syedzayyan/paper_mill_benchmark huggingface dataset:
Response Surface Analysis of Genomic Prediction Accuracy Values Using Quality Control Covariates in Soybean.

An important and broadly used tool for selection purposes and to increase yield and genetic gain in plant breeding programs is genomic prediction (gp).Genomic prediction is a technique where molecular marker information and phenotypic data are used to predict the phenotype (eg, yield) of individuals for which only marker data are available.Higher prediction accuracy can be achieved not only by using efficient models but also by using quality molecular marker and phenotypic data.The steps of a typical quality control (qc) of marker data include the elimination of markers with certain level of minor allele frequency (maf) and missing marker values and the imputation of missing marker values.In this article, we evaluated how the prediction accuracy is influenced by the combination of 12 maf values, 27 different percentages of missing marker values, and 2 imputation techniques (it; naïve and random forest (rf)).We constructed a response surface of prediction accuracy values for the two its as a function of maf and percentage of missing marker values using soybean data from the university of nebraska-lincoln soybean breeding program.We found that both the genetic architecture of the trait and the it affect the prediction accuracy implying that we have to be careful how we perform qc on the marker data.For the corresponding combinations maf-percentage of missing values we observed that implementing the rf imputation increased the number of markers by 2 to 5 times than the simple naïve imputation method that is based on the mean allele dosage of the non-missing values at each loci.We conclude that there is not a unique strategy (combination of the qcs and imputation method) that outperforms the results of the others for all traits.

Journal: Evolutionary bioinformatics online (2019)
Publication types: Journal Article;Review
COVID-19 Adaptive Humoral Immunity Models: Weakly Neutralizing Versus Antibody-Disease Enhancement Scenarios.

The interplay between the virus, infected cells and immune responses to sars-co v-2 is still under debate.By extending the basic model of viral dynamics, we propose here a formal approach to describe neutralisation versus weak (or non-)neutralisation scenarios and compare them with the possible effects of antibody-dependent enhancement (ade).The theoretical model is consistent with the data available in the literature; we show that both weakly neutralising antibodies and ade can result in final viral clearance or disease progression, but that the immunodynamics are different in each case.As a significant proportion of the world's population is already naturally immune or vaccinated, we also discuss the implications for secondary infections after vaccination or in the presence of immune system dysfunctions.

Journal: Acta biotheoretica (2022)
Publication types: Journal Article
Parvovirus B19 Infection Is Associated with Autoimmune Thyroid Disease in Adults.

Autoimmune thyroid diseases are the most frequent autoimmune disorders, with a global prevalence of about 10%.Several mechanisms have been proposed to induce autoimmune thyroid responses by infectious agents.In this study, we aimed to evaluate the association between parvovirus b19 infection and autoimmune thyroid disorders.Methods adult patients with newly diagnosed graves' disease (gd) and hashimoto's thyroiditis (ht) and healthy euthyroid controls were recruited.Various clinical and biochemical parameters, including thyroid function tests and serum parvovirus b19 antibody level (ig g), were assessed and compared between the groups.Results in this study, data from 404 cases with ht, 248 cases with gd, and 480 healthy individuals as a control group were analyzed.The prevalence of parvovirus b19 infection in patients with ht and gd and controls was 61.1%, 58.9%, and 47.1%, respectively.In the group of patients with ht, there was a significant positive correlation between the b19 ig g and tpoab (r = 0.764, p < 0.001) and tg ab (r = 0.533, p < 0.001).Also, in patients with gd, the b19 ig g had a significant positive correlation with tpoab (r = 0.779, p < 0.001) and tg ab (r = 0.467, p < 0.001).Conclusions parvovirus b19 infection is commonly seen in patients with autoimmune thyroid disorders.

Journal: International journal of endocrinology and metabolism (2021)
Publication types: Journal Article
A Spatial Analysis of Access to Physical Activity Infrastructure and Healthy Food in Regional Tasmania.

Prevalence of physical inactivity and obesity continues to increase in regional areas such as north-west (nw) tasmania and show no signs of abating.It is possible that limited access to physical activity infrastructure (pai) and healthier food options are exacerbating the low levels of habitual physical activity and obesity prevalence in these communities.Despite a burgeoning research base, concomitant exploration of both physical activity and food environments in rural and regional areas remain scarce.This research evaluated access (i.e., coverage, variety, density, and proximity) to physical activity resources and food outlets in relation to socioeconomic status (ses) in three nw tasmanian communities.In all three study areas, the pai and food outlets were largely concentrated in the main urban areas with most recreational tracks and natural amenities located along the coastline or river areas.Circular head had the lowest total number of pai (n= 43) but a greater proportion (30%) of free-to-access outdoor amenities.There was marked variation in accessibility to infrastructure across different areas of disadvantage within and between sites.For a considerable proportion of the population, free-to-access natural amenities/green spaces and recreational tracks (73 and 57%, respectively) were beyond 800 m from their households.In relation to food accessibility, only a small proportion of the food outlets across the region sells predominantly healthy (i.e., tier 1) foods (~6, 13, and 10% in burnie, circular head and devonport, respectively).Similarly, only a small proportion of the residents are within a reasonable walking distance (i.e., 5-10 min walk) from outlets.In contrast, a much larger proportion of residents lived close to food outlets selling predominantly energy-dense, highly processed food (i.e., tier 2 outlets).Circular head had at least twice as many tier 1 food stores per capita than devonport and burnie (0.23 vs.0.10 and 0.06; respectively) despite recording the highest average distance (4.35 and 5.66 km to tier 2/tier 1 stores) to a food outlet.As such, it is possible that both food and physical activity environment layouts in each site are contributing to the obesogenic nature of each community.

Journal: Frontiers in public health (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Do changes in network structure explain why unemployment damages health? Evidence from German panel data.

We use german panel data and apply fixed effects regressions to test whether changes in social network size or composition explain why unemployment harms individuals' health.We consider whether the number of weak ties, the number of strong ties, the share of relatives or the share of unemployed individuals among strong ties mediate the negative relation between unemployment and health.We look at various health and health behavior outcomes, such as self-rated health, mental health, physical health, the number of doctor visits and the number of cigarettes smoked.We find no evidence that structural features of the social network play a role in mediating the health-damaging effect of unemployment.We conduct a variety of supplementary analyses that support and extend our results, including mediation tests for emotional support and contact intensity.

Journal: Social science & medicine (1982) (2022)
Publication types: Journal Article
Cortical surface abnormalities are different depending on the stage of schizophrenia: A cross-sectional vertexwise mega-analysis of thickness, area and gyrification.

Brain magnetic resonance imaging studies have not investigated the cortical surface comprehensively in schizophrenia subjects by assessing thickness, surface area and gyrification separately during the first-episode of psychosis (fep) or chronic schizophrenia (ch sch).Methods we investigated cortical surface abnormalities in 137 fep patients and 240 ch sch subjects compared to 297 healthy controls (hc) contributed by five cohorts.Maps showing results of vertexwise between-group comparisons of cortical thickness, area, and gyrification were produced using t1-weighted datasets processed using free surfer 5.3, followed by validated quality control protocols.Results fep subjects showed large clusters of increased area and gyrification relative to hc in prefrontal and insuli cortices (cohen's d: 0.049 to 0.28).These between-group differences occurred partially beyond the effect of sample.Ch sch subjects displayed reduced cortical thickness relative to hc in smaller fronto-temporal foci (d: -0.73 to -0.35), but not beyond the effect of sample.Differences between fep and hc subjects were associated with male gender, younger age, and earlier illness onset, while differences between ch sch and hc were associated with treatment-resistance and first-generation antipsychotic (fga) intake independently of sample effect.Conclusions separate assessments of fep and ch sch revealed abnormalities that differed in regional distribution, phenotypes affected and effect size.In fep, associations of greater cortical area and gyrification abnormalities with earlier age of onset suggest an origin on anomalous neurodevelopment, while thickness reductions in ch sch are at least partially explained by treatment-resistance and fga intake.Associations of between-group differences with clinical variables retained statistical significance beyond the effect of sample.

Journal: Schizophrenia research (2021)
Publication types: Journal Article
To isolate or not to isolate: the impact of changing behavior on COVID-19 transmission.

The covid-19 pandemic has caused more than 25 million cases and 800 thousand deaths worldwide to date.In early days of the pandemic, neither vaccines nor therapeutic drugs were available for this novel coronavirus.All measures to prevent the spread of covid-19 are thus based on reducing contact between infected and susceptible individuals.Most of these measures such as quarantine and self-isolation require voluntary compliance by the population.However, humans may act in their (perceived) self-interest only.Methods we construct a mathematical model of covid-19 transmission with quarantine and hospitalization coupled with a dynamic game model of adaptive human behavior.Susceptible and infected individuals adopt various behavioral strategies based on perceived prevalence and burden of the disease and sensitivity to isolation measures, and they evolve their strategies using a social learning algorithm (imitation dynamics).Results this results in complex interplay between the epidemiological model, which affects success of different strategies, and the game-theoretic behavioral model, which in turn affects the spread of the disease.We found that the second wave of the pandemic, which has been observed in the us, can be attributed to rational behavior of susceptible individuals, and that multiple waves of the pandemic are possible if the rate of social learning of infected individuals is sufficiently high.Conclusions to reduce the burden of the disease on the society, it is necessary to incentivize such altruistic behavior by infected individuals as voluntary self-isolation.

Journal: BMC public health (2022)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.
Insomnia in Chinese patients with chronic schizophrenia: prevalence, clinical correlates and relationship with cognitive impairment.

Insomnia is a major public health concern that often occurs in patients with schizophrenia, complicating the treatment and prognosis of patients.This study aimed to investigate the prevalence of insomnia and its relationship with cognitive function in chinese patients with chronic schizophrenia.Methods we recruited patients with schizophrenia and collected their clinical and demographic data.Insomnia data were collected through a self-reported questionnaire consisting of three questions.The positive and negative syndrome scale (panss) was used to measure psychopathological symptoms, while the repeatable battery for the assessment of neuropsychological status (rbans) was used to measure cognitive performance.Results of 957 chinese patients with chronic schizophrenia 20.2% reported having insomnia (193/957).Male patients (107/630, 17.0%) had a lower rate of insomnia than female patients (86/327, 26.3%) (x2= 11.60, p = 0.001).Patients with insomnia exhibited significantly higher panss total score and positive symptom, negative symptom, and general psychopathology scores, but significantly lower rbans total score, language, attention and delayed memory scores compared to patients without insomnia (all p < 0.05).Logistic regression analysis showed that female sex, high panss total score and the use of diazepam were independently associated with insomnia (all p < 0.05).Conclusions insomnia is relatively common in chinese patients with chronic schizophrenia.Some demographic data and clinical symptoms are associated with insomnia.Patients with schizophrenia and insomnia perform poorly on cognition tests suggesting that insomnia and cognitive function are closely related in patients with schizophrenia.

Journal: Sleep & breathing = Schlaf & Atmung (2023)
Publication types: Journal Article
Severe COVID-19 and coagulopathy: A systematic review and meta-analysis.

Introduction coronavirus disease 2019 (covid-19)-induced coagulopathy (cic) has been widely reported in the literature.However, the spectrum of abnormalities associated with cic has been highly variable.Methods we conducted a systematic review of the literature (until 1 june 2020) to assess cic and disease severity during the early covid-19 pandemic.Primary outcomes were pooled mean differences in platelet count, d-dimer level, prothrombin time, activated partial thromboplastin time (a ptt) and fibrinogen level between non-severe and severe patients, stratified by degree of hypoxaemia or those who died.The risk factors for cic were analysed.Random-effects meta-analyses and meta-regression were performed using r version 3.6.1, and certainty of evidence was rated using the grading of recommendation, assessment, development, and evaluation approach.Results of the included 5,243 adult covid-19 patients, patients with severe covid-19 had a significantly lower platelet count, and higher d-dimer level, prothrombin time and fibrinogen level than non-severe patients.Pooled mean differences in platelet count (-19.7×109/l, 95% confidence interval [ci] -31.7 to -7.6), d-dimer level (0.8μg/m l, 95% ci 0.5-1.1), prothrombin time (0.4 second, 95% ci 0.2-0.6) and fibrinogen level (0.6g/l, 95% ci 0.3-0.8) were significant between the groups.Platelet count and d-dimer level were significant predictors of disease severity on meta-regression analysis.Older men had higher risks of severe coagulopathic disease.Conclusion significant variability in cic exists between non-severe and severe patients, with platelet count and d-dimer level correlating with disease severity.Routine monitoring of all coagulation parameters may help to assess cic and decide on the appropriate management.

Journal: Annals of the Academy of Medicine, Singapore (2021)
Publication types: Journal Article;Meta-Analysis;Systematic Review
Population Pharmacokinetics of Vancomycin in Chinese ICU Neonates: Initial Dosage Recommendations.

The main goal of our study was to characterize the population pharmacokinetics of vancomycin in critically ill chinese neonates to develop a pharmacokinetic model and investigate factors that have significant influences on the pharmacokinetics of vancomycin in this population.The study population consisted of 80 neonates in the neonatal intensive care unit (icu) from which 165 trough and peak concentrations of vancomycin were obtained.Nonlinear mixed effect modeling was used to develop a population pharmacokinetic model for vancomycin.The stability and predictive ability of the final model were evaluated based on diagnostic plots, normalized prediction distribution errors and the bootstrap method.Serum creatinine (scr) and body weight were significant covariates on the clearance of vancomycin.The average clearance was 0.309 l/h for a neonate with scr of 23.3 μmol/l and body weight of 2.9 kg.No obvious ethnic differences in the clearance of vancomycin were found relative to the earlier studies of caucasian neonates.Moreover, the established model indicated that in patients with a greater renal clearance status, especially scr < 15 μmol/l, current guideline recommendations would likely not achieve therapeutic area under the concentration-time curve over 24 h/minimum inhibitory concentration (auc24h/mic) ≥ 400.The exceptions to this are british national formulary (2016-2017), blue book (2016) and neofax (2017).Recommended dose regimens for neonates with different scr levels and postmenstrual ages were estimated based on monte carlo simulations and the established model.These findings will be valuable for developing individualized dosage regimens in the neonatal icu setting.

Journal: Frontiers in pharmacology (2018)
Publication types: Journal Article
Plasma membrane phosphatidylinositol (4,5)-bisphosphate is critical for determination of epithelial characteristics.

Epithelial cells provide cell-cell adhesion that is essential to maintain the integrity of multicellular organisms.Epithelial cell-characterizing proteins, such as epithelial junctional proteins and transcription factors are well defined.However, the role of lipids in epithelial characterization remains poorly understood.Here we show that the phospholipid phosphatidylinositol (4,5)-bisphosphate [pi(4,5)p2] is enriched in the plasma membrane (pm) of epithelial cells.Epithelial cells lose their characteristics upon depletion of pm pi(4,5)p2, and synthesis of pi(4,5)p2in the pm results in the development of epithelial-like morphology in osteosarcoma cells.Pm localization of pard3 is impaired by depletion of pm pi(4,5)p2in epithelial cells, whereas expression of the pm-targeting exocyst-docking region of pard3 induces osteosarcoma cells to show epithelial-like morphological changes, suggesting that pi(4,5)p2regulates epithelial characteristics by recruiting pard3 to the pm.These results indicate that a high level of pm pi(4,5)p2plays a crucial role in the maintenance of epithelial characteristics.

Journal: Nature communications (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Drive-Through Testing: A Unique, Efficient Method of Collecting Large Volume of Specimens During the SARS-CoV-2 (COVID-19) Pandemic.

The world health organization declared covid-19 a global pandemic in march 2020.A major challenge in this worldwide pandemic has been efficient and effective large-scale testing for the disease.In this communication, we discuss lessons learned in the set up and function of a locally organized drive-through testing facility.

Journal: Mayo Clinic proceedings (2020)
Publication types: Journal Article
Porcine circovirus-like virus P1 activates pancreatic secretion pathway by interacting with CHRM3 protein.

The porcine circovirus-like virus p1, a member of the circovirus family, causes post-weaning multisystemic wasting syndrome (pmws) in weaned piglets with progressive wasting as the main clinical symptom.The pancreatic secretion pathway induces pancreatic acinar cells to secrete various digestive enzymes and as such is an important signaling pathway for the digestive system and somatic growth.This study examined the effects and mechanism of p1 virus infection on the pancreatic secretion pathway.The experiment was conducted by transfecting double-copy plasmid p1 into pk-15 and 3d4 cells and by infecting cells with the p1 virus.Samples were collected at various times after transfection or infection.The pathway's transcription and translation levels of chrm3, gq, plc-β2, prkca, rab3d, rho a, rac1, and amy a proteins were detected by real-time pcr and western blots; these analyses confirmed that the p1 virus infection could upregulate the expression level of key pancreatic secretion signaling molecules.Then, we confirmed that the vp1 protein of the p1 virus could interact with the pathway initiation protein chrm3 using co-ip, pull-downs, and confocal fluorescence microscopy.Finally, we demonstrated that the vp1 protein activates the pancreatic secretory pathway through the chrm3 protein.In conclusion, this study demonstrated that the p1 virus can interact with the chrm3 receptor protein to activate the pancreatic secretion pathway and promote the secretion of various digestive enzymes downstream of the pathway, thereby providing a basis for p1 virus pathogenesis.

Journal: Veterinary microbiology (2022)
Publication types: Journal Article
Comparison of 12-cm versus 6-cm long peripheral catheters in patients with difficult intravenous access (DIVA).

Long peripheral catheter is 6-15 cm long vascular device.The aim of the study was to compare the frequency of complications of two types of long peripheral catheters with different length inserted in diva patients.Methods under ultrasound navigation 2.7f 6.4 cm or 4fr 12 cm long peripheral catheter was inserted.Complications of both long peripheral catheters were prospectively observed and their relationship to the patient's age, gender, selected vein, number of punctures and barthel score system was evaluated.Results ninety-three 12 cm and fifty-five 6.4 cm long peripheral catheters were inserted.Median of dwelling time was 8 days for 6.4 cm and 9 days for 12 cm long peripheral catheter.There were 17 (26%) complications in 6.4 cm (38/1000 catheter days) and 15 (16%) in 12 cm catheter (17/1000 catheter days),p= 0.04.The complications of both peripheral catheters were not associated with the age of patients, gender, number of punctures and selected vein for insertion.Unlike 12 cm catheter, the complications of 6.4 cm long peripheral catheter were significantly associated with the result of barthel scoring system (p= 0.003).Conclusion the frequency of complications was more common with 6,4 cm than with 12 cm catheter.

Journal: The journal of vascular access (2022)
Publication types: Journal Article