure, and predicted mesh structure are input into a wide residual neural network for regression. The loss function comprises local and global, aimed at minimizing the loss of image information within the mesh and global target. This method not only significantly reduces information loss during rectification but also adapting to different images with various rigid structures. Validation on the DIR-D dataset shows this method outperforms state-of-the-art methods in image rectification.

Cancer is the second major cause of disease-related dead worldwide, and its accurate early diagnosis and therapeutic intervention are fundamental for saving the patient’s life. Cancer, as a complex and heterogeneous disorder, results from disruption and alteration of a wide variety of biological entities, including genes, proteins, mRNAs, miRNAs, and metabolites that eventually emerge as clinical symptoms. Traditionally, diagnosis is based on clinical examination, blood tests for biomarkers, histopathology of biopsy, and imaging (MRI, CT, PET, US). Additionally, omics biotechnologies help to further characterize the genome, metabolome, microbiome traits of the patient that could have an impact on the prognosis and patient’s response to the therapy. The integration of all these data relies on gathering of several experts and may require considerable time, and, unfortunately, it is not without the risk of error in the interpretation and therefore in the decision. Systems biology algorithms exploit Artificial Intelligence (AI) combined with omics technologies to perform a rapid and accurate analysis and integration of patient’s big data and support the physician in making diagnosis and tailoring the most appropriate therapeutic intervention. However, AI is not free from possible diagnostic and prognostic errors in the interpretation of images or biochemical-clinical data. Here, we first describe the methods used by systems biology for combining AI with omics and then discuss the potential, challenges, limitations, and critical issues in using AI in cancer research.

Background and objectives: Colorectal cancer (CRC) is the second most common cause of cancer-related death in the world, but early diagnosis ameliorates the survival of CRC. This report directed to identify molecular biomarker signatures in CRC. Materials and Methods: We analyzed two microarray datasets (GSE35279 and GSE21815) from Gene Expression Omnibus (GEO) to identify mutual differentially expressed genes (DEGs). We integrated DEGs with protein-protein interaction and transcriptional/post-transcriptional regulatory networks to identify reporter signaling and regulatory molecules; utilized functional overrepresentation and pathway enrichment analyses to elucidate their roles in biological processes and molecular pathways; performed survival analyses to evaluate their prognostic performance; and applied drug repositioning analyses through Connectivity map (CMap) and geneXpharma tools to hypothesize possible drug candidates targeting reporter molecules. Results: A total of 727 up-regulated and 99 down-regulated DEGs were detected. The PI3K-Akt signaling, Wnt signaling, ECM-interaction, and cell cycle were identified as significantly enriched pathways. Ten hub proteins (ADNP, CCND1, CD44, CDK4, CEBPB, CENPA, CENPH, CENPN, MYC, and RFC2), 10 transcription factors (ETS1, ESR1, GATA1, GATA2, GATA3, AR, YBX1, FOXP3, E2F4, and PRDM14) and 2 miRNAs (miR-193b-3p and miR-615-3p) were detected as reporter molecules. The survival analyses through Kaplan Meier curves indicated remarkable performance of reporter molecules in estimation of survival probability in CRC patients. In addition, several drug candidates including anti-neoplastic and immunomodulating agents were repositioned. Conclusions: This study presents biomarker signatures at protein and RNA levels with prognostic capability in CRC. We think that the molecular signatures and candidate drugs presented in this study might be useful in future studies indenting development of accurate diagnostic and/or prognostic biomarker screens and efficient therapeutic strategies in CRC.

Shigella and Salmonella have been implicated in neonatal sepsis, food poisoning, and bacteremia. Their increasing resistance to antibiotics has undermined treatment options, constituting a public health crisis. Also, the scarcity of new antibiotics in the development pipeline compounds multidrug-resistance (MDR). Hence, there is a need to potentiate antibiotics to mitigate resistance. This study leveraged riboflavin to re-sensitize fluoroquinolones and carbapenems against MDR Shigella and Salmonella spp. Disk diffusion, microbroth-dilution, chequerboard, and time-kill assays were used to determine resistance profiles and riboflavin-antibiotic activity. Biofilm-formation and bacterial viability (after riboflavin-antibiotic challenge) was determined with crystal-violet and Macrophage infection assays, respectively. Strains exhibited &gt;80% resistance to fluoroquinolones and carbapenems, with 160–320 µg MIC ranges and 0.5–2 FIC, indicating no synergy. At 40–80 µg riboflavin, there was two-fold reduction in bacterial survival, with meropenem-riboflavin exhibiting significant reduction and FIC of 0.075 indicating high synergistic activity. Biofilm-formation was altered (from strong to weak phenotype) with 40 µg riboflavin-antibiotic treatment. There was a 40–70% reduction in bacterial survival in THP-1 cells treated with meropenem-riboflavin after 3 hours, and complete clearance between 24-48 hpi. Riboflavin potentiated fluoroquinolones and meropenem, leading to modulation of the host immune response for the clearance of the strains.

Europium is one of the most reactive lanthanides and humans use it in many different applica-tions, but we still know little about its potential toxicity and cellular response to its exposure. Two strains of the eukaryotic microorganism model Tetrahymena thermophila adapted to high concentrations of two Eu(III) compounds (EuCl3 or Eu2O3) were obtained and compared to a control strain and cultures treated with both compounds. In this ciliate, EuCl3 is more toxic than Eu2O3. LC50 values show that this microorganism is more resistant to these Eu(III) compounds than other microorganisms. Oxidative stress originated mainly by Eu2O3 is minimized by overexpression of genes encoding important antioxidant enzymes. The overexpression of metallothionein genes under treatment with Eu(III) compounds supports the possibility that this lanthanide may interact with the -SH groups of the cysteine residues from metallothi-oneins and/or displace essential cations of these proteins during their homeostasis function. Both lipid metabolism (lipid droplets that fuse with europium-containing vacuoles) and au-tophagy are involved in the cellular response to europium stress. Bioaccumulation, together with a possible biomineralization to europium phosphate, seems to be the main mechanism of Eu(III) detoxification in these cells.

Metabarcoding of prokaryotic and fungal ribosomal DNA was used to describe the microbial communities in soils of remnant equatorial rainforest, maize-bean intercrop, and sugarcane in western Kenya. Cropping systems influenced the microbial community composition and functional traits (energy source and nutrient cycling) of bulk soil in each crop. Microbial richness and diversity tended to increase with cultivation intensity. Soil of maize-bean intercrop had lower percentages and sugarcane had higher percentages of unique amplicon sequence variants of both bacteria and fungi compared to the remnant forest. Functional traits were altered by cultivation intensity. Compared to remnant forest soils, maize-bean intercrop soil had lower percentages of aerobic chemoheterotrophic bacteria and higher percentages of N-cycling bacteria, while sugarcane had higher percentages of aerobic chemoheterotrophic bacteria and lower percentages of N-cycling bacteria. In the face of increasing forest loss and pressures for agricultural productivity, this landscape provides a rich site for studying the impacts of cropping systems on soil health.

Antioxidant, anti-inflammatory and chemo-preventive features have been reported for the carotenoid diatoxanthin. Diatoxanthin is only produced by a few groups of microalgae where it functions in photoprotection. Its large-scale production in microalgae is currently not feasible. In fact, rapid conversion into the inactive pigment diadinoxanthin is triggered when the cells are removed from the high-intensity light source, which will be the case during large-scale harvesting of microalgae biomass. Zeaxanthin epoxidase (ZEP) 2 and/or ZEP3 have been suggested to be responsible for the back-conversion of high-light accumulated diatoxanthin to diadinoxanthin in low light in diatoms. Using the CRISPR/Cas9 gene editing technology we knocked out the ZEP2 and ZEP3 genes in the already commercially used marine diatom Phaeodactylum tricornutum to investigate their role in the diadinoxanthin-diatoxanthin cycle, and to determine if one of the mutant strains could function as a diatoxanthin production line. Light shift experiments proved that ZEP3 encodes the enzyme converting diatoxanthin to diadinoxanthin in low light. Loss of ZEP3 caused the high-light accumulated diatoxanthin to be stable for several hours after the cultures had been returned to low light, suggesting that zep3 mutant strains could be suitable as commercial production lines of diatoxanthin.

Relationships of the three bryophyte lineages (liverworts, mosses, and hornworts) to vascular plants is a pivotal question in the study of origin and evolution of land plants. In recent decades, this question has been subject to intense phylogenetic analyses using morphological characters, multigene DNA sequences, and genome structural characters. A tentative consensus reached ten years ago suggested that bryophytes are a paraphyletic group, with liverworts being sister to all other land plants and hornworts being sister to vascular plants. However, several more recent nuclear phylogenomic studies have concluded that bryophytes represent a monophyletic group that is sister to vascular plants. A discussion is presented here on strengths and weaknesses of different types of characters (morphological traits, nucleotide sequences, and genome structural arrangements), and their suitability for resolving deep phylogenetic relationships. Moreover, several criteria for credible phylogenetic reconstruction are proposed. Strong statistical support for reconstructed relationships should be derived from high quality, independent characters selected for suitability to the particular question being addressed. The relationships inferred in a study should be congruent with those from as many other lines of phylogenetic evidence as possible. Any incongruities should be explicable by well-understood biological mechanisms. It is concluded that the relationships of the three bryophyte lineages to vascular plants should currently be viewed as unresolved. This is a difficult phylogenetic problem; the land plants underwent a rapid radiation a long time ago. Yet, further exploration of analytical methods and careful choice of characters should lead to eventual elucidation of diversification patterns among early land plants.

The self-assembly is an intriguing process of great importance in general soft matter and thus re-ceives an ever-growing scientific interest. Its most trivial example is the entropy-driven crystalli-zation of hard spheres. Past works have established the similarities and differences in the phase behavior of monomers and chains made of hard spheres. In the present work, inspired by the dif-ference in the melting points of the pure components, we study, through Monte Carlo simulations, the phase behavior of athermal mixtures composed of fully flexible polymers and individual monomers of uniform size. We analyze how the relative number fraction and the packing density affect crystallization and the established ordered morphologies. A synergetic effect is observed in the crystallization leading to synchronous crystallization of the two species. Structural analysis of the resulting ordered morphologies shows perfect mixing and thus no phase separation, which could split the system into polymer-rich and monomer-rich domains. Due to the constraints imposed by chain connectivity, the local environment of the individual spheres is systematically more spherical and more symmetric compared to the one of spheres belonging to chains. In general, increasing polymer content leads to reduction of the degree of crystallinity. According to the present findings, relative concentration is another determining factor to control the phase behavior of hard colloidal systems based on polymers.

Water footprint has been widely used to illustrate the consumption of water in many situations; for instance, in products, processes or regions of interest. In this work, we analyzed – using a sensitivity analysis approach – the effect of some variables in the calculation of the water footprint in the viticulture in Brazilian Serra Gaúcha (the major producing region of Brazilian Wine).The classical Penman-Monteith model for evapotransporation was considered, with uncertainties in some parameters (dead mulch covering fraction in the vineyard, maximum temperatures for some months, altitudes and latitudes of the site). The sensitivity analysis was conducted using the SAFE toolbox under Octave framework. The results indicated that the the portion of the water footprint corresponding to the evapotranspiration is more sensitive to the values of mulch covering fraction and the altitude of the site in comparison with the latitude and the maximum temperatures.

As critical biocontrol agents, Trichoderma and Metarhizium have demonstrated vast potential in disease prevention and pest control respectively. Current applications, however, are predominantly confined to singular use or simplistic combinations of the two fungi. This study innovatively utilizes Metarhizium and Trichoderma as experimental subjects, employing non-targeted metabolomics to compare the differences in metabolites between co-culture and separate fermentation. The metabolite distinctions in co-culture are meticulously analyzed using sample correlation, least squares discriminant analysis, cluster analysis, and KEGG enrichment analysis. Metabolome sequencing analysis is then applied to compare the co-culture fermentation filtrate with Trichoderma atroviride and Metarhizium anisopliae. Differential metabolite analysis found that co-culture had significantly up-regulated or down-regulated metabolites compared to singular cultures.However,significant metabolite discrepancies are discovered in singular cultures, notably the up-regulated metabolites such as osthole and spirocyclic amine, which have documented antibacterial functions that may prove effective against Fusarium graminearum. Ultimately, the findings from this research contribute to the exploration of synergistic applications of biocontrol fungi and serve as a valuable reference for future development of bio-pesticides for disease and pest control.

Large datasets play a crucial role in the progression of surgical robotics, facilitating advancements in the fields of surgical task recognition and automation. Moreover, public datasets enable the comparative analysis of various algorithms and methodologies, thereby assessing their effectiveness and performance. The ROSMA (Robotics Surgical Maneuvers) dataset provides 206 trials of common surgical training tasks performed with the da Vinci Research Kit (dVRK). In this work, we extend ROSMA dataset with two annotated subsets: ROSMAT24, which contains bounding box annotations for instrument detection, and ROSMAG40, which contains high and low level gesture annotations. We propose an annotation method that provides independent labels for the right-handed tool and the left-handed tool. For instrument identification, we validate our proposal with a YOLOv4 model in two experimental scenarios. We demonstrate the generalization capabilities of the network to detect instruments in unseen scenarios. For gesture segmentation, we propose two label categories: high-level annotations that describe gestures at a maneuvers level, and low-level annotations that describe gestures at a fine-grain level. To validate this proposal, we have designed a recurrent neural network based on a bidirectional long-short term memory layer. We present results for four cross-validation experimental setups, reaching up to a 77.35% mAP.

As a complementary and alternative medicine in the western countries for decades, traditional Chinese medicine (TCM) has been used for more than 2000 years in China. Because of the characteristics of the philosophical style and the unknown mechanism of action, TCM sometimes has been biasedly described as "fraught with pseudoscience". From the scientific basis of the systems biology, here we promoted a novel medical model called the entropic systems medicine which could be applied to scientize TCM in future. In entropic systems medicine, TCM and Western modern biomedicine target the different variables of the entropic system. For instance, while Western modern biomedicine directly targets the phenotypes and its SOCs of macrostates, TCM differently targets the microstates, entropy and entropic force to generate SOTFs gradually causing the differentiated syndromes to be slowly rearranged. The prerequisites to modernize TCM are the entropic systems biology having been well established so that the variables could be precisely monitored and mathematically calculated.

Axon guidance is a crucial process for growth of the central and peripheral nervous systems. In this study, 3 axon guidance related disorders, namely- Duane Retraction Syndrome (DRS) , Horizontal Gaze Palsy with Progressive Scoliosis (HGPPS) and Congenital fibrosis of the extraocular muscles type 3 (CFEOM3) were studied using various Systems Biology tools to identify the genes and proteins involved with them to get a better idea about the underlying molecular mechanisms including the regulatory mechanisms. Based on the analyses carried out, 7 significant modules have been identified from the PPI network. Five pathways/processes have been found to be significantly associated with DRS, HGPPS and CFEOM3 associated genes. From the PPI network, 3 have been identified as hub proteins- DRD2, UBC and CUL3.

Abstract Octreotide is the first synthetic peptide hormone, consisted of eight amino acids, that mimics the activity of somatostatin, a natural hormone in the body. During the past decades, advanced instrumentation and crystallographic software established X-ray Powder Diffraction (XRPD) as a valuable tool for extracting structural information of biological macromolecules. The latter was demonstrated by the successful structural determination of octreotide at a remarkably high d-spacing resolution (1.87 Å) (PDB code: 6vc1). This study focuses on the response of octreotide to different humidity levels and temperatures, with a particular focus on the stability of the polycrystalline sample. XRPD measurements were accomplished employing an Anton Paar MHC-trans humidity-temperature chamber installed within a laboratory X’Pert Pro diffractometer (Malvern Panalytical). The chamber is employed to control and maintain precise humidity and temperature levels of samples during XRPD data collection. Pawley analysis of the collected data sets revealed that the octreotide polycrystalline sample is remarkably stable and no structural transitions were observed. The compound retains its orthorhombic symmetry (space group: P212121, a = 18.57744(4) Å, b = 30.17338(6) Å, c = 39.70590(9) Å, d~ 2.35 Å). However, a characteristic structural evolution in terms of lattice parameters and volume of the unit-cell is reported mainly upon controlled relative humidity variation. In addition, an improvement of signal-to-noise ratio in the XRPD data under a cycle of dehydration/rehydration is reported. These results underline the importance of considering the impact of environmental factors, as humidity and temperature, in the context of structure-based drug design, thereby contributing to the development of more effective and stable pharmaceutical products.

The global increase in population has placed significant pressure on food security, leading to the emergence of aquaculture as a vital source of aquatic foods. However, rising costs and the limited availability of fishmeal in aquafeeds have spurred the search for alternative protein sources. While plant-based ingredients have been integrated into commercial aquafeeds, they come with challenges, including low protein content, palatability issues, and the presence of antinutritional factors. In this context, fish silage, derived from fish waste and discarded fish, stands out as a promising alternative technology due to its cost-effectiveness and sustainability attributes. The production of fish silage involves the addition of organic/inorganic acids or lactic acid bacteria to homogenized fish waste. This process yields a valuable mixture rich in peptides, free amino acids, and partially hydrolyzed proteins, offering significant nutritional benefits for animal diets. Beyond its nutritional advantages, fish silage contributes to environmental sustainability by reducing the impact of waste disposal and enhancing the value of fish waste. The objective of this review is to promote sustainable practices in the aquaculture industry in response to the increasing demand for high-quality feed nutrients. To achieve this, it includes an analysis of research results related to silage technology, an appraisal of the advantages and disadvantages of using fish silage as a feed additive, and a focus on emerging trends in this field.

The article delves into the crucial realm of compressing hydrogen in its gaseous state, a pivotal process for enhancing its viability in both civil and industrial sectors. The study initiates by providing a concise overview and comparison of diverse hydrogen storage methodologies, laying the groundwork with an in-depth analysis of hydrogen's thermophysical properties. It scrutinizes plausible configurations for hydrogen compression, aiming to strike a delicate balance between energy consumption, predominantly derived from the fuel itself, and the requisite number of compression stages. Notably, to render hydrogen storage competitive in terms of volume, pressures of at least 350 bar are deemed essential, albeit at an energy cost amounting to approximately 10% of the fuel's calorific value. Multi-stage compression emerges as a crucial strategy, not solely for energy efficiency, but also to curtail temperature rise, with an upper limit set at 200°C. This nuanced approach is underlined by the exploration of compression levels commonly cited in the literature, particularly 350 bar and 700 bar. Ultimately, the study advocates for a three-stage compression system as a pragmatic compromise, capable of achieving high-pressure solutions while keeping compression work below 10 MJ/kg, a threshold indicative of sustainable energy utilization.

This paper analyzes and compares models for predicting average magnet losses in interior permanent-magnet motors with fractional-slot concentrated windings due to harmonics in the armature reaction (assuming sinusoidal phase currents). Particularly, loss models adopting different formulations and solutions to the Helmholtz equation to solve for the eddy currents are compared to a simpler model relying on an assumed eddy-current distribution. Boundaries in terms of magnet dimensions and angular frequency are identified (numerically and using an identified approximate analytical expression) to aid the machine designer whether the more simple loss model is applicable or not. The assumption of a uniform flux-density variation (used in the loss models) is also investigated for the case of V-shaped and straight interior permanent magnets. Finally, predicted volumetric loss densities are exemplified for combinations of slot and pole numbers common in automotive applications.

Light is a crucial environmental factor that influences the phenotypic development of plants. Despite extensive studies on the physiological, biochemical, and molecular mechanisms of the impact of light on phenotypes, genetic investigations regarding light-induced transgenerational plasticity in Arabidopsis thaliana remain incomplete. In this study, we used Arabidopsis thaliana as the material, then gathered phenotypic data regarding leaf number and plant height under high- and low-light conditions from two generations. In addition to the developed genotype data, a functional mapping model was used to locate a series of significant SNPs. Under low-light conditions, a noticeable adaptive change in the phenotype of leaf number in the second generation suggests the presence of transgenerational genetic effects in Arabidopsis thaliana under environmental stress. Under different lighting treatments, 33 and 13 significant genes associated with transgenerational inheritance were identified, respectively. These genes are largely involved in signal transduction, technical hormone pathways, light responses, and the regulation of organ development. Notably, genes identified under high-light conditions more significantly influence plant development, whereas those identified under low-light conditions focus more on responding to external environmental stimuli.

Leucine is an essential amino acid that cannot be produced endogenously in the human body and therefore needs to be obtained from dietary sources. Leucine plays a pivotal role in stimulating muscle protein synthesis along with isoleucine and valine as the group of branched-chain amino acids making them as one of the most popular dietary supplements for athletes and gym-goers. Individual effects of leucine, however, are not fully clarified, as most of the studies focused on the grouped effects of branched-chain amino acids. In recent years, leucine and its metabolites have been shown to stimulate muscle protein synthesis mainly via mammalian target of rapamycin complex 1 signaling pathway, thereby improving muscle atrophy in cancer cachexia. Interestingly, cancer research suggests that leucine may have either anti-cancer or carcinogenic effects. In the current manuscript, we aim to review leucine's roles in muscle protein synthesis, tumor suppression, and tumor progression, specifically summarizing the molecular mechanisms of leucine's action. The role of leucine is controversial in hepatocellular carcinoma, whereas its carcinogenic effects have been demonstrated in breast and pancreatic cancers. In summary, leucine being used as nutritional supplement for athletes needs more attention, as its oncogenic effects may have been identified by recent studies. Anti-cancer or carcinogenic effects of leucine in various cancers should be further investigated to have clear conclusions.

The Aspergillus genus comprises fungi that are widely distributed in nature. The Terrei section is particularly important due to its functions in recycling organic matter. Aspergillus hortae is a species from this section that has been isolated from clinical samples, but its role as a pathogenic agent is unclear. In this study, three clinical A. hortae isolates from Colombia, initially identified as A. terreus, were characterised by micro and macro-morphological analysis at 26°C and 37°C. A bioinformatic pipeline was used for molecular typing, which included analysis of whole genome sequences for accurate species identification. Susceptibility assays were also conducted using the microdilution broth method (EUCAST). It was confirmed that this species is intrinsically resistant to Amphotericin B with a minimum inhibitory concentration (MIC) of 2-4 mg/L, and is also thermotolerant. We obtained the in vitro susceptibility profiles for three azole drugs (MIC, 0.25-1 mg/L). The three isolates showed phylogenetic divergence from the reference genome strain. A mutation (M769K) in the MelA ortholog of a hypopigmented isolate, which had the lowest MIC value for AmB (2 mg/L), was identified. This study presents the morphological characterization, molecular typing through whole-genome analysis and identification of susceptibility profiles to azoles and amphotericin B of three clinical isolates of A. hortae from Colombia.

Brain aging causes a wide variety of changes at molecular and cellular levels, leading to the decline of cognitive functions and increased vulnerability to neurodegenerative disorders. The research aimed at understanding the aging of the brain has made much progress in recent decades. Technological innovations such as single-cell RNA-sequencing (scRNA-seq), proteomic analyses, and spatial transcriptomic analyses have facilitated the research on the dynamic changes occurring within neurons, glia, and other cells along with their impacts on intercellular communication during aging. In this review, we introduce recent trends of how neurons and glia change during aging and discuss the impact of the brain microenvironment such as the blood-brain barrier (BBB).

The transition to cleaner energy sources, particularly in hard-to-abate industrial sectors, often requires gradual integration of new technologies. Hydrogen, crucial for decarbonization, is explored as a fuel in blended combustions. Blending or replacing fuels impacts combustion stability and heat transfer rates due to differing densities. An extensive literature review examines blended combustion, focusing on hydrogen-methane mixtures. While industrial burners claim to accommodate up to 20% hydrogen, theoretical support is lacking. A novel thermodynamic analysis methodology is introduced, evaluating methane-hydrogen combustion using the Wobbe index. Findings highlight practical limitations beyond 25% hydrogen volume, necessitating a shift to "totally hydrogen" combustion. Blended combustion can be proposed as a medium-term strategy, acknowledging hydrogen's limited penetration. Higher percentages require burner and infrastructure redesign.

With a predominantly humid tropical climate and a large area for expanding agricultural activities, Angola has in principle favorable conditions for bioenergy production. The focus of this study was to evaluate the availability of suitable land for producing sugarcane. This crop is highly efficient in converting solar energy into biomass for energy purposes in Angola. To this end, the Global Agro-Ecological Zones database, GAEZ v4, developed by IIASA and FAO, with the aid of the QGIS version 3.22.5, has been used to identify areas suitable for sugarcane cultivation, considering four levels of suitability. Aiming at the sustainability of bioenergy production, areas dedicated to food production, protected areas, and areas with slopes above 16% were excluded. Under these criteria, this study identified the existence of 6.3 Mha in lands of good agricultural suitability, with water resources, corresponding to 5% of the Angolan territory, distributed in seven provinces of the country, especially in the provinces of Cuando Cubango and Cunene, where 85% of the very suitable land under irrigation is located. Adopting a model of agricultural productivity, assuming irrigation and adequate agricultural practices, such area could produce approximately 956 million ton of sugarcane annually, which is significantly higher than the current production in this country, This amount of feedstock, processed using current technology could potentially produce 81.3 GL of ethanol and 176,9 TWh of electricity with low GHG emission per year, able to mitigate, as a whole, circa 60.3 MtCO2-eq/year by displacing gasoline in light vehicles and diesel and natural gas consumed in power generation.

Circulating tumor cells (CTCs) are cells released from the primary tumor and intravasate into the blood or lymphatic vessels, where they are transported to distant sites and act as seeds that initiate cancer metastases. Recent advances in CTC research have shown their relevance as prognostic markers for early and metastatic disease detection, predictive biomarkers for relapse, and response to medical intervention or therapy. The rapidly evolving landscape of CTC biology has opened new avenues for understanding cancer progression, metastasis, and treatment response. Additionally, translating these findings into clinical applications holds promise for improving cancer diagnostics, prognosis, and personalized therapeutic strategies. This review discusses the significance of CTCs in cancer research and their associated challenges. We explore recent developments in the detection and characterization of CTCs and their implications in cancer research and clinical practice.

Advances in early detection of Breast cancer and treatment improvements have significant-ly increased survival rates. Traditional screening methods, including mammography, MRI, ultrasound, and biopsies, while effective, often come with high costs and risks. Recently, thermal imaging has gained attention due to its minimal risks compared to mammography, although it is not widely adopted as a primary detection tool since it depends on identifying skin temperature changes and lesions. The advent of machine learning (ML) and deep learning (DL) has enhanced the effectiveness of breast cancer detection and diagnosis using this technology. In this study a novel methodology for developing an interpretable computer-aided diagnosis (CAD) system for breast cancer detection, leveraging explaina-ble Artificial Intelligence (XAI) throughout its various phases. To achieve these goals, we proposed a new multi-objective optimization approach named Hybrid Particle Swarm Optimization algorithm (HPSO) and Hybrid spider Monkey Optimization algorithm (HSMO). These algorithms simultaneously combine the continuous and binary representations of PSO and SMO to effectively manage trade-offs between Accuracy, feature selection and hyperparameter tuning. We evaluate several CAD models and investigate the impact of handcrafted methods such as Local Binary Patterns (LBP), Histogram of Oriented Gradients (HOG), Gabor filters, and edge detection. We further shedding light on the effect of feature selection and optimization on feature attribution and model decision-making processes using the SHapley Additive exPlanations (SHAP) framework, with a particular emphasis on cancer classification using the DMR-IR dataset. The results of our experiments demonstrate in all trials that the performance of the model is improved. Also with HSMO our models achieved a high accuracy of 98.27% and F1- score of 98.15% while selecting only 25.78% of the HOG features. This approach not only boosts the performance of CAD models but also ensures comprehensive interpretability. This method emerges as a promising and transparent tool for early breast cancer diagnosis.

Shape memory alloys (SMA) are becoming a more important factor in actuation technology. Due to their unique features, they bring the potential to safe weight, installation space and reduce energy consumption. The system integration of the generally small diameter NiTi wires is an important cornerstone for the emerging technology. Crimping, a common method for the mechanical and electrical connection of SMA wires, has several drawbacks when it comes to miniaturization and high force outputs. For high force applications for example, multiple SMA wires in parallel are needed to keep actuation frequencies high, while scaling up the actuation force. To meet these challenges, the proposed study deals with the development of a resistance welding process for manufacturing NiTi wire bundles. The wires are welded to sheet metal substrate, resulting in promising functional properties and high joint strengths. The welding process benefits from low cost, easy to control parameters and good automation potential. A method for evaluating the resistance welding process parameters is presented. With these parameters in place, a manufacturing process for bundled wire actuators is discussed and implemented. The welded joints are examined by peel tests, microscopy, and fatigue experiments. The performance of the manufactured bundle actuators is demonstrated by comparison to a single wire with the same accumulated cross-sectional area.

Systemic Lupus Erythematosus (lupus) and B-cell lymphoma (lymphoma) are serious diseases. Lupus and lymphoma co-occur at higher-than-expected rates and primarily depend on B-cells for their pathology, implicating shared inflammation-related B-cell molecular mechanisms as a potential cause of co-occurrence. We consequently implemented a novel Immune Imbalance Transcriptomics (IIT) algorithm and applied IIT to lupus, lymphoma, and healthy B-cell RNA-seq data to find shared- and contrasting mechanisms potentially targetable for treatment. We observed 8,562 genes significantly dysregulated in both lupus and lymphoma. Of those genes, we found 5,335 to have a significant immune imbalance, defined as significant dysregulation by both diseases, as determined by IIT. Gene Ontology (GO) term and pathway enrichment of IIT genes yielded immune-related “Neutrophil Degranulation” and “Adaptive Immune System”, validating that the IIT algorithm isolates biologically relevant genes in immunity and inflammation. We found that 389 IIT gene products are drug-targetable with established or repurposed drugs. Among our results, we found 40 known and 349 novel lupus targets, along with 151 known and 238 novel lymphoma targets. Known disease drug targets in our IIT results further validate that IIT isolates genes with disease-relevant mechanisms. We anticipate the IIT algorithm and shared and contrasting gene mechanisms uncovered here will contribute to the development of immune-related therapeutic options for lupus and lymphoma patients.

Small interfering RNA (siRNA) holds significant therapeutic potential by silencing target genes through RNA interference. Current clinical applications of siRNA have been primarily limited to liver diseases, while achievements in delivery methods are expanding its applications to various organs, including the lungs. Cholesterol-conjugated siRNA emerges as a promising delivery approach due to its low toxicity and high efficiency. This study focuses on developing a cholesterol-conjugated anti-Il6 siRNA and the evaluation of its potency for the potential treatment of inflammatory diseases using the example of acute lung injury (ALI). The biological activities of different Il6-targeted siRNAs containing chemical modifications were evaluated in J774 cells in vitro. The lead cholesterol-conjugated anti-Il6 siRNA after intranasal instillation demonstrated dose-dependent therapeutic effects in a mouse model of ALI induced by lipopolysaccharide (LPS). The treatment significantly reduced Il6 mRNA levels, inflammatory cell infiltration, and the severity of lung inflammation. IL6 silencing by cholesterol-conjugated siRNA proves to be a promising strategy for treating inflammatory diseases, with potential applications beyond the lungs.

In this paper, we present an experimental procedure to enhance the dimensional accuracy of fabrication via Stereolithography (SLA) of features at the micro-scale. Using a custom benchmark part, deviations in feature dimensions (micro-pores diameters and depths) were detected and measured by confocal microscopy. Samples characterization and experimental observations allowed the identification of inaccuracy sources, mainly due to the laser beam scanning strategy and to the incomplete removal of uncured liquid resin in post-processing (i.e., IPA washing). As a technology baseline, the measured dimensional errors on pores diameters were up to -46%. A compensation method of the nominal laser spot diameter (85m) was defined and implemented resulting in relevant improvements in dimensional accuracy of 9.8% and 11.3% on full-open pores diameter and depth, respectively. Further investigation was performed on a customized test part to adjust the calibration procedure. The measurements revealed that the estimate of the laser beam spot size is 968m. Measurements on micro-pores having different sizes revealed that a constant compensation parameter (i.e., C=85, 96, 120m) is not fully effective at the micro-scale, where average errors still remain at -24%, -18.8%, and -16% for compensations equals to 85, 96 and 120m, respectively. A further experimental campaign allowed the identification of an effective nonlinear compensation law where the compensation parameter depends on the micro-feature size C= f (D). Results show a sharp improvement in dimensional accuracy on micro-pore fabrication, with errors consistently below +8.2%. The proposed compensation method can be extended for the fabrication of any micro-features without restrictions on the specific technology implementation. Concerning the inaccuracy introduced by the laser path, experimentation with a customized part allowed the optimization of the part orientation to reduce the errors and their differences along the X and Y machine axes.

In the face of escalating climate concerns and the push for sustainable development, the global shift towards renewable and decentralized energy systems presents new challenges and opportunities. This study investigates integrating decentralized energy production, particularly photovoltaic (PV) systems, into national energy planning, aiming to optimize energy strategies that balance local production and consumption with national objectives. By analyzing the Swiss energy model, the research employs the EnergyScope and REHO models to assess the strategic implications of decentralized versus centralized energy systems. Results show that a decentralized approach can significantly reduce PV installation needs to 35 GW, about 23% of potential capacity, and decrease annual system costs by 10% to CHF 1230 per capita. This strategy emphasizes local consumption, minimizes grid reinforcement demands, and leverages economic advantages while addressing overproduction challenges through effective energy storage and grid management. Conclusions underline the strategic value of combining centralized and decentralized methods for resilient and sustainable energy planning. The study contributes to the discourse on energy policy and infrastructure planning, advocating for a hybrid model that accommodates both local conditions and broader energy objectives, urging further research into climate impacts and technology integration for a comprehensive energy future.

Abstract: The SARS-CoV-2 pandemic has reemphasized the urgent need for broad-spectrum antiviral therapies. We developed a computational workflow using scRNA-Seq data to assess cellular metabolism during viral infection. With this workflow we predicted the capacity of cells to sustain SARS-CoV-2 virion production in patients and found a tissue-wide induction of metabolic pathways that support viral replication. Expanding our analysis to influenza A and dengue viruses, we identified metabolic targets and inhibitors for potential broad-45 spectrum antiviral treatment. These targets were highly enriched for known interaction partners of all analyzed viruses. Indeed, phenformin, an NADH:ubiquinone oxidoreductase inhibitor, suppressed SARS-CoV-2 and dengue virus replication. Atpenin A5, blocking succinate dehydrogenase, inhibited SARS-CoV-2, dengue virus, respiratory syncytial virus, and influenza A with high selectivity indices. In vivo, phenformin showed antiviral activity against SARS-CoV-2 in a Syrian hamster model. Our work establishes host metabolism as druggable for broad-spectrum antiviral strategies, providing invaluable tools for pandemic preparedness.

The seed habit is the most complex and successful method of sexual reproduction in vascular plants. It represents a remarkable moment in the evolution of plants that afterwards spread on land. In particular, seed size had a pivotal role as for evolutionary success and agronomic trait, especially in the field of crop domestication. Given that crop seeds constitute one of the primary products for consumption, it follows that seed size represents a fundamental determinant of crop yield. This adaptative feature is strictly controlled by genetic traits from both maternal and zygotic tissues, although seed development and growth are also affected by environmental cues. Despite being a highly exploited topic for both basic and applied research, there are still many issues to be elucidated as for developmental biology as well as for agronomic science. This review addresses a number of open questions related to cues that influence seed growth and size, and how developmental processes are influenced by them. Besides, new insights on the genetic-molecular control of this adaptive trait are presented.

The p53 tumor suppressor protein shows antiviral activity. The replication of viruses is also antagonized by interferons (IFNs) – cytokines, which control immunity genes by the STAT transcription factors. The best studied interferons belong to type I (e.g. IFNα) and type II (IFNγ) groups. IFNα and IFNγ both induce activating phosphorylation of STAT1 on Tyr701. Previously, we noticed that p53 activates SOCS1, which is a negative regulator of STAT1 phosphorylation. Thus, we hypothesized that p53 by activating SOCS1 expression reduces phosphorylation of STAT1 and attenuates activation of genes stimulated either by IFNα or IFNγ. To test this hypothesis, we exposed p53-proficient and p53-deficient cells to strong p53 activators, and either to IFNα or IFNγ. Subsequently, we estimated the phosphorylation status of STAT1 and the expression of genes regulated by either of these cytokines. Strong activation of p53 reduced the phosphorylation of STAT1 on Tyr701, however surprisingly it did not lead to reduced expression of most tested interferon-stimulated genes. On contrary, p53 and IFNγ synergized in the activation of CASP1, IFIT1 and IFIT3 genes. We conclude that the interactions between p53 and interferon-activated pathways are more complicated than initially expected, but the apparent cooperation between p53 and IFNγ deserves further studies.

Although phylogenetic analysis shows coronaviruses (CoV) share similar genome sequences, CoVs encode different number of proteins (5 to 14), which has implication on viral pathogenicity and infection. Here, we aimed to identify (in-silico) the similarities between different members of coronavirus family. The analysis included 50 coronavirus proteomes, including SARS-CoV-2 (COVID-19), to find the variation of the number of protein functional motifs and domain in each coronavirus. For this role, we used the experimentally validated domain (motif) that known to be crucial for viral infection. Although human CoVs are classified within one genus, we found variations among them. SARS-CoV-1, SARS-CoV-2 and MERS-CoV encode different type of domains, which has implications on the molecular interactions triggered by each virus within human cells. Secondly, we used functional motifs to reconstruct the potential molecular pathways or interactions triggered by SARS-CoV-2 proteins within human cell.