syedzayyan/paper_mill_benchmark huggingface dataset:
The sphingosine-1-phosphate receptor modulator, FTY720, prevents the incidence of diabetes in Spontaneously Diabetic Torii rats.

The sphingosine-1-phosphate (s1p) receptor modulator regulates lymphocyte trafficking, resulting in its depletion from circulation, which ultimately causes immunosuppression.In this study, we investigated the preventive effect of fingolimod (fty720) in the non-obese type 2 diabetic model, spontaneously diabetic torii (sdt) rats.The s1p receptor modulator, fty720 (0.3 mg/kg p.o.), was administered for 12 weeks to sdt rats from 5 to 17 weeks of age.Based on our findings, fty720 could suppress the incidence of diabetes in sdt rats.Further, glucose intolerance was improved in fty720-treated sdt rats at 14 weeks of age.Based on the haematological and histological analyses performed at 17 to 18 weeks of age, a decrease in lymphocytes and monocytes in the peripheral blood and a decrease in lymphocyte and atrophy in spleen occurred in the fty720-treated sdt rats.Furthermore, the pancreatic changes, such as inflammation, atrophy, and fibrosis in islets observed in sdt rats were improved by fty720 treatment.These findings suggest that the immunomodulatory effects of fty720 reduced the pancreatic lesion in sdt rats, thereby demonstrating its preventive effect against diabetes.The development of diabetes in sdt rats is related to disorders of the immune system.However, the s1p receptor modulator may be useful for treating type 2 diabetes.

Journal: Clinical and experimental pharmacology & physiology (2021)
Publication types: Journal Article
Food safety lessons learned from the COVID-19 pandemic.

The covid-19 pandemic has ushered in a new era of food safety.To date, there is no evidence to suggest that consuming food is associated with covid-19.Nevertheless, covid-19's impact on food safety and security has been grave.The world is currently experiencing several supply chain issues as a direct result of extensive lockdowns and impacts on essential workers' safety.However, disruption in the food supply, while catastrophic in nature, has created opportunities for the advancement of medical science, data processing, security monitoring, foodborne pathogen detection, and food safety technology.This article will discuss the key components for food safety during the covid-19 pandemic.The discussion will draw from lessons learned early in the outbreak and will analyze the etiology of the disease through a food safety perspective.From there, we will discuss personal protective equipment, detection of sars-co v-2, useful surrogates to study sars-co v-2, and the expanding field of data science, from the food safety point of view.In the future, scientists can apply the knowledge to the containment of covid-19 and eventually to future pandemics.

Journal: Journal of food safety (2021)
Publication types: Journal Article;Review
Effect of thermal liquefying of crystallised honeys on their antibacterial activities.

Thermal liquefying of crystallised honey is the most convenient option for beekeepers to fully liquefy honey.A controlled mild thermal treatment is widely used for effective and safe liquefying of crystallised honey.In this study, we demonstrated that thermal liquefying at different temperatures of 45, 55 and 65 °c does not affect the overall honey antibacterial activity against pseudomonas aeruginosa and staphylococcus aureus, and, in some cases, it may even increase the antibacterial potential of honey.A mild thermal treatment of crystallised honey was able to significantly increase its glucose oxidase (gox) enzyme activity.On the other hand, the increased gox activity in treated honey samples did not affect levels of accumulated h2o2, suggesting that some phytochemicals may contribute to or modulate antibacterial activity.Taken together, a mild thermal liquefaction of crystallised honey may increase the potential bioactivity of this matrix, which is also affected by the botanical origin.

Journal: Food chemistry (2018)
Publication types: Journal Article
Effect of long-term acid suppression therapy with proton pump inhibitors or H2receptor blockers on serum vitamin B12levels in elderly population.

Long-term usage of acid suppression drugs like proton pump inhibitors (ppis) or h2receptor blockers in the elderly population has been found to result in vitamin b12deficiency.However, the reports are equivocal.Objective to determine the serum vitamin b12levels in elderly patients under chronic acid suppression therapy.Methods patients aged above 60 years and on any of the ppis or h2blockers for at least 6 months were recruited.Out of 77 patients recruited, 60 patients were included for the final analysis.The serum vitamin b12levels were measured using the accu diagtm-vitamin b12 elisa system.Results out of 60 patients, pantoprazole (40%) and omeprazole (37%) were the commonly prescribed acid-suppressing drugs.Nearly 50% of the patients on prolonged acid suppression therapy were either "deficient" (less than 200 pg/ml) or "insufficient" (200 to 300 pg/ml) in serum vitamin b12levels.Neither the average serum vitamin b12levels (p = 0.994) nor the vitamin b12status (p = 0.226) varied significantly across the drug groups of pantoprazole, omeprazole, and ranitidine.Conclusions prolonged acid suppression therapy with ppis or h2blockers may result in serum vitamin b12deficiency.However, there was no class (ppis vs.H2receptor blockers)- or drug (pantoprazole vs.Omeprazole vs.Ranitidine)-based differences found in the vitamin b12deficiency caused.

Journal: Irish journal of medical science (2021)
Publication types: Journal Article
Nucleation in sessile saline microdroplets: induction time measurementviadeliquescence-recrystallization cycling.

Induction time, a measure of how long one will wait for nucleation to occur, is an important parameter in quantifying nucleation kinetics and its underlying mechanisms.Due to the stochastic nature of nucleation, efficient methods for measuring large numbers of independent induction times are needed to ensure statistical reproducibility.In this work, we present a novel approach for measuring and analyzing induction times in sessile arrays of microdropletsviadeliquescence/recrystallization cycling.With the help of a recently developed image analysis protocol, we show that the interfering diffusion-mediated interactions between microdroplets can be eliminated by controlling the relative humidity, thereby ensuring independent nucleation events.Moreover, possible influence of heterogeneities, impurities, and memory effect appear negligible as suggested by our 2-cycle experiment.Further statistical analysis (k-sample anderson-darling test) reveals that upon identifying possible outliers, the dimensionless induction times obtained from different datasets (microdroplet lines) obey the same distribution and thus can be pooled together to form a much larger dataset.The pooled dataset showed an excellent fit with the weibull function, giving a mean supersaturation at nucleation of 1.61 and 1.85 for the 60 p l and 4 p l microdroplets respectively.This confirms the effect of confinement where smaller systems require higher supersaturations to nucleate.Both the experimental method and the data-treatment procedure presented herein offer promising routes in the study of fundamental aspects of nucleation kinetics, particularly confinement effects, and are adaptable to other salts, pharmaceuticals, or biological crystals of interest.

Journal: Faraday discussions (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Virus blocking textile for SARS-CoV-2 using human body triboelectric energy harvesting.

Effective mitigation technology to prevent the spread of severe acute respiratory syndrome coronavirus 2 (sars-co v-2) is required before achieving population immunity through vaccines.Here we demonstrate a virus-blocking textile (vbt) that repulses sars-co v-2 by applying repulsive coulomb force to respiratory particles, powered by human body triboelectric energy harvesting.We show that sars-co v-2 has negative charges, and a human body generates high output current of which peak-to-peak value reaches 259.6 μa at most, based on triboelectric effect.Thereby, the human body can sustainably power a vbt to have negative electrical potential, and the vbt highly blocks sars-co v-2 by repulsion.In an acrylic chamber study, we found that the vbt blocks sars-co v-2 by 99.95%, and sars-co v-2 in the vbt is 13-fold reduced.Our work provides technology that may prevent the spread of virus based on repulsive coulomb force and triboelectric energy harvesting.

Journal: Cell reports. Physical science (2022)
Publication types: Journal Article
Combined hyperforin and lanicemine treatment instead of ketamine or imipramine restores behavioral deficits induced by chronic restraint stress and dietary zinc restriction in mice.

Clinical and preclinical studies show evidence that chronic stress or nutritional deficits in dietary zinc (zn) intake may be risk factors for developing major depressive disorder (mdd).Furthermore, there may be possible links between low serum zn levels and development of treatment-resistant depression.In the present work, we combined chronic restraint stress (crs) and a low-zinc diet (zn d) in mice and carried out a set of behavioral and biochemical studies.The mice were treated with four different antidepressant compounds, namely, ketamine, ro 25-6981 (ro), hyperforin and lanicemine (hyp + lan), and imipramine (imi).We show that crs or zn d alone or a combination of crs and zn d (crs + zn d) induces anhedonia observed in the sucrose preference test (spt).The behavioral effects of crs were restored by ketamine or imi.However, only hyp + lan restored the deficits in behavioral phenotype in mice subjected to crs + zn d.We also showed that the antidepressant-like effects observed in hyp + lan-treated crs + zn d mice were associated with changes in the morphology of the dendritic spines (restored physiological level) in the hippocampus (hp).Finally, we studied the metabolism of ketamine and its brain absorption in crs and crs + zn d mice.Our results suggest that crs + zn d does not alter the metabolism of ketamine to (2r,6r;2s,6s)-hnk; however, crs + zn d can induce altered bioavailability and distribution of ketamine in the hp and frontal cortex (fc) in crs + zn d animals compared to the control and crs groups.

Journal: Frontiers in pharmacology (2022)
Publication types: Journal Article
Clinical Proteomics for Meningioma: An Integrated Workflow for Quantitative Proteomics and Biomarker Validation in Formalin-Fixed Paraffin-Embedded Tissue Samples.

Clinical proteomics is a rapidly emerging frontier in laboratory medicine.High-throughput proteomic investigations of biopsy tissues provide mechanistic insights into complex human diseases.For large-scale proteomics, formalin-fixed and paraffin-embedded (ffpe) tissue samples offer a viable alternative to fresh-frozen (ff) tissues that have restricted availability.In this context, meningioma is one of the most common primary brain tumors where innovation in diagnostics and therapeutic targets can benefit from clinical proteomics.We present here an integrated workflow for quantitative proteomics and biomarker validation of meningioma ffpe tissues.Applying label-free quantitative (lfq) proteomics, we reproducibly (pearson's correlation: 0.84-0.91) obtained an in-depth proteome coverage (nearly 4000 proteins per sample) from 120 min gradient of single unfractionated mass spectrometry run.Furthermore, building upon lfq data and literature curated set of meningioma-associated proteins, we validated vim,ahnak, and clufrom ffpe tissues using selected reaction monitoring (srm) assay and compared its performance with ff tissues.This study illustrates how knowledge from label-free proteomics can be integrated for selecting peptides for targeted validation and suggests that ffpe tissues are comparable to ff tissues for srm assays.This quantitative clinical proteomics workflow is scalable for large-scale clinical diagnostics studies in the future, for example, utilizing the global repository of ffpe tissues in meningioma and possibly in other cancers.

Journal: Omics : a journal of integrative biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Effects of heavy ions (12C6+) on malignant melanoma B16F10 cells.

This study aimed to investigate the effects of heavy ion (12c6+) irradiation on the proliferation, apoptosis, cell cycle, migration, and epithelial-mesenchymal transition (emt) of b16f10 cells.Methods the b16f10 cells, which is a malignant melanoma cell line widely used in research, irradiated by12c6+and x-ray were detected by hoechst 33342/propidium iodide double staining, western blot, flow cytometry, and cell scratch tests to evaluate cell proliferation, expression of apoptosis-related proteins, g2/m phase arrest, cell migration, cell invasion and emt.Results compared with the same physical x-ray dose,12c6+could effectively inhibit the proliferation of b16f10 cells, inhibit the expression of b-cell lymphoma-2 (bcl-2) and cellular-myelocytomatosis viral oncogene (c-myc), and induce the expression of bax to promote the apoptosis of b16f10 cells.After12c6+irradiation, the b16f10 cells exhibited g2/m phase arrest.B16f10 cells were highly sensitive to12c6+irradiation.Moreover, compared with x-ray, the12c6+irradiation significantly inhibited the migration of b16f10 cells and inhibited extracellular matrix cleavage, induced e-cadherin expression, enhanced cell adhesion, and further inhibited cell invasion, migration, and emt.Conclusions the b16f10 cells were highly radiosensitive to12c6+.Compared with x-ray, b16f10 cells irradiated by12c6+significantly reduced the expressions of matrix metalloproteinases to inhibit extracellular matrix cleavage and, thus, effectively inhibit cell invasion and metastasis.However, although the issue of the different therapeutic effects of heavy ion and x-ray radiotherapy on malignant melanoma was investigated and preliminary research results were obtained, several problems must be further studied.

Journal: Translational cancer research (2022)
Publication types: Journal Article
Corrosion Behavior and Mechanical Properties of 30CrMnSiA High-Strength Steel under an Indoor Accelerated Harsh Marine Atmospheric Environment.

In this work, the corrosion behavior and mechanical properties of 30cr mn si a high-strength steel under a harsh marine atmosphere environment were systematically studied using accelerated test technology, along with corrosion kinetic analysis, microstructure and phase composition analysis, electrochemical measurements, and mechanical property tests.The influence of corrosion time on corrosion kinetics was characterized by the weight loss method.The corrosion layer and its product evolution were analyzed by sem, eds, xrd, and xps.The corrosion behavior of steel was studied by a potentiodynamic polarization curve and eis.Finally, the influence of corrosion on mechanical properties was studied by tensile and fatigue tests.The results show that 30cr mn si a high strength steel has good corrosion resistance in a harsh marine atmosphere environment.Its corrosion behavior is cyclical: the outer rust layer exfoliated, the inner rust layer became the outer rust layer, and the matrix became inner rust due to the attack by the corrosive medium.The rust layer had a great protective effect on the matrix.The mechanical properties of 30cr mn si a high-strength steel were reduced under the corrosive environment, and corrosion had a significant effect on its fatigue resistance.

Journal: Materials (Basel, Switzerland) (2022)
Publication types: Journal Article
Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples.

Microbiome research relies on next-generation sequencing and on downstream data analysis workflows.Several manufacturers have introduced multi-amplicon kits for microbiome characterization, improving speciation, but present unique challenges for analysis.The goal of this methodology study was to develop two analysis pipelines specific to mixed-orientation reads from multi-hypervariable (v) region amplicons.A secondary aim was to assess agreement with expected abundance, considering database and variable region.Mock community sequence data (n = 41) generated using the ion16stm metagenomics kit and ion torrent sequencing platform were analyzed using two workflows.Amplicons from v2, v3, v4, v6-7, v8 and v9 were deconvoluted using a specialized plugin based on cut primers.A separate workflow using cutadapt is also presented.Three reference databases (ribosomal database project, greengenes and silva) were used for taxonomic assignment.Bray-curtis, euclidean and jensen-shannon distance measures were used to evaluate overall annotation consistency, and specific taxon agreement was determined by calculating the ratio of observed to expected relative abundance.Reads that mapped to regions v2-v9 varied for both cut primers and cutadapt-based methods.Within the cut primers-based pipeline, v3 amplicons had the best agreement with the expected distribution, tested using global distance measures, while v9 amplicons had the worst agreement.Accurate taxonomic annotation varied by genus-level taxon and v region analyzed.For the first time, we present a microbiome analysis pipeline that employs a specialized plugin to allow microbiome researchers to separate multi-amplicon data from the ion16s metagenomics kit into v-specific reads.We also present an additional analysis workflow, modified for ion torrent mixed orientation reads.Overall, the global agreement of amplicons with the expected mock community abundances differed across v regions and reference databases.Benchmarking data should be referenced when planning a microbiome study to consider these biases related to sequencing and data analysis for multi-amplicon sequencing kits.

Journal: PloS one (2023)
Publication types: Journal Article;Research Support, N.I.H., Intramural
How to build a cognitive map.

Learning and interpreting the structure of the environment is an innate feature of biological systems, and is integral to guiding flexible behaviors for evolutionary viability.The concept of a cognitive map has emerged as one of the leading metaphors for these capacities, and unraveling the learning and neural representation of such a map has become a central focus of neuroscience.In recent years, many models have been developed to explain cellular responses in the hippocampus and other brain areas.Because it can be difficult to see how these models differ, how they relate and what each model can contribute, this review aims to organize these models into a clear ontology.This ontology reveals parallels between existing empirical results, and implies new approaches to understand hippocampal-cortical interactions and beyond.

Journal: Nature neuroscience (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Clinical evaluation of the GSD NovaPrime® SARS-CoV-2 RTq-PCR assay.

Faced with the emergence of severe acute respiratory syndrome coronavirus 2 (sars-co v-2), high-throughput respiratory tests are in high demand.We evaluated the clinical performance of the gsd nova prime® sars-co v-2 rtq-pcr assay, a new assay that detects 2 specific rna sequences of the nucleocapsid (n) gene.It was assessed using 99 nasopharyngeal samples and compared in parallel with the allplex® assay.Among those samples, 72 and 27 were included in the positive (ppa) and negative (npa) percent agreement analyses, respectively.In case of discordance, samples were reanalyzed with another amplification technique, the aptima® sars-co v-2 assay.Cross-reactivity, including specimens positive for another respiratory virus and collected before the covid-19 outbreak, was also evaluated (n = 32).Based on the patients' clinical history, the ct (cycle threshold) values obtained, and the results of the aptima® assay, the clinical performances were deemed satisfactory, with the ppa reaching a minimum percentage of 87.5% and the npa reaching 100%.No cross-reactivity with other respiratory viruses was observed.

Journal: Diagnostic microbiology and infectious disease (2022)
Publication types: Journal Article
Impaired wound healing in diabetes.

Impaired wound healing for patients with diabetes is due to a constellation of structural, biochemical, cellular and microbial factors.Hyperglycaemia and its associated inflammation contribute to immune dysfunction, vascular damage, neuropathy, cellular senescence, impaired transition beyond the inflammatory stage, microbiome disruptions, failed extracellular matrix formation, growth factor and cytokine imbalance, limited re-epithelialisation, and alterations in fibroblast migration and proliferation.Optimising glycaemic control remains the primary intervention to prevent continual dysfunction and comorbid disease progression.

Journal: Journal of wound care (2022)
Publication types: Journal Article
Antioxidant interventions in autism spectrum disorders: A meta-analysis.

Autism spectrum disorder (asd) might be associated with oxidative stress, and antioxidants are commonly used in the treatment of young people with asd.However, the evidence about the effectiveness of these interventions remains debatable.We performed a meta-analysis to evaluate the effect of antioxidants on the symptoms of patients with autism.Methods data sources: pub med and web of science databases.Study selection we selected placebo-controlled, double-blind, randomized clinical trials published until february 2021 to evaluate the efficacy of antioxidant interventions on asd.Data analysis aberrant behavior checklist (abc), repetitive behavior scale-revised (rbs), social responsiveness scale (srs), developmental behavior checklist (dbc) and clinical global impressions severity scale (cgis) were used to evaluate the 22 different symptom outcomes.The hedges-adjusted g value was used to estimate the effect of each dietary intervention relative to the placebo.Results in this meta-analysis, we examined 13 double-blind randomized clinical trials, comprising a total of 570 patients with asd: 293 in the intervention group and 277 in the placebo group.Antioxidants (n-acetylcysteine (nac), other antioxidants) are more effective than placebos in improving the irritability among symptoms in the abc and communication disturbance symptoms in the dbc.There was a good trend of improvement in the stereotypic behavior symptoms in the abc.Treatment with nac antioxidants showed a good trend of improvement in irritability in the abc and symptoms of hyperactivity.The effect size was small, and there was a low risk of statistical heterogeneity and publication bias.Limitations the number of studies in this meta-analysis was small and the sample size was small.Conclusion this meta-analysis suggests that antioxidant intervention has a potential role in the management of some symptoms in patients with asd, and indicates the feasibility of using antioxidants to treat autism in the future.

Journal: Progress in neuro-psychopharmacology & biological psychiatry (2022)
Publication types: Journal Article;Meta-Analysis;Research Support, Non-U.S. Gov't