Miracle-dz/UniFAR-FTUs huggingface dataset:
WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans

Abstract WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.
Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution

Abstract Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least two species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene–Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.
Digital Teaching in Medical Education: Scientific Literature Landscape Review

Background Digital teaching in medical education has grown in popularity in the recent years. However, to the best of our knowledge, no bibliometric report to date has been published that analyzes this important literature set to reveal prevailing topics and trends and their impacts reflected in citation counts. Objective We used a bibliometric approach to unveil and evaluate the scientific literature on digital teaching research in medical education, demonstrating recurring research topics, productive authors, research organizations, countries, and journals. We further aimed to discuss some of the topics and findings reported by specific highly cited works. Methods The Web of Science electronic database was searched to identify relevant papers on digital teaching research in medical education. Basic bibliographic data were obtained by the “Analyze” and “Create Citation Report” functions of the database. Complete bibliographic data were exported to VOSviewer for further analyses. Visualization maps were generated to display the recurring author keywords and terms mentioned in the titles and abstracts of the publications. Results The analysis was based on data from 3978 papers that were identified. The literature received worldwide contributions with the most productive countries being the United States and United Kingdom. Reviews were significantly more cited, but the citations between open access vs non–open access papers did not significantly differ. Some themes were cited more often, reflected by terms such as virtual reality, innovation, trial, effectiveness, and anatomy. Different aspects in medical education were experimented for digital teaching, such as gross anatomy education, histology, complementary medicine, medicinal chemistry, and basic life support. Some studies have shown that digital teaching could increase learning satisfaction, knowledge gain, and even cost-effectiveness. More studies were conducted on trainees than on undergraduate students. Conclusions Digital teaching in medical education is expected to flourish in the future, especially during this era of COVID-19 pandemic.
Organoid-based expansion of patient-derived primary alveolar type 2 cells for establishment of alveolus epithelial Lung-Chip cultures

Development of effective treatment strategies for lung tissue destruction as seen in emphysema would greatly benefit from representative human in vitro models of the alveolar compartment. Studying how cellular cross talk and/or (altered) biomechanical cues affect alveolar epithelial function could provide new insight for tissue repair strategies. Preclinical models of the alveolus ideally combine human primary patient-derived lung cells with advanced cell culture applications such as breathing-related stretch, to reliably represent the alveolar microenvironment. To test the feasibility of such a model, we isolated primary alveolar type 2 cells (AEC2s) from patient-derived lung tissues including those from patients with severe emphysema, using magnetic bead-based selection of cells expressing the AEC2 marker HTII-280. We obtained pure alveolar feeder-free organoid cultures using a minimally modified commercial medium. This was confirmed by known AEC2 markers as well as by detection of lamellar bodies using electron microscopy. Following (organoid-based) expansion, cells were seeded on both cell culture inserts and the Chip-S1 Organ-Chip that has a flexible polydimethylsiloxane (PDMS) membrane enabling the application of dynamic stretch. AEC2s cultured for 7 days on inserts or the chip maintained expression of HTII-280, prosurfactant protein C (SP-C), SP-A and SP-B, and zonula occludens-1 (ZO-1) also in the presence of stretch. AEC2s cultured on the chip showed lower expression levels of epithelial-mesenchymal transition-related vimentin expression compared with static cultures on inserts. The combination of a straightforward culture method of patient-derived AEC2s and their application in microfluidic chip cultures supports successful development of more representative human preclinical models of the (diseased) alveolar compartment.
Induced Cognitive Impairments Reversed by Grafts of Neural Precursors: A Longitudinal Study in a Macaque Model of Parkinson's Disease

Parkinson's disease (PD) evolves over an extended and variable period in humans; years prior to the onset of classical motor symptoms, sleep and biological rhythm disorders develop, significantly impacting the quality‐of‐life of patients. Circadian‐rhythm disorders are accompanied by mild cognitive deficits that progressively worsen with disease progression and can constitute a severe burden for patients at later stages. The gold‐standard 6‐methyl‐1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridin (MPTP) macaque model of PD recapitulates the progression of motor and nonmotor symptoms over contracted periods of time. Here, this multidisciplinary/multiparametric study follows, in five animals, the steady progression of motor and nonmotor symptoms and describes their reversal following grafts of neural precursors in diverse functional domains of the basal ganglia. Results show unprecedented recovery from cognitive symptoms in addition to a strong clinical motor recuperation. Both motor and cognitive recovery and partial circadian rhythm recovery correlate with the degree of graft integration, and in a subset of animals, with in vivo levels of striatal dopaminergic innervation and function. The present study provides empirical evidence that integration of neural precursors following transplantation efficiently restores function at multiple levels in parkinsonian nonhuman primates and, given interindividuality of disease progression and recovery, underlines the importance of longitudinal multidisciplinary assessments in view of clinical translation.
Slovenian Validation of the Mental Health Literacy Scale (S-MHLS) on the General Population: A Four-Factor Model

The aim of the present validation study is to determine the psychometric properties of the Slovenian version of the Mental Health Literacy Scale. For this purpose, the factorial structure, internal consistency, cross-cultural, convergent and discriminant validity were assessed. The measure was translated and adapted to Slovenian context through a blind back-translation process. It was applied to a representative sample of the Slovenian adult population via an online research panel. A total of 1189 participants (598 women), aged between 18 and 95 years (M = 46.7, SD = 16.2) completed the survey. Confirmatory and exploratory factor analyses, reliability analyses, hypothesis testing, and correlational analyses were conducted. The analyses rejected a hypothesised unidimensional model and demonstrated that a four-factor model with 27 items was the most theoretically and psychometrically adequate. The Slovenian version of Mental Health Literacy Scale (S-MHLS) consists of the following factors: (1) Attitudes Towards People With Mental Health Problems, (2) General Attitudes Towards Mental Health Problems and Help-Seeking, (3) Recognition of Mental Health Disorders and (4) Knowledge About Seeking Mental Health Information. The factors have adequate construct validity and internal consistency, which is also adequate for the entire S-MHLS. However, a decreased scope of the content might result in an inadequate representation of the construct of mental health literacy. In addition, the psychometric interpretation of the MHLS varies widely in validation studies across different linguistic contexts. Therefore, we propose a further improvement of the instrument with a psychometrically and theoretically sound multifactorial structure that demonstrates strong cross-cultural validity.
Simulation and Optimization of four-phase Wound-field Doubly Salient Generator

The Wound-field Doubly Salient Generator(WFDSG) has the prominent advantages of simple structure,high reliability,high power and controllable excitation.A lot of research works on the topologies of this kind of machines were done by the scholars at home and abroad.A four-phase 24 /18 poles WFDSG is modeled by Ansoft.The influences of different structure parameters on steady characteristics were investigated.Finite element analysis was carried out to investigate its steady characteristics,such as field distribution,air gap magnetic density,field flux,inductance,armature current,armature voltage and electro-magnetic torque.It is found that the widened rotor pole and stator pole are helpful to improve the power characteristic.The optimization results provide the design references for the four-phase WFDSG.
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi

Abstract Whole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic data sets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of single nucleotide polymorphisms extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomize the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than 2 million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the data set to nonintrogressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome data sets. [Incomplete lineage sorting; introgression; linkage disequilibrium; multispecies coalescence; rapid radiation; soft polytomy. ]
Residual concentrations of antimicrobial growth promoters in poultry litter favour plasmid conjugation among Escherichia coli

Considering that plasmid conjugation is a major driver for the dissemination of antimicrobial resistance in bacteria, this study aimed to investigate the effects of residual concentrations of antimicrobial growth promoters (AGPs) in poultry litter on the frequencies of IncFII‐FIB plasmid conjugation among Escherichia coli organisms. A 2 × 5 factorial trial was performed in vitro, using two types of litter materials (sugarcane bagasse and wood shavings) and five treatments of litter: non‐treated (CON), herbal alkaloid sanguinarine (SANG), AGPs monensin (MON), lincomycin (LCM) and virginiamycin (VIR). E. coli H2332 and E. coli J62 were used as donor and recipient strains, respectively. The presence of residues of monensin, lincomycin and virginiamycin increased the frequency of plasmid conjugation among E. coli in both types of litter materials. On the contrary, sanguinarine significantly reduced the frequency of conjugation among E. coli in sugarcane bagasse litter. The conjugation frequencies were significantly higher in wood shavings compared with sugarcane bagasse only in the presence of AGPs. Considering that the presence of AGPs in the litter can increase the conjugation of IncFII‐FIB plasmids carrying antimicrobial resistance genes, the real impact of this phenomenon on the dissemination of antimicrobial resistant bacteria in the poultry production chain must be investigated.
Behaviour change theories and techniques used to inform nutrition interventions for adults undergoing bariatric surgery: A systematic review

Abstract Aim This systematic review aimed to describe behaviour change theories and techniques used to inform nutrition interventions for adults undergoing bariatric surgery. Methods A systematic search was conducted across PubMed, PsycInfo, CENTRAL, EMBASE and CINAHL from inception until 09 March 2021. Eligible studies were randomised controlled trials involving nutrition interventions performed by a healthcare provider, to adults that were waitlisted or had undergone bariatric surgery and received a nutrition intervention explicitly informed by one or more behaviour change theories or behaviour change techniques. Screening was conducted independently by two authors. Behaviour change techniques were examined using the behaviour change technique taxonomy version one which includes 93 hierarchical techniques clustered into 16 groups. Quality of included studies was assessed using Cochrane risk of bias 2.0. Results Twenty‐one publications were included, involving 15 studies and 14 interventions, with 1495 participants. Bias was low or had some concerns. Two interventions reported using behaviour change theories (transtheoretical model and self‐determination theory). Thirteen behaviour change technique taxonomy groupings and 29 techniques were reported across 14 interventions. Common techniques included ‘1.2 Problem solving’ (n = 9 studies), ‘3.1 Social support (unspecified)’ (n = 9 studies), ‘1.1 Goal setting (behaviour)’ (n = 6 studies) and ‘2.3 Self‐monitoring of behaviour’ (n =‐ 6 studies). Conclusion While behaviour change techniques have been included, behaviour change theory is not consistently reported and/or adopted to inform nutrition interventions for adults undergoing bariatric surgery. Integrating behaviour change theory and techniques in nutrition interventions is important for researchers and bariatric surgery teams, including dietitians, to effectively target behaviours for this population.
The associations between motivational climate, basic psychological needs and dropout in volleyball – A comparison across competitive levels

ABSTRACT The purpose of this study was to investigate the importance of motivational climate for the satisfaction of psychological needs and dropout in recreational, intermediate and elite volleyball. Seven thousand nine hundred thirty six volleyball players from all 321 volleyball clubs across Denmark were invited to participate in the study. Three thousand three thirty answered the questionnaire and 2150 were included in the analysis. Dropout from Volleyball was measured as the proportion of players that had stopped playing volleyball over the last year. The coach-created motivational climate was measured using the Motivational Climate Scale for Youth Sports. The satisfaction of players’ psychological needs was measured using an adapted version of the basic psychological needs in exercise scale. The psychometric scales were validated and showed good model fit. For volleyball players of all levels, the degree of mastery climate predicted the satisfaction of the players’ basic psychological needs satisfaction during volleyball which was, in turn, associated with lower dropout rates. Performance climate had a weak negative association with the satisfaction of psychological needs on the intermediate level only. When adjusting the models for the negative association between performance climate and mastery climate this negative association became nonsignificant and a weak positive association to needs satisfaction emerged for players at the elite level. Findings confirm that the coach-created mastery climate in volleyball teams is important for the satisfaction of players’ basic psychological needs and continuation within the sport across the recreational, intermediate and elite levels. Highlights Coach-created mastery climate in volleyball teams was positively associated with the satisfaction of the players’ basic psychological and negatively associated with dropout. These associations between coach created climate, need satisfaction and dropout were similar across different sporting levels. Performance orientation had little influence and seemed mainly problematic if it was at the expense of mastery climate.
Myokine-mediated exercise effects: the role of myokine meteorin-like hormone (Metrnl)

Abstract Meterorin-like hormone (Metrnl), as a novel secreted factor, has been shown to be involved in physiological and pathophysiological processes. The behaviour of Metrnl in metabolic conditions like type 2 diabetes is conflicting. Metrnl-mediated (treatment with Metrnl) auto/paracrine actions in skeletal muscle are glucose uptake, fat oxidation and muscle regeneration. Exercise-induced Metrnl actions are increased fat oxidation in both skeletal muscle and adipose tissue, the control of inflammation in adipose tissue (metainflammation), and the regulation of muscle regeneration. Based on the current knowledge, Metrnl as a myokine can establish the muscle-fat crosstalk; however, the ability of Metrnl as a myokine to create other crosstalks remains unclear yet. Additionally, given the considerable anti-inflammatory roles of Metrnl in muscle regeneration, it could be a potential therapeutic candidate for muscle-related inflammatory diseases and ageing skeletal muscle which need to be addressed in the future studies.
HIV Stress Exchange: Queer Men, Intergenerational Stress, and Intimacy Amidst the Time of HIV

ABSTRACT HIV remains a principal inequity for queer men across the United States. Biomedical practices all but dominate interventions, and HIV-related stress persists among queer men. Regarding HIV as discourse is not well represented in prevention and care. This study is a response, then, to this need that seeks to build an HIV-informed model of praxis, entitled HIV Stress Exchange. A Queer Discourse Study was conducted with 20 queer men across two generations, pre-AIDS and post-AIDS. The data included in-depth interviews and material resources participants brought to the conversation. In all, this data speaks to the ways in which HIV is given life in discourse and what meaning it holds in embodied lives. Resultantly, five themes materialized, inclusive of all ages and sero-statuses: HIV provided meaning as in-/validated, un-/voiced, un-/intelligible, holding intimacy/-ies, and being PrEP/-ared. Based on the findings, the conceptual model for HIV Stress Exchange is presented along with an HIV-informed model of practice.
Trends in Global, Regional, and National Burden and Quality of Care Index for Liver Cancer by Cause from Global Burden of Disease 1990‐2019

Despite the tremendous burden of liver cancer and its underlying causes on humankind, there appear to be heterogeneities in coping approaches. The objective of this study was to compare the burden and the quality‐of‐care of liver cancer by causes among different countries and regions in both sexes and various age groups 1990‐2019. Data of liver cancer and underlying causes, including hepatitis B virus (HBV), hepatitis C virus (HCV), alcohol use, nonalcoholic steatohepatitis (NASH), and other causes were obtained from the Global Burden of Diseases 2019. Incidence, prevalence, death, and disability‐adjusted life‐years (DALYs) were assessed. Principal component analysis was used to combine age‐standardized mortality‐to‐incidence ratio, DALY‐to‐prevalence ratio, prevalence‐to‐incidence ratio, and years of life lost–to–years lived with disability into a single proxy named Quality of Care Index (QCI). Globally, the age‐standardized incidence, DALYs, and death rates decreased from 1990 to 2019, while the QCI scores increased by 68.5%. The QCI score of liver cancer was from as high as 83.3 in high Sociodemographic Index (SDI) countries to values as low as 26.4 in low SDI countries in 2019. Japan had the highest QCI score (QCI = 100). The age‐standardized death rates of liver cancer due to all underlying causes were decreasing during the past 30 years, with the most decrease for HBV. Consistently, the global QCI scores of liver cancer due to HBV, HCV, alcohol use, NASH, and other causes reached 53.5, 61.8, 54.3, 52.9, and 63.7, respectively, in 2019. Conclusion: Although the trends in burden are decreasing and the QCI improved from 1990 to 2019 globally, there is a wide gap between countries. Given the inequities in health care quality, there is an urgent need to address discrimination and bridge the gap.