syedzayyan/paper_mill_benchmark huggingface dataset:
Effects of Renaming Schizophrenia on Destigmatization among Medical Students in One Taiwan University.

The stigma associated with serious mental illnesses causes a huge burden on patients, their families, and society.In october 2012, in taiwan, schizophrenia was renamed to reduce the stigma associated with this disease.The aim of this study was to compare the differences of public stigma, self-stigma, and social distance associated with schizophrenia between old and new name of schizophrenia in medical students.A cross-sectional survey was administered to 180 medical students of taipei medical university from october 2014 to february 2015.In total, 123 complete questionnaires were included in this study.Participants completed the modified attribution questionnaire, the perceived psychiatric stigma scale, and modified social distance scale to assess public stigma, self-stigma, and social distance, respectively.We also collected basic demographic data and previous experience of contact with people with mental illness.In total, 52 and 71 of the first- and fourth-year medical students, respectively, participated in the study.Among them, there were 51 females and 72 males.A significant difference in age was observed between the first- and fourth-year groups (20.2 ± 1.7 years vs.22.7 ± 0.9 years,p< 0.001).After renaming schizophrenia, we noted significant differences in the scores in the modified attribution questionnaire, the perceived psychiatric stigma scale, and the modified social distance scale in all participants and the fourth-year students, respectively.Female gender (beta = 0.230,p= 0.018) was significantly associated with the difference in the score of the modified attribution questionnaire after name change.The difference in the score of the perceived psychiatric stigma scale after the name change (beta = 0.277,p= 0.004) and age (beta = -0.186,p= 0.049) were significantly associated with the difference in the score of the modified social distance scale after name change.In conclusion, renaming was associated with the changes in the scores of the modified attribution questionnaire, the perceived psychiatric stigma scale, and the modified social distance scale toward individuals with schizophrenia in medical students of one taiwan university.Further studies with large sample sizes, diverse participant backgrounds, and that monitor the subsequent behavioral changes are warranted.

Journal: International journal of environmental research and public health (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Temperature induces metabolic reprogramming in fish during bacterial infection.

Water temperature elevation as a consequence of global warming results in increased incidence of bacterial disease, such as edwardsiellosis, in fish farming.Edwardsiellosis is caused by the bacterial pathogen edwardsiella tardaand affects many farmed fish including flounder (paralichthys olivaceus).Currently, the effect of temperature on the metabolic response of flounder to e.Tardainfection is unclear.In this study, we found that compared to low temperature (15°c), high temperature (23°c) enhanced e.Tardadissemination in flounder tissues.To examine the impact of temperature on the metabolism of flounder induced by e.Tarda, comparative metabolomics were performed, which identified a large number of metabolites responsive to e.Tardainvasion and temperature alteration.During e.Tardainfection, the metabolic profile induced by elevated temperature was mainly featured by extensively decreased amino acids and tca intermediates such as succinate, a proven immune regulator.Further, 38 potential metabolite markers of temperature effect (mmte) in association with bacterial infection were identified.When used as exogenous supplements, two of the mmte, i.e., l-methionine and udp-glucose, effectively upregulated the expression of pro-inflammatory cytokines and suppressed e.Tardainfection in flounder leukocytes.Taken together, the results of this study indicate an important influence of temperature on the metabolism of flounder during bacterial infection, which eventually affects the survivability of the fish.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Eotaxin-1/CCL11 promotes cellular senescence in human-derived fibroblasts through pro-oxidant and pro-inflammatory pathways.

Introduction eotaxin-1/ccl11 is a pivotal chemokine crucial for eosinophil homing to the lungs of asthmatic patients.Recent studies also suggest that ccl11 is involved in the aging process, as it is upregulated in elderly, and correlated with shorter telomere length in leukocytes from asthmatic children.Despite its potential pro-aging effects, the precise contribution of ccl11 and the underlying mechanisms involved in the promotion of cellular senescence remains unclear.Therefore, the primary goal of this study was to explore the role of ccl11 on senescence development and the signaling pathways activated by this chemokine in lung fibroblasts.Methods to investigate the targets potentially modulated by ccl11, we performed anin silicoanalysis using pseudo cell.We validatedin vitrothe activation of these targets in the human lung fibroblast cell line mrc-5 following rh ccl11 exposure.Finally, we performed differential gene expression analysis in human airway epithelial cells of asthmatic patients to assess ccl11 signaling and activation of additional senescent markers.Results our study revealed that eotaxin-1/ccl11 promote reactive oxygen secretion (ros) production in lung fibroblasts, accompanied by increased activation of the dna damage response (ddr) and p-tp53 and γh2ax.These modifications were accompanied by cellular senescence promotion and increased secretion of senescence-associated secretory phenotype inflammatory cytokines il-6 and il-8.Furthermore, our data show that airway epithelial lung cells from atopic asthmatic patients overexpress ccl11 along with aging markers such as cdkn2a (p16ink4a) and serpine1.Discussion these findings provide new insights into the mechanisms underlying the pro-aging effects of ccl11 in the lungs of asthmatic patients.Understanding the role of ccl11 on senescence development may have important implications for the treatment of age-related lung diseases, such as asthma.

Journal: Frontiers in immunology (2023)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
TLR9/FCRL3 regulates B cell viability, apoptosis, and antibody and IL-10 production through ERK1/2, p38, and STAT3 signaling pathways.

B cells play a role in the progression of multiple sclerosis (ms) and are closely related to fc-receptor like-3 (fcrl3), but little is known about fcrl3 in b cells and ms.Activation of tlr9 in b cells with cp g found that cp g promoted fcrl3 expression in a dose- and time-dependent manner.Cp g significantly activated erk1/2, p38, and stat3 pathways, and fcrl3 overexpression further promoted the activation of these pathways, while fcrl3 si rna significantly inhibited the activation of these pathways by cp g.Cp g stimulation significantly promoted the viability of b cells, inhibited cell apoptosis, and enhanced the production of antibodies and secretion of il-10 by b cells.Fcrl3 si rna blocked most of the above regulatory effects of cp g, but promoted the further production of antibodies by b cells.Fcrl3 overexpression enhanced the pro-survival, anti-apoptotic, and il-10-inducing effects of cp g, but inhibited the effect of cp g on promoting antibody production.After adding inhibitors of erk1/2, p38, and stat3 pathways, respectively, the effects of cp g on promoting cell viability, antibody production, and il-10 secretion were significantly reduced, but the anti-apoptotic effect of cp g was only affected by the blockade of stat3 pathway.In addition, fcrl3 regulated b cell antibody and il-10 secretion mainly through its itims.These results indicate that tlr9 activation affects b cell proliferation, apoptosis, antibody production, and il-10 secretion by upregulating fcrl3 expression, and is associated with erk1/2, p38, and stat3 pathways.Therefore, fcrl3 may be an important target for the diagnosis and treatment of b cell-related diseases.

Journal: In vitro cellular & developmental biology. Animal (2022)
Publication types: Journal Article
An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants.

The spike s of sars-co v-2 recognizes ace2 on the host cell membrane to initiate entry.Soluble decoy receptors, in which the ace2 ectodomain is engineered to block s with high affinity, potently neutralize infection and, because of close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape.Here, we directly test this hypothesis.We find that an engineered decoy receptor, s ace22v2.4, tightly binds s of sars-associated viruses from humans and bats, despite the ace2-binding surface being a region of high diversity.Saturation mutagenesis of the receptor-binding domain followed by in vitro selection, with wild-type ace2 and the engineered decoy competing for binding sites, failed to find s mutants that discriminate in favor of the wild-type receptor.We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of sars-associated betacoronaviruses.

Journal: Science advances (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural
α4β1and αMβ2Integrin Expression and Pro-Proliferative Properties of Eosinophil Subtypes in Asthma.

Eosinophilic inflammation is one of the main pathophysiological features in asthma.Two subtypes of eosinophils exist in the lung and systemic circulation: lung-resident eosinophils (r eos) and inflammatory eosinophils (i eos).We evaluated the expression of α4β1and αmβ2integrins of eosinophil subtypes and their influence on airway smooth muscle (asm) cell proliferation and viability in asthma.We included 16 severe non-allergic eosinophilic asthma (snea) patients, 13 steroid-free, non-severe allergic asthma (aa) patients, and 12 healthy control subjects (hs).For aa patients, a bronchial allergen challenge with dermatophagoides pteronyssinuswas performed.The eosinophil subtypes were distinguished using magnetic bead-labeled antibodies against surface cd62l, and individual combined cell cultures were prepared with asm cells.The integrins gene expression was analyzed by a quantitative real-time polymerase chain reaction.Proliferation was assessed by the alamar blue assay, and viability by annexin v and propidium iodide staining.R eos-like cells were characterized by the relatively higher gene expression of the β1integrin subunit, whereas i eos-like cells were characterized by the αmand β2integrin subunits.The inclusion of either eosinophil subtypes in co-culture significantly increased the proliferation of asm cells, and the effect of r eos-like cells was stronger than i eos-like cells (p< 0.05).Furthermore, r eos-like cells had a more pronounced effect on reducing asm cell apoptosis compared to that of i eos-like cells (p< 0.05).Lastly, the bronchial allergen challenge significantly enhanced only the i eos-like cells' effect on asm cell proliferation and viability in aa patients (p< 0.05).These findings highlight the different expression of α4β1and αmβ2integrins on distinct eosinophil subtypes in asthma.Therefore, r eos-like cells have a stronger effect in stimulating asm cell proliferation and viability; however, contact with specific allergens mainly enhances pro-proliferative i eos-like cell properties.

Journal: Journal of personalized medicine (2021)
Publication types: Journal Article
Predictors of adverse pregnancy outcomes among Kenyan women with HIV on antiretroviral treatment in pregnancy.

The aim of this study was to understand predictors of adverse pregnancy outcomes (apos) among women on antiretroviral treatment (art).Design a longitudinal cohort.Methods participants from the mobile wach x trial were evaluated for apos, including stillbirth (fetal death at ≥20 weeks' gestation), preterm birth (ptb, livebirth at 1000 copies/ml) at enrollment.Half (55.1%) started art prepregnancy, 89.1% on tenofovir-based regimens.Women with depression had a higher risk of stillbirth (adjusted hazard ratio [a hr] 2.93, 95% confidence interval (95% ci) 1.04-8.23), and women with lower social support score had higher risk of late stillbirth (a hr 11.74, 2.47-55.86).Among 740 livebirths, 201 (27.2%) were preterm and 22 (3.0%) experienced nnd.Ptb was associated with unsuppressed maternal viral load (adjusted prevalence ratio [a pr] 1.28, 95% ci 1.02-1.61), intimate partner violence (ipv) in pregnancy (a pr 1.94, 95% ci 1.28-2.94), and history of any sexually transmitted infection (sti) (a pr 1.63, 95% ci 1.06-2.51).Nnd was associated with ptb (a pr 2.53, 95% ci 1.10-5.78) and sti history (a pr 4.25, 95% ci 1.39-13.06).Most associations retained significance in the subgroup of women with viral suppression.Conclusion maternal viremia during pregnancy predicted ptb as did ipv, lower education, and sti history, while psychosocial stressors predicted stillbirth.Implementing mental health services, art adherence, partner support, and routine sti screening and treatment could reduce apos among women with hiv in sub-saharan africa settings.

Journal: AIDS (London, England) (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Exploring the mechanistic link between SF3B1 mutation and ring sideroblast formation in myelodysplastic syndrome.

Acquired sideroblastic anemia, characterized by bone marrow ring sideroblasts (rs), is predominantly associated with myelodysplastic syndrome (mds).Although somatic mutations in splicing factor 3b subunit 1 (sf3b1), which is involved in the rna splicing machinery, are frequently found in mds-rs, the detailed mechanism contributing to rs formation is unknown.To explore the mechanism, we established human umbilical cord blood-derived erythroid progenitor-2 (hudep-2) cells stably expressing sf3b1k700e.Sf3b1k700eexpressing cells showed higher proportion of rs than the control cells along with erythroid differentiation, indicating the direct contribution of mutant sf3b1 expression in erythroblasts to rs formation.In sf3b1k700eexpressing cells, abcb7 and alas2, known causative genes for congenital sideroblastic anemia, were downregulated.Additionally, mis-splicing of abcb7 was observed in sf3b1k700eexpressing cells.Abcb7-knockdown hudep-2 cells revealed an increased frequency of rs formation along with erythroid differentiation, demonstrating the direct molecular link between abcb7 defects and rs formation.Alas2 protein levels were obviously decreased in abcb7-knockdown cells, indicating decreased alas2 translation owing to impaired fe-s cluster export by abcb7 defects.Finally, rna-seq analysis of mds clinical samples demonstrated decreased expression of abcb7 by the sf3b1 mutation.Our findings contribute to the elucidation of the complex mechanisms of rs formation in mds-rs.

Journal: Scientific reports (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Caulifigura coniformis gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from a red biofilm sampled in a hydrothermal area.

Pan44t, a novel strain belonging to the phylum planctomycetes, was isolated from a red biofilm in a hydrothermal area close to the island panarea in the tyrrhenian sea north of sicily, italy.The strain forms white colonies on solid medium and displays the following characteristics: cell division by budding, formation of rosettes, presence of matrix or fimbriae and long stalks.The cell surface has an interesting and characteristic texture made up of triangles and rectangles, which leads to a pine cone-like morphology of the strain.Strain pan44tis mesophilic (temperature optimum 26 °c), slightly alkaliphilic (p h optimum 8.0), aerobic and heterotrophic.The strain has a genome size of 6.76 mb with a g + c content of 63.2%.Phylogenetically, the strain is a member of the family planctomycetaceae, order planctomycetales, class planctomycetia.Our analysis supports delineation of strain pan44tfrom all known genera in this family, hence, we propose to assign it to a novel species within a novel genus, for which we propose the name caulifigura coniformis gen.Nov., sp.Nov., represented by pan44t(dsm 29405t= lmg 29788t) as the type strain.

Journal: Antonie van Leeuwenhoek (2020)
Publication types: Journal Article
Reliability, validity and responsiveness of the Dutch version of the AOSpine PROST (Patient Reported Outcome Spine Trauma).

To validate the dutch version of aospine prost (patient reported outcome spine trauma).Methods patients were recruited from two level-1 trauma centers from the netherlands.Next to the aospine prost, patients also filled out sf-36 for concurrent validity.Descriptive statistics were used to analyze the characteristics.Content validity was assessed by evaluating the number of inapplicable or missing questions.Also floor and ceiling effects were analyzed.Internal consistency was assessed by calculating cronbach's α and item-total correlation coefficients (itcc).Spearman correlation tests were performed within aospine prost items and in correlation with sf-36.Test-retest reliability was analyzed using intraclass correlation coefficients (icc).Responsiveness was assessed by calculating effect sizes (es) and standardized response mean (srm).Factor analysis was performed to explore any dimensions within aospine prost.Results out of 179 enrolled patients, 163 (91.1%) were included.Good results were obtained for content validity.No floor or ceiling effects were seen.Internal consistency was excellent (cronbach's α = 0.96, itcc 0.50-0.86), with also good spearman correlations (0.25-0.79).Compared to sf-36, the strongest correlation was seen for physical functioning (0.79; p 1), explaining 65.4% of variance.Conclusions very satisfactory results were obtained for reliability, validity and responsiveness of the dutch version of aospine prost.Treating surgeons are encouraged to use this novel and validated tool in clinical setting and research to contribute to evidence-based and patient-centered care.

Journal: European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer.

Motivation genetic alterations lead to tumor progression and cell survival but also uncover cancer-specific vulnerabilities on gene dependencies that can be therapeutically exploited.Results vulcan spot is a novel computational approach implemented to expand the therapeutic options in cancer beyond known-driver genes unlocking alternative ways to target undruggable genes.The method integrates genome-wide information provided by massive screening experiments to detect genetic vulnerabilities associated to tumors.Then, vulcan spot prioritizes drugs to target cancer-specific gene dependencies using a weighted scoring system based on well known drug-gene relationships and drug repositioning strategies.Availability and implementation supplementary information supplementary data are available at bioinformatics online.

Journal: Bioinformatics (Oxford, England) (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
COVID-19 detection in radiological text reports integrating entity recognition.

Covid-19 diagnosis is usually based on pcr test using radiological images, mainly chest computed tomography (ct) for the assessment of lung involvement by covid-19.However, textual radiological reports also contain relevant information for determining the likelihood of presenting radiological signs of covid-19 involving lungs.The development of covid-19 automatic detection systems based on natural language processing (nlp) techniques could provide a great help in supporting clinicians and detecting covid-19 related disorders within radiological reports.In this paper we propose a text classification system based on the integration of different information sources.The system can be used to automatically predict whether or not a patient has radiological findings consistent with covid-19 on the basis of radiological reports of chest ct.To carry out our experiments we use 295 radiological reports from chest ct studies provided by the ''ht médica" clinic.All of them are radiological requests with suspicions of chest involvement by covid-19.In order to train our text classification system we apply machine learning approaches and named entity recognition.The system takes two sources of information as input: the text of the radiological report and covid-19 related disorders extracted from snomed-ct.The best system is trained using svm and the baseline results achieve 85% accuracy predicting lung involvement by covid-19, which already offers competitive values that are difficult to overcome.Moreover, we apply mutual information in order to integrate the best quality information extracted from snomed-ct.In this way, we achieve around 90% accuracy improving the baseline results by 5 points.

Journal: Computers in biology and medicine (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Associations between MRI T1 mapping, liver stiffness, quantitative MRCP, and laboratory biomarkers in children and young adults with autoimmune liver disease.

Define relationships between quantitative magnetic resonance imaging (mri) metrics and clinical/laboratory data in a pediatric and young adult cohort with autoimmune liver disease (aild).Materials and methods this prospective, cross-sectional study was institutional review board-approved.Patients enrolled in an institutional aild registry were divided into groups: (1) autoimmune hepatitis (aih) or (2) primary sclerosing cholangitis (psc)/autoimmune sclerosing cholangitis (asc).Participants underwent serum liver biochemistry testing and research mri examinations, including 3d magnetic resonance cholangiopancreatography (mrcp), magnetic resonance elastography (mre), and iron-corrected t1 mapping (c t1).Mrcp + and liver multi scan (perspectum ltd., oxford, uk) were used to post-process 3d mrcp and c t1 data.Multiple linear regression models were used to assess relationships.Results 58 patients, 35 male, median age 16 years were included; 30 in the aih group, 28 in the psc/asc group.After statistical adjustments for patient age, sex, presence of inflammatory bowel disease (ibd), specific diagnosis (psc/asc vs.Aih), and time from diagnosis to mri examination, left hepatic bile duct maximum diameter was a statistically significant predictor of whole liver mean c t1, c t1 interquartile range (iqr), and mre liver stiffness (p = 0.01-0.04).Seven laboratory values were significant predictors of whole liver c t1 iqr (p < 0.0001-0.04).Eight laboratory values and right hepatic bile duct median and maximum diameter were significant predictors of liver stiffness (p < 0.0001-0.03).Conclusions bile duct diameters and multiple laboratory biomarkers of liver disease are independent predictors of liver stiffness and c t1 iqr in pediatric patients with aild.

Journal: Abdominal radiology (New York) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't