syedzayyan/paper_mill_benchmark huggingface dataset:
Determination of COVID-19 PCR positivity and mutation status in coronaVac vaccinated individuals in Turkey.

Corona vac is an inactivated virus-based covid-19 vaccine used in turkey and approved for emergency use by the world health organization (who).In this study, it was aimed to retrospectively evaluate the mutation status and clinical status in individuals who received two doses of corona vac vaccine and were infected with covid-19 at least two weeks after the second dose.Methods 164 people were included in the study and covid-19 diagnosis and mutation analyses were determined by rt-pcr using the bioseepdy sars co v-2 double gene rt-q pcr kit and the biospeedy sars-co v-2 variant plus kit in accordance with the protocol determined by the manufacturer.Results 116 (70.7%) uk (alpha, b.1.1.7) mutation and 3 (1.8%) south africa (beta, b.1.351), brazil (gamma, p.1) mutations were determined in 164 double doses corona vac vaccinated patients; 45 (27.5%) patients were mutation negative.Nine patients (5.5%) developed pneumonia.Eight patients (4.9%) had ct findings compatible with corona virus infection.Seven (4.3%) of the patients received treatment in the intensive care unit, and 5 (3%) of the patients were intubated.Discussion in conclusion, people who receive two doses of corona vac vaccine can be reinfected with mutant viruses, vaccine significantly reduces the need for hospitalization, ct findings and intensive care.

Journal: Turkish journal of medical sciences (2022)
Publication types: Journal Article
One Week Prevalence and Incidence of Diarrhea: Baseline Status of Cluster Randomised Controlled Trial of Nano Maji Filter System in Geita, Tanzania.

We have developed nano maji (nmm) filter system for water treatment which is currently being evaluated in a definitive cluster randomised controlled trial.Objectives this paper descriptively presents the baseline status of one-week incidence and prevelence of diarrhoea water, sanitation and hygiene and their determinants.Methods recruited households in the three villages of geita district were allocated to either intervention (nnm filter system) or control (usual practice).The primary outcome of the trial is to reduce episodes of diarrhoea at 6 months post-randomisation.Secondary outcomes are to improve water, sanitation and hygiene (wash) status.Although households were sampled, individuals living in the selected households are used as unit of analysis for estimation of prevalence and incidence of diarrhea.Results a total of 1,281 individuals (1,070 above 5 years and 211 under the age of 5 year children) lived in 186 households (7 individuals per household).The reported one-week prevalence and incidence of diarrhea was 10.8% and 8.4% respectively.Children under the age of five years had high incidence (22.7%) of diarrhea than individuals aged 5 years and above (5.6%).Among under five children, boys had high incidence and prevalence of diarrhea than girls.Individuals with diarrhea were likely to live in poor household, not using safe water and toilet.Over 70% of households had unacceptable latrines 135 (72.7%) and poor water situation 138 (74.3%) in terms of practice of storing, treating and drawing water from storage container.Majority of respondents had limited knowledge on handwashing and rarely used soap when washing hands.Conclusion substantial proportion of individuals living in project areas are affected by diarrhea.Children below the age of five years are more affected than individuals aged five years and above.The baseline findings are representative of local status of wash, and reflects the prevailing poor water, sanitation and hygiene status in rural areas of tanzania.Trial approval number nimr/hq/r.8a/vol.Ix/3045.

Journal: The East African health research journal (2022)
Publication types: Journal Article
Glucagon-like peptide-1 analog liraglutide leads to multiple metabolic alterations in diet-induced obese mice.

Liraglutide, a glucagon-like peptide-1 analog, has beneficial metabolic effects in patients with type 2 diabetes and obesity.Although the high efficacy of liraglutide as an anti-diabetic and anti-obesity drug is well known, liraglutide-induced metabolic alterations in diverse tissues remain largely unexplored.Here, we report the changes in metabolic profiles induced by a 2-week subcutaneous injection of liraglutide in diet-induced obese mice fed a high-fat diet for 8 weeks.Our comprehensive metabolomic analyses of the hypothalamus, plasma, liver, and skeletal muscle showed that liraglutide intervention led to various metabolic alterations in comparison with diet-induced obese or nonobese mice.We found that liraglutide remarkably coordinated not only fatty acid metabolism in the hypothalamus and skeletal muscle but also amino acid and carbohydrate metabolism in plasma and liver.Comparative analyses of metabolite dynamics revealed that liraglutide rewired intertissue metabolic correlations.Our study points to a previously unappreciated metabolic alteration by liraglutide in several tissues, which may underlie its therapeutic effects within and across the tissues.

Journal: The Journal of biological chemistry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Hemoglobin Mass and Blood Volume in Patients With Altitude-Related Polycythemia.

Patients with chronic mountain sickness (cms) have a high hemoglobin concentration [hb] due to increased hemoglobin mass (hbmass) and possibly reduced plasma volume (pv).The values of hbmass, pv and blood volume (bv) have been described differently, and the relationships between [hb] and hbmass or pv are poorly understood.This study obtained representative hbmass, pv and bv data from healthy, high-altitude residents and cms patients and quantified the dependency of [hb] on hbmass and pv.Methods eighty-seven subjects born at high altitude (∼3,900 m) were enrolled.Thirty-four had cms (cms), 11 had polycythemia without cms (intermediate, im), 20 were healthy highlanders (hh), and 22 living near sea level (sl, 420 m) served as the sea level (sl) control group.Hbmass, pv and bv were determined using a co-rebreathing method modified for assessing polycythemia patients.Furthermore, [hb], hematocrit (hct), plasma erythropoietin concentration [epo] and blood gas and acid-base status were determined.Results in the hh group, hbmass was 27% higher (940 ± 105 g) than in the sl group (740 ± 112 g) and 72% (1,617 ± 265 g) lower than in the cms group.The pv in the hh group was similar to that in the sl group (-6%) and 15% higher than that in the cms group (p< 0.001).In the hh group, the bv (5,936 ± 673 ml) did not differ from that in the sl group and was 28% lower than in the cms group (7,606 ± 1075 ml,p< 0.001).Log [epo] was slightly increased in the cms group relative to the hh group (p< 0.01).All values in the im group were between those in the hh and cms groups.Hbmass and bv were positively correlated, and pv was negatively correlated with peripheral o2saturation.Increased hbmass and decreased pv contributed approximately 65 and 35%, respectively, to the difference in [hb] between the hh (17.1 ± 0.8 g/dl) and cms (22.1 ± 1.0 g/dl) groups.Conclusions in cms patients, the decrease in pv only partially compensated for the substantial increase in hbmass, but it did not prevent an increase in bv; the decrease in pv contributed to an excessively high [hb].

Journal: Frontiers in physiology (2022)
Publication types: Journal Article
Understanding Pixel-Level 2D Image Semantics With 3D Keypoint Knowledge Engine.

Pixel-level 2d object semantic understanding is an important topic in computer vision and could help machine deeply understand objects (e.g., functionality and affordance) in our daily life.However, most previous methods directly train on correspondences in 2d images, which is end-to-end but loses plenty of information in 3d spaces.In this paper, we propose a new method on predicting image corresponding semantics in 3d domain and then projecting them back onto 2d images to achieve pixel-level understanding.In order to obtain reliable 3d semantic labels that are absent in current image datasets, we build a large scale keypoint knowledge engine called keypoint net, which contains 103,450 keypoints and 8,234 3d models from 16 object categories.Our method leverages the advantages in 3d vision and can explicitly reason about objects self-occlusion and visibility.We show that our method gives comparative and even superior results on standard semantic benchmarks.

Journal: IEEE transactions on pattern analysis and machine intelligence (2022)
Publication types: Journal Article
Early division of the paramedian forehead interpolated flap using cutaneous ultrasound.

And objectives the paramedian forehead flap is an interpolated flap, consisting of the transfer of tissue from the forehead region to the nasal area, irrigated by the supratrochlear artery.Traditionally, the vascular pedicle is divided at between 14 and 21 days.However, this time could be overestimated.Our objective is to demonstrate that the paramedian forehead flap can be divided before that set out in the literature and to demonstrate the usefulness of cutaneous ultrasound to determine the optimal time for division.Patients and methods a prospective observational study, including patients who required nasal defect reconstruction with a paramedian forehead flap, was designed.The inclusion criteria were: nasal tip, dorsum or alar skin defects following oncological surgery, larger than 2 cm.Twelve patients were included.A retrospective cohort was used to perform a cost reduction analysis.Results the average time to flow, measured by ultrasound, was 6.6 days.The average number of days to division of the pedicle was 6.9 days.No serious complications were reported.Conclusions the paramedian forehead flap can be divided before the traditional reported time.Ultrasound is a reliable and cost-effective technique to determine and individualize pedicle division time.

Journal: Journal der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : JDDG (2022)
Publication types: Observational Study;Journal Article
PaRent InterventiOn to pRevent dIsordered eating in children with TYpe 1 diabetes (PRIORITY): Study protocol for a feasibility randomised controlled trial.

S increasing evidence suggests that children and young people with type 1 diabetes (t1d) are at greater risk of disordered eating compared to children without t1d.Disordered eating in t1d has been linked to impaired wellbeing, increased health service use and early mortality.To address this problem, we will co-develop a psycho-education intervention for parents of children and young people with t1d, informed by the information motivation behavioural skills model.Methods the objective of this study is to assess the feasibility and acceptability of the intervention compared to a waitlist control group using a feasibility randomised controlled trial (rct) design.We aim to recruit 70 parents of children and young people with t1d (11-14 years), 35 in each arm.Those assigned to the intervention will be invited to participate in two workshops of 2 h each.Parents will be asked to complete outcome measures regarding eating habits, diabetes management, as well as a questionnaire based on the information motivation behavioural skills model which provides a theoretical foundation for the intervention.These will be completed at baseline, 1- and 3-month post-intervention.Children and young people will be asked to complete questionnaires on their eating behaviours at the same time intervals.Parents randomised to receive the intervention will be invited to take part in interviews to feedback on the intervention and research protocol acceptability.Conclusion it is anticipated that the psycho-education intervention aimed at parents will help prevent the development of disordered eating in children and young people with t1d and improve parental wellbeing.The results of this feasibility trial will determine whether this intervention approach is acceptable to families living with t1d, and whether a definitive rct of intervention effectiveness is justified.Qualitative findings will be used to refine the intervention and study protocols.Trial registration this protocol has been registered with clinical trials.gov [identifier: nct04741568].

Journal: Diabetic medicine : a journal of the British Diabetic Association (2022)
Publication types: Clinical Trial Protocol;Journal Article;Research Support, Non-U.S. Gov't
Effectiveness of an Ultrasound Visual Biofeedback Training for Tongue Shape Assessment During Speech Sound Production.

This proof-of-concept study examined the effectiveness of an ultrasound visual biofeedback (uvb) training within the participatory adult teaching strategy framework for instructing speech-language pathologists (slps) on the assessment of sonographic tongue configuration for remediation of speech sound errors.Method this research followed a multiple-baseline, multiple-probe single-case research methodology replicated across behaviors for data collection and analysis.Two school-based spls with no previous knowledge or experience with uvb were recruited.Results visual analysis of data and effect size calculations using the percentage of nonoverlapping data indicated that training was highly effective in teaching slps skills for the assessment of sonographic tongue configuration and how to promote changes in tongue configuration for the remediation of speech sound errors.Conclusions this study addressed the current gap in the literature regarding the lack of empirical evidence of uvb training for slps.Our findings support the exploration of evidence-based teaching strategies to train slps in the use of uvb for assessment of tongue configuration and remediation of speech sound errors.This can be of interest to academic programs and organizers of training opportunities through continued education units.

Journal: Language, speech, and hearing services in schools (2022)
Publication types: Journal Article
ACGME Interventional Cardiology Milestones 2.0-an overview: Endorsed by the Accreditation Council for Graduate Medical Education.

This document provides an overview of the rationale, development, interpretation, and practical suggestions for implementation of the new accreditation council for graduate medical education (acgme) interventional cardiology (ic) milestones 2.0.Previously, ic programs used the general acgme milestones for internal medicine.The ic milestones version 2.0 updates the acgme competencies to be specific to training in ic.In 2019 an acgme working group consisting of ic program directors, a lay representative, and representatives from the american board of internal medicine met to develop the ic milestones version 2.0.The acgme ic milestones 2.0 establishes a framework for formative feedback for trainees within domains of patient care, medical knowledge, systems-based practice, practice-based learning and improvement, professionalism, and interpersonal and communication skills.The 2021 ic milestones 2.0 provides a framework for ic mentors and trainees to identify areas for improvement or commendation help stimulate meaningful educational discussions, and provide the basis for self-reflection and self-improvement.

Journal: Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions (2022)
Publication types: Journal Article
Staging Chronic Hepatitis B Related Liver Fibrosis with a Fractional Order Calculus Diffusion Model.

Rationale and objectives accurately staging liver fibrosis is of great clinical significance.We aimed to evaluate the clinical potential of the non-gaussian fractional order calculus (froc) diffusion model in staging liver fibrosis.Materials and methods a total of 82 patients with chronic hepatitis b (chb) were included in this prospective study.Diffusion weighted imaging (dwi)-derived parameters including the diffusion coefficient (d), fractional order parameter (β) and microstructural quantity (μ) sourced from froc-dwi, and apparent diffusion coefficient (adc) derived from mono-exponential dwi, as well as the aspartate aminotransferase-to-platelet ratio index (apri) and fibrosis-4 (fib-4) were calculated.Their correlations with fibrosis stages and the diagnostic efficacy in predicting liver fibrosis were assessed and compared.Results d (r = -0.667), β (r = -0.671), μ (r = -0.481), and adc (r = -0.665) displayed significant correlations with fibrosis stages (p 0.05).The diagnostic performance of the combined index with four diffusion metrics was better than d, β, μ or adc used alone (p < 0.05) as well as apri or fib-4 (p < 0.01) in fibrosis staging.Conclusion froc-dwi was valuable in staging liver fibrosis in patients with chb, but there were no significant differences between the froc-dwi parameters and the classical adc.However, the combined dwi-derived index including d, β, μ and adc offered the best diagnostic efficacy and may serve as a reliable tool for fibrosis evaluation, superior to apri and fib-4.

Journal: Academic radiology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Mercury can be transported into marine copepod by polystyrene nanoplastics but is not bioaccumulated: An increased risk?

Plastic pollution is a serious problem in the global marine environment because it can produce negative effects at the biological and ecological levels.Due to large surface-area-to-volume ratio and inherent hydrophobicity, nanoplastics can serve as carriers of contaminants, and may affect their fate and toxicity in marine environments.However, the combined effects of nanoplastics and mercury (hg) in marine organisms have not been well characterized.In this study, after verifying the ingestion of polystyrene nano-size plastics (ps nps, 50 nm) by the copepod tigriopus japonicus and adsorption of hg to ps nps, we investigated the effects of ps nps and hg exposure (alone or in combination) for 48 h on the copepods.Specifically, a 72-h depuration was performed after 48 h exposure.The results showed that after 48 h exposure, the copepod's hg concentration was significantly increased in the combined exposure group compared to that in the hg treatment group, but these differences did not persist following 24 h of depuration.Therefore, ps nps transported hg into the copepods but did not promote hg bioaccumulation.Treatment with ps nps alone did not induce toxicity in t.Japonicus, but co-exposure to ps nps and hg resulted in elevated transcription of genes related to energy production, antioxidant response, and detoxification/stress defense when compared with hg treatment alone, demonstrating the synergistic interaction between ps nps and hg.Our findings contribute to a comprehensive understanding about the combined toxicity of nanoplastics and metals and the potential ecological risks of associated with these effects in marine environments.

Journal: Environmental pollution (Barking, Essex : 1987) (2022)
Publication types: Journal Article
Bioactivity of micropatterned TiO2nanotubes fabricated by micro-milling and anodic oxidation.

Although many methods have been proposed to fabricate a micro/nanostructure on titanium surface for enhanced cellular responses to implants, it has been challenging to construct an orderly micro/nanostructure.In this study, an ordered structure of micropatterned ti o2nanotubes was produced on titanium surface by the combined use of micro-milling and anodic oxidation.The surface properties of different modified titanium samples were investigated by field emission scanning electron microscopy, laser scanning microscope, x-ray diffraction, and contact angle goniometer.The corrosion resistance of different samples was evaluated by an electrochemical workstation.A series of cell experiments were performed to evaluate the responses of osteoblasts to the modified titanium substrates.The results indicated that the surface roughness and hydrophilicity of micro/nanostructured titanium remarkably increased compared to the polished titanium.In addition, the corrosion resistance of micro/nanostructured titanium samples was also improved in comparison to the polished titanium samples.More importantly, the proliferation and differentiation of cells were significantly promoted on micro/nanostructure titanium substrates.This study provides a promising method to construct a regular micro- and nano-structure on titanium surface for cytocompatibility improvement.

Journal: Materials science & engineering. C, Materials for biological applications (2019)
Publication types: Journal Article
Characterization of Herves-like transposable elements (hATs) in Drosophila species and their evolutionary scenario.

A monophyletic group of drosophila h at transposable elements, referred to as herves-like, was characterized and found to be present in 46% of 57 screened drosophila species.A remarkable characteristic of these elements is the presence of a long array of minisatellite repeats (mn rs) in both subterminal extremities of the elements.The copy number of these minisatellites was highly variable between and within populations.Twenty-three strains of drosophila willistoni, covering its geographic distribution, were screened for polymorphism in the copy number of 5' mn rs, showing a variation from 7 to 20 repeat copies.These mn rs are well conserved among drosophila species and probably function as transposase binding sequences, as provided by short subterminal repeats in other h at elements.Miniature inverted repeat transposable elements were found in 27% of species carrying herves-like elements.Phylogenetic analysis showed incongruences between transposable elements and species phylogenies, suggesting that at least four horizontal transfer events have occurred.

Journal: Insect molecular biology (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The effect of key DNA methylation in different regions on gene expression in hepatocellular carcinoma.

Hepatocellular carcinoma (hcc) is a common cancer with high morbidity and mortality.As we all know, the alteration of dna methylation has a crucial impact on the occurrence of hcc.However, the mechanism of the effect of dna methylation in different regions on gene expression is still unclear.Here, by computing and analyzing the distribution of differential methylation in 12 different regions in hcc tissues and adjacent normal tissues, not only the hypermethylation of cp g islands and global hypomethylation were found, but also a stable distribution pattern of differential methylation in hcc was found.Then the correlations between dna methylations in different regions and gene expressions were calculated, and the diversity of correlations in different regions was determined.The key genes of differential methylation and differential expression related to the survival of hcc patients were obtained by using cox regression analysis, a four-gene prognostic risk scoring model was constructed, and the prognostic performance was well verified.The regions of the differentially methylated cp g sites corresponding to the four key genes were located and their influences on the expression were analyzed.The results indicate that the promoter, first exon, 5'utr, sixth exon, n_shore, and s_shore hypomethylation promotes the expression of key oncogenes, which together lead to the occurrence of hcc.These results might help to study the role of dna methylation in hcc and provide potential biomarkers for the diagnosis of hcc.

Journal: Molecular omics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't