This mini-review discusses the importance of microorganisms in various biological processes and the paradigm shift in researchers' perception of microorganisms' biology and genetics. Microorganisms are now understood to interact with their associated microorganisms, and advanced sequencing technology is used to study these interactions. The article highlights the importance of careful study design to efficiently generate and integrate data derived from meta-omics approaches such as (meta)genomics, (meta)transcriptomics, (meta)proteomics, and (meta)metabolomics to fully explore the extent of interactions between host organisms and their associated microbiota. The article also discusses the usefulness of metabarcoding and metagenomics in studying coral holobiont diversity and composition. While metabarcoding can comprehensively explore the genetic diversity of various biological taxa, it has limitations in classifying prokaryotes based on 16S rRNA amplicons. On the other hand, metagenomics generates vast amounts of short reads sequencing data that can be used to examine microbial diversity with greater precision and predict the possible functions of the gene set that is presented in the sample. However, the ability to link species to their functional capabilities is challenging, especially for microbes with uncertain evolutionary relationships, hidden microbes, and microeukaryotes. Finally, the article highlights the potential usefulness of these approaches in conservation biology and molecular and environmental science.

Advanced genomics, transcriptomics and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids, and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research, the principles of genomics, transcriptomics and epigenomics, alongside their most advanced technologies (like single cell omics and spatial omics), which allows to investigate the molecular events that occur at single cell resolution retaining the spatial information.

The literature was scoped to help place mass spectrometric (MS) platforms in the spotlight of the life sciences, as a tool of OMICS and OMICS 2.0 technologies. Moreover, today’s appliances are so handy, that they literally place a whole lab on a single chip. Methods of OMICS (and the most recently developed term OMICS 2.0) are tackled, having in mind their aptness for educational purposes, as well as their feasibility. This same topic was highlighted in many reviews that have been periodically published. The author’s initial interest was the forensic application of MS, but since these interests changed, terms such as “biosensors” were also examined, so the review included means of discovery of efficient biomarkers and clinical therapeutic targets. Aside from simply reviewing the research status and the future perspectives, this article tackles terms such as Society 5.0 and OMICS 2.0. However, within the framework of this review, physical chemistry, bioinformatics, or specific software solutions were not specifically studied. Since the topic of generating permanent collections of digital content for retrospective analysis was also reviewed, the need for loads of data – cloud storage was discussed in the context of MS. These large quantities of data are easier to operate with if generated by MS, rather than by any other commercially available assay. In this manner, the review has strengthened an in-depth understanding of the applications of MS.

In recent years, the ecological and economic values of forest plants have been gradually recognized worldwide. However, the growing global demand for new forest plant varieties with higher wood production capacity and better stress tolerance cannot be satisfied by conventional phenotype-based breeding, marker-assisted selection, and genomic selection. In the recent past, diverse omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and metabolomics, have been developed rapidly, providing powerful tools for the precision genetic breeding of forest plants. Genomics lays a solid foundation for understanding complex biological regulatory networks, while other omics technologies provide different perspectives at different levels. Multi-omics integration has combined the different omics technologies, becoming a powerful tool for genome-wide functional element identification in forest plant breeding. This review summarizes the recent progress of omics technologies and their applications in the genetic studies of forest plants. It will provide forest plant breeders with an elementary knowledge of multi-omics techniques for future breeding programs.

For consciousness to exist, an entity must have prerequisite characteristics and attributes to give rise to it. We explore these “building blocks” of consciousness in detail in this paper, which range from perceptive to computational to higher-order characteristics of an entity’s cognitive architecture. We show how each cognitive attribute is strictly necessary for the emergence of consciousness, and how the building blocks are collectively sufficient for any entity to be classified as being conscious. The list of building blocks is not limited to human or organic consciousness and may be used to classify artificial and organisational conscious entities. We further explore a list of attributes that seem intuitively necessary for consciousness, but on further investigation, are neither required nor sufficient. The building blocks do not represent a theory of consciousness but rather a meta-theory on the emergence and classification of consciousness.

Meta-analysis has increasingly been used to synthesize the ecosystem services literature, with some testing of the use of such analyses to transfer benefits. These are typically based on local primary studies. However, meta-analyses associated with ecosystem services are a potentially powerful tool for transferring benefits, especially for environmental assets for which no primary studies are available. In this study we use the Ecosystem Service Valuation Database (ESVD), which brings together 1350 value estimates from more than 320 studies around the world, to estimate meta-regression functions for provisioning, regulating & maintenance and cultural ecosystem services across 12 biomes. We tested the reliability of these meta-regression functions and found that even using variables with high explanatory power, transfer errors could still be large. We show that meta-analytic transfer performs better than simple value transfer and, in addition, that local meta-analytical transfer (i.e. based on local explanatory variable values) provides more reliable estimates than global meta-analytical transfer (i.e. based on mean global explanatory variable values). Thus, we conclude that when taking into account the characteristics of the study area under analysis, including explanatory variables such as income, population density and protection status, we can determine the value of ecosystem services with greater accuracy.

Maize (Zea mays L.) stands as one of the most extensively cultivated crops globally, offering significant contributions to food, animal feed, and biofuel production. Maize yield is significantly impacted by diverse climate and soil variables, yet its productivity faces hindrances due to abiotic stresses, including drought, salinity, extreme temperatures, and cold conditions. In confronting these hurdles, the field of crop breeding has undergone a transformation thanks to high-throughput sequencing technologies (HSTs). These advancements have streamlined the identification of beneficial quantitative trait loci (QTL), associations between markers and traits (MTAs), as well as genes and alleles that contribute to crop improvement. Presently, well-established omics techniques such as genomics, transcriptomics, proteomics, and metabolomics are being amalgamated into maize breeding studies. These approaches have unveiled new biological markers that are being employed to bolster maize's capacity to withstand an array of challenges. In this chapter, we explore the current knowledge regarding the morpho-physiological and molecular mechanisms that underlie the resistance and tolerance of maize to biotic and abiotic stresses. The focus is on utilizing omics techniques to augment maize's ability to withstand these challenges. Moreover, it emphasizes the significant potential of integrating various omics techniques to tackle the challenges presented by biotic and abiotic stress in maize productivity, contrasting with singular approaches.

For a significant period, conventional breeding and genetic modification were the key techniques that were effective in managing biotic and abiotic stresses in crops and adding desirable traits. However, the recent appearance of novel diseases and unexpected climatic changes that have substantial implications for agriculture worldwide have urged scientists to look for alternative methods to quickly manage seasonal crises. The primary emphasis of this chapter is on the obstacles and diverse biotechnological methods employed to enhance crop resilience against a range of biotic and abiotic stressors in plants. Furthermore, we consider gene transformation, omics techniques, genome editing, and other sophisticated biotechnological tools that utilize transcriptomic, proteomic, metabolomic, phenomics, RNA interference, and epigenome modifications for enhancing plant resilience. Lastly, we examine the potential of merging these eco-friendly and innovative methods with conventional breeding to promote modern agriculture and aid in enhancing tolerance to different biotic, abiotic stresses and growth promotion.

Identifying groups that share common features among datasets through clustering analysis is a typical problem in many fields of science, particularly in post-omics and systems biology research. In respect of this, quantifying how a measure can cluster or organize intrinsic groups is important since currently there is no statistical evaluation of how ordered is, or how much noise is embedded in the resulting clustered vector. Many of the literature focuses on how well the clustering algorithm orders the data, with several measures regarding external and internal statistical measures; but none measure has been developed to statistically quantify the noise in an arranged vector posterior a clustering algorithm, i.e., how much of the clustering is due to randomness. Here, we present a quantitative methodology, based on autocorrelation, to assess this problem.

Jujube (Ziziphus jujuba Mill.) stands as a pivotal fruit tree with significant economic, ecological, and social value. Recent years have witnessed remarkable strides in multi-omics-based biological re-search on jujube. This review began by summarizing advancements in jujube genomics. Subse-quently, we provided a comprehensive overview of the integrated application of genomics, tran-scriptomics, and metabolomics to explore pivotal genes governing jujube domestication traits, quality attributes (including sugar synthesis, terpenoids, and flavonoids), and responses to abiotic stress, and discussed the transcriptional regulatory mechanisms underlying these traits. Further-more, challenges in multi-omics research on jujube biological traits were outlined, and we pro-posed the integration of resources such as pan-genomics and sRNAome to unearth key molecules and regulatory networks influencing diverse biological traits. Incorporating these molecules into practical breeding strategies, including gene editing, transgenic approaches, and progressive breeding, holds the potential for achieving molecular-design breeding and efficient genetic en-hancement of jujube.

In this review, we will cover a general overview of the current panorama on lncRNAs with an actual or potential role as biological markers in cancer. We will discuss examples of multi-omics approaches that integrates information on somatic aberrations, gene expression and epigenomics, with the scope of providing a more comprehensive view of the functional impact of lncRNA profiles and how these paradigm can be exploited for the discovery and selection of lncRNAs with a functional role and their use as variables informing on progression and prognostic and help guiding the selection of therapeutic strategies for cancers. Finally, we propose a perspective for future evolution of the study of lncRNAs and the discovery of their functional and harnessing their potential to assist in clinical management of malignancies.

Omics technologies, viz., genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal breeding program because they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in cereal-omics promise—in combination with time efficiency—the cost benefits. In this review, we provide a comprehensive overview of the established cereal-omics methods in five major cereals, viz., rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants, (2) high-density transcriptomics data to study gene expression patterns, (3) global and targeted proteome profiling to study protein structure and interaction, (4) metabolomic profiling to quantify organ level small-density metabolites and their composition, and (5) high-resolution high-throughput image-based phenomics approaches are surveyed in this review.

Metabolomics deals with multiple and complex chemical reactions within living organisms and how these are influenced by external or internal perturbations. It lies at the heart of omics profiling technologies not only as the underlying biochemical layer that reflects information expressed by the genome, the transcriptome and the proteome, but also as the closest layer to the phenome. The combination of metabolomics data with the information available from genomics, transcriptomics, and proteomics offers unprecedented possibilities to enhance current understanding of biological functions, elucidate their underlying mechanisms and uncover hidden associations between omics variables. As a result, a vast array of computational tools have been developed to assist with integrative analysis of metabolomics data with different omics. Here, we review and propose five criteria – hypothesis, data types, strategies, study design and study focus – to classify statistical multi-omics data integration approaches into state-of-the-art classes under which all existing statistical methods fall. The purpose of this review is to look at various aspects that lead the choice of the statistical integrative analysis pipeline in terms of the different classes. We will draw a particular attention to metabolomics and genomics data to assist those new to this field in the choice of the integrative analysis pipeline.

Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence, and heavy metals. The effective management at molecular level is mandatory for thorough understanding of plant response to abiotic stress. The molecular mechanism of stress tolerance is complex and requires information at the omic level to understand it effectively. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. The emerging field of ionomics is also being employed for investigating abiotic stress tolerance in wheat. Omic approaches generate a huge amount of data, and adequate advancements in computational tools have been achieved for effective analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. In this review, we have described advances in omic tools in the view of conventional and modern approaches being used to dissect abiotic stress tolerance in wheat. Emphasis was given to approaches such as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). Comparative genomics and candidate gene approaches are also discussed considering identification of potential genomic loci, genes, and biochemical pathways involved in stress tolerance mechanism in wheat. This review also provides a comprehensive catalog of available online omic resources for wheat and its effective utilization. We have also addressed the significance of phenomics in the integrated approaches and recognized high-throughput multi-dimensional phenotyping as a major limiting factor for the improvement of abiotic stress tolerance in wheat.

Improvements in the treatment of childhood cancer have considerably enhanced survival rates over the last decades, to over 80% as per today. However, this great achievement has been accompanied by the occurrence of several early and long-term treatment-related complications major of which is the cardiotoxicity. The chemotherapeutic agents that have been implicated as a cause of cardiotoxicity, are mostly anthracyclines and mitoxantrone, alkylating agents, proteasome inhibitors and to a lesser extent anti-microtubule agents, cisplatin, monoclonal antibodies, small molecular tyrosine kinase inhibitors, and nucleotide synthesis inhibitors. Routine diagnosis and monitoring of cardiotoxicity rely on electrocardiography and echocardiography. For the early detection of cardiotoxicity, in recent years, major studies have been conducted using biomarkers such as troponin, N-terminal pro b-natriuretic peptide, etc. Despite refinements in diagnostics still severe limitations exist, due to the increase of the above-mentioned biomarkers, only after significant cardiac damage has occurred. Lately, research has been expanded by introducing new technologies and finding new markers by omics approach. These new markers could be used not only for early detection, but also for early prevention of cardiotoxicity. The omics science, which includes genomics, transcriptomics, proteomics, and metabolomics, offers new opportunities for biomarker discovery in cardiotoxicity and may provide understanding of mechanisms of cardiotoxicity, beyond traditional technologies. This article reviews the contemporary definition of cardiotoxicity, older and newer chemotherapeutic agents mainly involved in cardiotoxicity and the methods of early and preventive diagnosis, using omics technology.

Given the importance of menstrual blood in the pathogenesis of endometriosis and the multifunctional roles of menstrual mesenchymal stem cells (MenSCs) in regenerative medicine, this issue has gained prominence in the scientific community. Moreover, recent reviews highlight how robust the integrated assessment of omics data is for endometriosis. To our knowledge, no study has applied the multi-omics approaches to endometriosis MenSCs. It is a case-control study at a university-affiliated hospital. MenSCs transcriptome and proteome data were obtained by RNA-seq and UHPLC-MS/MS detection. Among the differentially expressed proteins and genes, we emphasize ATF3, ID1, ID3, FOSB, SNAI1, NR4A1, EGR1, LAMC3, and ZFP36 genes and MT2A, TYMP, COL1A1, COL6A2, and NID2 proteins that were already reported in the endometriosis. Our functional enrichment analysis reveals integrated modulating signaling pathways such as epithelial-mesenchymal transition (↑) and PI3K signaling via AKT to mTORC1 (↓in proteome), mTORC1 signaling, TGF beta signaling, TNFA signaling via NFkB, and response to hypoxia via HIF1A targets (↑in transcriptome). Our findings highlight primary changes in the endometriosis MenSCs, suggesting that the chronic inflammatory endometrial microenvironment can modulate these cells, providing opportunities for endometriosis etiopathogenesis. Moreover, they identify challenges for future research leveraging knowledge for regenerative and precision medicine in endometriosis.

High-throughput screening technologies continues to produce large amounts of multiomics data from different populations and cell types for various diseases, such as cancer. However, analysis of such data encounters difficulties due to cancer heterogeneity, further exacerbated by human biological complexity and genomic variability. There is a need to redefine the drug discovery development pipeline, bringing an Artificial Intelligence (AI)-powered informational view that integrates relevant biological information and explores new ways to develop effective anticancer approaches. Here, we show SynPred, an interdisciplinary approach that leverages specifically designed ensembles of AI-algorithms, links omics and biophysical traits to predict synergistic anticancer drug synergy. SynPred exhibits state-of-the-art performance metrics: accuracy – 0.85, precision – 0.77, recall – 0.75, AUROC – 0.82, and F1-score - 0.76 in an independent test set. Moreover, data interpretability was achieved by deploying the most current and robust feature importance approaches. A simple web-based application available online at http://www.moreiralab.com/resources/synpred/ was constructed to predict synergistic anticancer drug combinations requiring only the upload of the two drug SMILES to be tested, allowing easy access by non-expert researchers.

Rapid development of high-throughput omics technologies generates an increasing interests in algorithms for cutoff point identification. Existing cutoff methods and tools identify cutoff points based on association of continuous variables with another variable, such as phenotype, disease state or treatment group. These approaches are not applicable for descriptive studies in which continuous variables are reported without known association with any biologically meaningful variables. The most common shape of the ranked distribution of continuous variables in high-throughput descriptive studies corresponds to a biphasic exponential/super-exponential curve, where the first phase includes big number of variables with values slowly growing with rank and the second phase includes smaller number of variables rapidly growing with rank. This study describes an easy algorithm to identify the boundary between these phases to be used as a cutoff point. The major assumption of that approach is that small number of variables with high values dominate biological system and determine its major processes and functions. This approach was tested on three different datasets: genes in the human cerebral cortex, mammalian genes sensitive to chemical exposures, and proteins expressed in human heart. In every case, the described cutoff identification method produced shortlists of variables (genes, proteins) highly relevant for dominant functions/pathways of the analyzed biological systems. Thus, our described method for cutoff identification may be used to prioritize variables for a focused functional analysis, in situations where other methods of dichotomization of data are inaccessible.

Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used to define the building blocks to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.

By providing useful tools to study host-pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, the depth of quantitative gene expression profiling has proven to be unsatisfactory when focusing on bacterial pathogens, thus preferentially requiring specific strategies or the development of novel methodologies based on complementary omics approaches. In this review, we focus on the difficulties encountered when making use of omics approaches to study bacterial pathogenesis. Besides, we review different omics strategies (i.e. transcriptomics, proteomics and secretomics) and their applications for studying interactions of pathogens with their host.

Systematic reviews and meta-analyses have become an important way to summarize data. The hierarchy of evidence-based medicine confers a high platform to meta-analyses. Hence, it is imperative that the analytical and reporting strategy associated with a meta-analysis be standardized. The modern tradition of reporting and publishing a meta-analysis is riddled with several methodological flaws. The most common of these flaws involve the choice of the model used to conduct the meta-analysis and the way that the heterogeneity of studies is assessed. The use of the I² statistic as a means of detecting within-study heterogeneity is a common methodological flaw encountered in reporting summary statistics.One of the ways to rectify the above flaws is to arm reviewers with an objective way to scrutinize the manuscript. This narrative review enlists six checklists for reviewers to improve the reporting of meta-analyses. The first two checklists address reporting of the risk of bias and assessment of publication bias with the help of a funnel plot. Checklists 3, 4, and 5 address the choice of model selected for the meta-analysis, the method to assess the confidence interval, and the measures of heterogeneity. The final checklist addresses the question asked in the meta-analysis, binary versus an effect size estimate. Although there are many more aspects which can help improve the assessment of a manuscript, these basic checklists can be employed by reviewers without the need for an external statistical analysis to enhance and improve meta-analyses.

Corn silage (Zea mays L.) is the most widely used energy resource in the diets of dairy cattle around the world; it stands out for its higher biomass yields, good palatability, homogeneous quality at harvest and ease of silage due to its higher soluble sugar content. It was carried out a search of studies related to dry matter yield (ton ha-1), population density (plant density ha-1), dry matter (DM), crude protein (CP), neutral detergent fiber (NDF), non-fibrous carbohydrates (NFC), organic matter (OM), DM digestibility (DMD) and neutral detergent fiber digestibility (NDFD) and milk production per hectare (kg of milk ha-1) that was determined using MILK2006®. It was carried out a cluster analysis (CL, PROC CLUSTER) obtaining six groups of corn silage: CL1: "Starch", which included DMD, DFDN, TDN1xDM, Mega calories per kg of DM and kg of milk/ton/DM; CL2: "Fats" which included TDN1xMS, Mcal/kg/DM and kg of milk/ton/DM; CL3: "Dry Matter", conformed only by DFDN; CL4: "Plant Density" including Yield of DM ha-1 and Milk Production ha-1; CL5: "Neutral Detergent Fiber" and CL6: "Raw Protein". It is concluded that CL1 was characterized by a higher DMD, DFND, CNF and starch that allow a higher TNDx1DM and an energy concentration (Mcal/kg/DM) that shows a higher milk production (kg of milk/ton/DM ha-1). The characteristics of CL2 with higher EE, allow a higher TNDx1DM and an energy concentration (Mcal/kg/DM) with a higher milk production (kg of milk/ton/DM ha-1).

A recent systematic review for 19 selected articles after searching through to 30 September 2017 showed vitamin D deficiency was associated with ischemic stroke (IS), not hemorrhagic stroke (HS). But a heterogeneity would be introduced with comparing the lowest and highest category of vitamin D. The aim of this article was to conduct an updated meta-analysis (UMA) with searching through to 31 March 2019. An interval collapsing method as information extraction was applied in order to decrease a heterogeneity among studies. Additional articles were selected from cited lists from 19 selected articles using citation discovery tools. Random effect model was applied if I-squared value was over 50%. A funnel plot and Egger’s test were used to detect a publication bias. After 5 new studies were added, the summary RRs [and their 95% confidence intervals] (I-squared value) were 1.52 [1.33–1.74] (0.0%) in IS, and 2.44 [1.34–4.46] (69.7%) in HS. This UMA supported the hypothesis that serum vitamin D deficiency was associated with an increased risk of HS as well as IS. Diverse public health programs against vitamin D deficiency status would be needed for higher risk group, especially elderly people.

Rice, as a staple crop feeding billions, faces constant threats from various diseases jeopardizing global food security. Precise understanding of disease resistance mechanisms is crucial for developing resilient rice varieties. Traditional genetic mapping methods, such as QTL mapping, provide valuable insights into the genetic basis of diseases. However, the complex nature of rice diseases demands a holistic approach to gain accurate knowledge of it. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, enable a comprehensive analysis of biological molecules, uncovering intricate molecular interactions within the rice plant. Integration of various mapping techniques using multi-omics data has revolutionized our understanding of rice disease resistance. By overlaying genetic maps with high-throughput omics datasets, researchers can pinpoint specific genes, proteins, or metabolites associated with disease resistance. This integration enhances the precision of disease-related biomarkers with better understanding of their functional roles in disease resistance. Improvement of rice breeding for disease resistance through this integration represents a significant stride in agricultural science because better understanding of the molecular intricacies and interactions underlying disease resistance architecture leads to more precise and efficient development of resilient and productive rice varieties. In this review, we explore how the integration of mapping and omics data can give a transformative impact on rice breeding for enhancing disease resistance.

The concept of omics-based technological approaches has promoted translational research by integrating knowledge from diverse areas to understand their dynamics by exploring the molecular mechanisms underlying various processes paving the way for further improvements in the crops quality by providing sound knowledge on controlling plant diseases. This area is not profoundly investigated a decade back and hence this knowledge has become exceedingly important in modern times as it has got potential for being utilized in crop improvement programs. In this review, the contributions of different omics technologies including genomics, transcriptomics, proteomics, and metabolomics in understanding and materializing the ways involved in the plant pathogen interaction (PPI) is discussed. Furthermore, opportunities, challenges, and perspectives of omics linked to signaling mechanisms have also been highlighted that are significantly linked to plant-microbe interactions.

Climate change has had a significant impact on many ecosystems worldwide, prompting native population species to adapt to the current weather patterns eventually. Pre-existing genetic variation in populations explains part of this adaptation. Still, recent studies have shown that new stable phenotypes can be generated through epigenetic modifications in just a few generations, thereby contributing to the stability and survival of plants in their natural habitat as they eventually adjust to the surrounding impacts. The state of chromatin inside plant cells varies, allowing cells to fine-tune their transcriptional profiles to better adapt to stimuli from the external environment. Within a cell, chromatin state changes such as post-transcriptional histone modifications and variations, DNA methylation, and non-coding RNA activity are all examples of chromatin state alterations that may epigenetically dictate certain transcriptional outputs. Recent advances in the field of ‘Omics’ in major crops has made it easier to identify epigenetic changes and their impact on plant responses to environmental stresses. These epigenetic mechanisms thus play an important role in improving crop adaptation and resilience to changing environments. This variation that has emerged can thus be exploited in crop breeding, ultimately leading to the generation of stable climate-resilient genotypes.

Increased severity of droughts, due to anthropogenic activities and global warming has imposed a severe threat on agricultural productivity ever before. This has further advanced the need for some eco-friendly approaches to ensure global food security. In this regard, application of plant growth-promoting rhizobacteria (PGPR) can be beneficial. PGPR through various mechanisms viz. osmotic adjustments, increased antioxidant, phytohormone production, regulating stomatal conductivity, increased nutrient uptake, releasing Volatile organic compounds (VOCs), and Exo-polysaccharide (EPS) production, etc not only ensures the plant’s survival during drought but also augment its growth. This review, extensively discusses the various mechanisms of PGPR in drought stress tolerance. We have also summarized the recent molecular and omics-based approaches for elucidating the role of drought responsive genes. The manuscript presents an in-depth mechanistic approach to combat the drought stress and also deals with designing PGPR based bioinoculants. Lastly, we present a possible sequence of steps for increasing the success rate of bioinoculants.

Bioethanol has been considered as an excellent alternative to fossil fuels since it importantly contributes to the reduced consumption of the crude oil and to the alleviation of environmental pollution [1]. Up to now, the baker yeast Saccharomyces cerevisiae is the most common eukaryotic microorganism used in ethanol production. The inability of S. cerevisiae to grow on pentoses, however, hinders its effective growth on plant biomass hydrolysates, which contain large amounts of C5 and C12 sugars. The industrial-scale bioprocessing requires high temperature bioreactors, diverse carbon sources, and the high titer production of volatile compounds [2]. These criteria indicate that the search for alternative microbes possessing useful traits that meet the required standards of bioethanol production is necessary. Compared to other yeasts, Kluyveromyces marxianus has several advantages over the others, e.g. it could grow on a broad spectrum of substrates (C5, C6 and C12 sugars) [3], tolerate to high temperature, toxin [4,5] and a wide range of pH values [6], and produce volatile short-chain ester [2]. K. marxianus also shows a high ethanol production rate at high temperature and is a Crabtree-negative species [7]. These attributes make K. marxianus a promise as an industrial host for the biosynthesis of biofuels and other valuable chemicals.

This investigation aimed to explore the impact of acute and regular physical exercise on Brain-Derived Neurotrophic Factor (BDNF) levels in individuals with obesity. Using the Population, Intervention, Comparator, Outcome, and Study design (PICOS) approach, the inclusion criteria were defined as follows: i) population - individuals with overweight or obesity of any age or gender; ii) intervention - acute or chronic interventions involving aerobic or anaerobic methodologies; iii) comparator - for acute effect studies, pre- and post-evaluations served as comparators, while interventions included at least one experimental group or the inclusion of a control group; iv) outcome - BDNF variability concerning the applied methodology; v) study design - restricted to experimental studies exclusively. Conducted in August 2022, the searches were carried out on PubMed, Academic Search Complete, and Web of Science. The risk of bias was assessed using the Risk of Bias in Non-randomized Studies (RoBANS) tool. Out of 98 potentially relevant articles, 16 met the eligibility criteria, encompassing 23 trials. Substantial heterogeneity was observed for both acute (I2 = 80.4%) and long-term effects (I2 = 88.7%). Additionally, RoBANS analysis indicated a low risk of bias for the included studies. The study's findings revealed a significant increase in the concentration of circulating BDNF in individuals with obesity compared to the control group following acute exercise. However, such an effect was not evident in the context of long-term physical exercise, with a small effect size (ES = 0.49) recorded in the latter scenario. The observed significant increase in BDNF levels post-acute exercise suggests a potential acute response mechanism contributing to the intricate interplay between exercise and neurotrophic factors in this population. Nevertheless, the absence of a similar effect in the context of long-term physical exercise implies a potential adaptation or ceiling effect. These findings underscore the importance of considering both the duration and nature of exercise interventions when exploring the neurobiological responses associated with obesity and exercise. The study provides valuable insights for future research and clinical implications in understanding the nuanced relationship between exercise, neurotrophic factors, and obesity.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with high heterogeneity and has a prevalence of 0.7% to 3.2% in children. Gut microbiota are a collection of microorganisms that inhabit in human guts, which can produce various metabolites that affect the homeostasis and functions of nervous and endocrine systems. There are many studies on the relationship between various gut microbiota and ASD, but the alteration pattern of microbial profiles in ASD children is not conclusive. In order to more robustly describe the deregulations of gut microbiota compositions in ASD, a meta-analysis was performed. The related investigations from PubMed, Embase and Web of Science were collected and manually reviewed. By procedure, 26 eligible studies until 2023, with a total of 1021 ASD and 951 typically developed children and adolescents, were included for the meta-analysis. RevMan5.4 was used to assess the overall effect of 8 microbes at the phylum level and 19 microbes at the genus level. Results demonstrated relatively up-regulated abundance of Bacteroidetes, Verrucomicrobia, Bacteroides, Clostridium, Dorea and Sutterella, and down-regulated abundance of Proteobacteria, Bifidobacterium, Coprococcus, and Akkermansia in ASD children, indicating partly agreement in the ASD-associated microbes, albeit the heterogeneity of ASD.

Background: Pharmacologic and non-pharmacologic treatments for stroke are essential but could be costly or harmful whereas probiotic has been a promising alternative. This scoping review aimed to synthesize the in vitro and in vivo evidence of probiotics on stroke-related neurological, biochemical, and histochemical outcomes. Method: We searched in PubMed, Embase, and Cochrane Central Register of Clinical up to May 7, 2021, and screened by two independent reviewers. We included the use of probiotics, prebiotics, and symbiotics both in vitro and in vivo for the prevention or treatment of the stroke-related model. Result: Of 6,293 articles, 4,990 passed the initial screen, of which 36 theme-related full-texts were assessed and 13 were included in this review. Probiotics could ameliorate the neurological deficit and show their property as an anti-inflammation and anti-oxidative stress. Histopathologically decreased loss of cerebral volume and inhibition of neuronal apoptosis were found. Conclusion: There are potential cognitive benefits of probiotic supplementation, especially among animal models, on decreasing cerebral volume, increasing neurological score, and decreasing the inflammatory response. However, further investigation is needed to validate these conclusions in various populations.

The pervasiveness of cardiovascular disease and physician misdiagnosis creates the urgent need for artificial intelligence models to improve diagnosis accuracy. The first objective of this study was to train machine learning models on publicly available data sets containing simple medical information of patients to diagnose cardiovascular disease. The Multilayer Perceptron (MLP) assembled for this task performed optimally with an F1 score of 0.8968. This prompted the creation of an open-source, automated cardiovascular disease diagnosis tool, powered by the MLP. The second objective of this study was to employ a meta-learning methodology called Local Interpretable Model-Agnostic Explanations (LIME) to understand the impact of different features on the model's diagnosis in the form of marginal probabilities. K-Means Clustering was employed to segment the data into ten clusters, after which each data example was passed through LIME. The resulting histograms depict the complex relationship between feature, cluster, and impact on diagnosis. A series of P-values with contrasting orders of magnitude shows the nuances in the MLP's understanding of patients from different clusters. The results of meta-learning analysis reveal that the most important features for cardiovascular disease diagnosis are fasting blood sugar, type of chest pain, and slope of the ST segment on an electrocardiogram. Future experiments should replicate the novel methodology introduced in this study on data sets containing more specialized medical features in order to gain practical medical insights about different types of cardiovascular disease represented by each cluster. Finally, feature engineering pathways should be explored with consideration of these results to create versatile diagnosis models not only for cardiovascular disease, but adaptable to other diseases as well.

SacreBLEU, by incorporating a text normalizing step in the pipeline, has been well-received as an automatic evaluation metric in recent years. With agglutinative languages such as Korean, however, the metric cannot provide a conceivable result without the help of customized pre-tokenization. In this regard, this paper endeavors to examine the influence of diversified pre-tokenization schemes –word, morpheme, character, and subword– on the aforementioned metric by performing a meta-evaluation with manually-constructed into-Korean human evaluation data. Our empirical study demonstrates that the correlation of SacreBLEU (to human judgment) fluctuates consistently by the token type. The reliability of the metric even deteriorates due to some tokenization, and MeCab is not an exception. Guiding through the proper usage of tokenizer for each metric, we stress the significance of a character level and the insignificance of a Jamo level in MT evaluation.

(1) Purpose: This work aims at developing a generalizable MRI reconstruction model in the meta-learning framework. The standard benchmarks in meta-learning are challenged by learning on diverse task distributions. The proposed network learns the regularization function in a variational model and reconstructs MR images with various under-sampling ratios or patterns that may or may not be seen in the training data by leveraging a heterogeneous dataset. (2) Methods: We propose an unrolling network induced by learnable optimization algorithms (LOA) for solving our nonconvex nonsmooth variational model for MRI reconstruction. In this model, the learnable regularization function contains a task-invariant common feature encoder and task-specific learner represented by a shallow network. To train the network we split the training data into two parts: training and validation, and introduce a bilevel optimization algorithm. The lower-level optimization trains task-invariant parameters for the feature encoder with fixed parameters of the task-specific learner on the training dataset, and the upper-level optimizes the parameters of the task-specific learner on the validation dataset. (3) Results: The PSNR increases 1.5 dB on average compared to the network trained through conventional supervised learning on the seen CS ratios. We test the result of quick adaption on the unseen tasks after meta-training, the average PSNR arises 1.22 dB compared to the conventional learning procedure that is directly trained on the unseen CS ratios in the meanwhile saving half of the training time. The average PSNR arises 1.87 dB for unseen sampling patterns comparing to conventional learning; (4) Conclusion: We proposed a meta-learning framework consisting of the base network architecture, design of regularization, and bi-level optimization-based training. The network inherits the convergence property of the LOA and interpretation of the variational model. The generalization ability is improved by the designated regularization and bilevel optimization-based training algorithm.

To evaluate the efficacy of fish oil for protection against coronary heart disease (CHD), we conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) evaluating the use of fish oil for protection against CHD. We retrieved relevant articles published from January 1966 to January 2020 by searching the PubMed, EMBASE, Cochrane CENTRAL, and Web of Science databases. RCTs of fish oil in preventing CHD were selected. The study quality was evaluated using the Cochrane Risk of Bias tool with RevMan 5.3 software. The first selection involved 350 citations. After screening and evaluation of suitability, 19 RCTs adjusted for clustering were included in the meta-analysis. All selected manuscripts considered that fish oil was effective in preventing CHD, secondary outcome measures included angina, sepsis and death. Compared with the control group, fish oil may confer significant protection against CHD (odds ratio = 0.84; 95% confidence interval: 0.72–0.98). There was no significant difference in the incidence of secondary outcomes between the observation group and the control group (P > 0.05). The above results show that fish oil plays an important role in reducing CHD and cardiovascular events. However, because of the suboptimal quality of the studies included into the meta-analysis, these results do not justify adding fish oils systematically to the heavy pharmaceutical assortment already recommended in CHD patients.

The effects of buckwheat intake on cardiovascular diseases (CVD) have not been systematically investigated. The aim of the present study was to comprehensively summarise studies in humans and animals evaluating the impact of buckwheat consumption on CVD risk markers and to conduct a meta-analysis of relevant data. Thirteen randomised, controlled human studies, two cross-sectional human studies and twenty-one animal studies were identified. Using random effects models, the weighted mean difference of post-intervention concentrations of blood glucose, total cholesterol and triglycerides were significantly decreased following buckwheat intervention compared with controls [differences in blood glucose: -0.85 mmol/L (95% CI: -1.31, -0.39), total cholesterol: 0.50 mmol/L (95% CI: -0.80, -0.20) and triglycerides: 0.25 mmol/L (95% CI: -0.49, -0.02)]. Responses of a similar magnitude were seen in two cross-sectional studies. For animal studies, nineteen of twenty-one studies showed a significant reduction in total cholesterol of between 12 and 54%, and fourteen of twenty studies showed a significant reduction in triglycerides of between 2 and 74%. All exhibited high unexplained heterogeneity. There was inconsistency in HDL cholesterol outcomes in both human and animal studies. It remains unclear whether increased buckwheat intake significantly benefits other markers of CVD risk, such as weight, blood pressure, insulin, and LDL-cholesterol, and underlying mechanisms responsible for any effects are unclear.

Acetamiprid is a broad-spectrum neonicotinoid insecticide used in agriculture to control aphids. While recent studies have documented resistance to acetamiprid in several aphid species, the underlying mechanisms are still not fully understood. In this study, we analyzed the transcriptome and metatranscriptome of a laboratory strain of the pea aphid, Acyrthosiphon pisum (Harris, 1776), with reduced susceptibility to acetamiprid after nine generations of exposure to identify candidate genes and the microbiome involved in the adaptation process. Sequencing of the transcriptome of both selected (RS) and non-selected (SS) strains allowed the identification of 14858 genes and 4938 new transcripts. Most of the differentially expressed genes were associated with catalytic activities and metabolic pathways involving carbon and fatty acids. Specifically, the alcohol-forming fatty acyl-CoA reductase (FAR) and acyl-CoA synthetase (ACSF2), both involved in the synthesis of epidermal wax layer components, were significantly upregulated in RS, suggesting that adaptation to acetamiprid involves the synthesis of a thicker protective layer. Metatranscriptomic analysis revealed subtle shifts in the microbiome of RS. These results contribute to a deeper understanding of acetamiprid adaptation by the pea aphid and provide new insights for aphid control strategies.

Inflammatory Bowel Disease (IBD) is a chronic and progressive inflammatory disorder affecting the gastrointestinal tract (GT) caused by a wide range of genetic, microbial, and environmental factors. IBD is characterized by chronic inflammation, decreased gut microbial diversity and dysbiosis, with a lower amount of beneficial bacteria and a concomitant increase of pathogenic species. It is well known that dysbiosis is closely related to the induction of inflammation and oxidative stress, this last caused by an imbalance between reactive oxygen species (ROS) production and cellular antioxidant capacity that leads to cellular ROS accumulation. ROS are responsible for the intestinal epithelium oxidative damage and the increased intestinal permeability found in IBD patients and their reduction could represent a potential therapeutic strategy to limit the IBD progression and alleviate its symptom. Recent evidence highlighted that dietary polyphenols, natural antioxidants, are able to maintain redox equilibrium in the GT preventing gut dysbiosis, intestinal epithelium damage and radical inflammatory responses. Here, we suggest that the relatively new foodomics approaches, together with new technologies for promoting the antioxidative properties of dietary polyphenols, including novel delivery systems, chemical modifications and combination strategies, may provide critical insight to determine the clinical value of polyphenols for IBD therapy and a comprehensive perspective for implementing natural antioxidants as potential IBD candidate treatment.

The advancement of mass spectrometry technologies has revolutionised plant metabolomics research by enabling the acquisition of raw metabolomics data. However, the identification, analysis, and visualisation of these data require specialised tools. Existing solutions lack a dedicated plant-specific metabolite database and pose usability challenges. To address these limitations, we developed PlantMetSuite, a web-based tool for comprehensive metabolomics analysis and visualisation. PlantMetSuite encompasses interactive bioinformatics tools and databases specifically tailored for plant metabolomics data, facilitating upstream-to-downstream analysis in metabolomics and supporting integrative multi-omics investigations. PlantMetSuite can be accessed directly through a user's browser without the need for installation or programming skills. The tool is freely available at https://plantmetsuite.verygenome.com/ and will undergo regular updates and expansions to incorporate additional libraries and newly published metabolomics analysis methods. The tool's significance lies in empowering researchers with an accessible and customisable platform for unlocking plant metabolomics insights.

If one considers chemical-biology toolsets that have had the greatest impact on numerous fields of life sciences over the most recent years, proximity-labeling tools, such as APEX, and Bio-ID arguably lead the way. This article reflects upon the current state-of-the-art and discusses key limitations underlying these emerging approaches, in particular, the limited functional knowledge they provide in understanding local proteomes / interactomes. This limitation is directly linked to the use of non-biologically- or non-pharmaceutically-relevant reactive intermediates in the course of covalently labeling the local proteomes. As such, these methods cannot report on specific functions of localized protein players, nor can they scrutinize whether the specific functions of such proteins/interactomes can be directly manipulated by pharmacologically-relevant small-molecule ligands. The latest data hint that precision localized electrophile delivery concept ushers a means to address this limitation with high spatiotemporal resolution, and ultimately, in relevant live animals.

The ability to read and quantify nucleic acids such as DNA and RNA using sequencing technologies has revolutionized our understanding of life. With the emergence of synthetic biology, these tools are now being put to work in new ways - enabling de novo biological design. Here, we show how sequencing is supporting the creation of a new wave of biological parts and systems, as well as providing the vast data sets needed for the machine learning of design rules for predictive bioengineering. However, we believe this is only the tip of the iceberg and end by providing an outlook on recent advances that will likely broaden the role of sequencing in synthetic biology and its deployment in real-world environments.

The study also found that older age was a protective factor in prospective studies. The consistency of results across different study designs and sensitivity analyses further supported the robustness of the findings. It is important to note that the existing literature on revictimization in women facing intimate partner violence is limited and exhibits significant heterogeneity in terms of methodology and conceptual frameworks.

Objective The aim of this study was to explore the prognosis and influencing factors of recurrent ependymoma in children. Methods PubMed, Embase, Cochrane Library, and Web of Science were searched to collect studies on survival outcomes and influencing factors of recurrent ependymoma in children. The search time frame was from the establishment of the database to September 2023. Two evaluators independently screened the literature, extracted data, and evaluated the quality of the included studies. Meta-analysis was performed using RevMan 5.4 software. Results A total of 11 studies involving 1120 patients were included. The integrated results of mOS from the 11 studies showed significant heterogeneity (I2 = 92%). Therefore, a random-effects model was used for merging, and the results showed statistically significant differences (P < 0.00001). In all the studies, the pooled estimate of median OS from the time of recurrence was 15.54 months (95% CI 8.80-27.45; P < 0.00001), and the combined median progression-free survival (PFS) from the time of first recurrence was 6.7 months (95% CI 5.59-7.64; P < 0.0001). The median OS for patients who underwent surgery at the time of recurrence was 20.7 months (95% CI 12.40–34.72; P < 0.00001), while the mOS for patients who received radiation therapy was 29.5 months (95% CI 18.97–46.00; P < 0.0001), and for patients who received chemotherapy mOS was 18.0 months (95% CI 8.62–37.75; P < 0.00001). The mOS for patients under 3 years old at the time of recurrence was 20.1 months (95% CI 1.98-204.50; P < 0.00001), while for patients over 3 years old at the time of recurrence mOS was 16.6 months (95% CI 9.40-29.35; P < 0.00001). Conclusion The results of the study show poor prognosis for children with recurrent ependymoma, and there are significant differences in these results. The influencing factors include patient age, tumor recurrence location, and treatment methods. These findings can further guide clinical research on new treatment methods and strategies to improve the prognosis of this population.

Background: Gestational diabetes is a common complication during pregnancy that can lead to numerous adverse outcomes. Some studies suggest that probiotics may be used to treat gestational diabetes, however, the results remain controversial. We conducted a systematic review and meta-analysis to evaluate the effect of probiotics on blood glucose and pregnancy outcomes in women with gestational diabetes. Methods: A systematic search of PubMed, Embase, and Cochrane databases was performed (start date to August 22, 2023). Primary outcomes included fasting blood sugar (FBS), fasting serum insulin (FSI), homeostasis model assessment of insulin resistance (HOMA-IR), and quantitative insulin sensitivity check index (QUICKI). Secondary outcomes included pregnancy and neonatal outcomes. Results: 15 articles (n = 1006 women) met the inclusion criteria and were included in the analysis. Compared to a placebo, probiotics can decrease FBS (MD -2.58, 95% CI -4.38 to -0.79, p &lt; 0.01), FSI (MD -2.29, 95% CI -3.40 to -1.18, p &lt; 0.01), HOMA-IR (MD -0.56, 95% CI -0.81 to -0.32, p &lt; 0.01), birthweight (MD -101.20, 95% CI -184.62 to -17.77, p = 0.02), neonatal intensive care unit (NICU) (RR 0.60, 95% CI 0.40 to 0.89, p = 0.01), and hyperbilirubinemia (RR 0.31, 95% CI 0.16 to 0.61, p &lt; 0.01), alongside higher QUICKI (MD 0.01, 95% CI 0.00 to 0.01, p &lt; 0.01). However, no other significant results were obtained. Conclusion: Probiotics may improve blood glucose indicators and reduce neonatal hyperbilirubinemia, NICU admissions, and birth weight in women with GDM.

It is a well-established fact that inadequate Vitamin D (Vit-D) levels have negative effects on the development and progression of malignant diseases, mainly cancer. The purpose of this paper was to elucidate the effects of Vit-D intake and serum 25-hydroxyvitamin-D (25(OH)D) levels on cancer incidence and mortality, the current evidence in this field, and the biases of this evidence using the meta-meta-analysis method. Meta-analyses focusing on Vit-D intake, serum 25(OH)D levels, and cancer risk/mortality were identified. A structured computer literature search was performed in PubMed/Medline, Web of Science (WoS), and Scopus electronic databases using predetermined keyword combinations. Primary and secondary meta-meta-analyses were carried out, combining odds ratios (ORs), risk ratios (RRs), and hazard ratios (HRs) for outcomes reported in selected meta-analyses. A total of 35 eligible meta-analyses assessing the association between Vit-D and cancer incidence and/or mortality were included in this study. In the pooled analysis, higher Vit-D intake and serum 25(OH)D levels were associated with lower cancer risk (OR = 0.93, 95% CI: 0.90-0.96, p < 0.001; OR = 0.80, 95% CI: 0.72-0.89, p < 0.001, respectively) and cancer-related mortality (RR = 0.89, 95% CI: 0.86-0.93, p < 0.001; RR = 0.67, 95% CI: 0.58-0.78, p < 0.001, respectively). When meta-analyses whose primary reports included only randomized controlled trials were pooled, there was no significant association between Vit-D intake and cancer risk (OR = 0.99, 95% CI: 0.97-1.01, p = 0.320). In subgroup analysis, Vit-D consumption was associated with a significant decrease in colorectal and lung cancer incidence (OR = 0.89, 95% CI: 0.83-0.96, p = 0.002; OR = 0.88, 95% CI: 0.83-0.94, p < 0.001, respectively). Taken together, both Vit-D intake and higher 25(OH)D levels may provide remarkable benefits in terms of cancer incidence and mortality, however, careful evaluation according to cancer types is critically important and recommended.

Objective: To carry out a bibliometric analysis study of systematic reviews and meta-analyses in dentistry, divided into different thematic areas. Material and method: A search was conducted in the Science Citation Index-Expanded on the core collection of Web of Science, they were selected from the area of Dentistry and Oral Surgery and Medicine categories, the data was downloaded on April 20, 2022 and The 100 most cited articles from each of the thematic areas were selected. Results: An increase in this type of articles was observed in the last decade in the areas of pediatric and medical dentistry and oral pathology. The thematic area that received the most citations was periodontics. The two authors with the most citations are Zwahlen, Marcel and Pjetursson, Bjarni Eluar. The countries that receive the most citations are European, along with the USA and China. The topics that are most published in this type of article deal with Cancer with 50 publications, caries treatment with 25 and fluoridation with 1. The entities that finance this type of articles the most are private companies (26.76%). Conclusions: Together with an exponential increase in the number of publications in dentistry, there has been an increase in the number of publications in systematic reviews. The areas publishing the most articles and having the most citations are Periodontics and Implantology, despite the fact that the most studied topic is cancer.

Purpose: Pitch plays an important role in auditory perception of music and language. This study provides a systematic review with meta-analysis to investigate whether individuals with autism spectrum disorder (ASD) have enhanced pitch processing ability and identify the potential factors associated with processing differences between ASD and neurotypicals. Method: We conducted a systematic search through six major electronic databases focusing on the studies that used nonspeech stimuli to provide a qualitative and quantitative assessment across existing studies on pitch perception in autism. We identified potential participant- and methodology-related moderators and conducted meta-regression analyses using mixed-effects models. Results: On the basis of 22 studies with a total of 464 participants with ASD, we obtained a small-to-medium positive effect size (0.26) in support of enhanced pitch perception in ASD.Moreover, the mean age and non-verbal IQ of participants were found to significantly moderate the between-studies heterogeneity. Conclusion: Our study provides the first meta-analysis on auditory pitch perception in ASD and demonstrates the existence of different developmental trajectories between individuals with ASD and neurotypicals. Non-verbal ability can be a significant contributor to the lower-level/ local processing bias in ASD. We highlight the need for further investigation of pitch perception in ASD under challenging listening conditions. Future neurophysiological and brain imaging research studies with a longitudinal design are also needed to better understand the nature of the atypical processing in ASD to obtain new insights into the underlying neural mechanisms and to help guide auditory-based interventions for improving language and social functioning.

The oral route remains one of the most popular and important routes of administration that warrants the development of advanced drug delivery systems such as the polymeric nanoparticles capable of enhancing the absorption and bioavailability of the used drugs. In this work, systematic reviewing through several databases followed by a meta-analysis study were utilized in order to navigate the published studies and reach literature-based evidence about the capability of polymeric nanoparticulate systems of augmenting the absorption and the bioavailability of the orally administered drugs. The pharmacokinetic parameter; area under the curve (AUC) was utilized as the “effect” of the meta-analysis study. The meta-analysis study demonstrated the significant increase AUC as compared to the conventional formulations. Furthermore, comparing the synthetic polymeric nanoparticles versus the naturally-based counterparts, as subgroups of the meta-analysis, revealed no significant differences.

The paper aims to illustrate the different roles that social sciences can play in the study of the energy transition. To this end, a scheme is developed that frames the relative position of the social sciences with respect to other disciplines (metaframe). Secondly, socialization is identified as a charismatic category capable of providing an original, typically sociological contribution to the complex and hesitant energy transition (masterframe)

In this paper, we implement a new method binary Particle Swarm Optimization (PSO) for solving the kidney exchange problem, which will improve the future decisions of kidney exchange programs. Because using a kidney exchange, we can help incompatible patient-donor couples to swap donors to receive a compatible kidney. Kidney paired donation programs provide an innovative approach for increasing the number of available kidneys. Further, we implementing binary particle swarm optimization in parallel with MATLAB with one, two, three and four threads and from the computations point of view, the authors compare the performance to reduce the running time for kidney exchange to match patients as fast as possible to help clinicians. Moreover, implementing binary particle swarm optimization in solving the kidney exchange problem is an effective method. The obtained results indicate that binary PSO outperforms other stochastic-based methods such as genetic algorithm, ant lion optimization, and efficient the number of resulting exchanges.

Background: Overweight and obese adults seek effective exercise interventions to reduce accumulated fat, but the effectiveness of these interventions vary across studies. The purpose of this meta-analysis was to investigate the effectiveness of exercise interventions in overweight and obese adults based on measurement of accumulated fat distributions. (2) Methods: Databases were used to select eligible studies for this meta-analysis. Randomized controlled trials with a control and experimental group were included. Degrees of effectiveness of exercise interventions were computed to assess the benefits on reducing weight and subcutaneous, visceral, and ectopic fat accumulation. (3) Results: A total of twenty-one studies were included in this meta-analysis. Participation in exercise interventions showed beneficial effects in reducing weight and subcutaneous and visceral fat. The effectiveness of exercise interventions on ectopic fat accumulation could not be assessed due to the limited number of studies measuring ectopic fat. Additionally, effectiveness of exercise interventions that depended on measurements of accumulated fat varied. The average exercise intervention for overweight and obese individuals was moderate to vigorous intensity, 4 times per week, 50 minutes per session, and 22 weeks duration. (4) Conclusions: Participating in exercise interventions has favorable effects on reducing weight and accumulation of subcutaneous and visceral fat.

Despite the considerable focus on job characteristics and individual differences in job crafting research, the influence of social factors on job crafting has not been well-acknowledged. This meta-analysis estimates the associations between social factors and job crafting, and how social factors contribute to employee outcomes through their job crafting. Based on a sample of 51 empirical studies that included 54 independent effect sizes (N = 17,863), we found that social factors of positive leadership styles (e.g., empowering and transformational) and coworker support were positively related to employee job crafting. Further, our study showed that employee job crafting positively mediate the relationships between social factors and work outcomes (e.g., job performance and well-being). Our study contributes to job crafting literature by integrating social factors into the job crafting model and demonstrating that the social context of work (in particular organizational-insiders) play a crucial role in shaping employees’ job crafting behavior. We also emphasize the critical role that job crafting plays in transmitting valuable social resources into improved work outcomes. Building on our results, we provide future direction for job crafting research and discuss how our results can imply practice in terms of job crafting training.

Stroke is one of the most prevalent cardiovascular diseases worldwide, both in high-income countries and in medium and low-medium income countries. The WHO report on non-communicable diseases (NCDs) indicates that the highest behavioral risk in NCDs is attributable to incorrect nutrition. The objective of our work is to present an overview of meta-analyses that have investigated the impact of different foods and / or drinks in relationship with the risk of stroke events (ischemic/ hemorrhagic). The papers to be included in the overview were sought in the MEDLINE, EMBASE, Scopus, Clinicaltrials.gov, Web of Science, and Cochrane Library and were selected according to PRIMA flow chart. Quality assessment were made according to AMSTAR scale. This overview shows that all primary studies came from countries with high income level. This evidence shows that many countries are not represented. Therefore, different lifestyles, ethnic groups, potentially harmful or virtuous eating habits are not reported. It is important to underline how the choose of foods may help reduce the risk of cardiovascular diseases and stroke in particular.

Background. Upper respiratory infections (URIs) remains as significant cause of morbidity in children. Evidence on efficacy of probiotics to prevent URIs in children is increasing. This systematic review was assembled to analyze evidence about the efficacy of probiotics to reduce duration of upper respiratory infections in ambulatory children. Methods. Randomized controlled trials (RCTs) comparing probiotics vs. placebo to prevent URIs, published between 2001 and 2016 were considered. Quality evaluation was evaluated using CONSORT. Standard mean difference (SMD) or risk ratio (RR) was calculated. Network Meta-Analysis (NMA), using a random effect model was assembled. Results. 31 RCTs were evaluated and 20 studies were included with 3,635 children randomized to probiotics and 3,433 to placebo. Lactobacillus reuteri [SMD -0.56 CI95% (-0.72 to -0.41), p 0.0001] and Lactobacillus acidophillus [SMD -0.33 CI95% (-0.60 to -0.06), p 0.01] were superior to placebo to reduce duration of URIs. L. rhamnosus GG showed tendency [SMD -0.14 CI95% (-0.28 to 0.0), p 0.048]. On the network forest plot L. reuteri showed preventive equivalence when was compared to L. rhamnosus GG, L. casei and BB12. Conclusions. Lactobacillus reuteri, Lactobacillus rhamnosus GG and Bifidobacterium BB12 are evidence-based alternatives to be considered to prevent URIs in children.

Theoretical studies propose an association between family violence and low self-control in adolescence, yet empirical findings of this association are inconclusive. The aim of the present research was to systematically summarize available findings on the relation between family violence and self-control across adolescence. We included 27 studies with 143 effect sizes, representing more than 25,000 participants of eight countries from early to late adolescence. Applying a multi-level meta-analyses, taking dependency between effect sizes into account while retaining statistical power, we examined the magnitude and direction of the overall effect size. Additionally, we investigated whether theoretical moderators (e.g., age, gender, country), and methodological moderators (cross-sectional/longitudinal, informant) influenced the magnitude of the association between family violence and self-control. Our results revealed that family violence and self-control have a small to moderate significant negative association (r = -.191). This association did not vary across gender, country, and informants. The strength of the association, however, decreased with age and in longitudinal studies. This finding provides evidence that researchers and clinicians may expect low self-control in the wake of family violence, especially in early adolescence. Recommendations for future research in the area are discussed.

Cow’s Milk (CM) is a healthy food consumed worldwide by individuals of all ages. Unfortunately, 'lactase deficient' individuals cannot digest milk's carbohydrate lactose depriving themselves of highly beneficial milk proteins like casein, lactoalbumin and lactoglobulin, due to lactose intolerance (LI), while other individuals develop cow milk allergy specifically against these proteins (CMPA). The management of these conditions is distinctly different and an inappropriate diagnosis or treatment may have significant implications for the patients, especially if they are infants or very young children, resulting in unnecessary dietary restriction or avoidable adverse reactions. Omics technologies play a pivotal role in elucidating the intricate interactions between nutrients and the human body, spanning from genetic factors to the microbiota profile and metabolites. This comprehensive approach enables the precise delineation and identification of distinct cohorts of individuals with specific dietary requirements, so that tailored nutrition strategies can be developed. This is what is called personalized nutrition or precision nutrition (PN), the area of nutrition that focuses on the effects of the nutrients over the genome, proteome and metabolome, promoting well-being and health, preventing diseases, reducing chronic disease incidence, and so increasing life expectancy. Here, we report the scientific community opinion proposing to replace the approach “one size fits all” with tailor-made nutrition programs, designed by integrating nutrigenomic data together with clinical parameters and microbiota profiles, taking into account the individual lactose tolerance threshold and needs in terms of specific nutrients intake. This customized approach could help LI patients to improve their quality of life, overcoming depression or anxiety, often resulting from the individual perception of this condition as different from a normal state.

A heterogeneous disease like cancer is activated through multiple pathways and different perturbations. Depending upon the activated pathway(s), patients’ survival vary significantly and show different efficacy to various drugs. Therefore, cancer subtype detection using genomics level data is a significant research problem. Subtype detection is often a complex problem, and in most cases, needs multi-omics data fusion to achieve accurate subtyping. Different data fusion and subtyping approaches have been proposed, such as kernel-based fusion, matrix factorization, and deep learning autoencoders. In this paper, we compared the performance of different deep learning autoencoders for cancer subtype detection. We performed cancer subtype detection on four different cancer types from The Cancer Genome Atlas (TCGA) datasets using four autoencoder implementations. We also predicted the optimal number of subtypes in a cancer type using the silhouette score. We observed that the detected subtypes exhibit significant differences in survival profiles. Furthermore, we also compared the effect of feature selection and similarity measures for subtype detection. To evaluate the results obtained, we selected the Glioblastoma multiforme (GBM) dataset and identified the differentially expressed genes in each of the subtypes identified by the autoencoders; the obtained results coincide well with other genomic studies and can be corroborated with the involved pathways and biological functions. Thus, it shows that the results from the autoencoders, obtained through the interaction of different datatypes of cancer, can be used for the prediction and characterization of patient subgroups and survival profiles.

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

Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer-review and increases the impact of datasets by enhancing their visibility, accessibility, and re-usability. We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivise researchers to publish high-quality data sets, we created a workflow for streamlined import of omics metadata directly into a data paper manuscript. An omics data paper template was designed by defining key article sections which encourage the description of omics datasets and methodologies. The workflow was based on REpresentational State Transfer services and Xpath to extract information from the European Nucleotide Archive, ArrayExpress and BioSamples databases, which follow community-agreed standards. The workflow for automatic import of standard-compliant metadata into an omics data paper manuscript facilitates the authoring process. It demonstrates the importance and potential of creating machine-readable and standard-compliant metadata. The omics data paper structure and workflow to import omics metadata improves the data publishing landscape by providing a novel mechanism for creating high-quality, enhanced metadata records, peer reviewing and publishing of these. It constitutes a powerful addition for distribution, visibility, reproducibility and re-usability of scientific data. We hope that streamlined metadata re-use for scholarly publishing encourages authors to improve the quality of their metadata to achieve a truly FAIR data world.

The objective of this study was to determine the effects of supplementing L-isoleucine (L-Ile) on milk protein synthesis, using an immortalized bovine mammary epithelial (MAC-T) cell line. In this case, the cells were treated with 0, 0.3, 0.6, 0.9, 1.2 and 1.5 mM of supplemental Isoleucine (Ile), and the most efficient time for protein synthesis for each amino acid was determined by measuring the cell, medium and total protein at 0, 24, 48, 72 and 96 h. Confirmatory tests showed that 48h incubation time and 0.6 mM dosage of L-Ile are considered as the optimal time and dosage. The mechanism of milk protein synthesis was elucidated through proteomics analysis to clarify the metabolic pathway. When the L-Ile was supplemented, extracellular protein (medium protein) reached a peak at 48h, whereas in the case of the intracellular cell protein, it was shown to have reached to its peak at 24h in all L-Ile dosage treatments. In total, it is noted that there were 63 upregulated and 52 downregulated proteins. The results of the protein pathway analysis showed that the L-Ile group stimulated insulin/IGF pathway-mitogen activated protein kinase kinase/MAP kinase cascade, insulin/IGF pathway-protein kinase B signaling cascade, p53 pathway, de novo purine biosynthesis, Wnt signaling pathway, glycolysis, pentose phosphate pathway, and ATP synthesis which are pathways involved and related to protein and energy metabolism. Together, these results demonstrate that L-Ile supplementation was effective in stimulating β-casein synthesis by stimulating genes and pathways which are significantly related to protein and energy metabolism.

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

Once discovered, cancer stem cells have become a hot topic in the research of cancer therapy. These cells possess stem cell-like self-renewal and differentiation capacities and are important factors that dominate cancer metastasis, therapy- resistance and recurrence. What's worse, their own characteristics make them difficult to be eliminated. Colorectal cancer is the third most common cancer and the second leading cause of cancer death worldwide. Targeting colorectal cancer stem cells (CRCSCs) can inhibit colorectal cancer metastasis, enhance therapeutic efficacy, and reduce recurrence. Here, we introduced the origin, marker proteins, identification, cultivation and research techniques of CRCSCs, summarized the signaling pathways that regulate the stemness of CRCSCs, such as Wnt, JAK/STAT3, Notch, and Hh signaling pathway. In addition to these, we also reviewed anti-CRCSC drugs targeting signaling pathways，markers，and other regulators in recent years. These will help researchers gain insight into the current agents targeting to CRCSCs, explore new cancer drugs, and propose potential therapy.

Demonstrating biosimilarity entails comprehensive analytical evaluations, clinical pharmacolo-gy profiling, and efficacy testing for at least one medical indication in patients. These require-ments are stipulated by the U.S. Biologics Price Competition and Innovation Act (BPCIA). The costliest element—efficacy testing—can be waived if other compliance benchmarks are satisfied, including comparing functional pharmacodynamic (PD) biomarkers, even when they do not di-rectly correlate with clinical outcomes. Most biological drugs, such as monoclonal antibodies (mAbs), lack identifiable PD biomarkers. The FDA has employed various 'omics' technologies to identify potential PD biomarkers, including proteomics, glycomics, transcriptomics, genomics, epigenomics, and metabolomics. Although these efforts provide a robust scientific basis for estab-lishing biosimilarity, they are neither practical nor necessarily superior to existing functional biomarkers, such as receptor binding and mode-of-action outcomes. As we report for the first time, these functional biomarkers can effectively serve as PD indicators for all FDA-licensed bio-logical drugs. We recommend that the FDA consider officially listing these functional biomarkers to expedite and reduce the cost of biosimilar development, thereby increasing the accessibility of biological drugs. PD surrogates, like the receptor binding and pharmacokinetic profiles, are more robust and offer a rational solution to finding PD markers to compare for establishing biosimi-larity.

The COVID-19 pandemic has presented an unprecedented challenge to the healthcare system. Identifying the genomics and clinical biomarkers for effective patient stratification and management is critical to controlling the spread of the disease. Omics datasets provide a wealth of information that can aid in understanding the underlying molecular mechanisms of COVID-19 and identifying potential biomarkers for patient stratification. Artificial intelligence (AI) and machine learning (ML) algorithms have been increasingly used to analyze large-scale omics and clinical datasets for patient stratification. In this manuscript, we demonstrate the recent advances and predictive accuracies in AI and ML-based patient stratification modeling linking omics and clinical biomarker datasets, focusing on COVID-19 patients. Our ML model not only demonstrates that clinical features are enough an indicator of COVID-19 severity and survival but also infers what clinical features are more impactful, which makes our approach a useful guide for clinicians for prioritization of best-fit therapeutics for a given cohort of patients. Moreover, with weighted gene network analysis, we are able to provide insights into gene networks that have a significant association with COVID-19 severity and clinical features. Finally, we have demonstrated the importance of clinical biomarkers in identifying high-risk patients and predicting disease progression.

The global threat of COVID-19 has led to the increasing use of metabolomics to study SARS-CoV-2 infection in humans and animals. Despite this, understanding SARS-CoV-2's metabolome during infection remains difficult and incomplete. Here, metabolic responses were characterized from sampled nasal washes collected from an asymptomatic ferret model (n = 20) at different time points before and after the SARS-CoV-2 challenge using an LC-MS-based metabolomics approach. Multivariate analysis of the nasal wash metabolome data resulted in several statistically significant features being observed. Despite no effects of gender or interaction between gender and time on the time course of SARS-CoV-2 infection, 16 metabolites were significantly different at every time point post-infection. Among these altered metabolites, the relative abundance of taurine was elevated post infection which could be an indication of hepatotoxicity, while the accumulation of sialic acids could indicate SARS-CoV-2 invasion. The pathway analysis identified several pathways influenced by SARS-CoV-2 infection. Of these, sugar, glycan, and amino acid metabolisms were the key altered pathways in the upper respiratory channel during infection. These findings provide some new insights into the progression of SARS-CoV-2 infection in ferrets at the metabolic level which could be useful for the development of early clinical diagnosis tools and new or repurposed drug therapies.

Abstract: Since ancient times aging has also been regarded as a disease, and humankind has always strived to extend the natural lifespan. Analyzing the genes involved in aging and disease allows for finding important indicators and biological markers for pathologies and possible therapeutic targets. An example of the use of omics technologies is the research regarding aging and the rare and fatal premature aging syndrome progeria (Hutchinson-Gilford progeria syndrome, HGPS). In our study, we focused on the in silico analysis of differentially expressed genes (DEGs) in progeria and aging, using a publicly available RNA Seq dataset (GEO dataset GSE113957) and a variety of bioinformatics tools. We identified several genes that appear to be involved both in natural aging and progeria (KRT8, KRT18, ACKR4, CCL2, UCP2, ADAMTS15, ACTN4P1, WNT16, IGFBP2). Further analyzing these genes and the pathways involved confirmed their possible roles in aging, suggesting the need for further in vitro and in vivo research. The graphical abstract illustrates the analysis workflow we used and will introduce in the following as an example to demonstrate the power of omics and bioinformatics.

The endothelium has multiple functions from maintaining vascular homeostasis, providing nutrition and oxygen to tissues, to evocating inflammation, under adverse conditions, and determining endo-thelial barrier disruption resulting in dysfunction. Endothelial dysfunction represents the typical condition associated with the pathogenesis of all the diseases of cardiovascular system, as well as of diseases of all the other human body’s systems, also including sepsis, acute respiratory distress syn-drome and COVID-19 respiratory distress. Such evidence is leading to identifying potential bi-omarkers and therapeutic targets for preserving, reverting, or restoring endothelium integrity and functionality by early treating its dysfunction. Here, it stresses some strategies for achieving these goals, even if diverse challenges exist and require a significant bench work associated with an in-creased number of clinical studies.

In the era of multi-omic sciences, dogma on singular cause-effect in physio-pathological processes is overcome and system biology approaches have been providing new perspectives to see through. In this context, extracellular vesicles (EVs) are offering a new level of complexity, given their role in cellular communication and their activity as mediators of specific signals to target cells or tissues. Indeed, their heterogeneity in terms of content, function, origin and potentiality contribute to the cross-interaction of almost every molecular process occurring in a complex system. Such features make EVs proper biological systems being, therefore, optimal targets of omic sciences. Currently, most studies focus on dissecting EVs content in order to either characterize it or to explore its role in various pathogenic processes at transcriptomic, proteomic, metabolomic, lipidomic and genomic levels. Despite valuable results are being provided by individual omic studies, the categorization of EVs biological data might represent a limit to be overcome. For this reason, a multi-omic integrative approach might contribute to explore EVs function, their tissue-specific origin and their potentiality. This review summarizes the state-of-the-art of EVs omic studies, addressing recent research on the integration of EVs multi-level biological data and challenging developments in EVs origin.

The indigenous communities across the globe especially in the rural areas consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many of the traditional food plants are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. TFPs are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in times of pandemics and other situations like COVID-19. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realising the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of traditional food plants for their improvements, further cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in few TFPs. This suggests that there is ample scope of integrated use of modern omics and editing tools/techniques for improvement of TFPs and their use for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

Polycyclic aromatic hydrocarbons (PAHs), which consist of low-molecular-weight PAHs (LMW-PAHs) and high-molecular-weight PAHs (HMW-PAHs), form an important class of pollutants. Pyrene and benzo[a]pyrene (BaP) are the main pollutants belonging to HMW-PAHs, and their degradation by microorganisms remains an important strategy for their removal from the environments. Extensive studies have been carried out on the isolation and characterisation of microorganisms that actively degrade LMW-PAHs, and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of “omics” approaches

French Guiana, located in the Guiana Shield, is a natural reservoir for many zoonotic pathogens that are of considerable medical or veterinary importance. Until now, there are few data available on the description of parasites circulating in this area, especially on protozoan belonging to the phy-lum Apicomplexa; conversely, the neighbouring countries describe a high parasitic prevalence in animals and humans. Epidemiological surveillance is necessary, as new potentially virulent strains may emerge from these forest ecosystems, such as Amazonian toxoplasmosis. However, there is no standard tool for detecting protozoa in wildlife. In this study, we developed Meat-Borne-Parasite, a high-throughput meta-barcoding workflow for detecting Apicomplexa based on Oxford Nanopore Technologies sequencing platform using the 18S gene of fourteen Apicomplexa-positive samples collected in French Guiana. Sequencing reads were then analysed with MetONTIIME pipeline. Thanks to a scoring rule, we were able to classify as Apicom-plexa-positive 10 samples out of 14 and reveal the presence of co-carriages. The same samples were also sequenced with Illumina platform, for validation purposes. On samples identified as Apicomplexa-positive by both platforms, a strong positive correlation at up to genus level was reported. Overall, the presented workflow represents a reliable method for Apicomplexa detec-tion, which may pave the way for more comprehensive biomonitoring of zoonotic pathogens.

A rapid synthesis of chiral sulfoxide-functionalized meta-terphenyl derivatives by a 2,5-[C4+C2] ring transformation reaction of pyrylium salts with in-situ generated enantio-merically pure .alpha.-sulfinylacetaldehydes is described. This synthetic method demonstrates for the first time the use of .alpha.-sulfinylacetaldehydes in a reaction sequence initiated by nu-cleophilic attack of pyrylium salts by .alpha.-sulfinylcarbanions to generate chiral aromatic systems. The method presented shows broad applicability starting with various methyl sulfoxides and a number of functionalized pyrylium salts, furnishing meta-terphenyls with complex substitution patterns from readily accessible starting compounds.

Dengue virus infection is caused by a positive stranded RNA virus called Dengue virus, which is spread by arthropods. It is a fast growing acute febrile disease with potentially lethal consequences that is a global public health problem, mostly in tropical and subtropical countries. In Ethiopia dengue fever is understudied despite the fact that the virus is still being transmitted and viral infection rates are rising. This systematic review and meta-analysis was aimed to estimate the pooled prevalence of DENV infection in Ethiopia. A literature search was done on PubMed, Hinari and Google Scholar databases to identify studies published before July, 2023. Random effects and fixed effects models were used to estimate pooled prevalence of all the three markers. The Inconsistency Index was used to assess the level of heterogeneity. A total of 11 articles were included in this review. Majority of the studies had moderate risk of bias and no study had a high risk of bias. A meta-analysis estimated pooled IgG prevalence of 21% (95% CI: 19-23), a pooled prevalence of IgM 9% (95%CI: 4-13) and a pooled DENV-RNA prevalence of 48% (95% CI: 33-62). There is evidence of possible publication bias in IgG but not found in the rest of markers. The prevalence of DENV infection is high in Ethiopia. Healthcare providers, researchers and policymakers should give more attention to dengue fever.

The dynamics of hydrological lateral nutrient fluxes contribute to our understanding of ecological functions related to energy, materials, and organism flows across various spatiotemporal scales. To explore the connectivity between multiple spatial flow processes, we conducted a one-year field measurement to assess lateral hydrologic carbon (C) and nitrogen (N) fluxes over the continental shelf in the Yangtze estuary. We observed a significant correlation between the differences in remote sensing-based estimates of gross primary production (GPP) (∆GPPMODIS) and the differences in eddy covariance (EC) tower-based GPP (∆GPPEC) at both high-elevation and low-elevation sites. Over the course of a year, our predicted daily maximum tidal elevation (TE) closely matched the observed values in the creek, which facilitated the development of theoretical models to simulate biogeochemical cycling processes and aquatic ecosystem functions. Our findings indicate that the studied saltmarsh acts as a net exporter of dissolved total C (DTC) while serving as a net sink for dissolved total N (DTN). Furthermore, there is a significant correlation in the total dissolved stoichiometry of the C/N ratio between imports and exports. These findings highlight the importance of integrating ecological stoichiometric principles to gain a deeper understanding of the complex relationships between physical, chemical, and biological processes, particularly within the context of the meta-ecosystem framework. Additionally, when considering reciprocal hydrological lateral C and N flows, single ecosystem can function both as sources and sinks within the meta-ecosystem framework.

Aims: The aims of this meta-analysis were to assess: the prevalence of Post-Acute COVID-19 sequalae in HIV positive patients; average time of diagnosis; and meta-regress for possible moderators of PACS.Methods: A standard search strategy was used in PubMed, and then later modified according to each specific database to get the best relevant results. These included Medline indexed journals; PubMed Central; NCBI Bookshelf and publishers' Web sites in line with the Preferred Reporting Items for Systematic Review and Meta-Analysis statement. Search terms included “long COVID-19 or post-acute COVID-19 syndrome/sequalae”, “persons living with HIV or HIV. The criteria for inclusion were published clinical articles reporting HIV in association with long COVID-19, further, the average time to an event of post-acute COVID-19 sequelae among primary infected patients with COVID-19. Random-effects model was used. Rank Correlation and Egger's tests were used to ascertain publication bias. Sub-group, sensitivity and meta-regression analysis were conducted. A 95% confidence intervals were presented and a p-value < 0.05 was considered statistically significant. Review Manager 5.4 and comprehensive meta-analysis version 4 (CMA V4) were used for the analysis. The review/trial was PROSPERO registered (CRD42022328509).Results: A total of 43 studies reported post-acute COVID-19 syndrome. Of those, five reported post-acute COVID-19 sequalae in PLHIV. Prevalence of post-acute COVID-19 sequalae was 43.1% (95% CI 20.5% to 68.9%) in persons living with HIV (PLWH). The average time to PACS diagnosis was 4 months at 64% [0.64 (95% CI 0.230, 0.913) (P < 0.0000), I²= 93%] and at one year to PACS diagnosis was at 70 %, however with non-significant correlation (P > 0.05). On comorbidities, asthenia was associated with PACS at 17.6 % [0.176 (95% CI 0.067, 0.385) (P = 0.008), I²= 86%] while fatigue at 82%, however not related with PACS event incidence (P < 0.05). Americas, Asian and European regions showed PACS events rates of 82%, 43% and 19 % respectively (P<0.05) relative to HIV infection. Conclusion: PACS prevalence in PLWH was 43% occurring at an average time of 4 months at 64% and 70 % at 12 months however non-significant with PACS. Asthenia was significantly associated with PACS at 17.6 % while fatigue at 82%, however not related with PACS event incidence. Americas recorded the highest PACS event rates in PLWH.

Background and Objectives: Angioembolization has emerged as an effective therapeutic approach for pelvic hemorrhages; however, its exact effect size remains uncertain. Therefore, we conducted this systematic review and meta-analysis to investigate the effect size of embolization-related pelvic complications after nonselective angioembolization compared to that after selective angioembolization in patients with pelvic injury accompanying hemorrhage. Materials and Methods Relevant articles were collected by searching the PubMed, EMBASE, and Cochrane databases until June 24, 2023. Meta-analyses were conducted using odds ratios (ORs) for binary outcomes. Quality assessment was conducted using the risk of bias tool in non-randomized studies of interventions. Results: Five studies examining 357 patients were included in the meta-analysis. Embolization-related pelvic complications did not significantly differ between patients with nonselective and selective angioembolization (OR 1.581, 95% confidence interval [CI] 0.592 to 4.225, I2 = 0%). However, in-hospital mortality was more likely to be higher in the nonselective group (OR 2.232, 95% CI 1.014 to 4.913, I2 = 0%) than in the selective group. In the quality assessment, two studies were found to have a moderate risk of bias, whereas two studies exhibited a serious risk of bias. Conclusions: Despite the favorable outcomes observed with nonselective angioembolization concerning embolization-related pelvic complications, determining the exact effect sizes was limited owing to the significant risk of bias and heterogeneity. Nonetheless, the low incidence of ischemic pelvic complications appears to be a promising result.

This study aimed to evaluate the diagnostic and prognostic roles of GATA3 immunohistochemistry in urothelial carcinoma (UC) through a meta-analysis. We investigated GATA3 immunohistochemical expression rates and performed a subgroup analysis based on tumor site, study location, and histological subtypes. The overall survival rates of patients with GATA3-positive and negative UC were compared. The estimated GATA3 expression rate was 0.748 (95% confidence interval [CI]: 0.704–0.787). GATA3 expression rates in the urinary bladder and urinary tract were 0.775 (95% CI: 0.727–0.818) and 0.614 (95% CI: 0.426–0.774), respectively. The GATA expression rates of noninvasive and invasive UCs were 0.965 (95% CI: 0.938–0.980) and 0.644 (95% CI: 0.581–0.702), respectively. In invasive UCs, there was a significant difference in GATA3 expression between non-muscular invasion and muscular invasion subgroups (0.937, 95% CI: 0.883–0.967 vs. 0.753, 95% CI: 0.645–0.836). GATA3 expression was the highest in the microcytic subtype among the histologic subtypes (0.952, 95% CI: 0.724–0.993). There was a significant correlation between GATA3 expression and better prognosis (hazard ratio: 0.402, 95% CI: 0.311–0.521). Taken together, GATA3 expression significantly correlated with low-stage and better prognosis in UC. GATA3 expression is highly variable across histological subtypes and it is careful interpreting GATA3 expression.

Recently, the move from cost-tied to open-access data has led to the mushrooming of research in pursuit of algorithms for estimating aboveground grass biomass (AGGB). Nevertheless, a comprehensive synthesis or direction on the milestones archived or an overview of how these models perform is lacking. This study synthesises the research work from decades of experiments in order to point researchers in the direction of what was done, the challenges faced, as well as how the models perform. A pool of findings from 108 remote sensing-based AGGB studies published from 1972 to 2020 show that about 62% of the remote sensing-based algorithms were tested in the Steppe grasslands, mostly in the temperate climate zone. An uneven annual publication yield was observed with approximately 36% of the research output from Asia whereas countries in the global south yielded few publications (&lt;10%). Optical sensors, particularly MODIS, remain a major source of satellite data for AGGB studies, whilst studies in the global south rarely use active sensors such as Sentinel-1. Optical data tend to produce poor regression accuracies that are highly inconsistent across the studies compared to Radar. Vegetation indices, particularly the Normalised Difference Vegetation Index (NDVI), remain a major predictor variable. Predictor variables such as Sward height, Red edge position and Backscatter coefficients produced slightly consistent accuracies. Deciding on the optimal algorithm for estimating AGGB is daunting due to the lack of overlap in the grassland type, location, sensor types, and predictor variables, signalling the need for further studies around the transferability of remote sensing-based AGGB models.

Objective: The objective of this review was to establish a modified meta-ethnography framework by integrating the traditional phases with methods from social constructivist grounded theory. The modified version was required to identify methods which can ensure analytic generalisability and honour critical inquiry. Method: A narrative synthesis review was undertaken using 4 electronic databases. Articles were located that described the methods and methodologies of meta-ethnography and social constructivist grounded theory. A synthesis was undertaken which integrated the methods of social constructivist grounded theory. Results: The meta-ethnography was undertaken in 5 phases: (1) The positionality of the researcher and the area of interest identified. (2) Identifying what is relevant. (3) Reading the study and determining how studies are related. (4) The iterative process of idea generation required for theory generation. And (5) Expression of the theory, model, or process. Conclusion: The current study provides a useful tool to support the development of a substantive theory (a theory in one area) which can be used then to consider its application in other areas. This approach will help create new lines of research and aid the explanation of problems in other areas.

Abstract: Background: Pain management is one of the main parts of treatments for Temporomandibular Disorders (TMDs). However, there is still a lack of high-quality evidence that compare the overall effects of these non-surgical treatments. The objective of this systematic review is to identify the most potential treatment protocol in dealing with pain caused by TMDs through a mixed comparison of interventions based on network meta-analysis. Methods: A systematic review and network meta-analysis of studies identified by searching PubMed, Embase, Medline, Ovid, and CINAHL. All the included studies should have characteristics that: (1) participants with TMDs of any age; (2) non-surgical treatments; (3) score of Visual Analog Scale (VAS) as the outcome measure; (4) randomized controlled trials. The Cochrane Bias Assessment Toll was used to assess the bias, the CINeMA website was applied to rate the confidence of evidence, and ADDIS software was used to conduct the network meta-analysis. Results: 46 studies were included in this review. The agreement between authors reached a kappa value of 0.78. The results of the network meta-analysis showed that wearable therapy devices are more likely to be the best choice for reducing the pain of patients with myogenic TMDs, whereas a combination of platelet-rich plasma injection and wearable therapy devices is more likely to be the best choice for reducing the pain in a long term after treatment for patients with mix-type TMDs. Moreover, the application of therapy equipment has the most potential in reducing pain in a long term after treatment for patients with articular TMDs. Discussion: Wearable devices have a great potential for pain syndrome caused by TMDs, the mechanism might come from a biomechanical perspective. However, the overall confidence rating of evidence is low. Studies with high quality are still needed in the future. Other: The PROSPERO Registration Number of this systematic review is CRD42021253442.

Overweight/obesity is one of the most important health problem worldwide. Birth by cesarean section has been shown to influence long-term health outcome including obesity. The aim of this systematic review-meta-analysis is to examine whether cesarean section increases the risk of offspring’ s overweight/obesity. The study follows the PRISMA and MOOSE guidelines. A systematic literature search was con-ducted on Scopus, PubMed, and WoS until December 2020. For inclusion, studies must have re-ported either (I) both Birth by cesarean section and adult (≥ 18 years) offspring BMI, (II) cohort or case–control study design and (III) a risk estimate. Heterogeneity testing was performed using Cochran's Q and I2 statistics. Publication bias was assessed by Egger’s test and Begg’s test. Me-ta-analysis was performed through a random effect model. Eleven studies with a combined population of 180.408 subjects were included in the meta-analysis. The overall analysis (n = 18) yielded a combined risk estimate for overweight/obesity of 1.19 (95% CI 1.08-1.31) and the test of heterogeneity resulted Q=53,37 (I2 = 70,37 %, P≤0•0001). The risk of offspring obesity is 1.23 (95% CI 1.09-1.39) and the test of heterogeneity resulted Q=39.50 (I2= 72,15%, P≤0•0001). Children born by cesarean section have an increased risk of developing obesity in adulthood

Background: Acute ischemic stroke is among the main causes of mortality worldwide; a rapid and opportune diagnosis is crucial to improve a patient's outcome. MicroRNAs are quite useful for a rapid and accurate diagnosis.Methods: We perform both structural networks approach and a meta-analysis (using a random-effect model to evaluate the heterogeneity and risk bias, according to the PRISMA statement) to analyze the feasibility to develop a microRNA-based biomarker panel for an opportune AIS diagnosis. Results: Structural networks identify a set of eight miRNAs (miR-16, miR-124-3p, miR-484, miR-15a, miR-4454, miR-107, miR-125b-5p and miR-320b) as preliminary microRNA-based biomarker panel, from these only three microRNAs are significantly associated with the main risk factors of AIS, (miR-107: hypertension, 95% CI 9.74-53.24 p<0.0001, type 2 Diabetes mellitus, 95% CI 2.18-19.26); p=0.0008; miR-16 hypertension, 95% CI 1.26-3.56 p=0.0046, smoking, 95% CI 1.07-3.54 p=0.0277; and miR-15a hypertension, 95% CI 1.26-3.56 p=0.0046; smoking, 95% CI 1.07-3.54 p=0.0277). However, the meta-analysis reveals that data is highly heterogeneous and biased; and only microRNAs isolated from plasma samples and further processed in microarrays are the most reliable to distinguish AIS patients.Conclusions: Together our results show that although there are some miRNAs that seem to be associated with AIS, we are still far to develop a miRNA-based biomarker for AIS diagnosis and it is necessary to harmonize the protocols, results and include more populations for further studies otherwise we will remain throwing punches in the dark.

This study presents a meta-analysis of studies that investigate the effectiveness of chitosan administration on lifestyle-related disease in murine models. A total of 34 published studies were used to evaluate the effect of chitosan supplementation. The effect sizes for various items after chitosan administration were evaluated using the standardized mean difference. Using Cochran’s Q test, the heterogeneity of effect sizes was assessed, after which a meta-ANOVA and –regression test was conducted to explain the heterogeneity of effect sizes using the mixed-effect model. Publication bias was performed using Egger’s linear regression test. Among the items evaluated, blood triglyceride and HDL-cholesterol showed the highest Q statistics and I2 values, respectively. Other than blood HDL-cholesterol, total cholesterol, and triglyceride in feces, most items evaluated showed a negative effect size with high significance in the fixed- and random-effect model (p<0.0001). In the meta-ANOVA and -regression test, administering chitosan and resistant starch was revealed to be most effective in lowering body weight. In addition, chitosan supplementation proved to be an effective solution for TNF-α inhibition. In conclusion, chitosan has been shown to be somewhat useful in improving symptoms of lifestyle-related disease. Although there are some limitations in the results of this meta-analysis due to the limited number of animal experiments conducted, chitosan administration nevertheless shows promise in enhancing the quality of human life.

Aim of study:Aim of this meta-analysis is to evaluate post-operative procalcitonin as a marker to predict post- operative infectious complications after pancreatic surgeries.Material and Methods:Systemic literature search was performed using MEDLINE, EMBASE and to identify studies evaluating the diagnostic accuracy of Procalcitonin (PCT) as a predictor for detecting infectious complications on postoperative days (POD) 3 and 5 following pancreatic surgery. A meta-analysis was performed using random effect model and pooled predictive parameters for POD 3 and 5 were derived. Geometric means were calculated for PCT cut offs. Results:6 studies included day 3 PCT analysis, 2 studies included both day 3 and day 5 analysis. Total data of 471 patients were derived. 161 patients developed infectious complications. Pooled sensitivity, specificity, pooled area under curve, diagnostic odds ratio (DOR), positive and negative like hood ratio of day 3 PCT were 74%,79%,0.8453, 11.03,3.17 and 0.31 respectively. Pooled sensitivity, specificity, diagnostic odds ratio (DOR), positive and negative like hood ratio of day 5 PCT were 83%,70%,12.91,2.91 and 0.25 respectively. Geometric means for PCT cut off for day 3 and 5 were 0.80 and 0.43. Conclusion:Postoperative procalcitonin particularly day 3 procalcitonin levels predict post-operative infectious complications following pancreatic surgeries.

Antibiotics (ABs) are common medications used for treating infections. In cancer patients treated with immune checkpoint inhibitors (ICIs), concomitant exposure to ABs may impair the efficacy of ICIs and lead to a poorer outcome compared to AB non-users. We report here the results of a meta-analysis evaluating the effects of ABs on the outcome of patients with solid tumors treated with ICIs. PubMed, the Cochrane Library, and Embase were searched from inception until September 2019 for observational or prospective studies reporting prognosis of adult patients with cancer treated with ICIs and with or without ABs. Overall survival (OS) was the primary endpoint, and progression-free survival (PFS) was the secondary endpoint. The effect size was reported as hazard ratios (HRs) with a 95% confidence interval (CI), and an HR > 1 associated with a worse outcome in ABs users compared to no-ABs users. Fifteen publications were retrieved for a total of 2363 patients. In the main analysis (n = 15 studies reporting data), OS was reduced in patients exposed to ABs before or during treatment with ICIs (HR = 2.07, 95%CI 1.51–2.84; P<.01). Similarly, PFS was inferior in ABs users in n = 13 studies with data available (HR = 1.53, 95%CI 1.22–1.93; p<.01). In cancer patients treated with ICIs, AB use significantly reduces OS and PFS. Short duration/course of ABs may be considered in clinical situations in which they are strictly needed.

Meta-aminobenzoic acid, an important model system in the study of polymorphism and crystallization of active pharmaceutical ingredients, exist in water in both the nonionic (mABA) and zwitterionic (mABA^±) forms. However, the constituent molecules of the polymorph that crystallizes from aqueous solutions are zwitterionic. This study reports atomistic simulations of the events surrounding the early stage of crystal nucleation of meta-aminobenzoic acid from aqueous solutions. Ab initio molecular dynamics was used to simulate the hydration of mABA± and mABA, and to quantify the interaction of these molecules with the surrounding water molecules. Density functional theory calculations were conducted to determine the low-lying energy conformers of meta-aminobenzoic acid dimers and compute the Gibbs free energies in water of nonionic, (mABA)₂, zwitterionic, (mABA^±)₂ and nonionic-zwitterionic, (mABA)(mABA^±), species. Classical molecular dynamics simulations of mixed mABA–mABA^± aqueous solutions were carried out to examine the aggregation of meta-aminobenzoic acid. According to these simulations the selective crystallization of the polymorph which constituent molecules are zwitterionic is driven by the formation of zwitterionic dimers in solution, which are thermodynamically more stable than (mABA)₂ and (mABA)(mABA^±) pairs. This work represents a paradigm of the role of molecular processes during the early stages of crystal nucleation in affecting polymorph selection during crystallization from solution.

Introduction Recent evidence from relatively small randomized controlled trials would seem to support a useful role of ranolazine for the prevention and treatment of atrial fibrillation (AF). The present study is aimed at providing information about the possible beneficial anti-arrhythmic properties of ranolazine. In particular, the meta-analysis carried out in this study focuses on the application of ranolazine to prophylaxis and treatment of atrial fibrillation.Methods Both randomized controlled trials (RCTs) and non randomized observational studies concerning the effects of ranolazine on AF were included in the meta-analysis. In each of the considered studies, a comparison was made between a group of patients taking ranolazine and a second group treated instead with another antiarrhythmic therapy , or assigned to placebo. Efficacy outcomes were the risk of new- onset AF, the probability of conversion to sinus rhythm of patients with recent occurrence(≤ 48 h)of AF and the time to conversion to sinus rhythm. Safety endpoints were death, adverse events, QTc prolongation and hypotension.Results Ten studies ( 8 RCTs and 2 nonrandomized observational studies) were gathered on the whole. Ranolazine was effective in preventing the occurrence of AF when compared to controls (RR= 0.60; 95% CI: 0.43–0.83; p = 0.002). Subgroup analysis showed a more pronounced preventive effect of ranolazine against AF in the postoperative setting of coronary artery bypass grafting(CABG) surgery (RR= 0.39; 95% CI: 0.18-0.83; p=0.02) when compared to non- postoperative AF (RR= 0.76; 95% CI: 0.63-0.92; p=0.04). Ranolazine enhanced the chances of successful cardioversion when added to intravenous amiodarone compared to amiodarone alone (RR 1.18; 95% CI: 1.05–1.33; p = 0.004) and significantly decreased the time to cardioversion(SMD= −10.35 h; 95% CI: −18.13 hours to − 2.57 hours; p < 0.001). Overall risks of death, adverse events, and QTc prolongation were shown to be similar in the comparison between patients treated with ranolazine and controls. Conclusions Ranolazine given orally at appropriate doses showed the property to significantly quicken the conversion of AF to sinus rhythm when combined with the iv amiodarone, compared to iv amiodarone alone . Furthermore, in patients in sinus rhythm, ranolazine proved to reduce the frequency of new onset AF as well as of its recurrences, especially in patients undergone CABG surgery, known to be at high risk of developing postoperative AF. In addition, ranolazine use seems to be safe and associated with relatively few adverse events.

Background: Diabetic retinopathy (DR) is one of the most prominent pathological microvascular complications in diabetes. A series of studies reported that vitamin D deficiency was associated with increased prevalence of retinopathy in diabetic patients but the results were inconsistent. In this study we focused on evaluating the relationship between vitamin D deficiency and DR by conducting a meta-analysis of observational studies. Methods: Systematic computerized searches were performed in PubMed, MEDLINE, and the Cochrane Library for relevant original articles till November 20, 2016. The pooled odds ratios (ORs) with corresponding confidence intervals (CIs) were calculated to assess the associated value of vitamin D deficiency to the risk of DR. 9 studies including 6332 participants were subjected to final analysis. Results: The results indicated that vitamin D deficiency increases the risk of DR (OR = 1.57, 95% CI 1.32-1.87) with a little heterogeneity (I2 = 23%). In addition, the subgroup analysis demonstrated that there were obvious heterogeneities in T2DM (I2 = 47.8%). Sensitivity analysis showed that the results were relatively stable and reliable. Conclusion: our meta-analysis demonstrated that vitamin D deficiency could increase the risk of DR.

Dietary patterns were recently applied to examine the relationship between eating habits and prostate cancer (PC) risk. While the associations between PC risk with glycemic index and Mediterranean score have been reviewed, no meta-analysis is currently available on dietary patterns defined by “a posteriori” methods. Search was carried out (PubMed, Web of Science) to identify studies reporting the relationship between dietary patterns and PC risk. Relevant dietary patterns were selected and the risk estimated were calculated by a random-effect model. Multivariable-adjusted odds ratios (ORs) for a 1st-percentile increase in dietary pattern score were combined by a dose response meta-analysis. 12 observational studies were included in the meta-analysis which identified “Healthy pattern” and “Western pattern”. The Healthy pattern was not related to PC risk (OR=0.96; 95% CI: 0.88-1.04) while the Western pattern significantly increased it (OR=1.34; 95% CI: 1.08-1.65). In addition, a “Carbohydrate pattern”, identified in four articles, was positively associated with a higher PC risk (OR=1.64; 95% CI: 1.35-2.00). A significant linear trend between the Western (p=0.011) and the Carbohydrate (p=0.005) pattern and the increment of PC risk was observed. The small numbers of studies included suggest that further investigations are necessary to support these findings.

As the era of omics continues to expand, omics-based experiments have become popular in industrial biotechnology. They promise deeper biological understanding, which may be leveraged to develop novel solutions to bioprocess optimization and cell line engineering strategies. Despite this expansion, naivety about what omic data offers and how to best handle such data can challenge the extraction of actionable value. However, the value of omic experiments in biotechnology research and development can be maximized with deliberate application of omic approaches and forethought about analysis techniques. Here we describe important considerations when designing and implementing omic-based experiments, and discuss how systems biology analysis strategies can enhance efforts to obtain actionable insights in biomanufacturing.

Metabolomics is now considered to be a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants. Investigating metabolomic regulation in plants is essential to understand their adaptation, acclimation and defense response to environmental stresses through the production of numerous metabolites. Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in molecular breeding and genome editing programs to develop superior next generation crops. This review describes the recent analytical tools and techniques available to study plants metabolome, along with their significance of sample preparation using targeted and non-targeted method. Advanced analytical tools, like gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectroscopy (LC-MS), capillary electrophoresis-mass spectrometry (CE-MS), fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) and matrix-assisted laser desorption/ionization (MALDI) have speed up metabolic profiling in plants. Further, we deliver a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.

The interaction of human immunodeficiency virus with human cells is responsible for all stages of the viral life cycle, from the infection of CD4+ cells to reverse transcription, integration, and the assembly of new viral particles. To date, a large amount of OMICs data as well as information from functional genomics screenings regarding the HIV-1-host interaction has been accumulated in the literature and in public databases. We processed databases containing HIV-host interactions and found 2910 HIV-1-human protein-protein interactions, mostly related to viral group M subtype B, 137 interactions between human and HIV-1 coding and non-coding RNAs, essential for viral lifecycle and cell defense mechanisms, 232 transcriptomics, 27 proteomics, and 34 epigenomics HIV-related experiments. Numerous studies regarding network-based analysis of corresponding OMICs data have been published in recent years. We overview various types of molecular networks, which can be created using OMICs data, including HIV-human protein-protein interaction networks, co-expression networks, gene regulatory and signaling networks, and approaches for the analysis of their topology and dynamics. The network-based analysis can be used to determine the critical pathways and key proteins involved in the HIV life cycle, cellular and immune responses to infection, viral escape from host defense mechanisms, and mechanisms mediating different susceptibility of humans to infection. The proteins and pathways identified in these studies may represent a basis for developing new anti-HIV therapeutic strategies such as new small-molecule drugs preventing infection of CD4+ cells and viral replication, effective vaccines, "shock and kill" and "block and lock" approaches to cure latent infection.

Colorectal cancer (CRC) with KRAS mutation is prone to develop metachronous metastasis. However, effective measures for prediction and prevention of such clinical issue are currently unavailable. In this study, we confirmed that KRAS mutation is a risk factor for CRC metachronous metastasis through meta-analysis and public database analysis. Based on the ICGC-AGRO database, we have constructed a risk scoring model for predicting metachronous metastasis in KRAS-mutant CRC using machine learning, which was validated in public datasets. Furthermore, we discovered that KRAS inhibitors can effectively suppress the migration and invasion capabilities of high risk CRC cells by wound healing assay and transwell experiment, which was validated ex vivo and in vivo using organoids and splenic liver metastatic mouse model. Finally, RNA sequencing, RT-qPCR, and western blots have proven that KRAS inhibitors can suppress the epithelial-mesenchymal transition (EMT) and transforming growth factor beta (TGF-beta) signaling pathway in CRC. Collectively, our study suggests that KRAS inhibitors may inhibit the metastatic ability of CRC by suppressing EMT and the TGF-beta pathway, suggesting their potential for the prevention of metachronous metastasis in CRC with KRAS mutation.

Today, LLMs are not good at personalization providing recommendation. They advise physicians and financial advisors to ask professionals in respective fields for help, even having user information available. Answering questions of software professionals, LLM needs to deliver in-depth answers with codes or algorithms, whereas for professionals in other fields would need definitions and main concepts. The intent of this chapter is to make LLM answer tailored to the needs of users, taking into account available information about them. To do that, we need to generalize available information about a person like her health record, maintaining the privacy of this person. We rely on meta-learning techniques to design a LLM prompt to produce a personalization prompt to obtain a suitable relevant information. Such “meta-prompt” is produced by generalization operation applied to available documents for the user. These documents need to be de-identified so that they are sufficient for personalization on one hand and will maintain user privacy on the other hand. The second neuro-symbolic technique to support personalization is abductive reasoning, acting in parallel to LLM fine-tuning. Traditional recommendation and personalization techniques as well as modern, deep learning – based are presented, and the comparison is drawn to the proposed approach. We also share the evaluation and comparative analyses of these approaches. We consider an example for how to build personalization LLM systems coming from Langchain platform. We will explore how to construct chains to form a personalization profile for a user and apply it to user search and recommendation requests.

Purpose: Understanding how older adults perceive and interpret emotional cues in speech prosody contributes to our knowledge of cognitive aging. This study provides a systematic review with meta-analysis to investigate the extent of the decline in affective prosody recognition (APR) among older adults in terms of overall and emotion-specific performance and explore potential moderators that may cause between-study heterogeneity. Method: Incorporated into the literature search were six electronic databases, with a specific emphasis on studies comparing the APR performance of older adults with that of younger adults. This comparison was focused on basic emotions. Meta-regression analyses were executed to pinpoint potential moderators related to demographic and methodological characteristics. Results: A total of 19 studies were included in the meta-analysis, involving 560 older adults with a mean age of 69.15 years. The findings indicated a substantial negative effect size (g = －1.21). Furthermore, the magnitude of aggregated effect sizes showed a distinct valence-related recognition pattern with positive prosody exhibiting smaller effect sizes. Years of education were found to moderate the overall performance effect estimate while age and gender significantly influenced the effect estimate of happiness. Conclusions: The results confirmed a significant decline in APR ability among older adults, but this decline was unbalanced across basic emotions. Educational level emerged as a significant factor influencing APR ability. Moreover, participants with a higher mean age exhibited notably poorer performance in recognizing happy prosody. These findings underscore the need to further investigate the neurobiological mechanisms for APR decline associated with aging.

Wireless sensor networks (WSN) are mostly utilized in many applications. Indeed, WSN is composed of sensors to evaluate some physical phenomena. However, the information brought by the sensor still missed if we don't know the exact location of the event. Several localization algorithms have been proposed in order to locate the nodes in WSN. The localization algorithms are categorized into range-based and range-free techniques. The range-based techniques use either distance or time to calculate the coordinates of unknown nodes. Nevertheless, those kinds of techniques need some additional material in computation purpose. Therefore, range-based techniques present an expensive solution for positioning in WSN. Alternatively, range-free techniques may do the same task without involving additional material. But they don’t offer a high precision of localization in comparison with range-based techniques. DVHOP is the most popular range-free technique that uses the hop count method in the localization process. In this work, we propose an improvement of DVHOP localization algorithm to create three improved versions of this algorithm and we have achieved that by adopting two meta-heuristic (simulated annealing, particle swarm optimization) and FMINCON solver dedicated to the optimization in the field of WSN nodes localization. The experimental results obtained in this work show clearly the gain and the good impact of our proposition.

The high costs of cancer treatment and lack of investment in health care are significant obstacles to public health on the African continent. The objective of this study was to estimate the financial cost of treating children suffering from cancer in Africa. We conducted a systematic review and meta-analysis of expert opinions between March 2000 and March 2020. The key search terms included ‘cost’, ‘cancer’ and ‘child’; we selected articles that specifically addressed the financial costs of childhood cancer in African countries. Of the 103 articles found, 18 met the inclusion criteria. Cancer care was a heavy financial burden in most of the countries studied, although costs varied from country to country; the average expenditure on healthcare was US$1017.39 ± US$319.1 per year. In countries without a health insurance system, the highest proportion of cancer care costs, 46.6%, was indirect, whereas in countries with a cancer financing system, the direct cost of treatment was low, 53.4%. The cost of treating childhood cancer is high in Africa in relation to the standard of living of individuals residing in this region.

The capacitated team orienteering problem with time windows (CTOPTW) is a NP-hard combinatorial optimization problem. In the CTOPTW, a set of customers is given each with a profit, a demand, a service time and a time window. A homogeneous fleet of vehicles is available for serving customers and collecting their associated profits. Each vehicle is constrained by a maximum tour duration and a limited capacity. The CTOPTW is concerned with the determination of a preset number of vehicle tours that begin and end at a depot, visit each customer no more than once while satisfying the time duration, time window and vehicle capacity constraints on each tour. The objective is to maximize the total profit collected. In this study we propose an iterated local search (ILS) algorithm to deal with the CTOPTW. ILS is a single solution based meta-heuristic that successively invokes a local search procedure to explore the solution space. A perturbation operator is used to modify the current local optimum solution in order to provide a starting solution for the local search procedure. As different problems and instances have different characteristics, the success of the ILS is highly dependent on the local search procedure, the perturbation operator(s) and the perturbation strength. The basic ILS uses a single perturbation operator and the perturbation strength remains the same during the optimization process. To address these issues, we use three different perturbation operators and a varying perturbation strength which changes as the algorithm progresses. The idea is to assign a larger perturbation strength in the early stages of the search in order to focus on exploring the search space. The perturbation strength is gradually decreased so that we focus more on exploitation. The computational results show that the proposed ILS algorithm is able to generate high quality solutions on the CTOPTW benchmark instances taken from the scientific literature, demonstrating its efficiency in terms of both the solution quality and computational time. Moreover, the proposed ILS produces 21 best known results and 5 new best solutions.

Background: Conclusions of meta-analyses of clinical studies may substantially influence opinions of perspective patients and stakeholders in health care. Nineteen meta-analyses of clinical studies on the management of primary knee osteoarthritis (pkOA) with stem cells, published between January 2020 and July 2021, came to inconsistent conclusions regarding the efficacy of this treatment modality. It is possible that a separate meta-analysis based on an independent, systematic assessment of clinical studies on the management of pkOA with stem cells may reach a different conclusion. Methods: PubMed, Web of Science and the Cochrane library were systematically searched for clinical studies and meta-analyses of clinical studies on the management of pkOA with stem cells. All clinical studies and meta-analyses identified were evaluated in detail, as were all sub-analyses included in the meta-analyses. Results: The inconsistent conclusions regarding the efficacy of treating pkOA with stem cells in the 19 assessed meta-analyses were most probably based on substantial differences in literature search strategies among different authors, misconceptions about meta-analyses themselves, and misconceptions about the biology of stem cells. An independent, systematic review of the literature yielded a total of 183 studies, of which 33 were randomized clinical trials, including a total of 6860 patients with pkOA. However, it was not possible to perform a scientifically sound meta-analysis. Conclusion: Clinicians should interpret the results of the 19 assessed meta-analyses of clinical studies on the management of pkOA with stem cells with caution, and should be cautious of the conclusions drawn therein. Clinicians and researchers should strive to participate in FDA and/or EMA reviewed and approved clinical trials to provide clinically and statistically valid efficacy.

Background: At present, the treatments for patients with advanced lung cancer focus on chemotherapy, targeted therapy, immunotherapy, or a combination of multiple treatments. Purpose: The main purpose of this study is to compare the various chemotherapy-based combination therapies and find the best one for patients with advanced lung cancer. Methods: Based on database (PubMed, EMBASE and Medline) for randomized controlled trials of advanced lung cancer with combination therapy from 2008 to 2020, we searched literatures with overall survival (OS), progression-free survival (PFS), objective response rate (ORR) and adverse as outcome indicators and established a Bayesian mesh meta-analysis for multiple treatment strategies. Then, we combined the results of four outcome indicators to find out the best chemotherapy-based combination therapy strategy for patients with advanced lung cancer, further, we tried to screen out the best drugs of which were commonly used now. Results: It contained a total of 51 studies, including five combination therapies: Chemotherapy/Chemotherapy plus placebo (CT), chemotherapy plus one targeted therapy drug (CT+T), chemotherapy plus two targeted therapy drugs (CT+T+T), chemotherapy combined with immunotherapy (CT+I) or chemotherapy combined with biotherapy (CT+B). In terms of four outcome indicators, CT+I showed the best therapeutic benefits. In the comparison of immunotherapy drugs, pembrolizumab showed the best effect. Conclusion: Our results showed that, among the multiple chemotherapy-based combination therapy strategies, chemotherapy combined with immunotherapy is the best choice for patients with advanced lung cancer, and pembrolizumab combined with chemotherapy has the best effect.