syedzayyan/paper_mill_benchmark huggingface dataset:
High-quality chromosome-scale de novo assembly of the Paspalum notatum 'Flugge' genome.

Paspalum notatum 'flugge' is a diploid with 20 chromosomes (2n = 20) multi-purpose subtropical herb native to south america and has a high ecological significance.It is currently widely planted in tropical and subtropical regions.Despite the gene pool of p.Notatum 'flugge' being unearthed to a large extent in the past decade, no details about the genomic information of relevant species in paspalum have been reported.In this study, the complete genome information of p.Notatum was established and annotated through sequencing and de novo assembly of its genome.Results the latest pac bio third-generation hi fi assembly and sequencing revealed that the genome size of p.Notatum 'flugge' is 541 m.The assembly result is the higher index among the genomes of the gramineous family published so far, with a contig n50 = 52mbp, scaffold n50 = 49mbp, and buscos = 98.1%, accounting for 98.5% of the estimated genome.Genome annotation revealed 36,511 high-confidence gene models, thus providing an important resource for future molecular breeding and evolutionary research.A comparison of the genome annotation results of p.Notatum 'flugge' with other closely related species revealed that it had a close relationship with zea mays but not close compared to brachypodium distachyon, setaria viridis, oryza sativa, puccinellia tenuiflora, echinochloa crusgalli.An analysis of the expansion and contraction of gene families suggested that p.Notatum 'flugge' contains gene families associated with environmental resistance, increased reproductive ability, and molecular evolution, which explained its excellent agronomic traits.Conclusion this study is the first to report the high-quality chromosome-scale-based genome of p.Notatum 'flugge' assembled using the latest pac bio third-generation hi fi sequencing reads.The study provides an excellent genetic resource bank for gramineous crops and invaluable perspectives regarding the evolution of gramineous plants.

Journal: BMC genomics (2022)
Publication types: Journal Article
Synchronous renal cell carcinoma and pheochromocytoma presenting as acute decompensated heart failure.

We report a 49-year-old woman who presented with a hypertensive crisis and acute heart failure and reduced left ventricular systolic function.An abdominal ultrasonography revealed a huge lobulated heterogeneous mass at the lower pole of the right kidney and a mass over the left suprarenal area, which were further delineated by magnetic resonance imaging.The patient underwent laparoscopic right radical nephrectomy and left adrenalectomy.Histopathological analysis confirmed the diagnoses of clear cell renal cell carcinoma of the right kidney with metastasis to the lung; and atypical pheochromocytoma of the left adrenal gland.Target therapy was initiated, which resulted in stabilization of the patient's tumors and the recovery of her heart function.To avoid a delayed diagnosis and catastrophic outcome, clinicians should consider such rare causes of acute decompensated heart failure.

Journal: Journal of postgraduate medicine (2019)
Publication types: Case Reports;Journal Article
Online re-examination of postgraduate medical students during the COVID-19 pandemic.

Postgraduate entrance examination (the unified national graduate entrance examination) is the major way for chinese medical undergraduate student to apply for postgraduate studies.It consists of two stages: the preliminary basic written test and the re-examination in form of both written tests and interviews.With the spread of covid-19, the traditional on-site re-examination of postgraduates must be changed to online re-examination.By comparing the re-examination process and admission results of online and on-site re-examination, we studied the feasibility of online re-examination for postgraduates and measures to improve it.Methods this was a retrospective cohort study using data from the unified national graduate entrance examination.Our sample population was the applicants to peking university third hospital (puth) who completed re-examinations.In total, 281 records were successively selected from march 2017 to may 2020.By comparing the re-examination process and admission results of the 2020 online re-examination with those of the 2017-2019 on-site re-examinations, we analyzed the process, difficulties and improvement of online re-examination.Results a total of 281 subjects were included, of whom 77.9% completed an on-site re-examination in 2017-2019 and 22.1% completed the 2020 online re-examination.In the on-site re-examinations, 70.8% of the students were admitted, and in the online re-examination, 74.2% of the students were admitted.There were no significant differences between the students who completed on-site and online re-examinations in terms of gender, recent graduation, cultivation type, graduate from a key university, and admission (p>0.05).The on-site and online re-examination results were very similar among the admitted students.The multivariable logistic regression analysis showed that online re-examination had no effect on student admissions.Students seeking professional degree were less likely to be admitted than those seeking academic degree, and those with a better standardized rank in medicine and a better standardized rank of re-examination score were more likely to be admitted.Conclusions the online re-examination implemented in 2020 during the covid-19 pandemic achieved the same selective effect as on-site re-examination.Effective time management, a standardized test question template, well-trained staff and effective technology are the keys to success.

Journal: BMC medical education (2022)
Publication types: Journal Article
The pain self-management paradox: why do we focus on the individual when life context plays such a major role?

Although there has been a drive toward pain self-management, self-management has not yet in my opinion been successfully defined or evaluated and neither has it been consistently translated from idea to practice.In this perspective article, i identify gaps in our approach to pain management and argue that even though we know life context plays a huge role in influencing our health, by and large we fail to take this into account.I argue for a shift in focus away from the 'self' and explore how we might be able to do this within the constraints of our tired and over-stretched health system.

Journal: Pain management (2021)
Publication types: Journal Article
Shyness Weakens the Agreeableness-Prosociality Association via Social Self-Efficacy: A Moderated-Mediation Study of Chinese Undergraduates.

Using a sample of 1383 undergraduate students (mage= 20.06,nfemale= 817), this study tested a moderated mediation model in which shyness moderated the association between agreeableness and prosocial behavior, as well as the relation between agreeableness and social self-efficacy (sse).Results showed (when gender, age, and family socio-economic status were controlled) that agreeableness exerted a positive effect on prosocial behavior (psb) toward three types of recipients (i.e., family members, friends/acquaintances, strangers), and this effect was mediated by sse and moderated by shyness.The relationships between agreeableness and psb were more positive under low shyness than that under high shyness condition.In addition, shyness also moderated the first stage of mediation model (i.e., the agreeableness-sse association), showing that the relation between agreeableness and sse was more positive under low shyness than that under high shyness condition.Identifying the moderation effect of shyness provides evidence that personality traits may operate in an interactive manner.This may shed new light on why there are inconsistent findings regarding the agreeableness-prosociality association.

Journal: Frontiers in psychology (2019)
Publication types: Journal Article
Sensory Analysis and Consumer Research in New Meat Products Development.

This review summarises the main sensory methods (traditional techniques and the most recent ones) together with consumer research as a key part in the development of new products, particularly meat products.Different types of sensory analyses (analytical and affective), from conventional methods (quantitative descriptive analysis) to new rapid sensory techniques (check all that apply, napping, flash profile, temporal dominance of sensations, etc.) have been used as crucial techniques in new product development to assess the quality and marketable feasibility of the novel products.Moreover, an important part of these new developments is analysing consumer attitudes, behaviours, and emotions, in order to understand the complex consumer-product interaction.In addition to implicit and explicit methodologies to measure consumers' emotions, the analysis of physiological responses can also provide information of the emotional state a food product can generate.Virtual reality is being used as an instrument to take sensory analysis out of traditional booths and configure conditions that are more realistic.This review will help to better understand these techniques and to facilitate the choice of the most appropriate at the time of its application at the different stages of the new product development, particularly on meat products.

Journal: Foods (Basel, Switzerland) (2021)
Publication types: Journal Article;Review
Effect of infection after liver cancer interventional therapy on T lymphocyte subsets and Toll-like receptors in peripheral blood mononuclear cells and its mechanism.

The t lymphocyte subset levels are an indicator used to evaluate the immune status of the body.In recent years, many studies have investigated the correlation between t lymphocyte subset levels and postoperative infection.Objectives to investigate the incidence of infection after liver cancer interventional therapy and its influence on t lymphocyte subset levels and toll-like receptors (tlrs).Material and methods a total of 325 patients with primary liver cancer receiving interventional therapy were divided into an infection group (n = 37) and a non-infection group (n = 288).The infection site and the distribution of pathogenic bacteria in the infection group were observed.The serum t lymphocyte subset level and tlr2 and tlr4 levels in peripheral blood mononuclear cells were compared.The clinical value of the postoperative tlr2 and tlr4 levels in evaluating infection was analyzed using receiver operating characteristic (roc) curves.Results among 51 strains of pathogens isolated from the infected patients, strains of escherichia coli (27.45%) and pseudomonas aeruginosa (19.61%) were the most commonly observed.After surgery, the levels of cd3+, cd4+ and cd4+/cd8+ decreased, while the level of cd8+ increased in both groups; the levels of tlr2 and tlr4 decreased in the non-infection group, while the levels of tlr2 and tlr4 increased in the infection group (all p < 0.05).Furthermore, the decreases and increases were more significant in the infection group than in the non-infection group (all p < 0.001).The area under the curve of postoperative tlr2 and tlr4 levels in evaluating infection were greater than 0.700 (p < 0.001).Conclusions gram-negative bacteria account for the majority of infections in patients after liver cancer interventional therapy, and the main infection sites are the lung and abdomen.The infected patients show changes in t lymphocyte level and decreased immune function.The tlr2 and tlr4 can be used as auxiliary indicators to evaluate infection after surgery.

Journal: Advances in clinical and experimental medicine : official organ Wroclaw Medical University (2022)
Publication types: Journal Article
Effect of Electrode Distances on Remediation of Eutrophic Water and Sediment by Sediment Microbial Fuel Cell Coupled Floating Beds.

Efficient and sustainable technologies for cleaning of contaminated water and sediments are in urgent demand.In this study, a new type of sediment microbial fuel cell coupled floating bed (fb-smfc) was developed to repair eutrophic water and sediment in a cleaner way.The effect of electrode spacing on the power generation capacity and the synchronous remediation of pollutants from eutrophic water and sediment were studied.When the electrode distance was 60 cm, the maximum power generation and pollutant removal effects were obtained.At the end of the experiment, the maximum output voltage was 0.4 v, and the chemical oxygen demand (codcr, potassium dichromate method), total nitrogen (tn), and total phosphorus (tp) contents in the overlying water were 8 mg/l, 0.7 mg/l, and 0.39 mg/l.The corresponding removal rates were 88.2%, 78.8%, and 59.0%, respectively.The removal rates of organic matter and tn in the sediment were 12.8% and 86.4%, respectively, and the fixation rate of tp was 29.2%.Proteobacteria was the dominant phylum of bacteria in the sediment and anode.Many anaerobic bacteria were found in the overlying water, which facilitated denitrification.Overall, the results of this research revealed a highly efficient and reliable strategy for eutrophic water and sediment remediation, aquatic ecosystems restoration, and human health protection.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Generation and Implementation of a Patient-Centered and Patient-Facing Genomic Test Report in the EHR.

Context communication of genetic laboratory results to patients and providers is impeded by the complexity of results and reports.This can lead to misinterpretation of results, causing inappropriate care.Patients often do not receive a copy of the report leading to possible miscommunication.To address these problems, we conducted patient-centered research to inform design of interpretive reports.Here we describe the development and deployment of a specific patient-centered clinical decision support (cds) tool, a multi-use patient-centered genomic test report (pgr) that interfaces with an electronic health record (ehr).Implementation process a pgr with a companion provider report was configured for implementation within the ehr using locally developed software (compasstm) to manage secure data exchange and access.Findings we conducted semi-structured interviews with patients, family members, and clinicians that showed they sought clear information addressing findings, family implications, resources, prognosis and next steps relative to the genomic result.Providers requested access to applicable, available clinical guidelines.Initial results indicated patients and providers found the pgr contained helpful, valuable information and would provide a basis for result-related conversation between patients, providers and family.Major themes direct patient involvement in the design and development of a pgr identified format and presentation preferences, and delivery of relevant information to patients and providers, prompting the creation of a cds tool.Conclusions research and development of patient-centered cds tools designed to support improved patient outcomes, are enhanced by early and substantial engagement of patients in contributing to all phases of tool design and development.

Journal: EGEMS (Washington, DC) (2018)
Publication types: Case Reports;Journal Article
Interactions between autophagy and phytohormone signaling pathways in plants.

Autophagy is a conserved recycling process with important functions in plant growth, development, and stress responses.Phytohormones also play key roles in the regulation of some of the same processes.Increasing evidence indicates that a close relationship exists between autophagy and phytohormone signaling pathways, and the mechanisms of interaction between these pathways have begun to be revealed.Here, we review recent advances in our understanding of how autophagy regulates hormone signaling and, conversely, how hormones regulate the activity of autophagy, both in plant growth and development and in environmental stress responses.We highlight in particular recent mechanistic insights into the coordination between autophagy and signaling events controlled by the stress hormone abscisic acid and by the growth hormones brassinosteroid and cytokinin and briefly discuss potential connections between autophagy and other phytohormones.

Journal: FEBS letters (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Neighborhood Disadvantage and Allostatic Load in African American Women at Risk for Obesity-Related Diseases.

Introduction african american women have higher rates of obesity and related chronic disease than other demographic groups.The poorer health of african american women compared with other groups may be explained by allostatic load, or cumulative physiologic stress, due to chronic socioeconomic disadvantage.The objective of this study was to evaluate neighborhood and individual factors contributing to allostatic load in african american women at risk for obesity-related diseases.Methods this study evaluated the relationship of allostatic load with neighborhood disadvantage, individual socioeconomic determinants, and synergism between neighborhood and socioeconomic disadvantage, along with health behaviors and other factors as mediators in african american women.Our sample consisted of 220 african american women at risk of obesity-related diseases enrolled in the better me within program (mean [standard deviation] age, 50.1 [11.2] y; mean [standard deviation] body mass index, 36.7 [8.4] kg/m2).Allostatic load score for each participant was calculated by summing the number of biomarkers (of 9 biomarkers) that were determined to be in the high-risk quartile.Results poisson regression of neighborhood disadvantage and individual socioeconomic determinants found that neighborhood disadvantage, but not education level or household income, was significantly associated with allostatic load (β = 0.22, se, 0.10, p = .04).Tests for mediators showed that household income and alcohol consumption partially mediated the relationship between allostatic load score and neighborhood disadvantage but were not significant.Conclusion more research is necessary to determine the mechanisms by which neighborhoods can exacerbate and attenuate cumulative disadvantage among african american women.Policies and interventions that focus on neighborhood health may improve the outcomes of individual-level health interventions among women who reside in disadvantaged communities.

Journal: Preventing chronic disease (2017)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Acquired G2032R Resistance Mutation in ROS1 to Lorlatinib Therapy Detected with Liquid Biopsy.

Lorlatinib, a third-generation anaplastic lymphoma kinase (alk)/receptor tyrosine kinase inhibitor (ros1), demonstrated efficacy in ros1 positive (ros1+) non-small cell lung cancer (nsclc), although approval is currently limited to the treatment of alk+ patients.However, lorlatinib-induced resistance mechanisms, and its efficacy against the resistance mutation g2032r in ros1, respectively, have not yet been fully understood.Furthermore, concomitant tumor suppressor gene p53 (tp53) mutations occur in driver alteration positive nsclc, but their prognostic contribution in the context of ros1 inhibition remains unclear.Here we report a ros1+ nsclc patient who developed an on target g2032r resistance mutation during second-line lorlatinib treatment, indicating the lack of activity of lorlatinib against ros1 g2032r.The resistance mutation was detected in plasma-derived ct dna, signifying the clinical utility of liquid biopsies.

Journal: Current oncology (Toronto, Ont.) (2022)
Publication types: Case Reports;Journal Article
Further observations on hydrogen peroxide antisepsis and COVID-19 cases among healthcare workers and inpatients.

The use of prophylactic antisepsis to protect against coronavirus disease 2019 (covid-19) has been suggested.This study investigated hydrogen peroxide antisepsis (hpa) at two hospitals in ghana.Methods cases of covid-19 among healthcare workers (hcws) using hydrogen peroxide (hp-hcws) or not using hydrogen peroxide (nhp-hcws), vaccinated or unvaccinated, were recorded at shai-osudoku hospital (sodh), dodowa, and mount olives hospital (moh), techiman, between may 2020 and december 2021.The effect of hpa in all inpatients at moh was also observed.Permutation tests were used to determine p values.Findings at sodh, there were 62 (13.5%) cases of covid-19 among 458 nhp-hcws but no cases among eight hp-hcws (p=0.622) from may to december 2020.Between january and march 2021, 10 (2.7%) of 372 nhp-hcws had covid-19, but there were no cases among 94 hp-hcws (p=0.206).At moh, prior to hpa, 17 (20.2%) of 84 hcws and five (1.4%) of 370 inpatients had covid-19 in july 2020.From august 2020 to march 2021, two of 54 (3.7%) hcws who stopped hpa had covid-19; none of 32 nhp-hcws contracted covid-19.At sodh, none of 23 unvaccinated hp-hcws and 35 (64%) of 55 unvaccinated nhp-hcws had covid-19 from april to december 2021 (p<0.0001).None of 34 vaccinated hp-hcws and 53 (13.6%) of 390 vaccinated nhp-hcws had covid-19 (p=0.015).No inpatients on prophylactic hpa (total 7736) contracted covid-19.Conclusion regular, daily hpa protects hcws from covid-19, and curtails nosocomial spread of sars-co v-2.

Journal: The Journal of hospital infection (2022)
Publication types: Journal Article
The geochemistry of geophagic material consumed in Onangama Village, Northern Namibia: a potential health hazard for pregnant women in the area.

Ingestion of geophagic materials might affect human health and induce diseases by different ways.The purpose of this study is to determine the geochemical composition of geophagic material consumed especially by pregnant women in onangama village, northern namibia and to assess its possible health effects.X-ray fluorescence and inductively coupled plasma mass spectrometry were used in order to determine the major, and trace elements as well as anions concentrations of the consumed material.The geochemical analysis revealed high concentrations of aluminium (al), calcium (ca), iron (fe), magnesium (mg), manganese (mn), potassium (k), sodium (na), and silica (si); and trace elements including arsenic (as), chromium (cr), mercury (hg), nickel (ni) and vanadium (v) as well as sulphate (so42-), nitrate (no3-), and nitrite (no2-) anions comparing to the recommended daily allowance for pregnant women.The p h for some of the studied samples is alkaline, which might increase the gastrointestinal tract p h (p h 1) revealed that al and mn might be a potential risk for human consumption.Based on the results obtained from the geochemical analysis, the consumption of the studied material might present a potential health risk to pregnant women including concomitant detrimental maternal and foetal effects.

Journal: Environmental geochemistry and health (2019)
Publication types: Journal Article