Hemoglobinopathies are a group of disorders in which the hemoglobin molecule has abnormal production or structure. The hemoglobin molecules in red blood cells (RBC) are impacted by the blood disease known as sickle cell disease (SCD), and Thalassemia is one of the major monogenic disorders that reduces hemoglobin production( Kohne et al ., 2011). This disorder results in a large number of red blood cells being destroyed, leading to anemia. India bears a huge burden of hemoglobinopathies; thalassemia is the most prevalent (Mondal SK et al., 2016). A key component of thalassemia prevention is a successful screening procedure to identify Thalassemia carriers. Effective screening programs have numerous obstacles, especially in environments with limited resources. Machine learning (ML) has been used to solve technical and domain-specific problems in a variety of prognostic and diagnostic medical jobs. In this work, we aimed to identify and analyze the most common mutation of β--thalassemia and sickle cell disease from the north Indian population by employing Machine learning-based algorithms. To accurately predict the carrier state from a simple blood test, and to predict pathogenic hemoglobin variants in a group of individuals, these results demonstrate the application of integrated bioinformatics and machine learning approaches. This study contributes to the validation of the models based on data from several individuals and hemoglobinopathies.

Goat milk's medicinal properties and potential cosmetic and health benefits have prompted extensive scientific investigation into its therapeutic applications, particularly for human skin conditions like eczema and psoriasis. Genetic factors, including genes such as lactoferrin (LTF), lysozyme (LYZ), and β-casein (CSN2), play a crucial role in shaping milk composition and its effects on skin health. This review explores the utilization of genomic tools to elucidate the genomic profiles of dairy goat breeds and the medicinal properties of goat milk, particularly in addressing key skin diseases. Genetic determinants of milk composition, quality, nutritional quality, and functional properties such as the growth hormone receptor (GHR), butyrophilin (BTN1A1) and lactoglobulin (LGB) genes, facilitating targeted breeding strategies to enhance the production of bioactive compounds with dermatological relevance have been identified. Future genomic approaches should aim at exploring goat milk's immunomodulatory, antimicrobial, and antioxidant activities, offering potential applications in skin care formulations for managing inflammatory skin conditions. Furthermore, the integration of genomic data with functional studies can provide valuable insights into the therapeutic effects of goat’s milk and its derivatives in addressing skin diseases.

Introduction: Biliary Atresia (BA) is a common cause of neonatal cholestatic jaundice which, if recognized and treated early, can be life-saving for the infant. If the liver biopsy suggests the presence of BA, exploratory laparotomy is then carried out to confirm the diagnosis, along with the Kasai procedure to provide drainage to the bile secreted by the liver. The purpose of this study is to get a deep dive into all the various imaging modalities that can diagnose BA more effectively and with absolute certitude, thus helping prevent several children from a grave prognosis.Methodology: For the collection of the data, a search was done by two individuals using PubMed, Google Scholar, and Cochrane Library databases for all relevant literature. Each qualifying paper was evaluated independently by two reviewers. Each article was analyzed for the number of patients, their age, procedure modality, complexity of ethology, and incidence of the pre-decided complications. The statistical software packages RevMan (Review Manager, version 5.3), SPSS (Statistical Package for the Social Sciences, version 20), Google Sheets, and Excel in Stata 14 were used to perform the statistical analyses. The data was obtained and entered into analytic software.Results: A total of 39 studies with 3,679 subjects were selected for the study, out of which 7 studies showed sensitivity above or equal to 95%, and an astounding 14 studies showed specificity above 95%. The value of True Positive (TP) was 1280, that of True Negative (TN) was 1817, that of False Positive (FP) was 239, and that of False Negative (FN) was 343. With a confidence interval of 95%, sensitivity, specificity, and positive predictive values were calculated. The sensitivity of Ultrasonography for Biliary Atresia is 0.79, with a CI of 95% in a range of 0.77 to 0.81. The specificity of Ultrasonography for Biliary Atresia is 0.88, with a CI of 95% in a range of 0.87 to 0.90. Conclusion: Even though several radiological techniques at present help to detect BA, USG of the abdomen proves to be an effective diagnostic and a modest screening test for the detection of BA.

Multiple sequence alignments and phylogenetic trees are rich in biological information and are fundamental to research in biology. PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for diverse analyses, including (i) constructing a phylogenomic supermatrix, (ii) detecting errors in orthology inference, (iii) quantifying biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution-based screens to facilitate gene function prediction. Several PhyKIT functions that streamline multiple sequence alignment and phylogenetic processing—such as renaming FASTA entries or tree tips—are also discussed. These protocols demonstrate how simple command-line operations in the unified framework of PhyKIT facilitate diverse phylogenomic data analysis and processing, from supermatrix construction and diagnosis to gene function prediction.

Fever control is essential in patients with severe traumatic brain injury (TBI). The efficacy of therapeutic hypothermia (TH) in severe TBI has been investigated over the last few decades; however, in contrast to experimental studies showing benefits, no evidence of efficacy has been demonstrated in clinical practice. In this review, the mechanisms and history of hypothermia were briefly outlined, while the results of major randomized controlled trials (RCTs) and meta-analyses investigating TH for adult TBI are introduced and discussed. The retrieved meta-analyses showed conflicting results, with a limited number of studies indicating benefits of TH. Some studies have shown benefits of long-term TH compared with short-term TH. Although TH is effective at lowering elevated intracranial pressure (ICP), reduced ICP does not lead to favorable outcomes. Low-quality RCTs overestimated the benefits of TH, while high-quality RCTs showed no difference or worse outcomes with TH. RCTs assessing standardized TH quality demonstrated the benefits of TH. As TBI has heterogeneous and complicated pathologies, applying a uniform treatment may not be ideal. A meta-analysis of young patients who underwent early cooling and hematoma removal showed better TH results. TH should not be abandoned, and its optimal should be advocated on an individual basis.

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

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

Background: Mental capacity is a fundamental aspect that enables patients to fully par-ticipate in various healthcare procedures. To assist healthcare professionals (HCPs) in assessing patients' capacity, especially in the mental health field, several standardized tools have been developed. These tools include the MacArthur Competence Assessment Tool for Treatment (MacCAT-T), the MacArthur Competence Assessment Tool for Clinical Research (MacCAT-CR), and the Competence Assessment Tool for Psychiatric Advance Directives (CAT-PAD). The core dimensions explored by these tools include Understanding, Appreciation, Reasoning, and Expression of a choice. Objective: This meta-analysis aimed to investigate potential differences in deci-sion-making capacity within the healthcare context among groups of patients with bi-polar disorder (BD) and schizophrenia spectrum disorder (SSD). Methods: A systematic search was conducted on Medline/Pubmed, and Scopus. Addi-tionally, Google Scholar was manually inspected, and a manual search of emerging re-views and reference lists of the retrieved papers was performed. Eligible studies were specifically cross-sectional, utilizing standardized assessment tools, and involving pa-tients diagnosed with BD and SSD. Data from the studies were independently extracted and pooled using random-effect models. Hedges g was used as a measure for outcomes. Results: Six studies were identified, with three studies using the MacCAT-CR, two studies the MacCAT-T, and one the CAT-PAD. The participants included 189 individuals with BD and 324 individuals with SSD. The meta-analysis revealed that patients with BD performed slightly better, and the difference was statistically significant, compared to patients with SSD, particularly in the domain of Appreciation (ES=0.23, 95% CI: 0.01 to 0.04, p=0.037). There was no statistically significant difference between the two groups for Understanding (ES=0.09, 95% CI: - 0.10 to 0.27, p=0.352), Reasoning (ES=0.18, 95% CI: - 0.12 to 0.47, p=0.074), and Expression of a choice (ES = 0.23, 95% CI: - 0.01 to 0.48, p=0.60). In the sensitivity analysis, furthermore, when considering only studies involving patients in symptomatic remission, the difference for Appreciation also resulted in non-significant (ES=0.21, 95% CI: -0.04 to 0.46, p=0.102). (ES=0.21, 95% CI: -0.04 to 0.46, p=0.102). Conclusions: These findings indicate that there are no significant differences between patients with BD and SSD during remission phases, while differences are minimal during acute phases. The usefulness of standardized assessment of capacity at any stage of the illness should be considered, both for diagnostic-therapeutic phases and for research and advance directives. Further studies are necessary to understand the reasons for the overlap in capacity between the two diagnostic categories compared in this study.

Adamantinomatous Craniopharyngioma (ACP) is a rare epithelial tumor located in the craniopharyngeal duct, often associated with high morbidity and a high long-term recurrence rate. ACP is predominantly diagnosed in children below the age of 15 and accounts for a majority of Craniopharyngioma cases in the United States. It is most commonly caused by a mutation in exon 3 of the CTNNB1 gene, which promotes overaccumulation of β-Catenin in the WNT pathway. As β-Catenin accumulates, it over-activates the transcription factor, causing an over-transcription of WNT proteins and uncontrolled cell growth. Current methods of treatment for ACP are centered around surgical intervention and radiotherapy, including gross-total resection (GTR), subtotal resection (STR), and a combination of subtotal resection and adjuvant radiotherapy (STR+XTR). These methods of treatment are associated with high risk due to the proximity of ACP to critical structures near the craniopharyngeal duct. High recurrence rates and morbidity are closely associated with current methods of treatment and other methods have yet to be attempted in craniopharyngioma. This review will explore two possible methods of non-surgical and non-radiological therapeutic interventions. The use of RNAi therapy and CRISPR may provide insight and be a potential way to treat ACP with increased quality of life and decreased recurrence rates.

With the inclusion of Internet Gaming Disorder (IGD) in both the DSM-5 and ICD-11, understanding the prevalence and diagnostic discrepancies is crucial for developing appropriate interventions. This study presents a meta-analysis of the prevalence of IGD based on two diagnostic criteria. We systematically searched PubMed, Web of Science databases. 17 studies were included in the final analysis, The analysis incorporated studies employing the DSM-5 and ICD-11 criteria and focused on the impact of various factors, including study location, sample size, and quality score, on the reported prevalence rates using a random-effects model. Heterogeneity and publication bias were analyzed using an I2 test and Galbraith plots , The prevalence of IGD varied among the selected studies, with a general pooled prevalence of 5% (95% CI: 3%–7%). Subgroup analysis indicated that the prevalence rates of IGD (DSM-5 criteria) and GD (ICD-11 criteria) do not show significant differences. DSM-5-based scales yielded varied results, while heterogeneity among the studies was high (I2 = 98.50). In contrast, ICD-11-based scales produced more consistent and less variable findings. Our findings highlight that assessment scales, not diagnostic criteria, impact IGD prevalence. This underscores the importance of adopting standardized methodologies to guide public health interventions. However, given the limited research based on ICD-11 diagnostic criteria, further investigation is necessary to determine the variations in prevalence rates of IGD under different diagnostic standards.

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.

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.

Psoriasis is a lifelong, systemic, immune mediated inflammatory skin condition, affecting 1-3% of the world’s population, with an impact on quality of life similar to diseases like cancer or diabetes. Genetics are the single largest risk factor in psoriasis, with GWAS studies showing that many psoriasis risk genes lie along the IL23/Th17 axis. Potential psoriasis risk genes determined through GWAS can be annotated and characterised using functional genomics, allowing the identification of novel drug targets and the repurposing of existing drugs. The pathogenesis of psoriasis is complex and focusing on the IL23/Th17 axis can provide insight into key cell types, cytokines and intracellular signaling pathways involved. Examination of currently available biological treatments, time to relapse post drug withdrawal and rates of drug primary/secondary drug failure show the need for greater understanding of the underlying genetic mechanisms of psoriasis and how they can impact treatment. This could allow for patient stratification towards the treatment most likely reduce dis-ease burden for the longest period possible.

Recently, there has been considerable research on deepfake detection. However, most existing methods face challenges in adapting to the advancements in new generative models within unknown domains. In addition, the emergence of new generative models capable of producing and editing high-quality images, such as Diffusion, Consistency, and LCM, poses a challenge for traditional deepfake training models. These advancements highlight the need for adapting and evolving existing deepfake detection techniques to effectively counter the threats posed by sophisticated image manipulation technologies. In this paper, our objective is to detect deepfake videos in unknown domains using unlabeled data. Specifically, our proposed approach employs Meta Pseudo Labels (MPL) with Supervised Contrastive Learning, so-called SupCon-MPL, allowing the model to be trained on unlabeled images. MPL involves the simultaneous training of both a Teacher model and a Student model, where the Teacher model generates Pseudo Labels utilized to train the Student model. This method aims to enhance the adaptability and robustness of deepfake detection systems against emerging unknown domains. Supervised Contrastive Learning utilizes labels to compare samples within similar classes more intensively, while encouraging greater distinction from samples in dissimilar classes. This facilitates the learning of features in a diverse set of deepfake images by the model, consequently contributing to the performance of deepfake detection in unknown domains. When utilizing the ResNet50 model as the backbone, SupCon-MPL exhibited an improvement of 1.58% in accuracy compared to traditional MPL in known domain detection. Moreover, in the same generation of unknown domain detection, there was a 1.32% accuracy enhancement, while in the detection of post-generation unknown domains, there was an 8.74% increase in accuracy.

Precision medicine (PM), also termed stratified, individualised, targeted or personalised medicine, embraces a rapidly expanding area of research, knowledge, and practice. It brings together two emerging health technologies to deliver better individualised care: the many “-omics” arising from increased capacity to understand the human genome; and “big data” and data analytics including Artificial Intelligence (AI). PM has the potential to transform an individual’s health, moving from population-based disease prevention to more personalised management. There is however a tension between the two, with a real risk that this will exacerbate health inequalities and divert funds and attention from basic healthcare requirements leading to worse health outcomes for many. All areas of medicine should consider how this will affect their practice, with PM now strongly encouraged and supported by government initiatives and research funding. In this review we discuss examples of PM in current practice and its emerging applications in primary care, such as clinical prediction tools that incorporate genomic markers and pharmacogenomic testing. We look towards potential future applications and consider some key questions for PM including evidence of real-world impact, its affordability, the risk of exacerbating health inequalities, and the computational and storage challenges of applying PM technologies at scale.

This comprehensive review traces the transformative journey of genomic mapping, ushering in the era of "Genomic Atlas 2.0," characterized by advanced strategies and cutting-edge technologies. Beginning with a historical overview, it highlights the evolution from early linkage analysis to the current landscape shaped by high-throughput sequencing. Key breakthroughs are emphasized, showcasing the pivotal role of platforms such as Illumina and Oxford Nanopore in accelerating the identification of genetic variations. Long-read sequencing technologies, including PacBio and Oxford Nanopore, are explored as transformative elements overcoming limitations associated with short-read sequencing. The review delves into spatial genomics and chromatin conformation capture techniques, revealing the three-dimensional intricacies of the genome, with a particular focus on the revolutionary impact of Hi-C in understanding chromatin interactions. CRISPR technologies emerge as indispensable tools in Genomic Atlas 2.0, enabling targeted genome editing and the generation of precise genetic models. Functional genomics screens, utilizing RNA interference and CRISPR-based techniques, are discussed for their scalable precision in deciphering genome functions. Navigating challenges, the review addresses complexities in data integration and ethical considerations, offering strategies to ensure the robustness and ethical conduct of genetic mapping. Looking optimistically towards the future, it explores opportunities such as improved sequencing accuracy and novel applications of CRISPR technologies. Envisioning the expansion of genomics into personalized medicine, agriculture, and conservation biology, the review serves as a guiding resource for researchers, scientists, and students navigating the intricate terrain of Genomic Atlas 2.0.

The exploration of three-dimensional (3D) DNA structures marks a pivotal shift in genomics, offering unprecedented insights into the intricacies of cellular regulation, disease genesis, and the potential for novel diagnostic and therapeutic strategies. This study delves into the dynamic nature of 3D genome organization, investigating how these structures influence cellular functions in response to environmental changes and over time. Through a combination of real-time imaging and advanced computational models, we aim to unravel the complex interplay between 3D DNA structures, non-coding RNAs, and chromatin organization, and their collective impact on gene expression and cellular differentiation. A significant focus is placed on understanding the role of 3D DNA structures in the development and progression of genetic disorders. By employing comprehensive genomic and epigenomic profiling, this research seeks to identify structural aberrations linked to diseases, paving the way for the development of targeted diagnostics and therapies. Additionally, the study explores the potential of genome editing technologies, such as CRISPR-Cas systems, in correcting these structural abnormalities, while also addressing the ethical, legal, and social implications (ELSI) of such interventions. Integrating data from various genomic analyses, we propose the development of advanced computational models to predict the effects of 3D DNA structures on gene expression and cellular function. This integrative approach not only promises to enhance our understanding of genomic regulation but also sets the stage for groundbreaking advances in genomics-based diagnostics and therapeutics. The findings of this study have the potential to revolutionize our approach to treating genetic disorders, offering a new frontier in personalized medicine.

Wastewater-based epidemiology (WBE) has emerged as a key method for continuous monitoring of COVID-19 prevalence including circulating SARS-CoV-2 lineages. WBE addresses limitations of traditional clinical COVID-19 surveillance such as clinical test availability, fluctuating testing rates and increased reliance on rapid antigen tests. Our study in Perth, Western Australia, found a significant positive correlation between SARS-CoV-2 concentrations in wastewater and clinical PCR positivity rates (rs = 0.772; p < 0.001) over an 18-month period that included four successive COVID-19 waves. A strong positive correlation was apparent between the proportions of SARS-CoV-2 lineages in wastewater and clinical cases within the same region (rs = 0.728; p < 0.001), including earlier detection of Omicron and recombinant lineages in wastewater before clinical case confirmation. The successful integration of WBE with healthcare data underscores its critical role in enhancing public health decision-making and pandemic management. This approach not only demonstrates the value of WBE in current global health surveillance efforts but also highlights the potential of WBE to address future public health challenges, as a comprehensive disease monitoring and response approach.

This review article offers an in-depth look at DNA, its discovery, structure, functions, and the significant role it plays in modern biomedical research. It begins by revisiting the landmark discovery of the DNA double helix by scientists Watson and Crick, a structure resembling a twisted ladder that forms the blueprint of life. The review explains the basic processes of DNA replication (copying DNA), transcription (converting DNA to RNA), and translation (turning RNA into proteins), which are fundamental to understanding how genetic information is passed on and used by living organisms. The article then explores gene regulation and epigenetics, which involve how genes are turned on or off and how environmental factors can affect gene expression without changing the DNA sequence itself. It examines how DNA interacts with various proteins and modifiers, which play crucial roles in these processes. A major focus is on the advancements in DNA sequencing technologies. From the initial Sanger sequencing method, which was labor-intensive and time-consuming, to the highly efficient next-generation sequencing (NGS) and the latest single-molecule sequencing techniques, the review covers how these technologies have revolutionized genomics and personalized medicine. It also highlights the importance of computational genomics and bioinformatics, fields that deal with analyzing and interpreting the vast amounts of data generated by DNA sequencing. The review discusses DNA's crucial role in understanding human diseases. It covers DNA-based research in cancer, rare genetic disorders, infectious diseases, and pharmacogenomics (how genes affect a person's response to drugs). It emphasizes studies that have led to new ways of diagnosing and treating diseases. The article looks at the future of DNA research. It talks about emerging technologies like CRISPR-Cas9, a revolutionary gene-editing tool that allows scientists to modify DNA with high precision. Synthetic biology, an interdisciplinary field that combines biology and engineering for designing and constructing new biological parts and systems, is also discussed. Furthermore, DNA nanotechnology, which involves designing DNA molecules for technological uses, is explored. Finally, the review addresses ethical issues in DNA research, such as privacy concerns and debates over genome editing.

Simple Summary: The distribution of typical bacterial redox enzymes such as pyruvate-ferredoxin oxidoreductase (PFOR) in protozoa remains interestingly puzzling. Previous studies have demonstrated diverse cellular localizations of PFOR in some amitochondriate anaerobic protozoa. PFOR is of particular pharmacological importance because it catalyzes the reductive bio-activation of nitro-based prodrugs to cytotoxic radical metabolites. Metronidazole was developed primarily as an antiprotozoal agent against infections caused by Trichomonas vaginalis. However, its antimicrobial spectrum was subsequently expanded to cover anaerobic bacterial infections. It has been shown that mutations in the genes encoding PFOR result in inherent resistance of PFOR-possessing anaerobic protozoa and bacteria to nitro-based prodrugs. Deciphering the evolutionary history of PFOR is crucial in deepening our understanding of the evolution of anaerobic pathogens and unfold new approaches for drug discovery and targeting in pathogen chemotherapy. Abstract: The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative bioinformatics approaches to test the hypothesis that PFOR was most likely acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other genes that were putatively acquired using proteome-wide and gene expression analyses. A plausible explanation for the patchy occurrence of PFOR in protozoa is based on the hypothesis that bacteria are potential sources of genes that enhance optimal adaptation of protozoa in hostile environments. The exclusively expressed proteins obtained from Entamoeba histolytica and the putative gene donor, Desulfovibrio vulgaris, showed an over-expression of eleven genes involved in intermediary metabolism. If these results can be reproduced in other PFOR-possessing protozoa, it would provide a more validated evidence to support the horizontal transfer of pfor from bacteria.

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.

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

Diagnosis of neonatal sepsis is difficult as signs and symptoms are nonspecific. Interleukin-6 (IL-6) is a promising marker for neonatal sepsis. We aimed to test the accuracy of IL-6 in term and preterm infants after 72 hours of life (late-onset sepsis-LOS). We searched for IL-6 diagnostic accuracy studies between 1990 and 2020 using the PubMed database. Study selection was performed. The range of reported IL-6 sensitivities and specificities was 68% to 100% and 28% to 100%, respectively, the median values were 85.7% and 82% from 15 studies including 1306 infants. Subgroup analysis was performed. Sensitivity (87% vs 82%), but not specificity (both 86%), was better in preterm infants than in preterm and term infants. Early sample collection had the highest sensitivity (84%), but the lowest specificity (86%). To assess quality we used a STARD checklist adapted for septic neonates. Limitation of this review include the heterogeneous group of studies on the one side and the small number of studies on the other side that analyzed different combinations of biomarker. We concluded that IL-6 had a good performance especially in the preterm infant population and best results are achieved by measurements at the time of LOS suspicion.

This review provides an overview of advancements in plant genomics, emphasizing key stages in genomics projects and addressing associated challenges. Long read sequencing enables the cost-effective sequencing of plant DNA and assembly of highly continuous genome sequences - often even separating haplophases. Incorporating external hints, such as cDNA sequences from RNA-seq or full length cDNA sequencing, enhances the identification of gene models. While these steps enable high-throughput exploration of numerous plant genomes, a significant bottleneck lies in elucidating gene functions. The classical approach based on wet lab methods is impractical when dealing with thousands of genes in a new genome sequence. To overcome this challenge, computational tools harnessing existing information for cross species knowledge transfer are essential for expediting the functional annotation process. In support of researchers entering the field of plant genomics, a collection of recommended tools has been curated and is accessible at https://github.com/bpucker/ToolOverview.

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.

Trimeresurus albolabris, also known as the white-lipped pit viper or white-lipped tree viper, is a highly venomous snake distributed across Southeast Asia and the cause of many snakebite cases. In this study, we report the first whole genome assembly of T. albolabris obtained with next-generation sequencing from a specimen collected in Mengzi, Yunnan, China. After genome sequencing and assembly, the genome of this male T. albolabris individual was 1.51 Gb in length and included 38.42% repeat-element content. Using this genome, 21,695 genes were identified, and 99.17% of genes could be annotated using gene functional databases. Our genome assembly and annotation process was validated using a phylogenetic tree, which included six species and focused on single-copy genes of nuclear genomes. This research will contribute to future studies on Trimeresurus biology and the genetic basis of snake venom.

Over recent years, the swine industry has witnessed the withdrawal of antibiotics and continuous regulation of zinc and copper oxides in the early-life nutrition of piglets. Due to this development, alternative ingredients or additives from plant sources have been tremendously explored. Therefore, this study's objective was to evaluate the effect of dietary supplementation with tannins on weaned piglets’ growth performance, serum antioxidant capacity, and immune status using a meta-analysis approach. With only the inclusion of non-challenged weaned piglets, a total of 16 studies with parameters of interest were deemed eligible after a two-step screening process following a comprehensive literature search in the scientific databases of Web of Science, Scopus, ScienceDirect, PubMed, and Google Scholar. Two main categories of data, including the study’s characteristics and response variables (growth performance, serum antioxidant, and immune indices), were extracted. Applying the random-effects models, Hedges’ g effect size of supplementation with tannins was calculated using the R software to determine the standardized mean difference (SMD) at a 95% confidence interval. Sub-group analysis and meta-regression further explored heterogeneity (PSMD 0.05, I2 50%, n ≥10). Supplementation with tannin reduced average daily gain (p = 0.20) and feed conversion ratio (p 0.01); however, it increased average daily feed intake (p = 0.07) and final body weight (p 0.01). Meta-regression models indicated that tannin dosage and supplementation duration were directly associated with tannins' effectiveness on productive performance. In the serum, the concentration of glutathione peroxidase, superoxide dismutase, and total antioxidant capacity were elevated (p 0.01) in response to tannins supplementation, while malondialdehydes was reduced (p 0.01). Likewise, decreased immunoglobin A (p = 0.47) and increased immunoglobin M and G levels (p 0.01) were detected. In conclusion, dietary supplementation with tannins, particularly with chestnut and grape seed proanthocyanidins, increases the productivity of weaned piglets. At the same time, it is a possible nutritional strategy to mitigate oxidative stress and stimulate gut health. Thus, supplementing chestnut and grape seed proanthocyanidin tannins in the early phase of swine production could be used to alleviate the incidence of diarrhea.

Novel genetic risk markers have helped to advance the field of cardiovascular epidemiology and refine our current understanding and risk stratification paradigms. Discovery and analysis of variants can help to tailor prognostication and management. However, populations underrepresented in cardiovascular epidemiology and cardiogenetics research may experience inequities in care if prediction tools are not applicable to them clinically. Therefore, the purpose of this article is to outline the barriers that underrepresented populations can face in participating in genetics research, describe current efforts to diversify cardiogenetics research, and outline strategies that researchers in cardiovascular epidemiology can implement to include underrepresented populations. Mistrust, a lack of diverse research teams, improper use of sensitive biodata, and constraints of genetic analyses are all barriers for including diverse populations in genetics studies. Current work is beginning to address the paucity of ethnically diverse genetics research and has already begun to shed light on the potential benefits of including underrepresented and diverse populations. Reducing barriers for individuals, utilizing community-driven research processes, adopting novel recruitment strategies, and pushing for organizational support for diverse genetics research are key steps that clinicians and researchers can take to develop equitable risk stratification tools and improve patient care.

The use of video in education has become ubiquitous as technological developments have markedly improved the ability and facility to create, deliver and view videos. The concomitant pedagogical transformation has created a sense of urgency regarding how video may be used to advance learning. Initial reviews have suggested only limited potential for the use of video in higher education. More recently, a systematic review of studies on the effect of video use on learning in higher education, published in the prestigious Review of Educational Research, found, overall, effects to be positive. In the present paper we critique this study and provide some needed clarity to the state of research on learning via video in higher education. We reveal significant gaps in the study methodology and write-up and use a cognitive processing lens to critically assess and reanalyse study data. We found results of this study to be only applicable to learning requiring lower-level cognitive processing and conclude, consistent with prior research, learning benefits remain limited.

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.

Malaxidinae is one of the confusing groups with classification in Orchidaceae. Previous phylogenetic analysis reveals that the relationships among the taxa in Malaxidinae have not yet been reliably established using a few plastome regions or nuclear ribosomal internal transcribed spacer (nrITS). In the present study, the complete plastomes of Oberonia integerrima and Crepidium purpureum were assembled using high-throughput sequencing. Combined with publicly available complete plastome data, this resulted in a data set of 19 plastomes, including 17 species of Malaxidinae. The plastome feature and phylogenetic relationship were compared and analyzed. The results showed that: (1) The plastomes of Malaxidinae species possessed the quadripartite structure of typical angiosperms, with sizes ranging from 142,996 bp to 158,787 bp and encoding from 125 to 133 genes. The ndh genes were lost or pseudogenized with varying degrees in six species. An unusal inversion was detected in the Large Single-Copy region (LSC) of Oberonioides microtatantha. (2) A total of 8 regions, including ycf1, matK, rps16, rpl32, ccsA-ndhD, clpP-psbB, trn-FGAA-ndhJ, and trnSGCU-trnGUCC, were identified as mutational hotspots. (3) Based on complete plastomes, 68 protein-coding genes and 51 intergenic regions, respectively, the phylogenetic analyses resolved genera-level relationships in this subtribe with strong support. The Liparis was supported as polyphyletic.

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.

Radiotherapy, also known as radiation therapy, is a treatment modality based on the use of high energy rays or radioactive substances, to damage tumoral cells and halt their growth and division. It is an effective tool for treating cancer of different kinds for more than 100 years with remarkable outcomes for cancer patients. This technique is characterised by notable technological innovations and methodologies, enhanced precision and effectiveness. Initially, precision and efficacy of radiotherapy are improved by technological advancements, such as the development of linear accelerators and brachytherapy. As a result, Radiotherapy has transformed the prognosis for cancer patients enhancing survival rates and improving quality of life. Also, it offers targeted and personalized treatment with advancements in imaging techniques such as Intensity-Modulated Radiation Therapy (IMRT) and Stereotactic Body Radiation Therapy (SBRT) and innovations like Image-Guided Radiation Therapy (IGRT), Adaptive Radiotherapy (ART) and Artificial Intelligence (AI). Additionally, techniques like proton therapy result in reduced side effects and collateral damage. Although, among the challenges and future perspectives we note the issue of affordability and accessibility. Ongoing research into immunotherapy and nanotechnology and their synergy with radiation therapy shows potential for further improving treatment outcomes. In conclusion, the evolution of radiotherapy has been a transformative journey, reshaping the prognosis and outcomes for cancer patients.

About half of the world's population is at risk of dengue infection. Epidemics of dengue fever caused an increased risk of morbidity and mortality in recent years, which led to the exploration of vaccines as a preventive measure. This systematic review and meta-analysis aimed to evaluate the efficacy, immune response, and safety of dengue vaccines in children by analyzing clinical trials. The review followed standard procedures for data extraction using PRISMA guidelines, and searching multiple databases including PubMed, CINAHL, Medline, Health Source, Science Direct, and Academic Search Premiere. Eligible studies involved children (0-17 years). Cochrane Collaboration criteria were used for quality assessment, with thematic data synthesis and meta-analysis. Among 38 selected studies, dengue vaccines showed varying efficacy against all four serotypes. CYD-TDV (Dengvaxia®), and Tekade (TAK-003) vaccines demonstrated strong protection against severe dengue, but their long-term efficacy varied. Vaccines triggered satisfactory immune responses, notably in those previously exposed to dengue. Safety profiles were mostly favorable, noting mild adverse events post-vaccination. Meta-analysis supported vaccine efficacy and immune response, but safety concerns warrant further exploration. In conclusion, dengue vaccines demonstrated promising efficacy and immune response, particularly against severe manifestations.

Few-shot fine-grained image classification (FSFGIC) methods refer to machine learning methods which aim to classify images (e.g., bird species, flowers, and airplanes) belonging to subordinate object categories of the same entry-level category with only a few samples. It is worth to note that feature representation learning is used not only to represent training samples, but also to construct classifiers for performing various FSFGIC tasks. In this paper, starting from the definition of FSFGIC, a taxonomy of feature representation learning for FSFGIC is proposed. According to this taxonomy, we discuss key issues on FSFGIC (including data augmentation, local or/and global deep feature representation learning, class representation learning, and task specific feature representation learning). The existing popular datasets and evaluation standards are introduced. Furthermore, a novel classification performance evaluation mechanism is designed with a 0.95 confidence interval for judging whether the classification accuracy obtained by a certain specified method is good or bad. Moreover, current challenges and future trends of feature representation learning on FSFGIC are elaborated.

The fungal order Entomophthorales in the Zoopagomycotina includes many fungal pathogens of arthropods. This review explores five genera in the Erynioideae subfamily, namely Erynia, Furia, Pandora, Strongwellsea, and Zoophthora. This is the largest subfamily in the Entomophthorales including 125 described species. The species diversity, global distribution, and host range of this subfamily are summarized, revealing that relatively few taxa are geographically widespread, and few have broad host ranges, contrasting with a large number of species with single reports, from one location and one host species. The insect orders infected by the greatest numbers of species are the Diptera and Hemiptera. Across the subfamily relatively few species have been cultivated in vitro and those that have require more specialized media than any fungi. Given their potential to attack arthropods and in the fungal evolutionary tree, which species might be adopted for biological control purposes or biotechnological innovations are highlighted. Current challenges in the implementation of these species in biotechnology include the limited ability or difficulty in culturing many in vitro, a correlated paucity in genomic resources, and considerations regarding the host ranges of different species.

The Swiss Personalized Health Network (SPHN) is a Swiss research infrastructure initiative that aims to facilitate the exchange of health-related data in a FAIR manner. The SPHN Dataset and SPHN RDF Schema form an essential part of the SPHN Semantic Interoperability Framework, which currently covers mostly clinical routine data. To facilitate the integration of omics data produced by the SPHN National Data Streams, a genomics extension was developed. This was done in close collaboration with clinicians, researchers, bioinformaticians, and data managers, from Swiss university hospitals, academic research groups and the omics platforms. Here, we present the genomics extension of the SPHN RDF Schema, which can be used to semantically describe genomics experiments and covers both clinical and research domains. The schema centers around the general omics process flow, with concepts that denote the individual steps, such as sample processing, assay, and data processing. Genomics-specific specializations are provided, such as library preparation, sequencing assay, and sequencing analysis. The schema also facilitates in capturing other important omics metadata, such as information about the sequencing instrument, standard operating procedure, and quality control metrics. The extension aligns with existing semantic data models and reuses common biomedical vocabularies, such as EDAM, OBI and FAIR genomes, as value sets, thereby facilitating semantic interoperability. It will be used to FAIRify data that is produced within the Swiss network and to facilitate sharing this data as one knowledge graph for reuse among its participants.

The pro-protein convertase FURIN (PCSK3) is implicated in a wide range of normal and pathological biological processes such as infectious disease, cancer and cardiovascular disease. Previously, we performed a systemic inhibition of FURIN in a mouse model of atherosclerosis and demonstrated significant plaque reduction and alterations in macrophage function. To understand the cellular mechanisms affected by FURIN inhibition in myeloid cells, we optimized a CRISPR-mediated gene deletion protocol for successfully deriving hemizygous (HZ) and nullizygous (NZ) FURIN knockout clones in U937 monocytic cells using lipotransfection based procedures and a dual guide RNA delivery strategy. We observed differences in monocyte and macrophage functions involving phagocytosis, lipid accumulation, cell migration, inflammatory gene expression, cytokine release patterns, secreted proteomics (cytokines) and whole-genome transcriptomics between wild-type, HZ and NZ FURIN clones. These studies provide a mechanistic basis on the possible roles of myeloid cell FURIN in cardiovascular disorders.

Sarcomas are a heterogenous group of tumours that commonly carry poor prognosis with limited therapeutic options. Adolescents and young adults (AYA) with sarcoma are a unique and under-studied patient population that have only achieved modest survival gains compared to other groups. We present our institutional experience of AYA with sarcoma who underwent comprehensive molecular profiling (CMP) using either large-panel targeted DNA sequencing or whole genome and transcriptome sequencing and evaluated the feasibility and clinical impact of this approach. Genomic variants detected were determined to be clinically relevant and actionable following the Molecular Tumour Board evaluation. Clinicians provided feedback regarding the utility of testing three months after reporting. Twenty-five patients who were recruited for CMP are included in this analysis. The median time from consent to final molecular report was 45 days (interquartile range 37-57). Potentially actionable variants were detected for 14 patients (56%) and new treatment recommendations were identified for 12 patients (48%). Pathogenic germline variants were identified in three patients (12%), and one patient had a change of diagnosis. Implementation for CMP for AYA with sarcoma is clinically valuable, feasible and should be increasingly integrated into routine clinical practice as technologies and turnaround times continue to improve.

In the modern era of genomic research, the scientific community is witnessing an explosive growth in the volume of published findings. While this abundance of data offers invaluable insights, it also places a pressing responsibility on genetic professionals and researchers to stay informed about the latest findings and their clinical significance. Genomic variant interpretation is currently facing a challenge in identifying the most up-to-date and relevant scientific papers, while also extracting meaningful information to accelerate the process from clinical assessment to reporting. Computer-aided literature search and summarization can play a pivotal role in this context. By synthesizing complex genomic findings into concise, interpretable summaries, this approach facilitates the translation of extensive genomic datasets into clinically relevant insights. To bridge this gap, we present VarChat (varchat.engenome.com), an innovative tool based on generative AI, developed to find and summarize the fragmented scientific literature associated with genomic variants into brief yet informative texts.VarChat provides users with a concise description of specific genetic variants, detailing their impact on related proteins and possible effects on human health. Additionally, VarChat offers direct links to related scientific trustable sources, and encourages deeper research. Availability: VarChat is freely available at varchat.engenome.com

Pea (Pisum sativum L.), like most legumes, forms mutualistic symbioses with nodule bacteria and arbuscular mycorrhizal (AM) fungi. The positive effect of inoculation is partially determined by the plant genotype, thus, pea varieties with high and low symbiotic responsivity have been described, but the molecular genetic basis of this trait remains unknown. Here, we compare the symbiotically responsive breeding line ‘Triumph’ of grain pea with its parental cultivars ‘Vendevil’ (a donor of high symbiotic responsivity) and ‘Classic’ (a donor of agriculturally valuable traits) using genome and transcriptome sequencing. We show that ‘Triumph’ inherited one-fourth of its genome from ‘Vendevil’, including the genes related to AM and nodule formation, and reveal that under combined inoculation with nodule bacteria and AM fungi, ‘Triumph’ and ‘Vendevil’, in contrast to ‘Classic’, demonstrate similar up-regulation of the genes related to solute transport, hormonal regulation and flavonoid biosynthesis in their roots. We also identify the gene PsGLP2, whose expression pattern distinguishing ‘Triumph’ and ‘Vendevil’ from ‘Classic’ correlates with difference within the promoter region sequence, making it a promising marker for the symbiotic responsivity trait. The results of the study may be helpful for future molecular breeding programs aimed at creation of symbiotically responsive cultivars of pea.

Peanuts, owing to their composition of complex carbohydrates, plant protein, unsaturated fatty acids, and essential minerals (magnesium, iron, zinc, and potassium), hold significant potential as a vital component of the human diet. Additionally, their low water requirements and nitrogen fixation capacity make them an appropriate choice for cultivation in adverse environmental conditions. The germination ability of seeds profoundly impacts the final yield of the crop, assessing seed viability of extreme importance. Conventional methods for assessing seed viability and germination are both time-consuming and costly. To address these challenges, this study investigated Visible-Near Infrared Spectroscopy (Vis/NIR) in the wavelength range of 500-1030 nm as a non-destructive and rapid method to determine the viability of two varieties of peanut seeds: North Carolina-2 (NC-2) and Spanish flower (Florispan). The study subjected the seeds to three levels of artificial aging through heat treatment, involving incubation in a controlled environment at a relative humidity of 85% and a temperature of 50°C over 24-hour intervals. The absorbance spectra noise was significantly mitigated and corrected to a large extent by combining the Savitzky-Golay (SG) and Multiplicative Scatter Correction (MSC) methods. To identify the optimal wavelengths for seed viability assessment, a range of meta-heuristic algorithms were employed, including world competitive contest (WCC), league championship algorithm (LCA), Genetics (GA), Particle Swarm Optimization (PSO), Ant Colony Optimization (ACO), imperialist competitive algorithm (ICA), learning automata (LA), heat transfer optimization (HTS), forest optimization (FOA), discrete symbiotic organisms search (DSOS), and cuckoo optimization (CUK). These algorithms offer powerful optimization capabilities for effectively extracting relevant wavelength information from spectral data. Results revealed that all the algorithms demonstrated remarkable accuracy in predicting the allometric coefficient of seeds, achieving correlation coefficients exceeding 0.985 and errors below 0.0036, respectively. In terms of execution time, the ICA (2.3635 seconds) and LCA (44.9389 seconds) algorithms exhibited the most and least efficient performance, respectively. Conversely, the FOA and the LCA algorithms excelled in identifying the least number of optimal wavelengths (10 wavelengths). Subsequently, the seeds were classified based on the wavelengths selected by the FOA (10 wavelengths) and (DSOS (16 wavelengths) methods, in conjunction with logistic regression (LR), decision tree (DT), Multilayer Perceptron (MP), support vector machine (SVM), k-nearest neighbor (K-NN), and NaiveBayes (NB) classifiers. The DSOS-DT and FOA-MP methods demonstrated the highest accuracy, yielding values of 0.993 and 0.983, respectively. Conversely, the DSOS-LR and DSOS-KNN methods obtained the lowest accuracy, with values of 0.958 and 0.961, respectively. Overall, our findings demonstrated that Vis/NIR spectroscopy, coupled with variable selection algorithms and learning methods, presents a suitable and non-destructive approach for detecting seed viability.

In our article in Genome Biology Ecology six years ago, one complete plastid genome of Belian was assembled for comparative analyses of the plastomes in Lauraceae. However, Ariati et al. (2023) concluded that our sequenced Belian individual could be located in the clade of Myristicaceae instead of that of Lauraceae. Here, we performed re-analyses of additional two Belian plastomes, along with 42 plastomes from plants spanning ten families of the Magnoliids. The plastomes of the three Belian individuals range from 157,535 to 157,577 bp in length. Comparative genomic analysis revealed 170 mutation sites in their plastomes, which include 111 substitutions, 53 indels, and six microinversions. Phylogeny was reconstructed using maximum likelihood and Bayesian approaches for 44 magnoliids species indicated that our three Belian individuals are nested among the species in the family Lauraceae rather than Myristicaceae.

Chronic Low Back Pain (CLBP), defined as pain persisting for at least 12 weeks, is a significant public health issue, with prevalence intensifying due to an ageing global population, amassing approximately 619 million cases in 2020 and projected to escalate to 843 million by 2050. Given the multitude of therapeutic modalities available for CLBP, this research sought to ascertain their respective efficacies in ameliorating pain and disability. We specifically scrutinized Multidisciplinary Biopsychosocial Rehabilitation (MBR) among adults enduring non-specific low back pain for over 12 weeks, excluding acute pain conditions and pre-study surgical interventions. MBR is an approach encompassing various modalities, including exercise, behavioral therapies, educational programs, and work conditioning aspects, necessitating a comprehensive Network Meta-Analysis (NMA) to fully grasp the extensive scope of its impact. The constructed network comprised diverse MBR modalities (behavioral, educational, and work conditioning) alongside exercise therapy (ET), minimal intervention, and usual care, serving as controls with pain and disability as outcomes. Through the analysis of 4,619 initially identified studies, 93 were included, encompassing a total of 8,059 participants. The NMA conducted substantiated that both ET and MBR modalities were notably effective in alleviating CLBP, with education-oriented MBR emerging as the most efficacious for pain mitigation and behavior-focused MBR for disability reduction. Nevertheless, the discerned differences amongst the treatments were minimal and uncertain, highlighting that no modality was definitively superior to the others. The analysis revealed low global and local inconsistency within the network, underscoring the reliability of the observed outcomes. Given the intricate nature of CLBP, embodying various facets, our findings advocate for a combined therapeutic approach to optimize treatment efficacy. Nonetheless, the presence of high study heterogeneity and potential biases necessitates cautious interpretation of the results, prompting future research.

In China, 65 types of venomous snakes exist, with the Chinese Cobra Naja atra being prominent and a major cause of snakebites in humans. Furthermore, N. atra is a protected animal in some areas, as it has been listed as vulnerable by the International Union for Conservation of Nature. Recently, due to the medical value of snake venoms, venomics has experienced growing research interest. In particular, genomic resources are crucial for understanding the molecular mechanisms of venom production. Here, we report a highly continuous genome assembly of N. atra, based on a snake sample from Huangshan, Anhui, China. The size of this genome is 1.67 Gb, while its repeat content constitutes 37.8% of the genome. A total of 26,432 functional genes were annotated. This data provides an essential resource for studying venom production in N. atra. It may also provide guidance for the protection of this species.

Trypanosoma cruzi, the protozoan causative of Chagas disease (ChD), exhibits striking genetic and phenotypic intraspecific diversity, along with ecoepidemiological complexity. Human-pathogen interactions lead to distinct clinical presentations of ChD. In 2009, an international consensus classified T. cruzi strains into six discrete typing units (DTUs), TcI to TcVI, later including TcBat, and proposed reproducible genotyping schemes for DTU identification. This article aims to review the impact of classifying T. cruzi strains into DTUs on our understanding of biological, ecoepidemio-logical, and pathogenic aspects of T. cruzi. We will explore the likely origin of DTUs and the intrinsic characteristics of each group of strains concerning genome organization, genomics, and suscepti-bility to drugs used in ChD treatment. We will also provide an overview of the association of DTUs with mammalian reservoirs, and summarize the geographic distribution, and the clinical implica-tions, of prevalent specific DTUs in ChD patients. Throughout this review, we will emphasize the crucial roles of both parasite and human genetics in defining ChD pathogenesis and chemotherapy outcome.

To systematically assess the effect size of different methods for patients with low back pain. PubMed, Cochrane Library, Web of Science, and Google Scholar. databases were searched in January 2023. This study has been developed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement. The key search terms were: “Low back pain”, “Back pain”, “SF-36”, “VAS”, “VASP”, “Roland-Morris”, “Oswestry Disability Index”, and “conservative treatment”. The risk of bias was determined for each randomized trial using the Cochrane Risk of Bias Tool, and the methodological index for non-randomized studies (MINORS). The outcomes included SF-36 Mental, SF-36 Physical, VAS, Roland-Morris, and Oswestry Disability Index. R 4.0.5 software was used, and standardized mean difference (SMD) and 95% confidence intervals (CI) were calculated for continuous outcomes, random model. Twenty-five studies were included. Depending on the outcome being measured, the effect size of different methods in treating low back pain varies from small to large as follows: SF-36 Mental (SMD = 0.39, p &lt; 0.0001), SF-36 Physical (SMD = 0.55, p &lt; 0.0001), VAS (SMD = -0.84, p &lt; 0.0001), Roland-Morris (SMD = -0.45, p &lt; 0.0001), and Oswestry Disability Index (SMD = -0.61, p &lt; 0.0001). Our meta-analysis indicates the positive effects of applying different methods in the treatment of low back pain. PROSPERO registration number: CRD42022371282

Objectives: Accumulating evidence suggests that physical activity (PA) is an efficient intervention to maintain functional capabilities and mitigate physiological changes in the older population. However, an attempt has yet to be made to comprehensively investigate the published landscape on the subject. Methods: This study had two aims. The first aim was to perform a bibliometric analysis for two keywords, “aging” and “PA”, to analyze the research trend. Since ‘frailty’ is the most noticeable co-occurring keyword with the two keywords, the second aim was to investigate the effects of PA, particularly resistance training (RT), on frailty via meta-analysis to provide a summary of the current evidence base. Results: Bibliometric analysis revealed that the number of publications on this research topic has gradually increased, highlighting the importance of understanding the role of PA in aging. A meta-analysis found that RT had significant beneficial effects on physical frailty factors, including handgrip strength, lower limb strength, balance, gait speed, and stair climbing ability. Conclusion: These findings demonstrate that RT is an effective intervention for improving physical function in frail populations; thus it has important implications for the development of PA programs for older adults with frailty. Future research is warranted to explore the optimal dose, frequency, and duration of RT programs for older adults, as well as the potential benefits of combining RT with other forms of PA, such as aerobic or balance exercises.

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.

Prostate cancer is a highly heterogeneous disease, and mortality is mainly due to metastases, but the initial steps of metastasis have not been well characterized. We have performed integrative whole exome sequencing and transcriptome analysis of primary prostate tumor foci and corresponding lymph node metastases (LNM) from 43 patients enrolled in clinical trial. We present evidence that while there are some cases of clonally independent primary tumor foci, 87% of primary tumor foci and metastases are descended from a common ancestor. We demonstrate that genes related to oxidative phosphorylation are upregulated in LNM and in African-American patients relative to White patients. We further show that mutations in TP53, FLT4, EYA1, NCOR2, CSMD3, and PCDH15 are enriched in prostate cancer metastases. These findings were validated in a meta-analysis of 3,929 primary tumors and 2,721 metastases and reveal a pattern of molecular alterations underlying the pathology of metastatic prostate cancer. We show that LNM contain multiple subclones that are already present in primary tumor foci. We observed enrichment of mutations in several genes including understudied genes such as EYA1, CSMD3, FLT4, NCOR2, and PCDH15 and find that mutations in EYA1 and CSMD3 are associated with poor outcome in prostate cancer.

Hearing loss stands as the most prevalent sensory deficit among humans, posing a significant global health challenge. Projections indicate that by 2050, approximately 10% of the world's population will grapple with disabling hearing impairment. While approximately half of these cases have a genetic etiology, traditional interventions such as hearing aids and cochlear implants do not completely restore normal hearing. The absence of biological treatment has prompted significant efforts in recent years, with a strong focus on gene therapy to address hereditary hearing loss. Although several studies have exhibited promising recovery of common forms of genetic deafness in mouse models, existing challenges must be overcome to make gene therapy applicable in the near future. Herein, we summarize the primary gene therapy strategies employed over past years, provide an overview of the recent achievements in the preclinical studies for genetic hearing loss, and outline the current key obstacles to cochlear gene therapy.

Asymmetry plays a major role in biology at all scales. This can be seen examining the helix of DNA, the fact that the human heart is on the left side, or that most people use their right hand. A single protein such as Myosin 1D can induce helical motion in another molecule. This causes cells, organs, and even entire bodies to twist in a domino effect, causing left-right behaviour. More in general, athlete movements are often asymmetric and, during the physical rehabilita-tion after injury the asymmetry is visually discernible. Herein we review the molecular basis of movement asymmetries and report on the available knowledge on the few therapeutics inves-tigated so far such as meloxicam. From a more rehabilitative perspective, it is very important to use effective methods to control the process of resolving the injury-related movement asym-metry through the complex use of specialized exercises, measurements and gait analysis which all can provide useful information on the effectiveness of rehabilitation plans. If for each athlete the normal range of asymmetry is known, the asymmetry can be treated individually and the evolution can be monitored over time. Appropriate measures should be taken if the movement asymmetry is outside this range. In addition, genetic, physiological, and psychological factors relevant to athlete health should be considered in the process of assessing and improving exer-cise asymmetry as we also discuss in this review. The main proposal of this work is that move-ment asymmetries in athletes should be treated individually, taking into account the athlete’s genetics, physical condition, and previous injuries.

Brown-Spotted Pit viper (Protobothrops mucrosquamatus), also known as the Chinese habu, is a widespread and highly venomous snake distributed from from northeastern India to eastern China. Genomics research can help provide much insight in understanding venom components and natural selection in vipers. Here, we collected, sequenced and assembled the genome of a male P. mucrosquamatus individual from China, producing a highly continuous reference genome, with the length of 1.53 Gb and 41.18% repeat element content. From this 24,799 genes were identified, and 97.97% genes could be annotated. Nuclear genome single-copy genes phylogenetic tree including 6 species verified the validity of our genome assembly and annotation process. This research will contribute to further study on Protobothrops biology and the genetic basis of the snake venom.

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 liver is not only a digestive gland, but also an immune tissue that receives a double infusion from the hepatic artery and the hepatic portal vein. Receiving 80% of its blood supply from the intestine through the hepatic portal vein system, the liver is enriched with a large number of innate immune cells, which carry out the process of immune response by detecting pathogens entering the organism through the intestine. The intestine and liver communicate extensively through the bile ducts, portal vein and the somatic circulation, a bidirectional communication known as the intestinal-liver axis. The mammalian gut is considered an important microbial ecosystem. The interplay between the natural immune system and microbes coordinates the physiology of the whole organism, and in specific mammalian lineages, there is a dependency between the host and its associated microbes. To this end, we explored the regulatory mechanisms of natural immunity genes at the genome-wide level. Based on comparative genomics, 1473 bovine natural immunity genes were obtained by collecting the latest reports of human natural immunity genes and updated bovine genomic data for comparison, and a bovine natural immunity gene database was initially constructed to screen and match calf liver natural immunity differential genes mainly affected by the phylum Mimosoidea and the phylum Thick-walled Bacteria, and 16 differentially expressed natural immunity genes were obtained. In addition, the results of IPA analysis indicated that the upstream factor IL-2 initiated the PI3K/AKt/mTOR, mitogen-activated protein kinase (MAPK) pathway and JAK/STAT5 pathway, leading to the liver's involvement in gut microbial immune regulation.

Understanding the genetic architecture of a disease is crucial for development of valid diagnostic and therapeutic interventions. The analysis of genomic variations associated with pathological conditions is the starting point for uncovering disease-causing pathways (candidate processes). However, the complexity of intergenic and genetic-environmental interactions hinders the identification of pathogenic values of genomic changes. Furthermore, heredity, epigenetics and somatic mosaicism make the interpretation of genomic data even more sophisticated. To succeed, a variety of bioinformatic techniques are applied. Here, reviewing own and literature data, knowledge-based prioritization of genomic variations is described. Theoretical basis of the knowledge-based prioritization is given with a special regard to gene ontology, heuristics, hermeneutics (genomic hermeneutics) and analytics. Practical and methodological issues of prioritization using ontology- or pathway-based systems analysis are considered in the light of optimistic and realistic scenarios of cumulative phenotypic effects of the variome (the whole set of genomic variations in an individual or specific set of genomic variations for a phenotypic outcome). In the present communication, copy number variants (CNVs) in children with neurodevelopmental diseases are used as a practical foundation for the prioritization, inasmuch as these genome variations are systematically overlooked in the so-called NGS era. Nonetheless, it is highly likely that the prioritization is applicable to almost all types of genomic variations (e.g. chromosome abnormalities, gene mutations, functional synonymous variants etc.). The present methodology seems to be a valuable addition to current biomedical science widening the opportunities for medical genomics and genetics.

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.

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.

Histone modifications, especially H3K27 and H3K36 methylations, are crucial for epigenetic regulation and are often dysregulated in cancer. In a comprehensive analysis of 11,194 patient samples across 32 cancer types, we identified significant genomic alterations in H3K27 and H3K36 modifiers, with the most common being in KDM6B, BRPF1, KDM6A, SETD2, and NSD1. Patients with these alterations also frequently exhibited mutations in genes like TP53 and PIK3CA. Moreover, the presence of these histone modifier alterations correlated with poorer overall survival, emphasizing their potential as both oncogenic drivers and prognostic markers in various cancers.

ABSTRACTBackground: Crohn's disease (CD) is a chronic inflammatory bowel disorder with limited treatment options. Mitochondrial dysfunction has been implicated in CD pathogenesis, and mitochondrial-based interventions have emerged as a potential therapeutic avenue. This systematic review aimed to assess the efficacy of mitochondrial-based interventions in the management of CD.Methods: A systematic search of multiple databases was conducted to identify relevant studies in accordance with the PRISMA protocol. Inclusion criteria encompassed studies investigating mitochondrial-targeted interventions in CD patients. Methodological quality and risk of bias assessments were performed. Data synthesis involved both quantitative meta-analysis and qualitative narrative synthesis.Results: A total of 23 studies were included in this review, comprising randomized controlled trials, observational studies, and case reports. Mitochondrial-based interventions encompassed nutraceuticals, probiotics, exercise, and dietary modifications. However, the overall quality of evidence was moderate, primarily due to methodological limitations in some studies.Conclusion: This systematic review suggests that mitochondrial-based interventions hold promise as adjunctive therapies for CD management. They appear to contribute to clinical remission and amelioration of disease activity. Nevertheless, the moderate quality of evidence underscores the need for further well-designed clinical trials to substantiate these findings and delineate optimal intervention strategies.

Polycystic ovary syndrome (PCOS) is a prevalent condition characterized by manifestations that can influence self-image and potentially result in psychological distress; however, data from literature on sexual function (SF) in PCOS women are contradictory. We aimed to evaluate sexual dysfunction (SD) in PCOS women by carrying out a systematic review and meta-analysis, using the gold-standard assessment tool SD-diagnosis (Female Sexual Function Index:FSFI). Seven databases were analyzed until August-2023; study quality was assessed by risk of bias and Newcastle Ottawa Scale. Our analysis encompassed 25 case-control studies (9933 women). PCOS group presented significantly lower scores in arousal (MD= -0.36 CI95%-0.60;-0.11), lubrication (MD= -0.52 CI95%-0.75;-0.28), orgasm (MD= -0.39 CI95%-0.57;-0.20), satisfaction (MD= -0.32 CI95%-0.50;-0.14) and pain subdomains (MD= -0.46 CI95%-0.75;-0.16), as in overall FSFI score (MD= -2.27 CI95%-3.23;-1.31). Overweight/obese (OW/O) patients exhibited significantly higher overall FSFI than OW/O controls (MD=1.98 CI95%0.68;3.27), particularly in lubrication (MD= -0.34), orgasm (MD= -0.26) and satisfaction (MD= -0.25) subdomains. These findings offer insights regarding SD in PCOS women and emphasize the need to incorporate SF assessment into multidisciplinary care. By this way, PCOS can be also considered a gateway diagnosis to other long-term consequences. Further research should focus on controlling variables, as ethnicity, culture, religion and economic disparities.

To determine the impacts of metabolizable energy levels on the performance indices of geese and to forecast the ideal range of dietary metabolizable energy levels, this study was carried out. Literature on the effects of dietary metabolized energy level on the performance of geese was searched from CNKI, Wanfang, VIP, PubMed, Web of Science, and ScienceDirect databases from January 1, 2000, to December 31, 2022. A dose-response meta-analysis was performed by STATA (14.0), data were calculated by the robust error meta-regression model (REMR), and nonlinear dose-effect curves were plotted by the restricted cubic spline method (RCS). 29 papers were chosen from the 1,475 literatures that fit the criteria and were included in the dose-response meta-analysis. There were 6,079 geese included in the sample. The following production performance indices included average daily gain (ADG), average daily feed intake (ADFI), feed-to-gain ratio (F/G), dressed percentage, percentage of half-eviscerated yield, percentage of eviscerated yield, percentage of breast muscle, percentage of leg muscle and percentage of abdominal fat. The Egger test assessed publication bias, while sensitivity analysis was used to examine the heterogeneity. The verified results are consistent and reliable. The results indicated that for each group, the optimal dietary metabolizable energy level was about 13 to 13.5MJ/kg for medium-sized geese aged 0 to 4 weeks, 12 to 13MJ/kg for medium-sized geese aged above 5 weeks, 12.5 to 13MJ/kg for small-sized geese aged 0 to 4 weeks, and 13 to 13.5MJ/kg for mall-sized geese over 5 weeks of age. Future research should be conducted on related diets of large-sized geese, small-sized geese, and higher metabolizable energy levels.

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.

Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct and analyze their genomes. The aDNA is commonly obtained from remains found in paleontological and archaeological sites, conserved in museums and in other archival collections. Herbarium collections represent a great source of phenotypic and genotypic information, and their exploitation allowed to infer and to clarify previously unsolved taxonomic and systematic relationships. Moreover, Herbarium specimens offered a new source to study phenological traits in plants and to disentangle biogeography and evolutionary scenarios of species. More recently, advances in the molecular technologies went in parallel with the decreasing costs of the next-generation sequencing (NGS) approaches, that paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and Herbarium specimens, this research field is still relatively unexplored, due to the need of improving strategies for aDNA manipulation and exploitation. The higher susceptibility of aDNA to degradation and contamination during the Herbarium conservation and manipulation, and the occurrence of biochemical post-mortem damages, can result in the more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical Herbarium plant materials, such as the best practices for aDNA extraction, amplification and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of Herbarium specimens for their exploitation in plant evolutionary studies.

With an ever increasing amount of research data available, it becomes constantly more important to possess data literacy skills to benefit from this valuable resource. An integrative course was developed to teach students the fundamentals of data literacy through an engaging genome sequencing project. Each cohort of students performed planning of the experiment, DNA extraction, nanopore sequencing, genome sequence assembly, prediction of genes in the assembled sequence, and assignment of functional annotation terms to predicted genes. Students learned how to communicate science through writing a protocol in the form of a scientific paper, providing comments during a peer-review process, and presenting their findings as part of an international symposium. Many students enjoyed the opportunity to own a project and to work towards a meaningful objective.

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 king ratsnake (Elaphe carinata) of the genus Elaphe is a common large non-venomous snake that is widely distributed in Southeast and East Asia, and is an economically important farmed snake species. As a non-venomous snake, the king snake that is predatory on venomous snakes such as cobras and pit vipers. The immune mechanisms of which has been unclear. Despite their economic and research importance, genomic resources which will benefit studies in toxicology, phylogeography and immunogenetics are lacking. In this study, we use single-tube long fragment read (stLFR) sequencing to display the first complete genome of a King ratsnake from Huangshan City, Anhui province in China. The genome size is 1.56GB with a scaffold N50 of 6.53M, the total length of the genome is approximately 621Mb, and the repeat content is 38.90%. Additionally, we predicted 22,339 protein-coding genes, of which 22,065 had functional annotations. Our genome is a potentially useful addition to those currently available for snakes.

The accumulation of loss of function mutations in the uricase gene well explains the high urate levels in hominoids (apes and humans) compared to other mammals. The loss of human uricase activity may have allowed humans to survive environmental stressors, evolution bottlenecks, and life-threatening pathogens. While high urate levels may contribute to developing cardiometabolic disorders such as hypertension and insulin resistance, low urate levels may increase the risk for neurodegenerative diseases. The double-edged sword effect of uric acid has resurrected a growing interest in the antioxidant role of urate and the role of the uricase gene in modulating the risk of obesity. Characterizing both the effect of uric acid levels and the uricase gene in different animal models may provide new insights into the potential therapeutic benefits of uric acid and novel uricase-based therapy.

The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pangenomes of several crops. The pan-genomes of crops constructed from various cultivars/accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novels genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding for mitigating the impact of global climate change. Here we summarize the tools used for pangenome assembly and annotations, web-portals hosting plant pangenomes. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and its future potential.

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.

In response to the issue of vehicle escape guidance, this manuscript proposes a unified intelligent control strategy synthesizing optimal guidance and Meta Deep Reinforcement Learning (DRL). Optimal control with minor energy consumption is introduced to meet terminal latitude, longitude and altitude. Maneuvering escape is realized by adding longitudinal and lateral direction maneuver overloads. Maneuver command decision model is calculated based on Soft-Actor-Critic (SAC) networks. Meta learning is introduced to enhance autonomous escape capability, which improves generalization performance to time-varying scenarios not encountered in the training process. In order to obtain training samples at a faster speed, this manuscript uses the prediction method to solve reward values, which avoiding a large number of numerical integration. The simulation results manifest that the proposed intelligent strategy can achieve high precise guidance and effective escape.

The Oriental ratsnake Ptyas mucosa is a common non-venomous snake of the colubrid family, with a wide geographic range spanning much of South and Southeast Asia. P. mucosa is widely cultivated dut to it used in traditional medicine, scientific research, and handicrafts. Therefore, genome resources could play an important role in the efficacy of traditional medicine and the analysis of the living environment of the species. We collected a snake sample in Hezhou, Guangxi, China, which was identified as P. mucosa by morphological identification. Here we present a highly continuous P. mucosa genome with a genome size of 1.74Gb. The scaffold N50 length is 9.57Mb and the maximal length of scaffold is 78.3Mb, the P. mucosa genome has a CG content of 37.9% and the integrity of the gene reached 86.6%.Assembled using long-reads, the total length of the repeat sequence in the genome reached 735 Mb, and its repeat content was as high as 42.19%. A total of 24,869 functional genes were annotated. This study will assist in the understanding of the P. mucosa, and also provide a basis for medicinal research.

Objective: To evaluate the existing meta-analytic evidence of associations between exposure to ultra-processed foods, as defined by the Nova food classification system, and adverse health outcomes. Design: Systematic umbrella review of existing meta-analyses. Data Sources: MEDLINE, PsycINFO, Embase, and the Cochrane Database of Systematic Reviews, as well as manually searching reference lists from 2009 to June 2023. Inclusion Criteria: Systematic reviews and meta-analyses of cohort, case-control, and/or cross-sectional study designs that evaluated the associations between exposure to ultra-processed foods and adverse health outcomes in humans across the lifespan. Results: The search identified 45 unique pooled analyses, including 13 dose-response and 32 non-dose-response associations (n=9,888,373). Overall, direct associations were found between exposure to ultra-processed foods and 32 (71%) health outcome domains spanning cardiometabolic, gastrointestinal, and respiratory conditions, cancer, mental health, and mortality. Based on a pre-specified evidence classification criteria, convincing evidence (Class I) supported direct associations between greater ultra-processed food exposure and higher risks of incident cardiovascular disease-related mortality (RR: 1.50; 95%CIs: 1.37 to 1.63), type two diabetes (dose-response RR: 1.12; 95%CIs: 1.11 to 1.13), and depressive outcomes (HR: 1.21; 95%CIs: 1.16 to 1.28), as well as higher risks of prevalent anxiety outcomes (OR: 1.48; 95%CIs: 1.37 to 1.59) and combined common mental disorder outcomes (OR: 1.53; 95%CIs: 1.43 to 1.63). Highly suggestive (Class II) evidence indicated that greater exposure to ultra-processed foods was directly associated with higher risks of incident all-cause mortality (RR: 1.21; 95%CIs: 1.15 to 1.27), heart disease-related mortality (dose-response HR: 1.66; 95%CIs: 1.51 to 1.84), and type two diabetes (OR: 1.40; 95%CIs: 1.23 to 1.59), together with higher risks of prevalent obesity (OR: 1.55; 95%CIs: 1.36 to 1.77), adverse sleep-related outcomes (OR: 1.41; 95%CIs: 1.24 to 1.60), and wheezing (RR: 1.40; 95%CIs: 1.27 to 1.55). Out of the remaining 34 pooled analyses, 21 were graded as suggestive or weak strength (Class III-IV) and 13 were graded as no evidence (Class V). Using the GRADE framework, 22 pooled analyses were rated as "Low" quality, with 19 rated as "Very Low” and four rated as "Moderate" quality. Conclusions: Higher exposure to ultra-processed food was associated with a greater risk of adverse health outcomes, especially cardiometabolic, common mental disorder, and mortality outcomes. These findings provide a rationale to evaluate the effectiveness of using population-based measures to target and reduce dietary exposure to ultra-processed foods for improved human health. Systematic Review Registration: PROSPERO CRD42023412732.

Gastric cancer (GC) is a highly heterogeneous, complex disease and the fifth most common cancer worldwide (about one million cases and 784 000 deaths worldwide in 2018). CG is lately diagnosed and guarantees a poor prognosis for GC (the 5-year survival rate is less than 20%, but in early detection can reach 90%). This study evaluated the transcriptional profile in tumor gastric samples to find genes highly expressed during tumor establishment and use the related proteins as targets to find new anticancer molecules. Data was collected at Gene Expression Omnibus (GEO) bank to obtain 3 dataset matrices that analyze gastric tumor tissue versus normal gastric tissue, performed microarray using GPL570 platform, and from different sources. The genes found in silico analysis were confirmed in several lines of GC cells by RT-qPCR. The protein data bank was used to find the correspondent proteins. Then a structural-based virtual screening was done to find molecules, and docking analysis was done using the DockThor server. Our results of transcriptomic analysis, together with RT-qPCR, confirm the high expression of the genes AJUBA, FBXL13, CCDC69, CD80 and NOLC1 in GC lines. Based on that, the correspondent proteins were used in SBVS analysis. Five molecules, one each target, MCULE-2386589557-0-6, MCULE-7343047040-0-1, MCULE-5230409338-0-3, MCULE-9178344200-0-1 and MCULE -5881513100-0-29. All molecules have favorable pharmacokinetic, pharmacodynamic and toxicological properties. Molecular docking analysis revealed that the molecules interact with proteins in critical sites for their activity. Using a virtual screening approach, a molecular docking study was performed for proteins encoded by genes that play important roles in cellular functions for carcinogenesis. Combining a systematic collection of public microarray data with a comparative meta-profiling, RT-qPCR, SBVS, and molecular docking analysis provided a suitable approach to find genes involved in GC and work the correspondent protein to strive for new molecules with anticancer properties.

The minimum dominating tree (MDT) problem consists of finding a minimum weight sub-graph from an undirected graph, such that each vertex not in this sub-graph is adjacent to at least one of the vertices in it, and the sub-graph is connected without any ring structures. This paper presents a Dual Neighborhoods Search (DNS) algorithm for solving the MDT problem, which integrates several distinguishing features, such as two neighborhoods collaboratively working for optimizing the objective function, a fast neighborhood evaluation method to boost the searching effectiveness, and several diversification techniques to help the searching process jump out of the local optimum trap thus obtaining better solutions. DNS improves the previous best-known results for 4 public benchmark instances while providing competitive results for the remaining ones. Several ingredients of DNS are investigated to demonstrate the importance of the proposed ideas and techniques.

Reinforcement Learning (RL) has demonstrated considerable potential in solving challenges across various domains, notably in autonomous driving. Nevertheless, implementing RL in autonomous driving comes with its own set of difficulties, such as the overestimation phenomenon, extensive learning time, and sparse reward problems. Although solutions like Hindsight Experience Replay (HER) have been proposed to alleviate these issues, the direct utilization of RL in autonomous vehicles remains constrained due to the intricate fusion of information and the possibility of system failures during the learning process. In this paper, we present a novel RL-based autonomous driving system technology that combines Obstacle Dependent Gaussian (ODG) RL, Soft Actor-Critic (SAC), and meta-learning algorithms. Our approach addresses key issues in RL, including the overestimation phenomenon and sparse reward problems, by incorporating prior knowledge derived from the ODG algorithm. We evaluated our proposed algorithm on official F1 circuits, using high-fidelity racing simulations with complex dynamics. The results demonstrate exceptional performance, with our method achieving up to 89% faster learning speed compared to existing algorithms in these environments.

The study of the currently known >3,000 species of snakes can provide valuable insights into the evolution of their genomes. Deinagkistrodon acutus, also known as Sharp-nosed Pit Viper, one hundred-pacer viper or five-pacer viper, is a venomous snake with significant economic, medicinal and scientific importance. Widely distributed in southeastern China and South-East Asia, D. acutus has been primarily studied for its venom. Here, we employed next-generation sequencing to assemble and annotate a highly continuous genome of D. acutus. The genome size is 1.46 Gb; its scaffold N50 length is 6.21 Mb, the repeat content is 42.81%, and 24,402 functional genes were annotated. This study helps to further understand and utilize D. acutus and its venom at the genetic level.

This study aimed to present a systematic meta-analysis examining the association between Helicobacter pylori (H. pylori) infection, hemoglobin A1c levels, and the development of type 1 diabetes mellitus. The initial search identified 451 articles related to the association between H. pylori infection and T1DM. Among them, 14 articles had 2,971 participants meeting the inclusion criteria for advanced meta-analysis. A significant association was observed between H. pylori infection and T1DM, with an odds ratio (OR) of 1.87 (95% confidence interval [CI]: 1.27–2.78, p = 0.002). A subgroup analysis on H. pylori status showed that a longer duration of diabetes diagnosis and higher hemoglobin A1c levels were significantly associated with H. pylori infection (p < 0.001 for both). However, there was no significant association between H. pylori infection and the diagnostic age of diabetes (p = 0.306). These findings contribute to the understanding of the association between H. pylori infection and T1DM, thereby highlighting the potential role of H. pylori in influencing the duration and glycemic control of diabetes.

This study aimed to evaluate the diagnostic roles of various immunohistochemical markers in urothelial carcinoma in situ (uCIS) through a meta-analysis and review of diagnostic test accuracy. Immunohistochemical markers CK20, CD44, AMACR, and p53 were evaluated in the present study. We analyzed the expression rates of immunohistochemical markers and compared their diagnostic accuracies. The estimated expression rates were 0.803 (95% confidence interval [CI]: 0.726–0.862), 0.142 (95% CI: 0.033–0.449), 0.824 (95% CI: 0.720–0.895), and 0.600 (95% CI: 0.510–0.683) for CK20, CD44, AMACR, and p53, respectively. In the comparison between uCIS and reactive/normal urothelium, the expression of CK20, AMACR, and p53 in uCIS was significantly higher than in reactive/normal urothelium. CD44 showed significantly lower expression in uCIS than in the reactive/normal urothelium. Among the markers, AMACR had the highest sensitivity, specificity, and diagnostic odds ratio. The AUC on SROC was the highest for CK20. In conclusion, immunohistochemical markers, such as CK20, CD44, AMACR, and p53, can be useful in differentiating uCIS from reactive/normal urothelium.

The field of mitochondrial genomics has advanced rapidly and revolutionized disciplines from molecular anthropology, population genetics, to medical/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated, mitogenome database and efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4,286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient and accurate means of sequence analysis for translational mitogenomics.

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.

The aims of this paper are 1) to explore the type of industry of SMEs that can survive for more than 5 years in ASEAN, and 2) to analyze the success factors of SMEs in ASEAN to be able to survive for more than 5 years. This paper employs a qualitative method, with a literature review and meta-analysis. From 2007 to 2017, data was extracted from Google Scholar, Emerald Insight, Sage Pub, and EBSCO databases. There are 14 factors that influence the success of SMEs in the main sectors, 20 factors in the manufacturing sectors, and 14 factors in the service sectors, depending on the type of industry. For instance: eCommerce, technology, and social media, international oriented, good management system, government support, working condition /environment, skill and competency labour/owner, market penetration/selection, policy, organizational performance, and characteristics, networking with government /supplier / customer, networking with government /supplier /customer, planned /strategy (business /market /operational /organizational). The findings of this literature review reveal several important factors that are critical to the success of SMEs in competing with other industries and can be developed for a longer period.

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.

Cryptosporidiosis is a widespread disease caused by the parasitic protozoan Cryptosporidium spp., which infects various vertebrate species, including humans. Once unknown as a gastroenteritis-causing agent, Cryptosporidium spp. is now recognized as a pathogen causing life-threatening disease, especially in immunocompromised individuals such as AIDS patients. Advances in diagnostic methods and increased awareness have led to a significant shift in the perception of Cryptosporidium spp. as a pathogen. Nowadays, genomic and proteomic studies have played a main role in understanding the molecular biology of this complex-life-cycle parasite. Genomics has enabled the identification of numerous genes involved in the parasite's development and interaction with hosts. Proteomics has allowed for the identification of protein interactions, their function, structure, and cellular activity. The combination of these two approaches has significantly contributed to the development of new diagnostic tools, vaccines, and drugs for cryptosporidiosis. In this review, we summarize the major accomplishments in the field of Cryptosporidium research using genomics and proteomics.

We compared the performance of matrix-assisted laser desorption/ionization followed by a time of flight (MALDI-TOF) mass spectrometry and genomic DNA extraction followed by sequencing, assembly, and alignment for phylogenetic assessment (Genomics method). We collected the samples from four contaminated rivers in the Dominican Republic and analyzed MALDI-TOF efficacy and accuracy for identifying bacteria in the samples. We evaluated the results for both methods (MALDI-TOF and Genomics) and reported a similarity percentage between each method's results. The MALDI-TOF method had a 72.41\% of coincidence with the Genomics method. This could have been sequence contamination found in the Genomics method. When it was later filtered, the result's coincidence rate went up to 90\%.

A review is here provided about the thermal effects on the optical chirality. To this goal, chiral objects dispersed in an embedding fluid are examined for their magnetoelectric coupling. Thermal effects on several chiral meta-atoms and their ensembles are examined. To this goal, DNA-like helical structures are examined in detail. Mechanical aspect of thermo-elasticity is reviewed along with transverse deformations, while drawing analogies from condensed-matter physics. In this respect, chirality-induced spin selection is reviewed along with the temperature-mediated elec-tron-phonon interactions. A wide range of materials such as polymers and biological cells are also examined for temperature effects. A transition temperature delineating a sign flip in the chirality parameter is identified as well. Chirality-associated functionalities such as ratchet motions, switching, and modulations are investigated for their respective thermal effects. Issues of fabri-cating chiral meta-atoms are also discussed.

Coronavirus Disease-19 (COVID-19) is caused by the infection of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The virus enters host cells through receptor-mediated endocytosis of angiotensin-converting enzyme-2 (ACE2), leading to systemic inflammation, also known as a “cytokine storm,” and neuroinflammation. COVID-19’s upstream regulator, interferon-gamma (IFNG), is downregulated upon the infection of SARS-CoV-2, which leads to the downregulation of ACE2. The neuroinflammation signaling pathway (NISP) can lead to neurodegenerative diseases, such as Parkinson's disease (PD), which is characterized by the formation of Lewy Bodies made of α-Synuclein protein encoded by synuclein alpha (SNCA). This study presents the pathways involved in the downregulation of ACE2 following SARS-CoV-2 infection and its effect on PD progression. Through QIAGEN’s Ingenuity Pathway Analysis, the study identifies the NISP as a top-five canonical pathway/signaling pathway and SNCA as a top-five upstream regulator. Core Analysis was also conducted on the associated molecules between COVID-19 and SNCA to construct a network connectivity map. The Molecule Activity Predictor tool was used to simulate the infection of SARS-CoV-2 by downregulating IFNG, which leads to the predicted activation of SNCA, and subsequently PD, through a dataset of intermediary molecules. Downstream Effect analysis was further used to quantify the downregulation of ACE2 on SNCA activation.

Background: The purpose of this study is to carry out bioinformatic analysis of lncRNA data obtained as a result of genomic analysis of kidney tissue samples taken from rats with nephrotoxicity induced by methotrexate (MTX) and from rats without pathology and modeling with tree-based machine learning method. Another aim of the study is to identify potential biomarkers for the diagnosis of nephrotoxicity and to provide a better understanding of the nephrotoxicity formation process by providing the interpretability of the model with explainable artificial intelligence methods as a result of the modeling. Methods: To identify potential indicators of drug-induced nephrotoxicity, 20 female Wistar Albino rats were separated into two groups: nephrotoxicity and control. Kidney tissue samples were collected from the rats, and genomic, histological, and immunohistochemical analyses were performed. The data set obtained as a result of genomic analysis was modeled with Random Forest (RF), one of the tree-based methods. Modeling results were evaluated with sensitivity (Se), specificity (Sp), balanced accuracy (B-Acc), negative predictive value (Npv), accuracy (Acc), positive predictive value (Ppv), and F1-score performance metrics. The Local Interpretable Model-Agnostic Annotations (LIME) method was used to determine the lncRNAs that could be biomarkers for nephrotoxicity by providing the interpretability of the RF model. Results: The outcomes of the histological and immunohistochemical analyses done in the study supported the conclusion that MTX use caused kidney injury. According to the results of the bioinformatics analysis, 52 lncRNAs showed different expression in the groups. As a result of modeling with RF for lncRNAs selected with Boruta variable selection, the B-Acc, Acc, Sp, Se, Npv, Ppv, and F1-score were 88.9%, 90%, 90.9%, 88.9%, 90.9%, 88.9% and 88.9%. respectively. lncRNAs with id rnaXR_591534.3 rnaXR_005503408.1, rnaXR_005495645.1, rnaXR_001839007.2, rnaXR_005492056.1 and rna_XR_005492522.1 the lncRNAs with the highest variable importance values produced from RF modeling can be used as nephroxicity biomarker candidates. Also, according to the LIME results, the high level of lncRNAs with id rnaXR_591534.3 and rnaXR_005503408.1 especially increased the possibility of nephrotoxicity. Conclusions: With the possible biomarkers obtained as a result of the analyses made within the scope of this study, it can be ensured that the procedures for the diagnosis of drug-induced nephrotoxicity can be carried out easily, quickly and effectively.

In response to escalating global demand for poultry, the industry grapples with an array of intricate challenges, from enhancing productivity to improving animal welfare and attenuating environmental impacts. This comprehensive review explores the transformative potential of digital phenotyping, an emergent technological innovation at the cusp of dramatically reshaping broiler production. The central aim of this study is to critically examine digital phenotyping as a pivotal solution to these multidimensional industry conundrums. Our investigation spotlights the profound implications of 'digital twins' in the burgeoning field of broiler genomics, where the production of exact digital counterparts of physical entities accelerates genomics research and its practical applications. Further, this review probes into the ongoing advancements in the research and development of a context-sensitive, multimodal digital phenotyping platform, custom-built to monitor broiler health. I critically evaluate this platform's potential in revolutionizing health monitoring, fortifying the resilience of broiler production, and fostering a harmonious balance between productivity and sustainability. Subsequently, the paper provides a rigorous assessment of the unique challenges that may surface during the integration of digital phenotyping within the industry. These span from technical and economic impediments to ethical deliberations, thus offering a comprehensive perspective. The paper concludes by highlighting the game-changing potential of digital phenotyping in the broiler industry and identifying potential future directions for the field, underlining the significance of continued research and development in unlocking digital phenotyping's full potential. In doing so, it charts a course towards a more robust, sustainable, and productive broiler industry. The insights garnered from this study hold substantial value for a broad spectrum of stakeholders in the broiler industry, setting the stage for an imminent technological evolution in poultry production.

Background Dietary guidelines typically recommend limiting the intake of fresh red meat, yet evidence linking red meat consumption with adverse health outcomes is inconsistent. Objective To assess the level of evidence from existing systematic reviews and meta-analyses and analyze the association between high consumption of red meat and cancer risk and adverse health outcomes. Methods Eight databases were searched to collect systematic reviews and meta-analyses from database inception to December 2022. Two independent reviewers screened and extracted data and used the AMSTAR 2 tool to evaluate methodological quality of the included studies. Meta-analysis was conducted using STATA 17.0. Results A total of 18 studies were included, of which 5 were rated as high quality, 4 as medium quality, 6 as low quality, and 3 as extremely low quality. Of the 9 SRs/MAs included, primary studies with overlap were identified, and 14 studies were eventually included. The meta-analysis results showed that compared with the lowest intake of red meat, the highest intake of red meat was associated with an increased risk of colorectal cancer (OR 1.21, 95% CI 1.07-1.37), gastric cancer (OR 1.37, 95% CI 1.18-1.59), non-Hodgkin's lymphoma (OR 1.10.95% CI 1.02-1.19), stroke (RR 1.11, 95% CI 1.03-1.20), type 2 diabetes (RR 1.19 95% CI 1.04-1.37), and ischemic heart disease (RR 1.09, 95% CI 1.06-1.12), as well as a negative effect on total cholesterol (WMD 0.264, 95% CI 0.144-0.383), triglycerides (WMD -0.181, 95% CI -0.349 to -0.013), low-density lipoprotein (WMD 0.198, 95% CI 0.065-0.330), and high-density lipoprotein (WMD -0.065, 95% CI -0.109 to -0.020). However, the associations with breast cancer (RR 1.05 95% CI 1.00-1.11), glycemic control (WMD 0.040, 95% CI 0.049-0.129), and changes in body weight status [overweight (β 0.89, 95% CI 0.48-1.64); obesity (β 1.06, 95% CI 0.30-3.71)] were not significant. Conclusions This comprehensive umbrella review suggests that high consumption of red meat may increase the risk of colorectal cancer, gastric cancer, non-Hodgkin lymphoma, stroke, type 2 diabetes, and cardiovascular disease, and that reducing red meat intake is a key modifiable dietary factor for reducing risk. However, there was no significant correlation with breast cancer, kidney stones, age-related eye disease or changes in body weight.

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.

Fungal plant diseases are a major threat to food security worldwide. Current efforts to identify and list loci involved in different biological processes are more complicated than originally thought, even when complete genome assemblies are available. Despite numerous experimental and computational efforts to characterize gene functions in plants, about ~ 40% of protein-coding genes in the model plant A. thaliana are still not categorized in the Gene Ontology Biological Process (BP) annotation. In non-model organisms, such as sunflower (Helianthus annuus), the number of BP term annotation is far fewer, ~22%. In the current study we performed gene co-expression network analysis using eight terabytes of public transcriptome datasets and performed expression-based functional prediction to categorize and identify loci involved in the response to fungal pathogens. We were able to construct a reference gene network of healthy green tissue (GreenGCN) and a gene network of healthy and stressed root tissues (RootGCN). Both networks achieved robust high quality scores on the metrics of guilt-by-association and selective constraints versus gene connectivity. We were able to identify eight modules enriched in defense functions, of which, two out of the three modules in the RootGCN were also conserved in the GreenGCN, suggesting similar defense-related expression patterns. We identified 16 WRKY genes involved in defense related functions and 65 previously uncharacterized loci now linked to defense response. In addition, we identified and classified 122 loci previously identified within QTL or near candidate loci reported in GWAS studies of disease resistance in sunflower linked to defense response. In all, we have implemented a valuable strategy to better describe genes within specific biological processes.

Rabies is a fatal zoonosis that is considered a re-emerging infectious disease. Although rabies remains endemic in canines throughout much of the world, vaccination programs have essentially eliminated dog rabies in the Americas and much of Europe. However, despite the goal of eradicating dog rabies in the European Union by 2020, sporadic cases of dog rabies still occur in Eastern Europe, including Georgia. To assess the genetic diversity of strains recently circulating in Georgia, we sequenced 78 RABV-positive samples from brain tissues of rabid dogs and jackals using Illumina short-read sequencing of total RNA shotgun libraries. Seventy-seven RABV genomes were successfully assembled and annotated, 74 of them to the coding complete status. Phylogenetic analyses of the nucleoprotein (N) and attachment glycoprotein (G) genes placed all the assembled genomes into the Cosmopolitan clade, consistent with the Georgian origin of the samples. Amino acid alignment of the G glycoprotein ectodomain identified twelve different sequences for this domain among the samples. Only one of the ectodomain groups contained a residue change in an antigenic site, an R264H change in the G5 antigenic site. Three isolates were cultured, and these were found to be efficiently neutralized by human monoclonal antibody A6. Overall, our data show that recently circulating RABV isolates from Georgian canines are predominantly closely related phylogroup I viruses of the Cosmopolitan clade. Current rabies vaccines should offer protection against infection by Georgian canine RABVs. The genomes have been deposited in GenBank (accessions: OQ603609-OQ603685).

Atopic dermatitis (AD) has been extensively investigated for genetic associations utilizing both candidate gene approaches and genome-wide scans. Here, we comprehensively evaluated the available literature to determine the association of candidate genes in AD to gain additional insight in the etiopathogenesis of the disease. We systematically screened all studies that explored the association between polymorphisms and AD risks in cases of European and Asian ancestry and synthesized the available evidence through random-effects meta-analysis. We identified 97 studies that met our inclusion/exclusion criteria that examined 17 candidate loci in Europeans and 14 candidate genes in Asians. We confirmed the significant associations between FLG variants in both European and Asian populations and AD risk, while additional synthesis of available data revealed novel loci mapped to IL18 and TGFB1 genes in Europeans and IL12RB1 and MIF in Asians, that have not yet been identified by genome-wide association studies. Our findings provide comprehensive evidence for AD risk loci in cases of both European and Asian ancestries, validating previous associations as well as revealing novel loci that could imply previously unexplored biological pathways.

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.

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.

Snakes are a vital component of wildlife resources and are widely distributed across the globe. Bungarus multicinctus, a highly venomous snake, is found in central and southern China. B. multicinctus is a highly venomous snake and is distributed in central and southern China. Snakes are an ancient group of reptiles, and their genome resources can provide important clues for understanding the evolutionary history of reptiles. Meanwhile, genomic resources play a crucial role in comprehending the evolution of species. So far, the genomic resources of snakes are a rarity. In 2021, a snake sample was collected from Beiliu Longgukeng, Guangxi, which was identified as B. multicinctus through morphological identification. In this study, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides a genomic basis for the genes involved in venom gland function.

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.

Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes, thus it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study we examined dispersal and connectivity patterns of rodents, one endemic (Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genomic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site we identified contrasting migration rates for each species, but these did not correspond to habitat-matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation.

GS provides exciting opportunities to rapidly identify a diagnosis in critically ill newborns and children with rare genetic conditions. But there are good reasons to remain cautious about the broad implementation of these strategies in babies and children. At best, rapid GS leads to diagnoses in many infants in highly selected populations. It sometimes leads to beneficial and changes in management. Parents and physicians both often find these results useful. We don’t know how useful such testing will be in the general population. It is almost inevitable that genetic counseling will be more challenging in a more general population. We don’t know how often GS helps improve outcome and survival or reduce symptoms in babies who receive a molecular diagnosis. We don’t know the relative cost-effectiveness of whole genome, whole exome, or targeted panels in different populations. We don’t know the relative contribution of a molecular diagnosis to the decision to withdraw life support. Each of these concerns will require careful study of both the technology and the ethical issues to allow us to harness the potential of these new technologies while avoiding foreseeable problems. Studies are underway to see how the tests are used in general populations. These studies should generate important information to guide clinicians and policymakers. In the meantime, parents should know that genetic results sometimes confirm an already suspected dismal prognosis and sometimes yield only ambiguous findings. Anticipatory discussions should try to give parents a realistic understanding of the likely impact of a genetic diagnosis. Both doctors and parents should recognize that the clinical usefulness of diagnostic genomic testing in newborns is a work in progress. We are only a decade into the age of true genomic medicine. We still have much to learn.