syedzayyan/paper_mill_benchmark huggingface dataset:
Effects of anti-resorptive treatment on the material properties of individual canine trabeculae in cyclic tensile tests.

Osteoporosis is defined as a decrease of bone mass and strength, as well as an increase in fracture risk.It is conventionally treated with antiresorptive drugs, such as bisphosphonates (bps) and selective estrogen receptor modulators (serms).Although both drug types successfully decrease the risk of bone fractures, their effect on bone mass and strength is different.For instance, bp treatment causes an increase of bone mass, stiffness and strength of whole bones, whereas serm treatment causes only small (4%) increases of bone mass, but increased bone toughness.Such improved mechanical behavior of whole bones can be potentially related to the bone mass, bone structure or material changes.While bone mass and architecture have already been investigated previously, little is known about the mechanical behavior at the tissue/material level, especially of trabecular bone.As such, the goal of the work presented here was to fill this gap by performing cyclic tensile tests in a wet, close to physiologic environment of individual trabeculae retrieved from the vertebrae of beagle dogs treated with alendronate (a bp), raloxifene (a serm) or without treatments.Identification of material properties was performed with a previously developed rheological model and of mechanical properties via fitting of envelope curves.Additionally, tissue mineral density (tmd) and microdamage formation were analyzed.Alendronate treatment resulted in a higher trabecular tissue stiffness and strength, associated with higher levels of tmd.In contrast, raloxifene treatment caused a higher trabecular toughness, pre-dominantly in the post-yield region.Microdamage formation during testing was not affected by either anti-resorptive treatment regimens.These findings highlight that the improved mechanical behavior of whole bones after anti-resorptive treatment is at least partly caused by improved material properties, with different mechanisms for alendronate and raloxifene.This study further shows the power of performing a mechanical characterization of trabecular bone at the level of individual trabeculae for better understanding of clinically relevant mechanical behavior of bone.

Journal: Bone (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Behavioral responses for facemask use messages to prevent COVID-19 among residents of Bahir Dar City, Ethiopia: an application of extended parallel process model.

The coronavirus disease 2019 (covid-19) pandemic causes major morbidity and mortality in the world.Timely behavioral response assessment of the community is important to shape the next effective interventions and risk communication strategies to adopt preventive behavior.Hence, this study aimed to assess behavioral responses for facemask-use messages to prevent covid-19 and its predictors among residents of bahir dar city, ethiopia, 2021 by using the extended parallel process model.Methods: a community-based cross-sectional study was conducted with the guide of the extended parallel process model in bahir dar city from march 9 to april 9, 2021.A multistage sampling technique was used, and data was collected through a face-to-face interviewer-administered questionnaire using epicollect5.Descriptive statistics and binary logistic regression were computed using spss v.25.Variable with p < 0.25 in the bivariable analysis was a candidate for multivariable analysis to control confounding effect.In multivariable analysis, variables with p < 0.05 were considered statistically significant and the result was presented using an adjusted odd ratio (aor) with a 95% confidence interval (ci).Results a total of 616 participants with a response rate of 97.1% were included.Of the total participants, 229(37.2%) were in the danger control response.The behavioral response was affected by occupational status [aor (95%ci) 3.53(1.67-7.46)], the number of people living together [aor (95%ci) 2.62(1.28-5.39)], self-control [aor (95%ci) 1.14(1.05-1.25)], a friend for the preferred source of information [aor (95%ci) 5.18(3.22-8.33)] and printed materials for the preferred channel [aor (95%ci) 2.14(1.35-3.43)].Conclusion above one-third of the participants were in the danger control response.Occupational status, number of people living together, self-control, a friend for the preferred source of information, and printed materials for the preferred channel were independent predictors of resident behavioral response to the use of facemasks.Policymakers should consider students and people who live alone.Message developers should use a friendly person to transmit messages and should prepare printed materials.Activities and strategies should also focus on self-control and perceived efficacy without ignoring the perceived threat.

Journal: BMC public health (2022)
Publication types: Journal Article
Genipin cross-linked carbon dots for antimicrobial, bioimaging and bacterial discrimination.

Multifunctional carbon dots (cds) present enormous potential in numerous applications and have attracted widespread attention for various applications in the biomedical field.Bacterial infection is a common health issue; the development of antibacterial materials with low toxicity and good biocompatibility is becoming more important.In this work, we synthesized a new type of nitrogen co-doped carbon dots-genipin covalent conjugate (n-cds-gp) via hydrothermal methods.The microstructure and chemical composition of the n-cds-gp were characterized.The biocompatibility, stability, antibacterial activity, and fluorescence performance of the n-cds-gp were assessed.The results revealed that n-cds-gp possessed high biocompatibility, high light stability, and broad antibacterial activity.Additionally, selective gram-positive bacterial imaging by n-cds-gp provided a more rapid method of bacterial detection.The n-cds-gp have the potential to be applied as bioimaging and antibacterial agents and for bacterial discrimination.

Journal: Colloids and surfaces. B, Biointerfaces (2020)
Publication types: Journal Article
Recurrent Amplification of the Osmotic Stress Transcription FactorNFAT5in Adrenocortical Carcinoma.

Tumorigenesis requires mitigation of osmotic stress and the transcription factor nuclear factor of activated t cells 5 (nfat5) coordinates this response by inducing transcellular transport of ions and osmolytes.Nfat5 modulates in vitro behavior in several cancer types, but a potential role of nfat5 in adrenocortical carcinoma (acc) has not been studied.A discovery cohort of 28 accs was selected for analysis.Coverage depth analysis of whole-exome sequencing reads assessed nfat5copy number alterations in 19 accs.Quantitative real-time pcr measured nfat5m rna expression levels in 11 accs and 23 adrenocortical adenomas.Immunohistochemistry investigated protein expression in representative adrenal samples.The cancer genome atlas database was analyzed to corroborate nfat5findings from the discovery cohort and to test whether nfat5expression correlated with ion/osmolyte channel and regulatory protein expression patterns in acc.nfat5was amplified in 10 accs (52.6%) and clustered in the top 6% of all amplified genes.M rna expression levels were 5-fold higher compared with adrenocortical adenomas (p< 0.0001) and nfat5overexpression had a sensitivity and specificity of 81.8% and 82.7%, respectively, for malignancy.Increased protein expression and nuclear localization occurred in representative accs.The cancer genome atlas analysis demonstrated concomitant nfat5amplification and overexpression (p< 0.0001) that correlated with increased expression of sodium/myo-inositol transporter slc5a3(r2= 0.237,p< 0.0001) and 14 other regulatory proteins (p< 0.05) previously shown to interact with nfat5.Amplification and overexpression of nfat5and associated osmotic stress response related genes may play an important role adrenocortical tumorigenesis.

Journal: Journal of the Endocrine Society (2020)
Publication types: Journal Article
Evidence for functional G-coupled protein receptors 43 and 120 in subcutaneous and intramuscular adipose tissue of Angus crossbred steers.

We conducted 3 independent experiments to demonstrate functional g-coupled protein receptor 43 (gpr43) and gpr120 in bovine intramuscular (i.m.) and subcutaneous (s.c.) adipose tissues.We hypothesized that media volatile fatty acids and long-chain fatty acids would affect c amp-activated protein kinase-alpha (ampkα) protein expression and c amp concentrations differently in i.m.And s.c.Adipose tissue.Experiment 1: oleic acid (18:1n-9) decreased phosphorylated ampkα protein (p-ampkα) and the p-ampkα/ampkα protein ratio in i.m.Preadipocytes, increased the p-ampkα/ampkα protein ratio in bovine satellite cells, and had no effect in s.c.Preadipocytes.Experment 2: ex vivo explants from the 5th to 8th longissimus thoracic rib muscle section of angus crossbred steers were cultured 48 hr in media containing 0.25 μm ciglitizone, 5 m m glucose, and 5 m m acetate, in the absence or the presence of 100 μm oleic acid.Oleic acid increased acetate incorporation into fatty acids and gpr43 gene expression in i.m.Adipose tissue (p < 0.05), but oleic acid had no effect on fatty acid synthesis or gpr43 expression in s.c.Adipose tissue.Experiment 3: fresh s.c.And i.m.Adipose tissue from the 5th to 8th longissimus thoracic rib muscle section of angus crossbred steers was transferred immediately to 6-well culture plates containing 3 m l of khb/hepes/5 m m glucose.Samples were preincubated with 0.5 m m theophylline plus 10 μm forskolin for 30 min, after which increasing concentrations of acetate or propionate (0, 10-3, 10-2.3, and 10-3 m) in the absence or the presence of 100 μm oleic acid or 100 μm palmitic acid (16:0) were added to the incubation media.Acetate had no effect on forskolin-stimulated c amp production in s.c.Adipose tissue but decreased c amp in i.m.Adipose tissue (p < 0.05); this indicates a functional gpr43 receptor in i.m.Adipose tissue.The combination of 10-2 m acetate and oleic acid decrease c amp production in s.c.Adipose tissue, consistent with gpr120 receptor activity, but oleic acid and palmitic acid attenuated the depression of c amp production caused by acetate in i.m.Adipose tissue.Palmitic acid depressed c amp production in s.c.Adipose tissue, and increased c amp production in i.m.Adipose tissue (p < 0.05).Propionate had no effect on c amp production in s.c.Or i.m.Adipose tissue.These results provide evidence for functional gpr43 receptors in i.m.Adipose tissue and gpr120 receptors in s.c.Adipose tissue, both of which would suppress lipolysis.

Journal: Journal of animal science (2021)
Publication types: Journal Article
Nudge with caution: targeting fruit and vegetable consumption in primary schools.

Most children in the uk are not eating enough fruit and vegetables to support optimum health.Evidence-based interventions are needed to change this trend.In the present pilot study, effectiveness of simple behavioural nudges on children's lunchtime consumption of fruit and vegetables was tested in two primary (elementary) schools.Children's (n = 107) lunchtime consumption was measured directly through the use of a validated digital photography protocol; measures were taken at baseline and again after a 3-week long intervention.Changes to the choice architecture of dining rooms included improved presentation and provision of target foods, attractive advertisements and labelling, and prompting by staff.For children who took school lunches (n = 67), both selection and consumption of fruit increased as the result of the intervention.Their selection of vegetables did not change over time, however, and their consumption ether remained unchanged or declined.No changes were observed in the comparison group (n = 40), who brought their lunch boxes from home.These results caution against using selection (serving sizes), as estimates of consumption or a measure of behaviour changes.They also show that all evaluations should consider the effects of each intervention on children's eating overall, rather than just report changes in target item consumption, to check for any unintended consequences of the intervention.

Journal: European journal of clinical nutrition (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Explainable artificial intelligence for omics data: a systematic mapping study.

Researchers increasingly turn to explainable artificial intelligence (xai) to analyze omics data and gain insights into the underlying biological processes.Yet, given the interdisciplinary nature of the field, many findings have only been shared in their respective research community.An overview of xai for omics data is needed to highlight promising approaches and help detect common issues.Toward this end, we conducted a systematic mapping study.To identify relevant literature, we queried scopus, pub med, web of science, bio rxiv, med rxiv and ar xiv.Based on keywording, we developed a coding scheme with 10 facets regarding the studies' ai methods, explainability methods and omics data.Our mapping study resulted in 405 included papers published between 2010 and 2023.The inspected papers analyze dna-based (mostly genomic), transcriptomic, proteomic or metabolomic data by means of neural networks, tree-based methods, statistical methods and further ai methods.The preferred post-hoc explainability methods are feature relevance (n = 166) and visual explanation (n = 52), while papers using interpretable approaches often resort to the use of transparent models (n = 83) or architecture modifications (n = 72).With many research gaps still apparent for xai for omics data, we deduced eight research directions and discuss their potential for the field.We also provide exemplary research questions for each direction.Many problems with the adoption of xai for omics data in clinical practice are yet to be resolved.This systematic mapping study outlines extant research on the topic and provides research directions for researchers and practitioners.

Journal: Briefings in bioinformatics (2023)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Effects of Epidural Labour Analgesia in Mother and Foetus.

Aim of study was to determine effect of epidural analgesia on progress of labour and mode of delivery, to find out its complications in labour and puerperium and to evaluate neonatal outcome in terms of apgar score.Method the present study was conducted in department of obstetrics and gynaecology at government medical college aurangabad over period of 2 years from june 2014 to june 2016 after taking approval from institutional ethical board.Hundred low-risk primigravidas were included in the study, 50 women received epidural analgesia for relief of labour pain at 3-4 cm and 50 women served as control.The important outcome factors studied were the following : (1) duration of active phase of i stage, and ii stage, (2) mode of delivery, (3) apgar scores, (4) untoward reactions and intrapartum complications, (5) overall satisfaction of the mother.Results the operative delivery rates were not significantly different in both the groups (8% in the control group and 6% in the study group:pvalue ns, i.e.> 0.05).The duration of first stage (our study showed no significant difference in the duration of first stage in both the study and control groupspvalue > 0.05) and second stage of labour (pvalue ns > 0.05) and the need for oxytocin were comparable in the two groups.The side effects observed were minimal.It has given excellent pain relief and improved neonatal outcome (5 min).Ea is associated with rates of vaginal delivery (88 v/s 84%) and lscs rate (8 v/s 6%) which are comparable with control group.Conclusion epidural analgesia is a very promising, safe and effective method of pain relief.No major complications and a good apgar score make it a good option of care in modern obstetrics.

Journal: Journal of obstetrics and gynaecology of India (2018)
Publication types: Journal Article
Machine Learning Prediction of the Transmission Function for Protein Sequencing with Graphene Nanoslit.

Protein sequencing has rapidly changed the landscape of healthcare and life science by accelerating the growth of diagnostics and personalized medicines for a variety of fatal diseases.Next-generation nanopore/nanoslit sequencing is promising to achieve single-molecule resolution with chromosome-size-long readability.However, due to inherent complexity, high-throughput sequencing of all 20 amino acids demands different approaches.Aiming to accelerate the detection of amino acids, a general machine learning (ml) method has been developed for quick and accurate prediction of the transmission function for amino acid sequencing.Among the utilized ml models, the xgboost regression model is found to be the most effective algorithm for fast prediction of the transmission function with a very low test root-mean-square error (rmse ∼0.05).In addition, using the random forest ml classification technique, we are able to classify the neutral amino acids with a prediction accuracy of 100%.Therefore, our approach is an initiative for the prediction of the transmission function through ml and can provide a platform for the quick identification of amino acids with high accuracy.

Journal: ACS applied materials & interfaces (2022)
Publication types: Journal Article
Actions of multiple doses of resveratrol on oxidative and inflammatory markers in plasma and brain of healthy and arthritic rats.

The actions of resveratrol in brain and plasma of rats with adjuvant-induced arthritis were investigated.Resveratrol was administered orally during a period of 23 days.A major concern of the present work was to explore an ample range of daily doses (10-200 mg/kg).Several oxidative and inflammatory markers were measured.Important effects of resveratrol treatment were the normalization of the plasma myeloperoxidase activity (inflammatory marker), the normalization of the brain xanthine oxidase activity (reactive oxygen species source) and the near-normalization of the catalase activity in the brain (antioxidant defence).These effects presented obvious dose dependencies in the range up to 200 mg/kg.Resveratrol also reduced protein and lipid damage within the lowest dose ranges investigated, and its action as a free radical scavenger activity was enhanced in brain mitochondria of arthritic rats.Resveratrol failed in restoring the diminished albumin levels and plasma protein thiols in arthritic rats.The latter, however, were substantially increased in healthy rats at low doses (up to 50 mg/kg), a sign of antioxidant action.This increase was reversed at higher doses, a sign of pro-oxidant action.The observations agree with the notion that low doses of resveratrol might be useful as an adjuvant to the conventional antirheumatic drugs.

Journal: Basic & clinical pharmacology & toxicology (2021)
Publication types: Journal Article
Nanoscale Interparticle Distance within Dimers in Solution Measured by Light Scattering.

We demonstrate a novel approach to quantify the interparticle distance in colloidal dimers using mie scattering.The interparticle distance is varied in a controlled way by changing the ionic strength of the solution and the magnetic attraction between the particles.The measured scaling behavior is interpreted using an energy-distance model that includes the repulsive electrostatic and attractive magnetic interactions.The center-to-center distances of particles with a 525 nm radius can be determined with a root-mean-square accuracy of 12 nm.The data show that the center-to-center distance is larger by 83 nm compared to perfect spheres.The underlying distance offset can be attributed to repulsion by charged protrusions caused by particle surface roughness.The measurement method accurately quantifies interparticle distances that can be used to study cluster formation and colloid aggregation in complex systems, e.g., in biosensing applications.

Journal: Langmuir : the ACS journal of surfaces and colloids (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
IgE antibodies increase honeybee venom responsiveness and detoxification efficiency of mast cells.

In contrast to their clearly defined roles in allergic diseases, the physiologic functions of immunoglobulin e antibodies (ig es) and mast cells (mcs) remain enigmatic.Recent research supports the toxin hypothesis, showing that mcs and ig e-related type 2 immune responses can enhance host defense against certain noxious substances, including honeybee venom (bv).However, the mechanisms by which mcs can interfere with bv toxicity are unknown.In this study, we assessed the role of ig e and certain mc products in mc-mediated bv detoxification.Methods we applied in vitro and in vivo fluorescence microscopyimaging, and flow cytometry, fibroblast-based toxicity assays and mass spectrometry to investigate ig e-mediated detoxification of bv cytotoxicity by mouse and human mcs in vitro.Pharmacologic strategies to interfere with mc-derived heparin and proteases helped to define the importance of specific detoxification mechanisms.Results venom-specific ig e increased the degranulation and cytokine responses of mcs to bv in vitro.Passive serum sensitization enhanced mc degranulation in vivo.Ig e-activated mouse or human mcs exhibited enhanced potential for detoxifying bv by both proteolytic degradation and heparin-related interference with toxicity.Mediators released by ig e-activated human mcs efficiently degraded multiple bv toxins.Conclusions our results both reveal that ig e sensitization enhances the mc's ability to detoxify bv and also assign efficient toxin-neutralizing activity to mc-derived heparin and proteases.Our study thus highlights the potential importance of ig e, mcs, and particular mc products in defense against bv.

Journal: Allergy (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Risk factors affecting ICU admission in COVID-19 patients; Could air temperature be an effective factor?

As the covid-19 pandemic has been spreading rapidly all over the world, there are plenty of ongoing works to shed on light to unknown factors related to disease.One of the factors questioned is also to be the factors affecting the disease course.In this study, our aim is to determine the factors that affect the course of the disease in the hospitalised patients because of covid-19 infection and to reveal whether the seasonal change has an effect on the disease course.Methods our study was conducted on 1950 pcr test positive patients who were hospitalised for covid-19 disease between march 16 and july 15.Results as the seasonal temperature increases, decrease in wbc, plt and albumin levels and increase in ldh and ast levels were observed.Risk of need for icu has been found statistically significant (p < .05) with the increase in the age, ldh levels and crp levels and with the decrease in the ca and albumin levels.Conclusions it is predicted with these results that, seasonal change might have affects on the clinical course of the disease, although it has no affect on the spread of the disease.And it might beneficial to check biochemical parameters such as ldh, crp, ca and albumin to predict the course of the disease.

Journal: International journal of clinical practice (2021)
Publication types: Journal Article