Miracle-dz/UniFAR-FTUs huggingface dataset:
Intake of selected foods and beverages and serum uric acid levels in adults: ELSA-Brasil (2008–2010)

Abstract Objective: To investigate the association between the intake of selected food groups and beverages and serum uric acid (UA). Design: Cross-sectional study using the baseline data (2008–2010) from the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil). Food intake was assessed by food frequency questionnaire with 114 items. Linear and logistic regressions investigated the associations between the daily intake of each food group (servings/d) and UA (mg/dl) and hyperuricemia (UA ≥ 6·8 mg/dl), respectively. All the analyses were adjusted for potential confounders, energy intake and all food groups. Setting: Teaching and research institutions from six Brazilians states. Subjects: The participants were 14 320 active and retired civil servants, aged 35–74 years. Results: Higher intake of dairy products was associated with lower serum UA levels in both sexes, with a statistical dose-response gradient. High meat intake was associated with high UA only in women, and high intake of organ meats, in men. Intake of fish and fruits, vegetables and legumes were not associated with serum UA. In men, moderate and high intake of alcoholic beverages, specifically beer and spirits, but not wine, increased UA. In women, only high intake of alcoholic beverages, specifically beer, was associated with increased serum UA. Similar associations were seen for hyperuricemia. Conclusions: Results suggest a potential beneficial role of dairy products consumption on UA levels. The association between alcohol intake and UA differed according to type of beverage and between sexes. Results reinforce the need to consider the whole diet in the analysis and to conduct sex stratified analysis.
Reluctance and Willingness for Organ Donation After Death Among the Slovene General Population

Abstract Introduction The paper presents the findings of the first large-scale survey on post-mortem organ donation among the general Slovenian population. It focuses on the reported donation willingness, the barriers to joining the register of organ donors and the position towards consent to donate organs of deceased relatives. Methods A face-to-face survey was conducted on a probability sample of 1,076 Slovenian residents between October and December 2017. The performed analyses included estimations of means and proportions for target variables, an evaluation of between-group differences and a partial proportional odds model to study the relations between organ donation willingness and socio-demographic characteristics. Results The mean reported willingness to donate one’s own organs after death was 3.77 on a 5-point scale, with less than a third of respondents claiming to be certainly willing. Only 6% of those at least tentatively willing to donate organs were certain to join the register of organ donors in the future. The most frequently reported barriers to registration were unfamiliarity with the procedure and a lack of considering it beforehand. The reported willingness to donate organs of a deceased relative strongly depended on the knowledge of the relative’s wishes, yet 80% of the respondents did not discuss their wishes with any family members. Conclusions The findings confirm the gap between the reported donation willingness and joining the register of donors. Future post-mortem organ donation strategies need to consider socio-demographic and attitudinal factors of donation willingness and help stimulate the communication about organ donation wishes between family members.
Suicide attempts by self-poisoning in the United States among 10–25 year olds from 2000 to 2018: substances used, temporal changes and demographics

Abstract Objective: To evaluate the substances used, outcomes, temporal and demographics associated with suicide attempts by self-poisoning in children and young adults aged 10–25 years old from 2000 to 2018. Methods: This is a retrospective review of suspected-suicide self-poisoning cases reported to the National Poison Data System (NPDS) from US Poison Centers from 2000 to 2018 for patients 10–25 years old. For comparison of annual rates, we obtained population data by year of age from the US Census Bureau. We evaluated changes in: monthly and annual incidence/rate per 100,000 population, substances used and outcome by patient age and demographics. Results: There were 1,677,435 cases of suicide attempt by self-poisoning among individuals 10–25 years old reported to US PCCs from 2000 to 2018. There were 410,940 self-poisoning cases (24.5%) with a serious medical outcome, and the proportion of exposures that resulted in a serious medical outcome increased with increasing age group. For the age groups of 10–12, 13–15 and 16–18 years of age, there was a significant increase after 2011, which was influenced primarily by females. The substance groups with the greatest number of serious medical outcomes were OTC analgesics, antidepressants, antihistamines and antipsychotics. ADHD medications were common in the younger age groups of 10–15 years, while the sedative/hypnotics occurred more commonly in the older age groups. The groups with the greatest increase in serious medical outcomes after 2011 were antidepressants, OTC analgesics, antihistamines and ADHD medications. Opiates were less commonly involved (7.4%) in cases with serious medical outcomes and decreased significantly in the 19–25 year-old age groups after 2012. States with a lower population per square mile had a greater number of reported cases with serious medical outcomes. There was a significant decrease in the number of cases in the age groups of 10–18 years during the traditional non-school months of June–August compared with September–May. This seasonal trend occurred among cases with all outcomes and among cases with serious medical outcomes. This decrease did not occur in the age group of 19–21 years, and there was an increase during summer months in the age group 22–25 years. Conclusions: The substances used during self-poisoning varies by age group but appears to include substances available to that age group, with a significant increase after 2011, increased rates in more rural states, and a seasonal variation of increased rates during school months among adolescents but not among young adults. Two of the top substances, OTC analgesics and antihistamines, in all age groups, comprising more than a third of all substances used, are widely available over-the-counter with no restrictions regarding access. Of additional concern, ADHD medications had the highest risk of a serious medical outcome.
Efficacy of enteric‐coated tilmicosin granules in pigs artificially infected with Actinobacillus pleuropneumoniae serotype 2

Abstract Background Porcine infectious pleuropneumonia caused by Actinobacillus pleuropneumoniae (App) is one of the most serious infectious diseases in pigs and has brought huge economic losses to the world pig industry. The aim of this trial was to evaluate the effect of enteric‐coated tilmicosin granule in the treatment and control of artificial infection of App. Methods Sixty Duroc and Yorkshire crossbred pigs (50 of which were artificially infected) were divided into six groups: BCG (Blank control group), ICG (Infection‐only control group), HDG (High‐dose enteric‐coated tilmicosin granules), MDG (Medium‐dose enteric‐coated tilmicosin granules), LDG (Low‐dose enteric‐coated tilmicosin granules) and TPG (Tilmicosin premix drug control group). The cure rate, mortality, clinical respiratory score, body temperature score, weight gain, lung score and so on were recorded. Results The cure rate of HDG and MDG was as high as 90%, the mortality was 10%, and the clinical signs recovered quickly. Conclusion The results showed that enteric‐coated tilmicosin granules had obvious therapeutic effect on artificial infection, which could reduce the damage caused by the disease and reduce the mortality.
EvoEF2: accurate and fast energy function for computational protein design

MOTIVATION The accuracy and success rate of de novo protein design remain limited, mainly due to the parameter overfitting of current energy functions and their inability to discriminate incorrect designs from correct designs. RESULTS We developed an extended energy function, EvoEF2, for efficient de novo protein sequence design, based on a previously proposed physical energy function, EvoEF. Remarkably, EvoEF2 recovered 32.5%, 47.9% and 22.3% of all, core and surface residues for 148 test monomers, and was generally applicable to protein-protein interaction design, as it recapitulated 30.9%, 42.4%, 31.3% and 21.4% of all, core, interface and surface residues for 88 test dimers, significantly outperforming EvoEF on the native sequence recapitulation. We further used I-TASSER to evaluate the foldability of the 148 designed monomer sequences, where all of them were predicted to fold into structures with high fold- and atomic-level similarity to their corresponding native structures, as demonstrated by the fact that 87.8% of the predicted structures shared a root-mean-square-deviation less than 2 Å to their native counterparts. The study also demonstrated that the usefulness of physical energy functions is highly correlated with the parameter optimization processes, and EvoEF2, with parameters optimized using sequence recapitulation, is more suitable for computational protein sequence design than EvoEF, which was optimized on thermodynamic mutation data. AVAILABILITY The source code of EvoEF2 and the benchmark datasets are freely available at https://zhanglab.ccmb. med.umich. edu/EvoEF. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Assessing the accuracy of contact predictions in CASP13

The accuracy of sequence‐based tertiary contact predictions was assessed in a blind prediction experiment at the CASP13 meeting. After 4 years of significant improvements in prediction accuracy, another dramatic advance has taken place since CASP12 was held 2 years ago. The precision of predicting the top L/5 contacts in the free modeling category, where L is the corresponding length of the protein in residues, has exceeded 70%. As a comparison, the best‐performing group at CASP12 with a 47% precision would have finished below the top 1/3 of the CASP13 groups. Extensively trained deep neural network approaches dominate the top performing algorithms, which appear to efficiently integrate information on coevolving residues and interacting fragments or possibly utilize memories of sequence similarities and sometimes can deliver accurate results even in the absence of virtually any target specific evolutionary information. If the current performance is evaluated by F‐score on L contacts, it stands around 24% right now, which, despite the tremendous impact and advance in improving its utility for structure modeling, also suggests that there is much room left for further improvement.
Microglia and astroglia proliferation within the normal appearing white matter in histologically active and inactive multiple sclerosis.

INTRODUCTION Multiple sclerosis (MS) is an autoimmune, neurodegenerative disease with the involvement of white and grey matter. Histopathological abnormalities can be also identified in normal appearing white matter (NAWM). AIM OF THE STUDY To compare the micro- and astroglia proliferation within NAWM in MS cases with and without inflammatory activity within central nervous system (CNS). MATERIAL AND METHODS In post-mortem brain examinations we investigated 13 MS cases and 5 individuals who suddenly died for cardiological reasons without neurological comorbidities. We analysed micro- and astroglia proliferation within NAWM in histologically active and inactive MS cases in relation to the control group. To avoid the possible influence of the modern disease modifying treatment (DMT) on NAWM histopathological appearance, we decided to investigate the individuals who died before the modern DMT was introduced in Poland. The morphometric analysis of micro- and astrogliosis was carried out at magnification 10 × 10 (microscopic lens × oculars = magnification 100×). The fields were expressed in mm2; each field = 0.364 mm2. In total, 775 fields of NAWM and 420 fields of white matter in the control group were morphometrically assessed. RESULTS Significantly higher microglia proliferation appeared both in MS active and inactive cases compared to controls, while there were no differences between active and inactive cases. There was a significantly higher proliferation within NAWM of active MS cases compared to the inactive ones and controls as well as between inactive cases and controls. There were no correlations between microglia and astrocytes proliferation either in active or inactive MS groups. CONCLUSIONS Our results suggest that within MS NAWM, which appears to be involved at the very least, intense diffuse micro- and astroglia reactions occur. Possibly, microglia rather support proinflammatory mechanisms, whereas astrocytes seem to be more neuroprotective. Diffuse microglia proliferation indicates that CNS immune system is chronically activated within the whole CNS.
Rapamycin for longevity: opinion article

From the dawn of civilization, humanity has dreamed of immortality. So why didn’t the discovery of the anti-aging properties of mTOR inhibitors change the world forever? I will discuss several reasons, including fear of the actual and fictional side effects of rapamycin, everolimus and other clinically-approved drugs, arguing that no real side effects preclude their use as anti-aging drugs today. Furthermore, the alternative to the reversible (and avoidable) side effects of rapamycin/everolimus are the irreversible (and inevitable) effects of aging: cancer, stroke, infarction, blindness and premature death. I will also discuss why it is more dangerous not to use anti-aging drugs than to use them and how rapamycin-based drug combinations have already been implemented for potential life extension in humans. If you read this article from the very beginning to its end, you may realize that the time is now.
Meta‐analytic and functional connectivity evidence from functional magnetic resonance imaging for an anterior to posterior gradient of function along the hippocampal axis

There is considerable evidence from non‐human animal studies that the anterior and posterior regions of the hippocampus have different anatomical connections and support different behavioural functions. Although there are some recent human studies using functional magnetic resonance imaging (fMRI) that have addressed this idea directly in the memory and spatial processing domains and provided support for it, there has been no broader meta‐analysis of the fMRI literature to determine if there is consistent evidence for functional dissociations in anterior and posterior hippocampus across all of the different cognitive domains in which the hippocampus participates. The purpose of this review is to address this gap in our knowledge using three approaches. One approach involved PubMed searches to identify relevant fMRI papers reporting hippocampal activation during episodic encoding and retrieval, semantic retrieval, working memory, spatial navigation, simulation/scene construction, transitive inference, and social cognition tasks. The second was to use a large meta‐analytic database (neurosynth) to find text terms and coactivation maps associated with the anterior and posterior hippocampal regions identified in the literature search. The third approach was to contrast the resting‐state functional connectivity of the anterior and posterior hippocampal regions using a publicly available database that includes a large sample of adults. These three approaches provided converging evidence that not only are cognitive processes differently distributed along the hippocampal axis, but there also are distinct areas coactivated and functionally connected with the anterior and posterior segments. This anterior/posterior distinction involving multiple cognitive domains is consistent with the animal literature and provides strong support from fMRI for the idea of functional dissociations across the long axis of the hippocampus.
[Staphylococcus aureus and its genotypes as a mastitis pathogen in dairy cattles - a review].

INTRODUCTION In the last decade the knowledge on Staphylococcus aureus as the etiologic agent of chronic mastitis in dairy cattle has increased. Molecular biology and increasingly whole genome sequencing provide an advanced technology far beyond the classical, phenotypic bacteriology. Staphylococcus aureus has different characteristics, thus clinical and epidemiological properties are massively dependent on the genotypes. In Switzerland, Staphylococcus aureus genotype B (GTB) is a common genotype that causes infectious mastitis. Often, half and more cows of the herd are infected. Conversely, genotype C (GTC) and some of the other Staphylococcus aureus genotypes are classified less problematic because they affect individual cows and only one mammary gland quarter. Since Staphylococcus aureus GTB causes herd problems, the associated costs are high in the dairy industry. This applies in particular in the alpine region, because GTB-positive and -negative cows are not separated during milking and the infectious pathogen can spread rapidly. The pathogen is transferred by contaminated milking liners. Staphylococcus aureus GTB is highly associated with the mammary gland. In contrast, the skin and the udder are identified as the reservoir for Staphylococcus aureus GTC and the other genotypes. Staphylococcus aureus GTC is a classic infectious pathogen in wounds and occasionally in mammary glands.
Is QUOTE-IBD a valid questionnaire for measurement of quality of care in IBD? A validation study of the Swedish version

Abstract Background: Quality of care has gained increased attention in IBD. The questionnaire Quality of Care Through the Patient’s Eyes – Inflammatory Bowel Disease (QUOTE-IBD) was the first published validated IBD-specific quality of care questionnaire. The aim of this study was to validate the Swedish version of the QUOTE-IBD. Methods: Adult outpatients (n = 400) at a gastroenterology clinic in the south-east of Sweden were asked to fill in the questionnaire. For evaluation of construct validity, patients also responded to one global item for each health care dimension in the QUOTE-IBD, as well as for their overall experience of quality of health care. Results: All quality of care dimensions (QI) correlated significantly (p < .05) with their respective global dimensional item (r = 0.016–0.43), except for accommodation (r = –0.02. Test–retest (n = 32) gave significant results for all the dimensions r = 0.31–0.80 (p < .05), except for accommodation (–0.15, p = ns). Conclusions: The construct validity of the Swedish version of QUOTE-IBD is moderate. This indicates that the QUOTE-IBD may not fully cover the health care aspects important to patients. The high number of item non-response for Performance may be related to the questions being too specific, which may also contribute to the moderate level of construct validity. The reliability is moderate and the internal consistency is good.
Extra‐pair paternity in birds

Since the first molecular study providing evidence for mating outside the pair bond in birds over 30 years ago, >500 studies have reported rates of extra‐pair paternity (EPP) in >300 bird species. Here, we give a detailed overview of the current literature reporting EPP in birds and highlight the sampling biases and patterns in the data set with respect to taxonomy, avian phylogeny and global regions, knowledge of which will be crucial for correct interpretation of results in future comparative studies. Subsequently, we use this comprehensive dataset to simultaneously test the role of several ecological and life history variables. We do not find clear evidence that variation in EPP across socially monogamous species can be explained by latitude, density (coloniality), migration, generation length, genetic structuring (dispersal distance), or climatic variability, after accounting for phylogeny. These results contrast previous studies, most likely due to the large heterogeneity within species in both EPP and the predictor of interest, indicating that using species averages might be unreliable. Despite the absence of broadscale ecological drivers in explaining interspecific variation in EPP, we suggest that certain behaviours and ecological variables might facilitate or constrain EPP, as indicated by our finding that EPP was negatively associated with latitude within noncolonial species, suggesting a role of breeding synchrony. Thus, rather than focussing on general explanations for variation in EPP across all species, a future focus should be on how various aspects of ecology or life history might have driven variation in EPP among groups of species or populations of the same species. Hence, we argue that variation in EPP can be partly explained when taking the right perspective. This comprehensive overview, and particularly the dataset provided herein will create a foundation for further studies.
WASPS: web-assisted symbolic plasmid synteny server

Abstract Motivation Comparative plasmid genome analyses require complex tools, the manipulation of large numbers of sequences and constitute a daunting task for the wet bench experimentalist. Dedicated plasmid databases are sparse, only comprise bacterial plasmids and provide exclusively access to sequence similarity searches. Results We have developed Web-Assisted Symbolic Plasmid Synteny (WASPS), a web service granting protein and DNA sequence similarity searches against a database comprising all completely sequenced natural plasmids from bacterial, archaeal and eukaryal origin. This database pre-calculates orthologous protein clustering and enables WASPS to generate fully resolved plasmid synteny maps in real time using internal and user-provided DNA sequences. Availability and implementation WASPS queries befit all current browsers such as Firefox, Edge or Safari while the best functionality is achieved with Chrome. Internet Explorer is not supported. WASPS is freely accessible at https://archaea.i2bc. paris-saclay.fr/wasps/. Supplementary information Supplementary data are available at Bioinformatics online.
LncRNA PTCSC3 inhibits the proliferation, invasion and migration of cervical cancer cells via sponging miR‐574‐5p

Dysregulation of long non‐coding RNA papillary thyroid carcinoma susceptibility candidate 3 (lncRNA PTCSC3) has been found to correlate with various types of cancers. Quantitative RT‐PCR showed a down‐regulation of PTCSC3 in cervical cancer tissues compared with normal cervical tissues. The present study aimed to investigate the role of lncRNA PTCSC3 in cervical cancer and the underlying mechanisms. PTCSC3 was overexpressed in cervical cancer cell lines C‐33A and Hela by transfection with pcDNA3.1‐lncRNA PTCSC3 expressing plasmid. Overexpression of lncRNA PTCSC3 inhibited cell proliferation, induced cell cycle arrest, and suppressed cell invasion and migration using CCK8 assay, flow cytometry, Transwell assay and wound healing examination, respectively. Western blotting analysis showed that PTCSC3 overexpression decreased the expression of cyclinD1, matrix metalloproteinases 9 (MMP9), N‐cadherin and β‐catenin and increased E‐cadherin expression. Further, PTCSC3 negatively regulated miR‐574‐5p expression and dual‐luciferase assay verified the binding activity between miR‐574‐5p and lncRNA PTCSC3. Enforced up‐regulation of miR‐574‐5p abolished the inhibitory effect of lncRNA PTCSC3 on cervical cancer cell proliferation, invasiveness and mobility. Taken together, lncRNA PTCSC3 inhibited cell growth and metastasis via sponging miR‐574‐5p in cervical cancer. Therefore, we demonstrate the tumour‐suppressive function of lncRNA PTCSC3 in cervical cancer and suggest that PTCSC3 is a potential therapeutic target for cervical cancer.