syedzayyan/paper_mill_benchmark huggingface dataset:
The effects of simulated transport conditions on the muscle tissue characteristics of white-strain layer pullets.

The objective of this study was to evaluate the effects of temperature (t)/relative humidity (rh) combinations and exposure duration (d) on the muscle tissue characteristics of layer pullets during simulated transport.While layer pullets are not processed for meat, muscle physiology can be used as an indicator to assess welfare.Pullets (n = 240) were randomly assigned to 1 of 5 t/rh combinations (-15°c uncontrolled rh [-15], 21°c 30%rh [21/30], 21°c 80%rh [21/80], 30°c 30%rh [30/30], and 30°c 80%rh [30/80]) and 2 d (4 or 8 h) in a 5 x 2 factorial arrangement (3 replications).Birds were weighed before exposure, crated (density 45.5 kg/m2) and exposed to the conditions above.After exposure, birds were weighed (live shrink calculated) and slaughtered using a small-scale facility.Postslaughter, carcasses were eviscerated, and an initial p h was obtained from the right breast and thigh.Final breast and thigh p h and color values (lightness [l∗], yellowness [b∗], and redness [a∗]) were obtained 30 h postslaughter.Left breast muscles were frozen and analyzed for thaw and cook loss 4 wk postslaughter.Data were analyzed as a randomized complete block design via anova (proc mixed; sas 9.4), with farm of origin as block.Differences were considered significant when p ≤ 0.05.Live shrink (kg) was higher for pullets exposed to 30/30 and 30/80 compared with those exposed to 21/80 (p = 0.04) and for pullets exposed for 8 h compared with 4 h (p < 0.01).Breast muscle thaw loss (%) was higher in pullets exposed for 4 h compared with 8 h (p = 0.01).Breast and thigh muscle a∗ were higher for pullets exposed to 30/30 compared with 21/30 (p = 0.02).Thigh muscle b∗ was lower for pullets exposed to -15 compared with 21/80 (p = 0.05).Breast b∗ was higher for pullets exposed for 8 h compared with 4 h (p = 0.04).The results from this study demonstrates that increasing exposure d had minor effects on pullet muscle characteristics.In addition, layer pullets coped well with thermal stressors associated with simulated transport.

Journal: Poultry science (2021)
Publication types: Journal Article
Betamethasone versus dexamethasone for inpatient preschool wheezing-A case-control study.

And objectives wheezing is one of the most common reasons for the presentation of children to primary care or the emergency ward, before 7 years of age.Current guidelines recommend a short course of oral corticosteroids (ocs) for those children with a wheezing attack severe enough to require hospitalization.However, the optimal choice of therapy is controversial.We aimed to compare the efficacy of betamethasone to that of dexamethasone in achieving clinical response in preschool children requiring hospitalization for an acute wheezing attack.Methods this was a retrospective study.Medical records of healthy children without significant comorbidities between 1 and 7 years of age (n = 234) admitted with a moderate-severity acute wheezing attack to two pediatric wards between 2014 and 2018 were included.All children were treated with either betamethasone or dexamethasone exclusively during the hospitalization.The primary outcome of interest was the length of hospital stay (los).Results the demographic parameters and the clinical severity of wheezing episodes were similar in the two study groups, as was the los.However, the dexamethasone cumulative dose used during hospitalization was significantly larger than the betamethasone cumulative dose (3.76 (1.88-5.64) vs.1.86 (1.24-3.1) mg/kg of prednisone-equivalent dose, p < .001).Conclusion in preschool children with acute wheezing requiring hospitalization, betamethasone achieved a similar clinical response when compared to dexamethasone, with a lower cumulative steroid dose.Further studies are needed to understand the additional benefits of betamethasone over other steroids or placebo.

Journal: Pediatric pulmonology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Identification of N, C-capped di- and tripeptides as selective immunoproteasome inhibitors.

A series of n, c-capped di- and tripeptides were designed as selective immunoproteasome inhibitors based on the known inhibitor 4-ca.Forty-eight new compounds were synthesized and evaluated, and the structure-activity relationship (sar) of this compound class as β5i selective inhibitors were explored.Most of these compounds showed significant inhibition against the β5i subunit of the immunoproteasome and the most potent β5i inhibitor (15) showed an ic50of 0.94 n m.A selective β5i inhibitor (54) with over 500-fold β5i/β5c selectivity was identified.Three of the inhibitors were found to selectively inhibit β5i and β5c, and showed no noticeable inhibition against the other four subunits.Six inhibitors with significant inhibitory activity against the hct-116 cells were recognized, and the most active inhibitors, 14 and 50, showed ic50values of 0.46 μm and 0.16 μm, respectively.Some selective β5i inhibitors exhibited significant inhibitory effects on the release of the cytokines tnf-α and il-6.The results not only afford effective chemical tools to elucidate the relationships between subunit selectivity and pharmacological profiles, but also offer useful clues for further optimization and development of selective immunoproteasome inhibitors.

Journal: European journal of medicinal chemistry (2022)
Publication types: Journal Article
Suitability of Human Mesenchymal Stem Cells Derived from Fetal Umbilical Cord (Wharton's Jelly) as an Alternative In Vitro Model for Acute Drug Toxicity Screening.

Preclinical toxicity screening is the first and most crucial test that assesses the safety of new candidate drugs before their consideration for further evaluation in clinical trials.In vitro drug screening using stem cells has lately arisen as a promising alternative to the "gold standard" of animal testing, but their suitability and performance characteristics in toxicological studies have so far not been comprehensively investigated.In this study, we focused on the evaluation of human mesenchymal stem cells isolated from the matrix (wharton's jelly) of fetal umbilical cord (wjscs), which bear enhanced in vitro applicability due to their unique biological characteristics.In order to determine their suitability for drug-related cytotoxicity assessment, we adopted a high-throughput methodology that evaluated their sensitivity to a selected panel of chemicals in different culture environments.Cytotoxicity was measured within 48 h by means of mts and/or nru viability assays, and was compared directly (in vitro) or indirectly (in silico) to adult human mesenchymal stem cells and to reference cell lines of human and murine origin.Our data clearly suggest that human wjscs can serve as a robust in vitro alternative for acute drug toxicity screening by uniquely combining rapid and versatile assay setup with high-throughput analysis, good representation of human toxicology, high reproducibility, and low cost.

Journal: Cells (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth.

In natural environments, bacteria must frequently cope with extremely scarce nutrients.Most studies focus on bacterial growth in nutrient replete conditions, while less is known about the stationary phase.Here, we are interested in global gene expression throughout all growth phases, including the adjustment to deep stationary phase.Results we monitored both the transcriptome and the proteome in cultures of the alphaproteobacterium rhodobacter sphaeroides, beginning with the transition to stationary phase and at different points of the stationary phase and finally during exit from stationary phase (outgrowth) following dilution with fresh medium.Correlation between the transcriptomic and proteomic changes was very low throughout the growth phases.Surprisingly, even in deep stationary phase, the abundance of many proteins continued to adjust, while the transcriptome analysis revealed fewer adjustments.This pattern was reversed during the first 90 min of outgrowth, although this depended upon the duration of the stationary phase.We provide a detailed analysis of proteomic changes based on the clustering of orthologous groups (cogs), and compare these with the transcriptome.Conclusions the low correlation between transcriptome and proteome supports the view that post-transcriptional processes play a major role in the adaptation to growth conditions.Our data revealed that many proteins with functions in transcription, energy production and conversion and the metabolism and transport of amino acids, carbohydrates, lipids, and secondary metabolites continually increased in deep stationary phase.Based on these findings, we conclude that the bacterium responds to sudden changes in environmental conditions by a radical and rapid reprogramming of the transcriptome in the first 90 min, while the proteome changes were modest.In response to gradually deteriorating conditions, however, the transcriptome remains mostly at a steady state while the bacterium continues to adjust its proteome.Even long after the population has entered stationary phase, cells are still actively adjusting their proteomes.

Journal: BMC genomics (2019)
Publication types: Comparative Study;Journal Article
Bacterial community composition of internal circulation reactor at different heights for large-scale brewery wastewater treatment.

This study analyzed bacterial community structure for large-scale brewery wastewater treatment at different heights in internal circulation (ic) reactor.Proteobacteria, bacteroidetes and chloroflexi were dominant bacteria, which accounted for 64.17%, 64.04%, 59.87% and 55.79% in phylum level, respectively.The unidentified bacteria were accounted for a large proportion in genus level, available data showed that longilinea, desulfomicrobium, caldithrix, geobacter and syntrophorhabdus were relatively abundant.Organic fermentation, hydrolysis, and acidification were mainly completed at the bottom, and production of hydrogen and methane were completed in the upper and middle part of reactor.Alpha diversity and cluster distance analysis showed the bacterial community could be divided into bottom, middle and upper part of ic reactor.The ic reactor possessed the codcrremoval efficiency of 80% - 84.09%, and bod5of 77.50% - 86% for brewery wastewater.This study would provide bacterial analysis references of ic reactor for industrial wastewater treatment in future.

Journal: Bioresource technology (2021)
Publication types: Journal Article
Functional Analysis of Sulfatide in Influenza A Virus Infection and Replication.

3-o-sulfation synthesizes sulfatide in the galactose moiety of galactosylceramide.Sulfatide is expressed in many organs such as the gastrointestinal tract, trachea, kidney, and central nervous system.Influenza a virus binds not only to glycoconjugates terminally containing sialic acid as a viral binding receptor but also to sulfatide not containing sialic acid.On the surface of infected cells, the envelope glycoprotein hemagglutinin of influenza a virus interacts with sulfatide.This interaction enhances the nuclear export of viral ribonucleoprotein complexes, resulting in efficient progeny viruses.Inhibiting this interaction would be a new potent anti-influenza drug that suppresses the progeny virus production in the infected cells.

Journal: Methods in molecular biology (Clifton, N.J.) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Symptom centrality and infrequency of endorsement identify adolescent depression symptoms more strongly associated with life satisfaction.

Although depression symptoms are often treated as interchangeable, some symptoms may relate to adolescent life satisfaction more strongly than others.To assess this premise, we first conducted a network analysis on the mood and feelings questionnaire (mfq) in a large (n = 1,059), cross-sectional sample of community adolescents (age m = 14.72 ± 1.79).The most central symptoms of adolescent depression, as indexed by strength, were self-hatred, loneliness, sadness, and worthlessness while the least frequently endorsed symptoms were self-hatred, anhedonia, feeling like a bad person, and feeling unloved.Moreover, the more central a depression symptom was in the network (i.e., higher strength), the more variance it shared with life satisfaction (r = 0.59, 95% ci: 0.27, 0.76).How frequently a symptom was endorsed was negatively associated with the variance symptoms shared with life satisfaction (r = -0.48, 95% ci: -0.63, -0.21).Cross-validated, prediction focused models found central symptoms were expected to predict more out of fold variance in life satisfaction than peripheral symptoms and frequently endorsed symptoms, but not the least frequently endorsed symptoms.These findings show certain depression symptoms may be more strongly associated with life satisfaction in adolescence and these symptoms can be identified by multiple symptom-level metrics.Limitations include use of cross-sectional data and utilizing a community sample.Better understanding which symptoms of depression share more variance with important outcomes like life satisfaction could help us develop a more fine-grained understanding of adolescent depression.

Journal: Journal of affective disorders (2021)
Publication types: Journal Article
Evaluating the Performance of Ball-Milled Silk Fibroin Films for Simultaneous Adsorption of Eight Pharmaceuticals from Water.

Pollutants mainly exist as multicomponent mixtures in the environment.Therefore, it is necessary to synthesize low-cost adsorbents that can simultaneously adsorb multiple compounds.This work presents the prospect of the adsorption of multiclass pharmaceuticals from the aqueous environment using an adsorbent derived from silk fibroin of the wild silkworm argema mimosae.The adsorbent was prepared by dissolving degummed silk fibroin and the resultant solution was cast to obtain films that were ball-milled to powder.Ftir results revealed bands corresponding to n-h and c=o stretching vibrations.Particle size distribution data generally showed two size groups in the range of 50-90 nm and 250-625 nm.The study focused on the adsorptive removal of multiple compounds consisting of eight pharmaceuticals representing various classes including a β-blocker (pindolol), anesthetic (lidocaine), stimulant (caffeine), antiviral (nevirapine), steroid (estriol), anti-epileptic (carbamazepine), and a non-steroidal anti-inflammatory drug (naproxen).The adsorption process was best fitted to the pseudo-second-order isotherm and an overall match to the freundlich model.Thermodynamic parameters suggested that the process was mainly exothermic and more spontaneous at lower temperatures.The performance of the adsorbent was further evaluated using environmental waters and the adsorbent demonstrated good potential for simultaneous adsorption of multicomponent pharmaceuticals.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Splice variant in ARX leading to loss of C-terminal region in a boy with intellectual disability and infantile onset developmental and epileptic encephalopathy.

Pathogenic variants in the x-chromosome aristaless-related homeobox (arx) gene contribute to intellectual disability, epilepsy, and associated comorbidities in affected males.Here, we report a novel splice variant in arx in a family with three affected individuals.The proband had early onset developmental and epileptic encephalopathy, his brother and mother had severe and mild intellectual disability, respectively.Massively parallel sequencing identified a novel c.1449-1g>c in intron 4 of the arx gene, predicted to abolish the splice acceptor site, retaining intron 4 and leading to a premature termination codon immediately after exon 4.As exon 5 is the last exon of the arx gene, the premature termination codon at position p.l484* would be predicted to escape nonsense-mediated m rna decay, potentially producing at least some c-terminally truncated protein.Analysis of c dna from patient lymphoblastoid cells confirmed retention of intron 4 and loss of detectable expression of arx m rna across exon 4 to exon 5.We review published cases of variants that lead to altered or early termination of the arx protein, but not complete loss of function, and are associated with phenotypes of intellectual disability and infantile onset developmental and epileptic encephalopathies, including ohtahara and west syndromes.Taken together, this novel splice variant retaining intron 4 is likely to be the cause of the early onset developmental and epileptic encephalopathy in the proband.

Journal: American journal of medical genetics. Part A (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Understanding Disclosure of Health Information to Workplace Friends.

The purpose of this study was to learn about the process of disclosing health information to a coworker friend using the lens of communication privacy management theory.The study explores emerging themes regarding health information disclosure and predicts associations between privacy, social support, risk, stigma, and the willingness to disclose health information to a friend at work.Employees were asked to recall a time they shared health information with a coworker friend and report about the interaction via open-ended items and scales on a survey.The study found that as emotional support, instrumental support, perceived risk, and stigma of the information increased, so did the tendency to disclose to a coworker friend.Increased privacy of the information was associated with a decrease in the tendency to disclose.A thematic analysis of the open-ended results also revealed that employees shared information associated with personal on-going health problems to seek support, to relate to their coworker friends, and to maintain their friendship.The findings also indicated that employees were likely to receive social support from their coworker friends even if they were not seeking it.

Journal: Behavioral sciences (Basel, Switzerland) (2022)
Publication types: Journal Article
The impact of proteostasis dysfunction secondary to environmental and genetic causes on neurodegenerative diseases progression and potential therapeutic intervention.

Aggregation of particular proteins in the form of inclusion bodies or plaques followed by neuronal death is a hallmark of neurodegenerative proteopathies such as primary parkinsonism, alzheimer's disease, lou gehrig's disease, and huntington's chorea.Complex polygenic and environmental factors implicated in these proteopathies.Accumulation of proteins in these disorders indicates a substantial disruption in protein homeostasis (proteostasis).Proteostasis or cellular proteome homeostasis is attained by the synchronization of a group of cellular mechanisms called the proteostasis network (pn), which is responsible for the stability of the proteome and achieves the equilibrium between synthesis, folding, and degradation of proteins.In this review, we will discuss the different types of pn and the impact of pn component dysfunction on the four major neurodegenerative diseases mentioned earlier.Graphical abstract.

Journal: Environmental science and pollution research international (2020)
Publication types: Journal Article;Review
Two new species of the millipede family Trichopolydesmidae from Bahia state, northeastern Brazil, including a remarkable threatened troglobiont (Diplopoda, Polydesmida).

Phaneromerium troglopterygotum sp.Nov.And moojenodesmus schubarti sp.Nov.Are described from bahia state, northeastern brazil.The former species is a remarkable troglobiont relict endemic to a single limestone cave from the serra do ramalho karst area; it shows some clear-cut troglomorphic traits, and particular biology and ecology.The latter species occurs close to limestone outcrops of the serra do iuiu karst area.Both regions generally support a typical dry tropical climate, but the cave and outcrop habitats represent sites with high humidity, this being essential for the survival of these and other species.

Journal: Zootaxa (2022)
Publication types: Journal Article
Enhanced Cellular Materials through Multiscale, Variable-Section Inner Designs: Mechanical Attributes and Neural Network Modeling.

In the current work, the mechanical response of multiscale cellular materials with hollow variable-section inner elements is analyzed, combining experimental, numerical and machine learning techniques.At first, the effect of multiscale designs on the macroscale material attributes is quantified as a function of their inner structure.To that scope, analytical, closed-form expressions for the axial and bending inner element-scale stiffness are elaborated.The multiscale metamaterial performance is numerically probed for variable-section, multiscale honeycomb, square and re-entrant star-shaped lattice architectures.It is observed that a substantial normal, bulk and shear specific stiffness increase can be achieved, which differs depending on the upper-scale lattice pattern.Subsequently, extended mechanical datasets are created for the training of machine learning models of the metamaterial performance.Thereupon, neural network (nn) architectures and modeling parameters that can robustly capture the multiscale material response are identified.It is demonstrated that rather low-numerical-cost nn models can assess the complete set of elastic properties with substantial accuracy, providing a direct link between the underlying design parameters and the macroscale metamaterial performance.Moreover, inverse, multi-objective engineering tasks become feasible.It is shown that unified machine-learning-based representation allows for the inverse identification of the inner multiscale structural topology and base material parameters that optimally meet multiple macroscale performance objectives, coupling the nn metamaterial models with genetic algorithm-based optimization schemes.

Journal: Materials (Basel, Switzerland) (2022)
Publication types: Journal Article