syedzayyan/paper_mill_benchmark huggingface dataset:
Androgens Alleviate Allergic Airway Inflammation by Suppressing Cytokine Production in Th2 Cells.

Asthma is more common in females than males after adolescence.However, the mechanism of the sex bias in the prevalence of asthma remains unknown.To test whether sex steroid hormones have some roles in t cells during development of asthma, we analyzed airway inflammation in t cell-specific androgen receptor (ar)- and estrogen receptor (er)-deficient mice.T cell-specific ar-deficient male mice developed severer house dust mite-induced allergic airway inflammation than did control male mice, whereas t cell-specific erα- and erβ-deficient female mice exhibited a similar degree of inflammation as for control female mice.Furthermore, administration of dihydrotestosterone reduced cytokine production of th2 cells from control, but not ar-deficient, naive t cells.Transfer of ot-ii transgenic ar-deficient th2 cells into wild-type mice induced severer allergic airway inflammation by ova than transfer of control th2 cells.Gene expression profiling suggested that the expression of genes related with cell cycle and th2 differentiation was elevated in ar-deficient th2 cells, whereas expression of dual specificity phosphatase (dusp)-2, a negative regulator of p38, was downregulated.In addition, a chromatin immunoprecipitation assay suggested that ar bound to an ar motif in the 5' untranslated region of the dusp2gene in th2 cells.Furthermore, the dusp2promoter with a wild-type ar motif, but not a mutated motif, was transactivated by dihydrotestosterone in a reporter assay.Finally, forced expression of dusp-2 by retrovirus vector reduced il-4 expression in th2 cells.Thus, these results suggest that androgen signaling suppresses cytokine production of th2 cells by inducing dusp-2, explaining, in part, the sex bias of asthma after adolescence.

Journal: Journal of immunology (Baltimore, Md. : 1950) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Effect of an Anaerobic Fermentation Process on 3D-Printed PLA Materials of a Biogas-Generating Reactor.

3d-printed materials are present in numerous applications, from medicine to engineering.The aim of this study is to assess their suitability for an application of interest today, that of testing of 3d-printed polylactic acid (pla)-based reactors for biogas production using anaerobic digestion.The impact of temperature, p h, and aqueous phase on the tested bioreactor is investigated, together with the effect of the gaseous phase (i.e., produced biogas).Two batches of materials used separately, one after another inside the bioreactor were considered, in a realistic situation.Two essential parameters inside the reactor (i.e., p h and temperature) were continuously monitored during a time interval of 25 to 30 days for each of the two biogas-generating processes.To understand the impact of these processes on the walls of the bioreactor, samples of 3d-printed material were placed at three levels: at the top (i.e., outside the substrate), in the middle, and at the bottom of the bioreactor.The samples were analyzed using a non-destructive imaging method, optical coherence tomography (oct).An in-house developed swept-source (ss) oct system, master-slave (ms) enhanced, operating at a central wavelength of 1310 nm was utilized.The 3d oct images related to the degradation level of the material of the pla samples were validated using scanning electron microscopy (sem).The differences between the impact of the substrate on samples situated at the three considered levels inside the reactor were determined and analyzed using their oct b-scans (optical cross-section images).Thus, the impact of the biogas-generating process on the interior of the bioreactor was demonstrated and quantified, as well as the capability of oct to perform such assessments.Therefore, future work may target oct for in situ investigations of such bioreactors.

Journal: Materials (Basel, Switzerland) (2022)
Publication types: Journal Article
Human Intelectin-1 Promotes Cellular Attachment and Neutrophil Killing of Streptococcus pneumoniae in a Serotype-Dependent Manner.

Human intelectin-1 (h int l-1) is a secreted glycoprotein capable of binding exocyclic 1,2-diols within surface glycans of human pathogens such as streptococcus pneumoniae, vibrio cholerae, and helicobacter pylori.For the latter, lectin binding was shown to cause bacterial agglutination and increased phagocytosis, suggesting a role for h int l-1 in pathogen surveillance.In this study, we investigated the interactions between h int l-1 and s.Pneumoniae, the leading cause of bacterial pneumonia.We show that h int l-1 also agglutinates s.Pneumoniae serotype 43, which displays an exocyclic 1,2-diol moiety in its capsular polysaccharide but is unable to kill in a complement-dependent manner or to promote bacterial killing by peripheral blood mononuclear cells.In contrast, h int l-1 not only significantly increases serotype-specific s.Pneumoniae killing by neutrophils but also enhances the attachment of these bacteria to a549 lung epithelial cells.Taken together, our results suggest that h int l-1 participates in host surveillance through microbe sequestration and enhanced targeting to neutrophils.

Journal: Infection and immunity (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
MEIOSIN Directs the Switch from Mitosis to Meiosis in Mammalian Germ Cells.

The mechanisms regulating meiotic initiation in mammals are enigmatic.It is known that retinoic acid (ra) signaling plays a pivotal role during meiotic initiation.Stra8, which is expressed in response to ra, is thought to be a key factor promoting meiotic initiation.However, the specific role of stra8 in meiotic initiation has remained elusive.Here, we identified meiosin as a germ-cell-specific factor that associates with stra8.Meiosin, like stra8, is expressed in response to ra and plays an essential role in meiotic initiation in both males and females.Functional analyses revealed that meiosin acts as a transcription factor together with stra8, and that both factors are critical for driving meiotic gene activation.Furthermore, temporally restricted expression of meiosin leads to meiotic entry decision during spermatogenesis.The present study demonstrates that meiosin, in collaboration with stra8, plays a central role in regulating the mitosis to meiosis germ cell fate decision in mammals.

Journal: Developmental cell (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Exogenous Abscisic Acid Mediates Berry Quality Improvement by Altered Endogenous Plant Hormones Level in "Ruiduhongyu" Grapevine.

Abscisic acid (aba) plays a key role in fruit development and ripening in non-climacteric fruit.A variety of metabolites such as sugars, anthocyanins, fatty acids, and several antioxidants, which are regulated by various phytohormones, are important components of fruit quality in grape.Here, grape cultivar "ruiduhongyu" was used to investigate the relationship between endogenous phytohormones and metabolites associated to grape berry quality under exogenous aba treatment.500 mg/l aba significantly improved the appearance parameters and the content of many metabolites including sugar, anthocyanin, and other compounds.Exogenous aba also increased the contents of aba, auxin (iaa), and cytokinins (ctks), and transcription level of aba biosynthesis and signaling related genes in fruit.Furthermore, a series of genes involved in biosynthesis and the metabolite pathway of sugars, anthocyanins, and fatty acids were shown to be significantly up-regulated under 500 mg/l aba treatment.In addition, pearson correlation analysis demonstrated that there existed relatively strong cooperativities in the aba/kinetin (kt)-appearance parameters, aba/iaa/kt-sugars, aba/indolepopionic acid (ipa)/zeatin riboside (zr)-anthocyanins, and gibberellin 3 (ga3)/methyl jasmonate (me ja)-fatty acids, indicating that 13 kinds of endogenous phytohormones induced by aba had different contributions to the accumulation of quality-related metabolites, while all of them were involved in regulating the overall improvement of grape fruit quality.These results laid a primary foundation for better understanding that exogenous aba improves fruit quality by mediating the endogenous phytohormones level in grape.

Journal: Frontiers in plant science (2021)
Publication types: Journal Article
Sorbent-incorporated dipstick for direct assaying of proteases.

Efficient removal of interferents from complex matrices would significantly improve the performance of state of the art dipstick assays.Herein, we evaluate a graphitized carbon black (gcb)-incorporated dipstick, a configuration that has not been explored before, for reliable and facile on-site analysis of complex matrices.Carrot juice, a highly pigmented sample matrix, is chosen for evaluating the retention of interferents within the sorbent-incorporated cleanup pad on the dipstick.A peptide with a specific cleavage site for botulinum neurotoxin a light chain (bo nt/a lc), a model protease for validation of the proposed dipstick assay, is incubated with the test samples containing bo nt/a lc.Subsequently, the bo nt/a lc digested substrate and sample matrix flow vertically through the gcb-deposited cleanup pad within which the matrix interferents are captured, while the substrate, with a minimum of interferents, continues to flow toward a conjugation pad for labelling with europium particles.Finally, the cleaved and uncleaved substrates flow toward a detection zone, where they bind to the test line producing a pinkish band which is not visible in the absence of gcb incorporation.The dipstick assay yields a lod of 0.1 n m (5 ng/m l) of bo nt/a lc in carrot juice, within 20 min.The reported approach enables detection of proteases in a wide range of matrices upon incorporation of appropriate sorbents, ultimately aiming to exclude tedious laboratory-based sample pre-treatment protocols.Thus, merging extraction, cleanup, and pre-concentration steps with a sensitive optical detection approach is an attractive strategy for on-site assaying in complex matrices.Graphical abstract.

Journal: Analytical and bioanalytical chemistry (2020)
Publication types: Journal Article
Metabolic and Anthropometric Parameters of Persons at Risk of Developing Type 2 Diabetes Mellitus Before and After 3 Months of Consuming Insoluble Dietary Fiber.

Observational studies have shown that insoluble fiber (if) can be effective in preventing type 2 diabetes (t2d), but there is a lack of experimental data on the effect of short-term consumption of if on metabolic parameters.We tried to investigate whether there was an improvement in glycemia and body composition in individuals at risk for t2d after 3 months of if consumption.Methods this "type 2 diabetes mellitus prevention ukraine (t2dpua)" study describes participants with impaired fasting glucose (ifg) as determined by ada criteria.The study involved 30 people, including 21 women (70%).Daily, 15 g of if derived from wheat was used.T2dpua did not have a placebo group and the intervention lasted 3 months.Evaluation of fasting plasma glucose (fpg) and 2h plasma glucose (2h pg), glycated hemoglobin (hb a1c), total cholesterol, hdl-cholesterol, triacylglycerols, uric acid, and γ-glutamyl transferase was performed.The baseline and 3-monthly anthropometric examinations included measurements of weight, waist and hip circumference.Fat mass was assessed by bioelectrical impedance analysis.Paired samplest-test or wilcoxon test were used.Result a decrease of fpg (p= .042), hb a1c (p< .001), 2h pg (p= .005), weight (p< .001), body mass index (p< .001), the proportion of body fat (p= .006), and the absolute amount of fat (p< .001), increases in systolic (p< .001) and diastolic (p= .008) blood pressure was shown.The number of people with hypertension did not change.The absolute amount of body fat decreased by almost 5% and tolerance to the standard glucose load improved by 15%.The dynamics of other metabolic parameters were not revealed.Conclusion and recommendation data about improvement of glycemia and body composition over a short period of using if by individuals with ifg are new and deserve larger studies.

Journal: Nutrition and metabolic insights (2022)
Publication types: Journal Article
Ovarian Cancer-SpecificBRCA-like Copy-Number Aberration Classifiers Detect Mutations Associated with Homologous Recombination Deficiency in the AGO-TR1 Trial.

Previously, we developed breast cancer brca1-like and brca2-like copy-number profile shrunken centroid classifiers predictive for mutation status and response to therapy, targeting homologous recombination deficiency (hrd).Therefore, we investigated brca1-and brca2-like classification in ovarian cancer, aiming to acquire classifiers with similar properties as those in breast cancer.experimental design:we analyzed dna copy-number profiles of germline brca1- and brca2-mutant ovarian cancers and control tumors and observed that existing breast cancer classifiers did not sufficiently predict mutation status.Hence, we trained new shrunken centroid classifiers on this set and validated them in the independent the cancer genome atlas dataset.Subsequently, we assessed brca1/2-like classification and obtained germline and tumor mutation and methylation status of cancer predisposition genes, among them several involved in hr repair, of 300 ovarian cancer samples derived from the consecutive cohort trial ago-tr1 (nct02222883).Results the detection rate of the brca1-like classifier for brca1mutations and promoter hypermethylation was 95.6%.The brca2-like classifier performed less accurately, likely due to a smaller training set.Furthermore, three quarters of the brca1/2-like tumors could be explained by (epi)genetic alterations in brca1/2, germline rad51cmutations and alterations in other genes involved in hr.Around half of the non-brca-mutated ovarian cancer cases displayed a brca-like phenotype.Conclusions the newly trained classifiers detected most brca-mutated and methylated cancers and all tumors harboring a rad51cgermline mutations.Beyond that, we found an additional substantial proportion of ovarian cancers to be brca-like.

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research (2021)
Publication types: Clinical Trial;Journal Article;Research Support, Non-U.S. Gov't
Effects of VHA Policy Directive 1163 on Acceptance and Employment Rates for Veterans with Substance Use Disorders Referred to VHA Vocational Rehabilitation.

Introduction research has shown that veterans with substance/alcohol use disorders (suds/auds) are at a greater risk for employment-related issues (eg, lower labor force participation rates), and interventions such as vocational rehabilitation (vr) have been used as a tool to reduce employment obtainment and maintenance.The purpose of the current study was to evaluate acceptance rates and employment rates at closure for veterans with suds/auds prior to the implementation of vha policy directive 1163 (mandated that veterans are not refused services based on prior or current sud/auds).Sud/auds were coded to reflect dsm 5-tr criteria of active use and in-remission.Methods data from a vha vocational rehabilitation program in the veterans integrated service network 12 network were obtained for the purpose of the current study.Results findings showed that veterans with auds were less likely to be accepted for vr services prior and after implementation of vha policy directive 1163.Conclusions when examining active and inactive suds/auds, findings showed that implementation of vha policy directive 1163 was not effective for veterans with auds.One factor that was not explored but could explain disparities in program acceptance rates is duration of program entry.If a veteran has a consult placed for vha vocational rehabilitation services, and their program entry date (date accepted) is a significant duration, then perhaps veterans with active auds start drinking again given that they are waiting for vocational assistance.Thus, it would be important to assist veterans with active auds into services in a timely manner (perhaps prior them being discharged from sud treatment).

Journal: Substance abuse : research and treatment (2022)
Publication types: Journal Article
Cyclic transitions of DNA origami dimers driven by thermal cycling.

It is widely observed that life activities are regulated through conformational transitions of biological macromolecules, which inspires the construction of environmental responsive nanomachines in recent years.Here we present a thermal responsive dna origami dimers system, whose conformations can be cyclically switched by thermal cycling.In our strategy, origami dimers are assembled at high temperatures and disassembled at low temperatures, which is different from the conventional strategy of breaking nanostructures using high temperatures.The advantage of this strategy is that the dimers system can be repeatedly operated without significant performance degradation, compared to traditional strategies such as conformational transitions via i-motif and g-quadruplexes, whose performance degrades with sample dilution due to repeated addition of trigger solutions.The cyclic conformational transitions of the dimers system are verified by fluorescence curves and afm images.This research offered a new way to construct cyclic transformational nanodevices, such as reusable nanomedicine delivery systems or nanorobots with long service lifetimes.

Journal: Nanotechnology (2022)
Publication types: Journal Article
Effects of Amoxicillin on the Structure and Mineralization of Dental Enamel and Dentin in Wistar Rats.

S the development of teeth is affected by genetic and environmental factors.Amoxicillin is a widely prescribed semi-synthetic antibiotic.Its most frequent side effects are gastrointestinal disorders and hypersensitivity reactions.The purpose of this study was to determine the effect produced by amoxicillin administration on dental enamel and dentin in wistar rats.Materials and methods twelve pregnant adult wistar rats were equally divided into four different groups.Negative controls were prescribed with a saline solution.Positive controls were prescribed with tetracycline (130 mg/kg).The other two groups were treated with amoxicillin doses of 50 and 100 mg/kg (every 8 hours), respectively.The treatments were daily administered by oral gavage from the 13th gestation day to the end of gestation.After birth, the offspring also received the same treatment as their mothers from day one to day twelve.After 24 hours, the newborns were sacrificed, the jaws were dissected, and the first molar teeth were collected.The samples were fixed in 10% formaldehyde solution and were histomorphologically and histopathologically observed to determine enamel and dentin abnormalities.Results the mean ameloblastic layer thickness, enamel thickness, odontoblastic layer thickness, and dentin thickness were significantly different in the tetracycline group and the amoxicillin 50 and 100 mg/kg groups compared to the control group.Also, dentin hypomineralization and vacuolization of the odontoblastic layer were observed in the tetracycline- and amoxicillin-treated groups.Conclusion this study showed that amoxicillin interferes with amelogenesis and dentinogenesis and reduces enamel and dentin thickness.

Journal: Frontiers in dentistry (2019)
Publication types: Journal Article
A comprehensive in silico analysis of multiple sclerosis related non-synonymous SNPs and their potential effects on protein structure and function.

Multiple sclerosis (ms) is an autoimmune and central nervous system disease characterized by an inflammatory demyelinating process in the brain.Although the exact cause of ms is still unclear, environmental, and genetic factors are known to play a role in the development of disease.New molecular markers must be identified to understand the mechanism of disease formation and progression.We investigated the effects of ms-related non-synonymous single-nucleotide polymorphisms (ns snps) on the structure and function of identified proteins in this study.Methods missense variations associated with ms were extracted from the nhgri-ebi gwas database.Functional and structural analysis of ns snps on mapped genes was performed using g:profiler, wikipathway, kegg, reactome and gene ontology programs (p < 0.05 was accepted statistically significant).Amino acid sequence-based analysis was performed to identify deleterious variants by using provean and predict snp tools.Finally, protein structure analyzes were performed on deleterious protein variants by dyna mut, mutabind2 and missense3d servers to identify changes in protein stability and flexibility.Results 10 target ns snps were identified.Among these rs34536443, rs10936599, rs2293152, rs11808092, rs1129183 were found deleterious according to amino acid sequence-based analysis.Furthermore, structure-based analyses show that tyk2 (p1104a), mynn (h6q), evi5 (q612h), and lztfl1 (d246n) substitutions increase protein stability and decrease structure flexibility, whereas stat3 (r426g) substitution decreases protein stability and increases structure flexibility.Conclusion we revealed that identified ns snps have potential effects on stability and flexibility of the target proteins.The prominent target genes are thought to have significant impacts on the pathogenesis of ms.Further in vitro and in vivo studies are required to validate our in silico results.

Journal: Multiple sclerosis and related disorders (2022)
Publication types: Journal Article
Focal ablation of apical prostate cancer lesions with irreversible electroporation (IRE).

Introduction and objective to assess the safety, oncological and quality-of-life (qo l) outcomes of focal ablation of apical prostate cancer (pca) lesions with irreversible electroporation (ire).Methods patients were included in the study if they had a pca lesion within 3 mm of the apical capsule treated with ire.The ire procedure was performed in our institution by a single urologist.The qo l and functional data was collected prospectively from patients who provided consent using the expanded prostate cancer index composite (epic).Oncological follow up included 3-month psa levels, mp mri at 6 months and transperineal biopsy at 1-year post treatment.Results a total of 50 patients had apical pca lesions treated between february 2013 and september 2018.Median follow-up was 44 months.There were no clavien-dindo grade 3 events or higher.No perioperative complications were recorded.No significant difference was observed in the epic urinary or bowel qo l domain between baseline and 12-month post-treatment.One patient (2%) required one pad per day for urinary incontinence 12-month post-treatment.There was a small but significant decline in epic sexual qo l (65 at baseline and 59 at 12-month post-ire).Of patient's potent pre-treatment, 94% remained potent after treatment.The median psa nadir decreased by 71% (6.25-1.7 ng/m l).Only one patient (2.5%) had in-field residual disease on repeat biopsy.Conclusion focal ablation using ire for pca in the distal apex appears safe and feasible with acceptable early qo l and oncologic outcomes.

Journal: World journal of urology (2021)
Publication types: Journal Article