syedzayyan/paper_mill_benchmark huggingface dataset:
Reduced electrocortical responses to pleasant pictures in depression: A brief report on time-domain and time-frequency delta analyses.

The late positive potential (lpp) to pleasant content is an electrocortical indicator of blunted emotional reactivity in depression.A reduced time-frequency delta power has never been investigated in clinical samples.The present study examined time-frequency delta in depression and at investigated whether the combination of time-domain and time-frequency data would explain additional variance in the depression status.Methods the study was a secondary analysis of data collected during a passive viewing task of pleasant and neutral pictures in a community-based sample of 75 participants with a current depressive disorder and 42 controls.A time-frequency analysis on event-related changes within delta frequency band was conducted.Results cluster-based statistics revealed a centro-parietal increase in delta power to pleasant relative to neutral pictures in the control group but not within the depression group.Moreover, a fronto-centro-parietal reduction in delta power to pleasant pictures emerged in depression relative to controls.Both a smaller lpp and delta power to pleasant pictures were related to depression status.The combination of lpp and delta power explained a greater amount of variance compared to the model where lpp was entered as the only predictor of depression status.Conclusions these data suggest that delta power might be a promising electrocortical correlate of the hypoactivation of the approach-related motivational system in depression.Additionally, a blunted delta and lpp might reflect unique processes related to depression.A combination of these measures can be leveraged together to enhance clinical utility and to shed light on the underlying mechanisms associated with depression.

Journal: Biological psychology (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Evaluation of the use of GeneXpert MTB/RIF in a zone with high burden of tuberculosis in Thailand.

Gene xpert mtb/rif is a reliable molecular diagnostic tool capable of detecting mycobacterium tuberculosis (mtb) and identifying genetic determinants of rifampicin (rif) resistance.This study aimed to assess physicians' diagnostic decision-making processes for tb based on gene xpert mtb/rif results and how this affected the initiation of multidrug resistance (mdr) treatment.This study employed a mixed method: data were collected retrospectively from the medical records of tb patients and in-depth interviews were conducted with healthcare workers in areas with a high tb burden in thailand.A total of 2,030 complete tb records from 2 patient groups were reviewed, including 1443 suspected cases with negative smear results and 587 with high risk of mdr-tb.Gene xpert mtb/rif was routinely used to assist the physicians in their decision-making for the diagnosis of pulmonary tuberculosis (ptb) and the initiation of mdr-tb treatment.The physicians used it as a "rule-in test" for all patients with negative chest x-rays (cxr) and smear results, to ensure timely treatment.Approximately one-fourth of the patients with negative cxr/smear and gene xpert mtb/rif results were diagnosed with ptb by the physicians, who based their decisions on other evidence, such as clinical symptoms, and did not use gene xpert mtb/rif as a "rule-out test." gene xpert mtb/rif proved effective in early detection within a day, thereby radically shortening the time required to initiate second-line drug treatment.Despite its high sensitivity for detecting ptb and mdr-tb, gene xpert mtb/rif had contradictory results (false positive and/or false negative) for 21.8% of cases among patients with negative smear results and 41.1% of cases among patients with high risk of mdr-tb.Therefore, physicians still used the results of other conventional tests in their decision-making process.It is recommended that gene xpert mtb/rif should be established at all points of care and be used as the initial test for ptb and mdr-tb diagnosis.

Journal: PloS one (2022)
Publication types: Journal Article
Fluorine MR Imaging Probes Dynamic Migratory Profiles of Perfluorocarbon-Loaded Dendritic Cells After Streptozotocin-Induced Inflammation.

The pathogenesis of type 1 diabetes (t1d) involves presentation of islet-specific self-antigens by dendritic cells (dcs) to autoreactive t cells, resulting in the destruction of insulin-producing pancreatic beta cells.We aimed to study the dynamic homing of diabetes-prone dcs to the pancreas and nearby organs with and without induction of pancreatic stress in a t1d susceptible model of repeated streptozotocin (stz) injection.Procedures in vitro labeling of activated bone marrow-derived dcs (bmdcs) from nod (nonobese diabetes) mice was performed using zonyl perfluoro-15-crown-5-ether nanoparticles (zpfce-nps).Internalization of particles was confirmed by confocal microscopy.Two groups of nod.scid (nonobese diabetic/severe combined immunodeficiency) mice with (induced by low dose stz administration) or without pancreatic stress were compared.Diabetogenic bmdcs loaded with bdc2.5 mimotope were pre-labeled with zpfce-nps and adoptively transferred into mice.Longitudinal in vivo fluorine mri (19f mri) was performed 24 h, 36 h and 48 h after transfer of bmdcs.For ex vivo quantification of labeled cells,19f nmr and flow cytometry were performed on dissected tissues to validate in vivo19f mri data.Results in vitro flow cytometry and confocal microscopy confirmed high uptake of nanoparticles in bmdcs during the process of maturation.Migration/homing of activated and zpfce-np- labeled bmdcs to different organs was monitored and quantified longitudinally, showing highest cell density in pancreas at 48-h time-point.Based on19f mri, stz induced mild inflammation in the pancreatic region, as indicated by high accumulation of zpfce-np-labeled bmdcs in the pancreas when compared to the vehicle group.Pancreatic draining lymph nodes showed elevated homing of labeled bmdcs in the vehicle groups in contrast to the stz group after 72 h.The effect of stz was confirmed by increased blood glucose levels.Conclusion we showed the potential of19f mri for the non-invasive visualization and quantification of migrating immune cells in models for pancreatic inflammation after stz administration.Without any intrinsic background signal,19f mri serves as a highly specific imaging tool to study the migration of diabetic-prone bmdcs in t1d models in vivo.This approach could particularly be of interest for the longitudinal assessment of established or novel anti-inflammatory therapeutic approaches in preclinical models.

Journal: Molecular imaging and biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A Quantitative High-Throughput Screening Data Analysis Pipeline for Activity Profiling.

The u.s.Tox21 program has developed in vitro assays to test large collections of environmental chemicals in a quantitative high-throughput screening (q hts) format, using triplicate 15-dose titrations to generate over 100 million data points to date.Counterscreens are also employed to minimize interferences from non-target-specific assay artifacts, such as compound autofluorescence and cytotoxicity.New data analysis approaches are needed to integrate these data and characterize the activities observed from these assays.Here, we describe a complete analysis pipeline that evaluates these q hts data for technical quality in terms of signal reproducibility.We integrate signals from repeated assay runs, primary readouts and counterscreens to produce a final call on on-target compound activity.

Journal: Methods in molecular biology (Clifton, N.J.) (2022)
Publication types: Journal Article
Refinement of Computational Access to Molecular Physicochemical Properties: From Ro5 to bRo5.

There is a need of computational tools to rank b ro5 drug candidates in the very early phases of drug discovery when chemical matter is unavailable.In this study, we selected three compounds: (a) a ro5 drug (pomalidomide), (b) a b ro5 orally available drug (saquinavir), and (c) a polar protac (cmp 98) to focus on computational access to physicochemical properties.To provide a benchmark, the three compounds were first experimentally characterized for their lipophilicity, polarity, imhbs, and chameleonicity.To reproduce the experimental information content, we generated conformer ensembles with conformational sampling and molecular dynamics in both water and nonpolar solvents.Then we calculated rgyr, 3d psa, and imhb number.An innovative pool of strategies for data analysis was then provided.Overall, we report a contribution to close the gap between experimental and computational methods for characterizing b ro5 physicochemical properties.

Journal: Journal of medicinal chemistry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Development of a distributed nonlinear Muskingum model by considering snowmelt effects for flood routing in the Red River.

This research paper presents the development of a nonlinear muskingum model which achieves precise flood routing through river reaches while considering lateral inflow conditions.Fourteen pairs of flood hydrograph found at two specific united states geological survey (usgs) stations located along the red river of the north, namely grand forks and drayton, are used for the calibrations and validations of the muskingum model.To enhance the accuracy of the procedure, a reach is divided into multiple sub-reaches, and the muskingum model calculations are performed individually for each interval using the distributed muskingum method.Notably, the model development process incorporates the use of the salp swarm algorithm.The obtained results demonstrate the effectiveness of the developed nonlinear muskingum model in accurately routing floods through the very gentle river with a bed slope of (0.0002-0.0003).The events were categorized into three groups based on their dominant drivers: group a (snowmelt-driven floods), group b (rain-on-snow-induced floods), and group c (mixed floods influenced by both snowmelt and rainfall).For the sub-reaches in group a, single sub-reach (nr = 1), the performance evaluation criteria (pec) yielded the highest value for sse, amounting to 404.9 × 106.In group b, when nr = 2, pec results the highest value were sse = 730.2 × 106.The number of sub-reaches in a model has a significant influence on parameter estimates and model performance, as demonstrated by the analysis of hydrologic parameters and performance evaluation criteria.Optimal performance varied across case studies, emphasizing the importance of selecting the appropriate number of sub-reaches for peak discharge predictions.

Journal: Scientific reports (2023)
Publication types: Journal Article
Do specific types of sleep disturbances represent risk factors for poorer health-related quality of life in inflammatory bowel disease? A longitudinal cohort study.

S poor global sleep quality is commonly reported in people with inflammatory bowel disease (ibd) and is linked to poorer health-related quality of life (hrqo l).However, understanding is currently limited by a lack of: (1) longitudinal research and (2) research investigating the impact of specific types of problems sleeping on ibd-related outcomes, particularly on hrqo l.Design observational longitudinal cohort study.Methods n = 276 participants with ibd completed measures at baseline (t1) and 4 weeks later at t2.Four specific sleep disturbances associated with ibd including sleep apnoea, insomnia, restless legs, and nightmares were measured alongside depression, anxiety and stress, and hrqo l.Results after controlling for participant demographics and clinical characteristics, t1 depression, anxiety, stress, and t1 hrqo l, more severe symptom severity of sleep apnoea (b = -0.30, p .87) and nightmares (b = -0.14, p > .11) at t1 did not predict hrqo l.Conclusion symptoms synonymous with sleep apnoea and insomnia might represent modifiable risk factors that provide independent contributions to hrqo l over time in those with ibd.These findings suggest that interventions designed to improve sleep apnoea and insomnia could confer benefits to hrqo l in those with ibd.However, more longitudinal research is needed to understand the contribution of sleep disturbances over the longer term, as well as more randomized controlled trials testing the effect of improving sleep on ibd-related outcomes.

Journal: British journal of health psychology (2021)
Publication types: Journal Article
Reflections on a Career in Plastic Surgery: A National Survey of Retired Surgeons.

Introduction retired plastic surgeons can provide valuable insights for the greater plastic surgery community.The purpose of this study was to gather demographics, personal reflections, and advice for a career in plastic surgery from retired american plastic surgeons.Methods an email survey was distributed to 825 members of the american society of plastic surgeons during september 2021.The survey distribution was designed to engage members of the plastic surgery community, who were retired from surgical practice in the united states.The form consisted of 29 questions, five of which were free response.Descriptive statistical analyses were performed.Results a total of 214 completed surveys were received, with a response rate of 25.9%.The average age at retirement was 67.6 years.The majority of respondents were men (87.6%) and white (93.3%); 46.9% of surgeons practiced at individual private practice.Ninety percent of surgeons indicated that they would choose to practice as a plastic surgeon again.Free responses provided positive career reflections and advice for young plastic surgeons regarding navigating the changing landscape of healthcare.Conclusions retired plastic surgeons are interested in engaging with the plastic surgery community and demonstrate continued interest in the future of the field.Efforts can be made to avail the field of their expertise and experience.

Journal: Plastic and reconstructive surgery. Global open (2022)
Publication types: Journal Article
Extensive prostatic abscess drained by CT-guided percutaneous approach: Case report.

Prostatic abscess is a rare entity that occurs most frequently after the age of 50.The main risk factors are immunosuppressive conditions such as diabetes, hiv infection and chronic renal failure.It is clinically manifested by signs of bladder irritation.The management of the disease involves antibiotic therapy and drainage of the abscess, which can be performed by various invasive methods.We report the case of a 60-year-old patient with a large prostatic abscess drained by ct-guided percutaneous approach.

Journal: Radiology case reports (2022)
Publication types: Case Reports;Journal Article
Unified Theory of Vapor-Wall Mass Transport in Teflon-Walled Environmental Chambers.

Secondary organic aerosol (soa) formation is studied in laboratory chambers, in which volatile organic compounds (vocs) are oxidized to produce low-volatility compounds that condense into the aerosol phase.It has been established that such oxidized low-volatility compounds can partition into the chamber walls, which traditionally consist of teflon film.Several studies exist in which the rates of uptake of individual vapor compounds to the chamber walls have been measured, but a unified theory capable of describing the range of experimental measurements has been lacking.Here, a two-layer model of observed short and long vapor-wall interaction time scales in teflon-walled environmental chambers is presented and shown to be consistent with experimental data on the rate of wall deposition of more than 90 compounds.Semiempirical relationships between key parameters in the model and vapor molecular properties are derived, which can be used to predict the fate of gas-phase vapor in the chamber under dry conditions.

Journal: Environmental science & technology (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Impacts of the COVID-19 pandemic on access to HIV and reproductive health care among women living with HIV (WLHIV) in Western Kenya: A mixed methods analysis.

Introduction the covid-19 pandemic has impacted access to health services.Our objective was to understand the pandemic's impact on access to hiv, pregnancy, and family planning (fp) care among women living with hiv (wlhiv).Methods data were collected after june 2020, when questions about the pandemic were added to two ongoing mixed methods studies using telephone surveys and in-depth interviews among wlhiv in western kenya.The chaguo langu (cl)study includes primarily non-pregnant wlhiv receiving hiv care at 55 facilities supported by ampath and the opt4mamasstudy includes pregnant wlhiv receiving antenatal care at five facilities supported by faces.Our outcomes were self-reported increased difficulty refilling medication, accessing care, and managing fp during the pandemic.We summarized descriptive data and utilized multivariable logistic regression to evaluate predictors of difficulty refilling medication and accessing care.We qualitatively analyzed the interviews using inductive coding with thematic analysis.Results we analyzed 1,402 surveys and 15 in-depth interviews.Many (32%)clparticipants reported greater difficulty refilling medications and a minority (14%) reported greater difficulty accessing hiv care during the pandemic.Most (99%)opt4mamasparticipants reported no difficulty refilling medications or accessing hiv/pregnancy care.Among the clparticipants, older women werelesslikely (a or = 0.95, 95% ci: 0.92-0.98) and women with more children weremorelikely (a or = 1.13, 95% ci: 1.00-1.28) to report difficulty refilling medications.Only 2% of clparticipants reported greater difficulty managing fp and most (95%) reported no change in likelihood of using fp or desire to get pregnant.Qualitative analysis revealed three major themes: (1) adverse organizational/economic implications of the pandemic, (2) increased importance of pregnancy prevention during the pandemic, and (3) fear of contracting covid-19.Discussion the two unique participant groups included in our study encountered overlapping problems during the covid-19 epidemic.Access to hiv services and antiretrovirals was interrupted for a large proportion of non-pregnant wlhiv in western kenya, but access to pregnancy/family planning care was less affected in our cohort.Innovative solutions are needed to ensure hiv and reproductive health outcomes do not worsen during the ongoing pandemic.

Journal: Frontiers in global women's health (2022)
Publication types: Journal Article
Scintillation index for the optical wave in the vertical oceanic link with anisotropic tilt angle.

The influence of the ocean depth and anisotropic tilt angle on vertical underwater wireless optical communication (uwoc) systems is considered in this study.We propose a power spectrum model of oceanic turbulence with an anisotropic tilt angle for the first time.Thereafter, the expression of the scintillation index is derived for a spherical wave propagating over anisotropic oceanic turbulence in the vertical link.In addition, considering the temperature and salinity, relevant data of the atlantic and pacific oceans at different depths are selected to study further the effect of ocean depth on the scintillation index.The results indicate that the scintillation index strongly depends on the ocean depth and anisotropic tilt angle.Moreover, the scintillation index is also related to other parameters, such as temperature and salinity, kinematic viscosity, the anisotropic factor, optical wavelength, and propagation distance.The presented results can be beneficial in designing optical wireless communication systems in the ocean environment.

Journal: Optics express (2022)
Publication types: Journal Article
Long-Term Connectome Analysis Reveals Reshaping of Visual, Spatial Networks in a Model With Vascular Dementia Features.

Connectome analysis of neuroimaging data is a rapidly expanding field that offers the potential to diagnose, characterize, and predict neurological disease.Animal models provide insight into biological mechanisms that underpin disease, but connectivity approaches are currently lagging in the rodent.Methods we present a pipeline adapted for structural and functional connectivity analysis of the mouse brain, and we tested it in a mouse model of vascular dementia.Results we observed lacunar infarctions, microbleeds, and progressive white matter change across 6 months.For the first time, we report that default mode network activity is disrupted in the mouse model.We also identified specific functional circuitry that was vulnerable to vascular stress, including perturbations in a sensorimotor, visual resting state network that were accompanied by deficits in visual and spatial memory tasks.Conclusions these findings advance our understanding of the mouse connectome and provide insight into how it can be altered by vascular insufficiency.

Journal: Stroke (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
MicroRNA-409-5p inhibits cell proliferation, and induces G2/M phase arrest and apoptosis by targeting DLGAP5 in ovarian cancer cells.

Micro rna (mi rna/mi r)-409-5p has been reported to be implicated in prostate and breast cancers; however, its functional role in ovarian cancer (oc) remains unclear.Therefore the aim of the present study was to investigate the clinical significance and biological function of mi r-409-5p in oc.Here, reverse transcription-quantitative pcr analysis was performed to detect mi r-409-5p expression in oc tissues and cell lines.The association between mi r-409-5p expression and the clinicopathological characteristics of patients with oc was assessed using the fisher's exact test.Furthermore, the cell counting kit-8 assay was performed to assess cell proliferation.Cell cycle distribution and apoptosis were evaluated via flow cytometric analysis, and the target gene of mi r-409-5p was validated via the dual-luciferase reporter assay.The results demonstrated that mi r-409-5p expression was significantly downregulated in oc tissues and cell lines compared with adjacent normal tissues and epithelial cells, respectively.In addition, low mi r-409-5p expression was significantly associated with tumor size (p=0.044) and the international federation of gynecology and obstetrics staging system (p=0.005).Notably, overexpression of mi r-409-5p suppressed cell proliferation, and induced g2/m phase arrest and apoptosis of oc cells.Mechanistically, discs large-associated protein 5 (dlgap5) was identified as a novel target of mi r-409-5p, which was negatively regulated by mi r-409-5p.Dlgap5 expression was significantly upregulated in oc tissues and cell lines compared with adjacent normal tissues and epithelial cells, respectively.Furthermore, overexpression of dlgap5 reversed the effects of mi r-409-5p on skov-3 cell proliferation, and g2/m phase and apoptosis.Taken together, these results suggest that mi r-409-5p acts as a tumor suppressor in oc by modulating dlgap5 expression.

Journal: Oncology letters (2022)
Publication types: Journal Article