Miracle-dz/UniFAR-FTUs huggingface dataset:
A Method to Automate the Discharge Summary Hospital Course for Neurology Patients

OBJECTIVE Generation of automated clinical notes has been posited as a strategy to mitigate physician burnout. In particular, an automated narrative summary of a patient's hospital stay could supplement the hospital course section of the discharge summary that inpatient physicians document in electronic health record (EHR) systems. In the current study, we developed and evaluated an automated method for summarizing the hospital course section using encoder-decoder sequence-to-sequence transformer models. MATERIALS AND METHODS We fine-tuned BERT and BART models and optimized for factuality through constraining beam search, which we trained and tested using EHR data from patients admitted to the neurology unit of an academic medical center. RESULTS The approach demonstrated good ROUGE scores with an R-2 of 13.76. In a blind evaluation, 2 board-certified physicians rated 62% of the automated summaries as meeting the standard of care, which suggests the method may be useful clinically. DISCUSSION AND CONCLUSION To our knowledge, this study is among the first to demonstrate an automated method for generating a discharge summary hospital course that approaches a quality level of what a physician would write.
On time-local solvability of the Navier-Stokes equations in Besov spaces

A time--local solution is constructed for the Cauchy problem of the $n$-dimensional Navier--Stokes equations when the initial velocity belongs to Besov spaces of nonpositive order. The space contains $L^\infty$ in some exponents, so our solution may not decay at space infinity. In order to use iteration scheme we have to establish the Holder type inequality for estimating bilinear term by dividing the sum of Besov norm with respect to levels of frequency. Moreover, by regularizing effect our solutions belong to $L^\infty$ for any positive time.
Bridges-Round 2: A study protocol to examine the longitudinal HIV risk prevention and care continuum outcomes among orphaned youth transitioning to young adulthood

Background Youth orphaned by HIV in sub–Saharan Africa experience immense hardships including social disadvantage, adverse childhood events and limited economic prospects. These adversities disrupt the normative developmental milestones and can gravely compromise their health and emotional wellbeing. The Bridges to the Future study (2012–2018) prospectively followed 1,383 adolescents, between 10–16 years, to evaluate the efficacy and cost-effectiveness of a family-based economic empowerment intervention comprising of child development accounts, financial literacy training, family income generating activities and peer mentorship. Study findings show efficacy of this contextually-driven intervention significantly improving mental health, school retention and performance and sexual health. However, critical questions, such as those related to the longitudinal impact of economic empowerment on HIV prevention and engagement in care remain. This paper presents a protocol for the follow-up phase titled, Bridges Round 2. Methods The Original Bridges study participants will be tracked for an additional four years (2022–2026) to examine the longitudinal developmental and behavioral health outcomes and potential mechanisms of the effect of protective health behaviors of the Bridges cohort. The study will include a new qualitative component to examine participants’ experiences with the intervention, the use of biomedical data to provide the most precise results of the highly relevant, but currently unknown sexual health outcomes among study participants, as well as a cost-benefit analysis to inform policy and scale-up. Discussion Study findings may contribute to the scientific knowledge for low-resource communities on the potential value of providing modest economic resources to vulnerable boys and girls during childhood and early adolescence and how these resources may offer long-term protection against known HIV risks, poor mental health functioning and improve treatment among the HIV treatment care continuum.
Quantifying climate conditions for the formation of coals and evaporites

ABSTRACT Coals and evaporites are commonly used as qualitative indicators of wet and dry environments in deep-time climate studies, respectively. Here, we combine geological records with climate simulations to establish quantitative relationships of coals and evaporites with temperature and precipitation over the Phanerozoic. We show that coal records were associated with a median temperature of 25°C and precipitation of 1300 mm yr−1 before 250 Ma. Afterwards, coal records appeared with temperatures between 0°C and 21°C and precipitation of 900 mm yr−1. Evaporite records were associated with a median temperature of 27°C and precipitation of 800 mm yr−1. The most remarkable result is that net precipitation associated with coal and evaporite records remained constant across time. The results here have important implications for quantifying climate conditions for other lithologic indicators of climate and for predicting exogenetic ore deposits.
Effects of tapering on performance in endurance athletes: A systematic review and meta-analysis

Objective To assess the responses to taper in endurance athletes using meta-analysis. Methods Systematic searches were conducted in China National Knowledge Infrastructure, PubMed, Web of Science, SPORTDiscus, and EMBASE databases. Standardized mean difference (SMD) and 95% confidence interval (CI) of outcome measures were calculated as effect sizes. Results 14 studies were included in this meta-analysis. Significant improvements were found between pre- and post-tapering in time–trial (TT) performance (SMD = −0.45; P < 0.05) and time to exhaustion (TTE) performance (SMD = 1.28; P < 0.05). However, There were no improvements in maximal oxygen consumption (V˙O2max) and economy of movement (EM) (P > 0.05) between pre- and post-tapering. Further subgroup analysis showed that tapering combined with pre-taper overload training had a more significant effect on TT performance than conventional tapering (P < 0.05). A tapering strategy that reduced training volume by 41–60%, maintained training intensity and frequency, lasted ≤7 days, 8–14 days, or 15–21 days, used a progressive or step taper could significantly improve TT performance (P < 0.05). Conclusions The tapering applied in conjunction with pre-taper overload training seems to be more conducive to maximize performance gains. Current evidence suggests that a ≤21-day taper, in which training volume is progressively reduced by 41–60% without changing training intensity or frequency, is an effective tapering strategy.
Partitioning and integrating of plant traits and phylogeny in assessing diversity along secondary forest succession in Loess Plateau of China

Abstract Assessing plant diversity during community succession based on plant trait and phylogenetic features within a community (alpha scale) and among communities (beta scale) could improve our understanding of community succession mechanism. However, whether changes of community functional diversity at alpha and beta scale are structured by different traits and whether integrating plant traits and phylogeny can enhance the ability in detecting diversity pattern have not been studied in detail. Thirty plots representing different successional stages were established on the Loess Plateau of China and 15 functional traits were measured for all coexisting species. We first analyzed the functional alpha and beta diversity along succession by decomposing species trait into alpha and beta components and then integrated key traits with phylogenetic information to explore their roles in shaping species turnover during community succession. We found that functional alpha diversity increased along successional stages and was structured by morphological traits, while beta diversity decreased during succession and was more structured by stoichiometry traits. Phylogenetic alpha diversity showed congruent pattern with functional alpha diversity because of phylogenetic conservation of trait alpha components (variation within community), while beta diversity showed incongruent pattern due to phylogenetic randomness of trait beta components (variation among communities). Furthermore, only integrating relatively conserved traits (plant height and seed mass) and phylogenetic information can raise the detecting ability in assessing diversity change. Overall, our results reveal the increasing niche differentiation within community and functional convergence among communities with succession process, indicating the importance of matching traits with scale in studying community functional diversity and the asymmetry of traits and phylogeny in reflecting species ecological differences under long‐term selection pressures.
Dodecamer assembly of a metazoan AAA+ chaperone couples substrate extraction to refolding

Ring-forming AAA+ chaperones solubilize protein aggregates and protect organisms from proteostatic stress. In metazoans, the AAA+ chaperone Skd3 in the mitochondrial intermembrane space (IMS) is critical for human health and efficiently refolds aggregated proteins, but its underlying mechanism is poorly understood. Here, we show that Skd3 harbors both disaggregase and protein refolding activities enabled by distinct assembly states. High-resolution structures of Skd3 hexamers in distinct conformations capture ratchet-like motions that mediate substrate extraction. Unlike previously described disaggregases, Skd3 hexamers further assemble into dodecameric cages in which solubilized substrate proteins can attain near-native states. Skd3 mutants defective in dodecamer assembly retain disaggregase activity but are impaired in client refolding, linking the disaggregase and refolding activities to the hexameric and dodecameric states of Skd3, respectively. We suggest that Skd3 is a combined disaggregase and foldase, and this property is particularly suited to meet the complex proteostatic demands in the mitochondrial IMS.
Development and characterization of chimera of yellow fever virus vaccine strain and Tick-Borne encephalitis virus

Tick-borne encephalitis virus (TBEV) is one of the most threatening pathogens which affects the human central nervous system (CNS). TBEV circulates widely in Northern Eurasia. According to ECDC, the number of TBE cases increase annually. There is no specific treatment for the TBEV infection, thus vaccination is the main preventive measure. Despite the existence of several inactivated vaccines currently being licensed, the development of new TBEV vaccines remains a leading priority in countries endemic to this pathogen. Here we report new recombinant virus made by infectious subgenomic amplicon (ISA) approach using TBEV and yellow fever virus vaccine strain (YF17DD-UN) as a genetic backbone. The recombinant virus is capable of effective replication in mammalian cells and induce TBEV-neutralizing antibodies in mice. Unlike the original vector based on the yellow fever vaccine strain, chimeric virus became neuroinvasive in doses of 107−106 PFU and can be used as a model of flavivirus neuroinvasiveness, neurotropism and neurovirulence. These properties of hybrid structures are the main factors limiting their practical use as vaccines platforms.
Changes in methodological study characteristics in psychology between 2010-2021

In 2015, the Open Science Collaboration repeated a series of 100 psychological experiments. Since a considerable part of these replications could not confirm the original effects and some of them pointed in the opposite direction, psychological research is said to lack reproducibility. Several general criticisms can explain this finding, such as the standardized use of undirected nil-null hypothesis tests, samples being too small and selective, lack of corrections for multiple testing, but also some widespread questionable research practices and incentives to publish positive results only. A selection of 57,909 articles from 12 renowned journals is processed with the JATSdecoder software to analyze the extent to which several empirical research practices in psychology have changed over the past 12 years. To identify journal- and time-specific changes, the relative use of statistics based on p-values, the number of reported p-values per paper, the relative use of confidence intervals, directed tests, power analysis, Bayesian procedures, non-standard α levels, correction procedures for multiple testing, and median sample sizes are analyzed for articles published between 2010 and 2015 and after 2015, and in more detail for every included journal and year of publication. In addition, the origin of authorships is analyzed over time. Compared to articles that were published in and before 2015, the median number of reported p-values per article has decreased from 14 to 12, whereas the median proportion of significant p-values per article remained constant at 69%. While reports of effect sizes and confidence intervals have increased, the α level is usually set to the default value of . 05. The use of corrections for multiple testing has decreased. Although uncommon in each case (4% in total), directed testing is used less frequently, while Bayesian inference has become more common after 2015. The overall median estimated sample size has increased from 105 to 190.
The effect of global warming on Western Mediterranean seagrasses: a preliminary agent-based modelling approach

Seagrasses are key structural elements in coastal ecosystems, and studying how temperature affects these species is crucial to anticipate the implications of global warming. In this work, we use an empirically-based numerical model to study the combined dynamics of {\it Posidonia oceanica} and {\it Cymodocea nodosa} and their resilience to sea warming. The model is parametrised using seagrass growth rates measured at the Western Mediterranean Sea. Under favorable growth conditions, our simulations predict the emergence of a coexistence region at the front between mono-specific meadows. This region can be characterised by its width and local shoot densities, which are found to depend on the coupling parameter between {\it Posidonia oceanica} and {\it Cymodocea nodosa} species. Such regions have been empirically observed in Ses Olles de Son Saura (Balearic Islands, Western Mediterranean Sea). A comparison between the field measurements at the study site with the model predictions has been used to fit the value of the coupling parameter. Field data also relates the width of the coexistence region to the average length of {\it Posidonia oceanica} leaves at the front. Remarkably, a linear relationship is found between the coupling parameter and the leaf length. In the presence of sea warming, the model predicts an exponential decay in the population of {\it Posidonia oceanica}, which is highly sensitive to temperature. This behaviour is a direct consequence of the clonal nature of the plant and can be characterised by the model parameters. Considering a scenario of high greenhouse emissions, our model forecasts that {\it Posidonia oceanica} meadows will lose 70$\%$ of their population by the year $2050$. {\it Cymodocea nodosa}, with higher thermal resilience, acts as an opportunistic species conquering the space left by the degraded {\it Posidonia oceanica}.
Qualitative analysis of a modified Leslie-Gower predator-prey model with Crowley-Martin functional responses

In this paper, we study a modified Leslie-Gower predator-prey model with Crowley-Martin functional response. We show the existence of a bounded positive invariant attracting set and establish the permanence conditions. The parameter regions for the stability and instability of the unique constant steady state solution are derived, and the existence of time-periodic orbits and non-constant steady state solutions are proved by bifurcation method.
Molecular characterization of vancomycin‐resistant Staphylococcus aureus isolated from bovine milk

Vancomycin‐resistant Staphylococcus aureus (VRSA) is a zoonotic life‐threatening pathogen. Vancomycin exhibits anti‐bacterial activity by inhibiting peptidoglycan synthesis by binding to the D‐ala‐D‐ala terminus of the peptidoglycan. But in VRSA, D‐ala‐D‐ala is replaced by D‐ala‐D‐lactate due to the presence of vanA, vanB or vanD genes. This study was intended to identify the molecular prevalence of VRSA in 768 bovine milk samples, risk factor association, antibiogram profile and bioinformatics analysis of VRSA by targeting vanB gene. Out of a total of 248 S. aureus isolates from mastitic milk samples, the phenotypic and genotypic prevalence of VRSA was estimated to be 17.74% and 10.89%, respectively. Farm‐level risk factors including use of improper milking technique, lack of milker's care during milking, unhygienic conditions during milking and no dry cow therapy were found to be significantly associated (p < 0.05). Anti‐microbial susceptibility testing of VRSA isolates exhibited the highest resistance to oxytetracycline, followed by oxacillin and Trimethoprim+sulfamethoxazole. The current study sequences showed more resemblance with reported sequences from Iraq (MN747834) and Egypt (MK095504, MK087830), which belong to vanB gene from S. aureus as compared to sequences from other countries, which belong to vanB gene from the genus Enterococcus. The Genetic Algorithm for Recombination Detection (GARD) found 234 potential breakpoints, translating into a search room of 123,883,305 models with up to 4 breakpoints. The phylogenetic motif profiling method discovered evolutionarily conserved residues across target genes' homologous protein sequences. These residues were discovered to be conserved in drug‐resistant target proteins over the evolutionary process and may play a key role in their function. The current study revealed a molecular prevalence of VRSA in dairy animals, along with molecular analysis of vancomycin resistance in S. aureus by targeting the vanB gene using standard bioinformatics tools. The occurrence of VRSA in animals requires serious attention because this pathogen has zoonotic potential, so it can become a greater risk to consumer health.
A Genetic Search Algorithm for Motion Estimation

Motion estimation is essential for many interframe video coding techniques, block matching algorithms, such as FSA and TSS, have been widely used for motion estimation. The easiest implementation is the FSA, which evaluates all the blocks in the search window and has the highest computational cost. Therefore,many fast search algorithm including TSS, have been proposed to reduce the computational complexity, but most of them are based on the assumption that there should be only one optimal solution in the search window, however, in normal cases, there always exist multitudinous local optima, so they will miss the global optima, but get a suboptimal solution. In this paper, we propose a genetic search algorithm for motion estimation(GSAME) which applies genetic operation to motion estimation. We also introduce a scheme called competition evolution, which can bring the better solutions into the next evolution, and can accelerate the iteration process converging. In this method, the motion vector of block is defined as chromosome, after crossover, mutation and competition evolution, the global optimal solutions will be got. Last we compare the GASME to TSS, FSA, and the result shows that the method not only solve the problem of being trapped to local optima, but also have speed close to that of TSS.
Effect of Family Size and Type on Maternal Rejection of Children With ADHD

Objective: This study examined the impact of family size and type on maternal rejection and its relationship with emotional-behavioral difficulties in children with ADHD compared to those typically developing. Method: The participants were mothers of 7- to 12-year-old children with ADHD (n = 102) and mothers of typically developing children (n = 102) in Kazakhstan. In this cross-sectional study, multiple linear regression analysis was performed to explore the relationship between variables. Results: Family size affected maternal rejection after accounting for children’s emotional-behavioral difficulties only in mothers of children with ADHD. The effect of family type on maternal rejection was statistically significant in both groups. Family size exacerbated the relationship between children’s emotional-behavioral difficulties and maternal rejection only in children with ADHD. The moderating effect of family type was not found in either group. Conclusion: Our findings suggest that family size and type contribute to maternal rejection of children with ADHD.
SELENOP modifies sporadic colorectal carcinogenesis and WNT signaling activity through LRP5/6 interactions

Although selenium deficiency correlates with colorectal cancer (CRC) risk, the roles of the selenium-rich antioxidant selenoprotein P (SELENOP) in CRC remain unclear. In this study, we defined SELENOP’s contributions to sporadic CRC. In human single-cell cRNA-Seq (scRNA-Seq) data sets, we discovered that SELENOP expression rose as normal colon stem cells transformed into adenomas that progressed into carcinomas. We next examined the effects of Selenop KO in a mouse adenoma model that involved conditional, intestinal epithelium-specific deletion of the tumor suppressor adenomatous polyposis coli (Apc) and found that Selenop KO decreased colon tumor incidence and size. We mechanistically interrogated SELENOP-driven phenotypes in tumor organoids as well as in CRC and noncancer cell lines. Selenop-KO tumor organoids demonstrated defects in organoid formation and decreases in WNT target gene expression, which could be reversed by SELENOP restoration. Moreover, SELENOP increased canonical WNT signaling activity in noncancer and CRC cell lines. In defining the mechanism of action of SELENOP, we mapped protein-protein interactions between SELENOP and the WNT coreceptors low-density lipoprotein receptor–related proteins 5 and 6 (LRP5/6). Last, we confirmed that SELENOP-LRP5/6 interactions contributed to the effects of SELENOP on WNT activity. Overall, our results position SELENOP as a modulator of the WNT signaling pathway in sporadic CRC.
Adherence to the Mediterranean Diet in medical students

Abstract Objective: The protective effect of the Mediterranean Diet (MeDi) is undisputed. However, adherence to MeDi has decreased in recent years, particularly in young people. The aim of this study was to evaluate adherence to MeDi in medical students and to assess the influence of knowledge acquisition as well as other factors on dietary compliance. Design: A cross-sectional study was conducted on medical students. The data were obtained through anonymous surveys that collected demographic characteristics, medical history, alcohol and tobacco consumption, physical activity and adherence to MeDi – using 14-point Mediterranean Diet Adherence Score (MEDAS) –. Adherence to MeDi and related factors were evaluated by univariate and multivariable analysis. Participants: Medical students from the first to the sixth year of the 2018–2019 academic year. Setting: The study was conducted at the university of Las Palmas de Gran Canaria. Results: Of 589 respondents (73 % women) mean aged 22 years (range 18–39), 58·9 % showed good adherence to MeDi. Adherence was significantly associated with age (P = 0·017) but not with sex or the presence of comorbidities. Independently, adherence to MeDi was higher in last academic courses (OR = 2·1; 95 % CI = 1·3, 3·2; P = 0·001), in those who consumed alcohol more frequently (OR = 1·5; 95 % CI = 1·0, 2·1; P = 0·039) and in those who practiced more exercise (OR = 1·5; 95 % CI = 1·2, 1·9; P < 0·001). Conclusions: Half of all medical students did not have a good adherence to MeDi. Adherence was higher at older age in higher academic years and related to greater physical activity. It would be convenient to quantify dietary knowledge as well as implement nutritional educational programmes, favouring a healthy lifestyle.