Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing Genetic Regulatory Elements in Ovine Tissues

The Ovine Functional Annotation of Animal Genomes (FAANG) project, part of the broader livestock species FAANG initiative, aims to identify and characterize gene regulatory elements in domestic sheep. Regulatory element annotation is essential for identifying genetic variants that affect health and production traits in this important agricultural species, as greater than 90% of variants underlying genetic effects are estimated to lie outside of transcribed regions. Histone modifications that distinguish active or repressed chromatin states, CTCF binding, and DNA methylation were used to characterize regulatory elements in liver, spleen, and cerebellum tissues from four yearling sheep. Chromatin immunoprecipitation with sequencing (ChIP-seq) was performed for H3K4me3, H3K27ac, H3K4me1, H3K27me3, and CTCF. Nine chromatin states including active promoters, active enhancers, poised enhancers, repressed enhancers, and insulators were characterized in each tissue using ChromHMM. Whole-genome bisulfite sequencing (WGBS) was performed to determine the complement of whole-genome DNA methylation with the ChIP-seq data. Hypermethylated and hypomethylated regions were identified across tissues, and these locations were compared with chromatin states to better distinguish and validate regulatory elements in these tissues. Interestingly, chromatin states with the poised enhancer mark H3K4me1 in the spleen and cerebellum and CTCF in the liver displayed the greatest number of hypermethylated sites. Not surprisingly, active enhancers in the liver and spleen, and promoters in the cerebellum, displayed the greatest number of hypomethylated sites. Overall, chromatin states defined by histone marks and CTCF occupied approximately 22% of the genome in all three tissues. Furthermore, the liver and spleen displayed in common the greatest percent of active promoter (65%) and active enhancer (81%) states, and the liver and cerebellum displayed in common the greatest percent of poised enhancer (53%), repressed enhancer (68%), hypermethylated sites (75%), and hypomethylated sites (73%). In addition, both known and de novo CTCF-binding motifs were identified in all three tissues, with the highest number of unique motifs identified in the cerebellum. In summary, this study has identified the regulatory regions of genes in three tissues that play key roles in defining health and economically important traits and has set the precedent for the characterization of regulatory elements in ovine tissues using the Rambouillet reference genome.
Prevalence of Sarcopenia and Its Association With Diabetes: A Meta-Analysis of Community-Dwelling Asian Population

Purpose: Sarcopenia is a major disease affecting mortality and quality of life in the elderly population. We performed a meta-analysis of studies on the community-dwelling population to investigate the prevalence of sarcopenia and its association with diabetes. Methods: Databases were searched for studies published up to February 3, 2021, reporting the prevalence of sarcopenia in patients with and without diabetes. Data extraction and quality assessment were performed according to the Newcastle-Ottawa scale. Results: Six articles were included in the systematic review. All the patients were Asian, aged ≥60 years (women 53.4%), and the diabetic and non-diabetic population was 1,537 and 5,485, respectively. In all six studies, the Asian Working Group for Sarcopenia criteria were used to diagnose sarcopenia. The prevalence of sarcopenia was 15.9% in diabetics and 10.8% in non-diabetics. Diabetics showed a significantly higher risk of sarcopenia than non-diabetics (pooled OR = 1.518, 95% CI = 1.110 to 2.076, Z-value = 2.611, p = 0.009). Conclusion: Among the Asian community-dwelling geriatric population, the prevalence of sarcopenia was significantly higher in diabetics than in non-diabetics. These results suggest that strategies for the management of sarcopenia are required in Asian elderly patients, especially with diabetes.
Genome-Wide Association Study Uncover the Genetic Architecture of Salt Tolerance-Related Traits in Common Wheat (Triticum aestivum L.)

Soil salinity is a serious threat to wheat yield affecting sustainable agriculture. Although salt tolerance is important for plant establishment at seedling stage, its genetic architecture remains unclear. In the present study, we have evaluated eight salt tolerance–related traits at seedling stage and identified the loci for salt tolerance by genome-wide association study (GWAS). This GWAS panel comprised 317 accessions and was genotyped with the wheat 90 K single-nucleotide polymorphism (SNP) chip. In total, 37 SNPs located at 16 unique loci were identified, and each explained 6.3 to 18.6% of the phenotypic variations. Among these, six loci were overlapped with previously reported genes or quantitative trait loci, whereas the other 10 were novel. Besides, nine loci were detected for two or more traits, indicating that the salt-tolerance genetic architecture is complex. Furthermore, five candidate genes were identified for salt tolerance–related traits, including kinase family protein, E3 ubiquitin-protein ligase-like protein, and transmembrane protein. SNPs identified in this study and the accessions with more favorable alleles could further enhance salt tolerance in wheat breeding. Our results are useful for uncovering the genetic mechanism of salt tolerance in wheat at seeding stage.
Virus Diversity and Loads in Crickets Reared for Feed: Implications for Husbandry

Insects generally have high reproductive rates leading to rapid population growth and high local densities; ideal conditions for disease epidemics. The parasites and diseases that naturally regulate wild insect populations can also impact when these insects are produced commercially, on farms. While insects produced for human or animal consumption are often reared under high density conditions, very little is known about the microbes associated with these insects, particularly those with pathogenic potential. In this study we used both target-free and targeted screening approaches to explore the virome of two cricket species commonly reared for feed and food, Acheta domesticus and Gryllus bimaculatus. The target-free screening of DNA and RNA from a single A. domesticus frass sample revealed that only 1% of the nucleic acid reads belonged to viruses, including known cricket, insect, bacterial and plant pathogens, as well as a diverse selection of novel viruses. The targeted screening revealed relatively high levels of Acheta domesticus densovirus, invertebrate iridovirus 6 and a novel iflavirus, as well as low levels of Acheta domesticus volvovirus, in insect and frass samples from several retailers. Our findings highlight the value of multiple screening approaches for a comprehensive and robust cricket disease monitoring and management strategy. This will become particularly relevant as-and-when cricket rearing facilities scale up and transform from producing insects for animal feed to producing insects for human consumption.
Satisfaction of Telehealth in Patients With Established Neuromuscular Disorders

Introduction/aims: Determine established neuromuscular disease patients' satisfaction with telehealth during the COVID-19 pandemic. Methods: We received 50 completed Utah telehealth satisfaction surveys from a cohort of 90 from April 2020 to June 2020. Returning neuromuscular disease patients rated seven aspects from 1 (strongly disagree) to 5 (strongly agree): Communication, timeliness of physician, picture quality, sound quality, protection of privacy, the comfort of the physical exam, the ease of healthcare, and whether patients would prefer “in-person” visits despite safety precaution. A favorable response was defined as a response of “Agree” or “Strongly Agree” to the survey questions. An independent t-test, Fisher's or chi-square test were used to compare demographic factors on outcomes for each survey question. Results: The average age was 47.54 ± 20.63, 54% were female, 70% from rural areas, 60% had family present “webside,” and 14% had family present remotely. The majority of patients reported “Agree” or “Strongly Agree” to each survey question assessing their telehealth satisfaction, except for whether patients preferred in-person appointments. Demographic factors, including location and clinical diagnosis, did not influence survey responses. Discussion: The vast majority of established neuromuscular disease patients responded favorably to their telehealth experience during the COVID-19 pandemic.
Evaluation of Patient Reported Safety and Efficacy of Cannabis From a Survey of Medical Cannabis Patients in Canada

With the medical use of cannabis permitted in Canada since 2001, patients seek to use this botanical drug to treat a range of medical conditions. However, many healthcare practitioners express the need for further scientific evidence around the use of medical cannabis. This real-world evidence study aimed to address the paucity of scientific data by surveying newly registered medical cannabis patients, before beginning medical cannabis treatment, and at one follow up 6 weeks after beginning medical cannabis treatment. The goal was to collect data on efficacy, safety and cannabis product type information to capture the potential impact medical cannabis had on patient-reported quality of life (QOL) and several medical conditions over a 6-week period using validated questionnaires. The 214 participants were mainly male (58%) and 57% of the population was older than 50. The most frequently reported medical conditions were recurrent pain, post-traumatic stress disorder (PTSD), anxiety, sleep disorders [including restless leg syndrome (RLS)], and arthritis and other rheumatic disorders. Here we report that over 60% of our medical cannabis cohort self-reported improvements in their medical conditions. With the use of validated surveys, we found significant improvements in recurrent pain, PTSD, and sleep disorders after 6 weeks of medical cannabis treatment. Our findings from patients who reported arthritis and other rheumatic disorders are complex, showing improvements in pain and global activity sub-scores, but not overall changes in validated survey scores. We also report that patients who stated anxiety as their main medical condition did not experience significant changes in their anxiety after 6 weeks of cannabis treatment, though there were QOL improvements. While these results show that patients find cannabis treatment effective for a broad range of medical conditions, cannabis was not a remedy for all the conditions investigated. Thus, there is a need for future clinical research to support the findings we have reported. Additionally, while real-world evidence has not historically been utilized by regulatory bodies, we suggest changes in public policy surrounding cannabis should occur to reflect patient reported efficacy of cannabis from real-world studies due to the uniqueness of medical cannabis's path to legalization.
Stress-Related Growth in Adolescents Returning to School After COVID-19 School Closure

The move to remote learning during COVID-19 has impacted billions of students. While research shows that school closure, and the pandemic more generally, has led to student distress, the possibility that these disruptions can also prompt growth in is a worthwhile question to investigate. The current study examined stress-related growth (SRG) in a sample of students returning to campus after a period of COVID-19 remote learning (n = 404, age = 13–18). The degree to which well-being skills were taught at school (i.e., positive education) before the COVID-19 outbreak and student levels of SRG upon returning to campus was tested via structural equation modeling. Positive reappraisal, emotional processing, and strengths use in students were examined as mediators. The model provided a good fit [χ2 = 5.37, df = 3, p = 0.146, RMSEA = 0.044 (90% CI = 0.00–0.10), SRMR = 0.012, CFI = 99, TLI = 0.99] with 56% of the variance in SRG explained. Positive education explained 15% of the variance in cognitive reappraisal, 7% in emotional processing, and 16% in student strengths use during remote learning. The results are discussed using a positive education paradigm with implications for teaching well-being skills at school to foster growth through adversity and assist in times of crisis.
Modulating Enzyme Function via Dynamic Allostery within Biliverdin Reductase B

The biliverdin reductase B (BLVRB) class of enzymes catalyze the NADPH-dependent reduction of multiple flavin substrates and are emerging as critical players in cellular redox regulation. However, the role of dynamics and allostery have not been addressed, prompting studies here that have revealed a position 15 Å away from the active site within human BLVRB (T164) that is inherently dynamic and can be mutated to control global micro-millisecond motions and function. By comparing the inherent dynamics through nuclear magnetic resonance (NMR) relaxation approaches of evolutionarily distinct BLVRB homologues and by applying our previously developed Relaxation And Single Site Multiple Mutations (RASSMM) approach that monitors both the functional and dynamic effects of multiple mutations to the single T164 site, we have discovered that the most dramatic mutagenic effects coincide with evolutionary changes and these modulate coenzyme binding. Thus, evolutionarily changing sites distal to the active site serve as dynamic “dials” to globally modulate motions and function. Despite the distal dynamic and functional coupling modulated by this site, micro-millisecond motions span an order of magnitude in their apparent kinetic rates of motions. Thus, global dynamics within BLVRB are a collection of partially coupled motions tied to catalytic function.
Bio-Based Hydrogels With Ion Exchange Properties Applied to Remove Cu(II), Cr(VI), and As(V) Ions From Water

Hydrogels with ion exchange properties were synthesized from compounds derived from wood biopolymer hemicellulose and from commercial vinyl monomers to be tested as active materials for the removal of Cu(II), Cr(VI), and As(V) ions. The hemicellulose O-acetyl galactoglucomannan (GGM) was used as the precursor material, and through a transesterification reaction, GGM was converted into a macromonomer GGM–glycidyl methacrylate (GGM-GMA). Subsequently, the GGM-GMA macromonomer, containing more than one methacrylate group, was used as a crosslinking agent in the synthesis of hydrogels through free-radical polymerization reactions in combination with a 2-acrylamido-2-methyl-1-propanesulfonic acid monomer to produce a cation exchange hydrogel. Also, (3-acrylamidopropyl)trimethylammonium chloride monomer was applied together with the GGM-GMA to form hydrogels that can be used as anion exchange hydrogel. The hydrogels were characterized by Fourier transform-infrared (FT-IR), 1H-NMR spectroscopy, and thermogravimetric analysis (TGA), as well as derivative thermogravimetry (DTG). The microstructure of the hydrogels was characterized by scanning electron microscopy (SEM) analysis with X-ray microanalysis energy-dispersive spectroscopy (EDS). The results obtained regarding the absorption capacity of the Cu(II), Cr(VI), and As(V) ions were studied as a function of the pH value and the initial concentration of the metal ions in the solutions. Absorption was carried out in consecutive batches, and it was found that the poly(GGM-GMA/AMPSH) hydrogel reached an absorption capacity of 90 mg g–1 for Cu(II). The poly(GGM-GMA/APTACl) hydrogel reached values of 69 and 60 mg g–1 for Cr(VI) and As(V) oxyanions, respectively. Tests with polymer blends (mixtures of anionic and cationic hydrogels) were also carried out to remove Cu(II), Cr(VI), and As(V) ions from multi-ionic solutions, obtaining satisfactory results.
Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell

A comprehensive annotation of transcript isoforms in domesticated species is lacking. Especially considering that transcriptome complexity and splicing patterns are not well-conserved between species, this presents a substantial obstacle to genomic selection programs that seek to improve production, disease resistance, and reproduction. Recent advances in long-read sequencing technology have made it possible to directly extrapolate the structure of full-length transcripts without the need for transcript reconstruction. In this study, we demonstrate the power of long-read sequencing for transcriptome annotation by coupling Oxford Nanopore Technology (ONT) with large-scale multiplexing of 93 samples, comprising 32 tissues collected from adult male and female Hereford cattle. More than 30 million uniquely mapping full-length reads were obtained from a single ONT flow cell, and used to identify and characterize the expression dynamics of 99,044 transcript isoforms at 31,824 loci. Of these predicted transcripts, 21% exactly matched a reference transcript, and 61% were novel isoforms of reference genes, substantially increasing the ratio of transcript variants per gene, and suggesting that the complexity of the bovine transcriptome is comparable to that in humans. Over 7,000 transcript isoforms were extremely tissue-specific, and 61% of these were attributed to testis, which exhibited the most complex transcriptome of all interrogated tissues. Despite profiling over 30 tissues, transcription was only detected at about 60% of reference loci. Consequently, additional studies will be necessary to continue characterizing the bovine transcriptome in additional cell types, developmental stages, and physiological conditions. However, by here demonstrating the power of ONT sequencing coupled with large-scale multiplexing, the task of exhaustively annotating the bovine transcriptome – or any mammalian transcriptome – appears significantly more feasible.
Assessment of the Safety Signal for the Abuse Potential of Pregabalin and Gabapentin Using the FAERS Database and Big Data Search Analytics

Introduction: The latest decade, an emerging issue has been the abuse potential of the gabapentinoids pregabalin and gabapentin. The aim of our study was to assess this safety signal combining two different methods of surveillance: search analytics big data and the FDA spontaneous reporting system database. Methods: Analysis of big data and the FAERS was used to detect pregabalin's and gabapentin's abuse potential in comparison with two controls, clonazepam and levetiracetam, and further, the correlation between these domains was investigated. Data from the United States between 2007 and 2020Q2 were analyzed. Results: The FAERS analysis revealed the following pattern of signals: clonazepam > pregabalin ≥ gabapentin > levetiracetam, for both the primary term “drug abuse and dependence” and the secondary terms (withdrawal, tolerance, overdose). The Google domain pattern was slightly different: clonazepam ≥ gabapentin ≥ pregabalin≥ levetiracetam. A monotonic correlation was found between FAERS and Google searches for gabapentin (r = 0.558; p < 0.001), pregabalin (r = 0.587; p < 0.001), and clonazepam (r = 0.295; p = 0.030). Conclusion: Our results revealed that there is preliminary evidence of a safety signal for the abuse potential of pregabalin and gabapentin. Analysis of the FAERS database, supplemented by big data search analytics, suggests that there is potential of using these methods as a supplementary tool to detect drug abuse-related safety signals in pharmacovigilance.
Advances in Biological Function and Clinical Application of Small Extracellular Vesicle Membrane Proteins

Small extracellular vesicles are membrane-bound vesicles secreted into extracellular spaces by virtually all types of cells. These carry a large number of membrane proteins on their surface that are incorporated during their biogenesis in cells. The composition of the membrane proteins hence bears the signature of the cells from which they originate. Recent studies have suggested that the proteins on these small extracellular vesicles can serve as biomarkers and target proteins for the diagnosis and treatment of diseases. This article classifies small extracellular vesicle membrane proteins and summarizes their pathophysiological functions in the diagnosis and treatment of diseases.
Stressors in Indoor and Field Brazilian Soccer: Are They Perceived as a Distress or Eustress?

Soccer players inescapably live under stress during the sportive career, and many real-life aspects of soccer situations operate in the ongoing performance. This study’s main objective was to elaborate the List of Stressors in Professional Indoor and Field Soccer, a self-report instrument designed to measure the impact of 77 soccer situations upon the sport performance. Participants were 138 indoor and field soccer players from the Brazilian Premier League. Each situation was evaluated on a 7-point scale, ranging from the most negative (−3) to the most positive (+3). Data were analyzed according to the players’ perception of the items: distress or eustress and its intensity, and after that, situations perceived as plus −1 and +1 were compared by time in which they were experienced and distributed among five categories established by the literature: Expectations about the Performance, Personal Factors, Competition Aspects, Training Demands, and Relationship with Significant People. Narratives of athletes’ experiences were also used to discuss the results. An Exploratory Structural Equation Modeling using Bi-factorial (BI-ESEM) was employed to assess the factor structure. For the total participants, 49 situations were perceived as distress and 28 as eustress. Using the criteria established a priori, the distribution was among the five categories in the remaining 32 situations. Differences in perception between less and more experienced players were found in 11 situations. The results revealed that Brazilian professional soccer players experience various stressful situations. These events are important representations of environmental demands and could predict the performance as they are perceived as eustress or distress. Some of these stressful situations are inherent in sport and others adjacent to the sports system or environment. Coach pressure to win and conflicts with teammates are examples of stressors in-sport, family problems and disputes with press or fans are examples of stressors external to the team, also called peripheral opponents, and showed the relative social influence of significant others in soccer performance. We can conclude that the knowledge of the direction of a given stress situation has important practical implications in preparing athletes and helping them face the performance stressors that are part of soccer daily life.
Triazole-Modified Peptidomimetics: An Opportunity for Drug Discovery and Development

Peptidomimetics play a fundamental role in drug design due to their preferential properties regarding natural peptides. In particular, compounds possessing nitrogen-containing heterocycles have been intensively studied in recent years. The triazolyl moiety incorporation decreases the molecule susceptibility to enzymatic degradation, reduction, hydrolysis, and oxidation. In fact, peptides containing triazole rings are a typical example of peptidomimetics. They have all the advantages over classic peptides. Both efficient synthetic methods and biological activity make these systems an interesting and promising object of research. Peptide triazole derivatives display a diversity of biological properties and can be obtained via numerous synthetic strategies. In this review, we have highlighted the importance of the triazole-modified peptidomimetics in the field of drug design. We present an overview on new achievements in triazolyl-containing peptidomimetics synthesis and their biological activity as inhibitors of enzymes or against cancer, viruses, bacteria, or fungi. The relevance of above-mentioned compounds was confirmed by their comparison with unmodified peptides.