syedzayyan/paper_mill_benchmark huggingface dataset:
Tumor-Specific T Cells Exacerbate Mortality and Immune Dysregulation during Sepsis.

Sepsis induces significant immune dysregulation characterized by lymphocyte apoptosis and alterations in the cytokine milieu.Because cancer patients exhibit a 10-fold greater risk of developing sepsis compared with the general population, we aimed to understand how pre-existing malignancy alters sepsis-induced immune dysregulation.To address this question, we assessed the impact of tumor-specific cd8+t cells on the immune response in a mouse model of cecal ligation and puncture (clp)-induced sepsis.Tumor-bearing animals containing thy1.1+tumor-specific cd8+t cells were subjected to clp, and groups of animals received anti-thy1.1 m ab to deplete tumor-specific cd8+t cells or isotype control.Results indicated that depleting tumor-specific t cells significantly improved mortality from sepsis.The presence of tumor-specific cd8+t cells resulted in increased expression of the 2b4 coinhibitory receptor and increased apoptosis of endogenous cd8+t cells.Moreover, tumor-specific t cells were not reduced in number in the tumors during sepsis but did exhibit impaired ifn-γ production in the tumor, tumor draining lymph node, and spleen 24 h after clp.Our research provides novel insight into the mechanisms by which pre-existing malignancy contributes to increased mortality during sepsis.

Journal: Journal of immunology (Baltimore, Md. : 1950) (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural
The evolution of survival of pulmonary arterial hypertension over 15 years.

The prognosis of pulmonary arterial hypertension (pah) remains dismal.Over the years, multiple therapeutic advances have been introduced.This study evaluates the evolution of pah survival over the past 15 years.We included 293 consecutive adult patients diagnosed with pah between 2005 and 2019 (median age: 61.8 years, 70.3% female).Patients were divided into three cohorts based on the time of diagnosis: 2005-2009, 2010-2014, and 2015-2019 (2005-2009:n= 56; 2010-2014:n= 111; 2015-2019:n= 126).Transplant-free survival was measured from the date of right heart catheterization until patients reached the composite endpoint of lung transplant or death.Multivariable cox-pulmonary hypertension regression was used to study the effect of the time of diagnosis.The final cox model was fitted in both younger and older patients to evaluate the difference between these groups.During a median follow-up time of 4.1 (interquartile range: 2.2-7.3) years, 9 patients underwent lung transplantation and 151 patients died.The median overall transplant-free survival was 6.2 (5.5-8.0) years.Patients older than 56 years at baseline who were diagnosed in 2005-2009 showed better survival compared to patients diagnosed in 2010-2014 and 2015-2019 with an adjusted hazard ratio of, respectively, 2.12 (1.11-4.03) and 2.83 (1.41-5.69).Patients younger than 56 years showed neither an improved nor deteriorated survival over time.In conclusion, survival in patients with pah did not improve over time, despite more available therapeutic options.This might be partly due to the changed demographic characteristics of the pah patients and a still important diagnostic delay.

Journal: Pulmonary circulation (2022)
Publication types: Journal Article
Electrochemical Signatures of Interface-Dominated Behavior in the Testing of Calcium Foil Anodes.

Fundamental research and practical assembly of rechargeable calcium (ca) batteries will benefit from an ability to use ca foil anodes.Given that ca electrochemistry is considered a surface-film-controlled process, understanding the interface's role is paramount.This study examines electrochemical signatures of several ca interfaces in a benchmark electrolyte, ca(bh4)2/tetrahydrofuran (thf).Preparation methodologies of ca foils are presented, along with ca plating/stripping through either pre-existing, native calcium hydride (ca h2), or pre-formed calcium fluoride (ca f2) interfaces.In contrast to earlier work examining ca foil in other electrolytes, ca foils are accessible for reversible electrochemistry in ca(bh4)2/thf.However, the first cyclic voltammetry (cv) cycle reflects persistent, history-dependent behavior from prior handling, which manifests as characteristic interface-derived features.This behavior diminishes as ca is cycled, though formation of a native interface can return the cv to interface-dominated behavior.Ca f2modification enhances such interface-dominance; however, continued cycling suppresses such features, collectively indicating the dynamic nature of certain ca interfaces.Cell configuration is also found to significantly influence electrochemistry.With appropriate preparation of ca foils, the signature of interface-dominated behavior is still present during the first cycle in coin cells, but higher current density compared to three-electrode cells along with moderate cycle life are readily achievable.

Journal: Journal of the Electrochemical Society (2020)
Publication types: Journal Article
Drug-coated balloon in the treatment of coronary left main true bifurcation lesion: A patient-level propensity-matched analysis.

S an increasing body of evidence suggests that drug-coated balloon (dcb) angioplasty represents a valuable option for revascularization in selected patients with coronary bifurcation disease.However, there remains a paucity of real-world observational evidence on the efficacy of dcb in left main (lm) true bifurcation lesion.We compared clinical and angiographic outcomes of hybrid [dcb + drug-eluting stent (des)] versus des-only strategy (provisional stenting or two-stent strategies) inde novo lm true bifurcated lesions.Methods the primary endpoint was the 2-year composite rate of target lesion failure (tlf): cardiac death, target vessel myocardial infarction (tvmi), or clinically driven target lesion revascularization (cd-tlr).A routine 1-year angiographic follow-up was scheduled.Propensity-score matching was utilized to assemble a cohort of patients with similar baseline characteristics.Results among 1077 eligible patients, 199 who received dcb treatment and 398 who were assigned to des therapy had similar propensity scores and were included in the analysis.Tlf within 2 years occurred in 13 patients (7.56%) assigned to dcb group, and 52 patients (14.36%) assigned to des group (odds ratio: 0.487; 95% confidence interval: 0.258-0.922;p= 0.025; log-rank p= 0.024).Compared with the des group, the dcb group resulted in a lower rate of cd-tlr (2.91%vs.9.42%;p= 0.007).Cardiac death, tvmi, all-cause mortality, and stent thrombosis were comparable between both groups.Patients treated with des-only were associated with a higher late lumen loss (0.42 ± 0.62 mmvs.0.13 ± 0.42 mm,p< 0.001) compared with the dcb group at 1 year.In sensitivity analysis, the dcb group also presented a lower incidence of tlf, cd-tlr and stent thrombosis both compared to the two-stent strategy and compared to provisional stenting (ps < 0.05).Conclusion the 2-year results of pci utilizing dcb for lm true bifurcation lesions are superior to employing des alone in terms of safety and effectiveness.

Journal: Frontiers in cardiovascular medicine (2022)
Publication types: Journal Article
Haloalkaline Lipase from Bacillus flexus PU2 Efficiently Inhibits Biofilm Formation of Aquatic Pathogen Vibrio parahaemolyticus.

A gene encoding lipase enzyme from bacillus flexus pu2 was cloned and expressed in e.Coli bl21 (de3) p lys s and purified protein having the molecular weight of 34 k da.This lipase was found to be alkaline (p h 9) and slightly thermophilic.This lipase was observed to retain its activity in the presence of methanol, ethanol, dmso, and acetone.Ferrous sulfate, copper sulfate, and manganese sulfate highly enhanced the lipase activity.All the surfactants and detergents were found to inhibit the enzyme activity, whereas the bleaching agent hydrogen peroxide was found to increase the activity.This lipase was observed as a metalloenzyme, and its activity was highly inhibited by edta.Also, it is moderately halophilic and can retain the activity between 0.2 and 0.8 m na cl.Biofilm inhibitory potential of purified lipase was tested against pathogenic vibrio parahaemolyticus, and the minimal inhibitory concentration observed was 350 u.Different concentration of this enzyme significantly changed the morphology and biofilm density of v.Parahaemolyticus and was evinced by sem and clsm imaging.The transcriptome levels of genes responsible for biofilm formation, motility, and virulence such as, mot x, fli g, and trh were significantly downregulated with lipase treatment.

Journal: Probiotics and antimicrobial proteins (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A Novel and Quantitative Detection Assay (effluxR) for Identifying Efflux-Associated Resistance Genes Using Multiplex Digital PCR in Clinical Isolates ofPseudomonas aeruginosa.

The rise of multidrug resistance of pseudomonas aeruginosahighlights an increased need for selective and precise antimicrobial treatment.Drug efflux pumps are one of the major mechanisms of antimicrobial resistance found in many bacteria, including p.aeruginosa.Detection of efflux genes using a polymerase chain reaction (pcr)-based system would enable resistance detection and aid clinical decision making.Therefore, we aimed to develop and optimize a novel method herein referred to as "efflux rdetection assay" using multiplex digital pcr (md pcr) for detection ofmexefflux pump genes in p.Aeruginosastrains.The annealing/extension temperatures and g dna concentrations were optimized to amplifymex b,mex d, andmex yusing the multiplex quantitative pcr (mq pcr) system.We established the optimal mq pcr conditions for the assay (ta of 59 °c with g dna concentrations at or above 0.5 ng/μl).Using these conditions, we were able to successfully detect the presence of these genes in a quantity-dependent manner.The limit of detection formexgenes using theefflux rdetection assay with md pcr was 0.001 ng/μl (7.04-34.81 copies/μl).Moreover, using blind sample testing, we show thatefflux rdetection assay had 100% sensitivity and specificity for detectingmexgenes in p.aeruginosa.In conclusion, theefflux rdetection assay, using md pcr, is able to identify the presence of multiplemexgenes in p.aeruginosathat may aid clinical laboratory decisions and further epidemiological studies.

Journal: Methods and protocols (2023)
Publication types: Journal Article
Topical netarsudil 0.02% as adjunctive therapy in refractory pediatric glaucoma.

To evaluate the efficacy of topical netarsudil 0.02% as adjunctive therapy in children with refractory pediatric glaucoma.Methods the medical records of patients ≤18 years diagnosed with pediatric glaucoma treated with topical netarsudil 0.02% from june 2019 to march 2022 were reviewed retrospectively.Data collected included age, sex, ethnicity, etiology of glaucoma, history of previous or subsequent glaucoma surgery, and intraocular pressure (iop) before and after the addition of topical netarsudil.Results a total of 21 eyes of 16 patients (11 males) were included.Five patients used topical netarsudil in both eyes.Eight patients were hispanic.The mean number of glaucoma surgeries and medications before initiating topical netarsudil was 1.8 ± 1.2 and 3.7 ± 0.5, respectively.The mean age prior to starting topical netarsudil was 8.9 ± 4.1 years.The mean follow-up after initiating topical netarsudil was 11.3 ± 8.2 months.The iop was significantly reduced from 26.3 ± 6.2 mm hg before topical netarsudil to 19.6 ± 6.02 mm hg at 1 month in 15 eyes (p < 0.01), 18.2 ± 6.9 mm hg at 3-months in 18 eyes (p < 0.01), 18.3 ± 7.3 mm hg at 6 months in 13 eyes (p = 0.01), 17.6 ± 5.07 mm hg at 9 months in 14 eyes (p = 0.002), and 17.4 ± 3.1 mm hg at 12 months in 13 eyes (p = 0.002).Nine eyes (43%) underwent additional glaucoma surgery due to long-term failure of topical netarsudil to reduce iop despite an initial reduction, and one eye had persistent iop elevation ≥21 mm hg despite the addition of topical netarsudil.Conclusions in our small cohort of patients with refractory pediatric glaucoma, the addition of topical netarsudil reduced iop, potentially delaying the need for surgery.

Journal: Journal of AAPOS : the official publication of the American Association for Pediatric Ophthalmology and Strabismus (2022)
Publication types: Journal Article
Bilateral testicular Leydig cell hyperplasia presented incidentally: A case report.

Introduction leydig cell hyperplasia or tumor represents less than 3% of all testicular tumors.It can be defined as an increase in the size and number of leydig cell within the testicles.These cells are responsible for the production of testosterone in human males.Case presentation our patient is a forty-eight-year-old male presented with erectile dysfunction and decreased libido for the past six months.Ultrasound of the scrotum show bilateral hypoechoic testicular masses larger on the left size thus left orchidectomy was performed.Histopathology confirmed our diagnosis.Discussion leydig cell hyperplasia (lch) is a rare and mostly benign entity that affects both children and adults.In adults, it might be associated with variety of condition including klinefelter's syndrome, exogenous human chorionic gonadotropin (h cg) therapy, and many others but it mostly occurs idiopathically.Scrotal ultrasound and tumor markers can be used to diagnose most of the patients with lch.Conclusion lch should be differentiated from leydig cell tumor to avoid unnecessary and sometimes harmful intervention in the future.

Journal: International journal of surgery case reports (2022)
Publication types: Journal Article
Longitudinal association of childhood physical activity and physical fitness with physical activity in adolescence: insights from the IDEFICS/I.Family study.

This study aimed to examine associations of early childhood physical fitness and physical activity (pa) with pa during later childhood/early adolescence while accounting for gender differences.Methods we selected data of n = 4329 children from the idefics/i.Family cohort (age 2.4-11.7 years) with data on baseline fitness and accelerometer measurements.At baseline, physical fitness tests were conducted including flamingo balance, backsaver sit and reach, handgrip strength, standing long jump, 40-m sprint and 20-m shuttle run (to estimate cardio-respiratory fitness levels).Pa was measured with actigraph accelerometers over 3 days at baseline (acti trainer or gt1m) and 7 days at follow-up (gt3x).Evenson cutpoints were used to determine moderate-to-vigorous pa (mvpa) time, and children with ≥60mins/day of average mvpa were deemed as having met who guidelines at baseline and follow-up.Linear and logistic regressions were performed to examine longitudinal associations between meeting who guidelines, mvpa, and physical fitness tests at baseline with meeting who guidelines and mvpa at follow-up.Models were conducted on the entire sample, the sex-stratified sample, and stratified by sex and pubertal status at follow-up.Results results showed that meeting who guidelines for mvpa at baseline was positively associated with mvpa (standardized beta (b) = 0.13, 95%ci:(5.6;11.1)) and meeting who guidelines at follow-up for the entire sample (or = 2.1, 95%ci:(1.5; 3.14), and stratified by males (or = 2.5, 95%ci:(1.5; 4.1)) and females (or = 1.8, 95%ci:(1.0; 3.2)).This was also found for both male pre/early pubertal and pubertal groups but only in the female pre/early pubertal group, and not the female pubertal group (mvpa: b = .00, 95%ci:(- 6.1; 5.6), who: or = 0.61, 95%ci:(0.23;1.6)).Models indicated that standing long jump, 40-m sprint, shuttle run and flamingo balance at baseline were associated with mvpa and meeting the guidelines at follow-up.Conclusions meeting who guidelines and certain fitness tests at baseline were strongly associated with mvpa and meeting who guidelines at follow-up, but this association varied with sex and pubertal status.Consequently, these findings underline the importance of ensuring sufficient physical activity in terms of quality and quantity for children at the earliest stages of life.Trial registration isrctn62310987.

Journal: The international journal of behavioral nutrition and physical activity (2022)
Publication types: Journal Article
Inherited myopathy plus: Double-trouble from rare neuromuscular disorders.

A rare disorder in the usa is one that affects <200,000 people, making inherited myopathies rare diseases.Increasing access to genetic testing has been instrumental for the diagnosis of inherited myopathies.Genetic findings, however, require clinical correlation due to variable phenotype, polygenic etiology of certain inherited disorders, and possible co-existing independent neuromuscular disorders.We searched the mayo clinic rochester medical record (2004-2020) to identify adult patients carrying pathogenic variants or likely pathogenic variants in genes causative of myopathies and having a coexisting independent neuromuscular disorder classified as rare at one additional patient was identified at nationwide children's hospital.Clinical and laboratory findings were reviewed.We identified 14 patients from 13 families fulfilling search criteria.Seven patients had a "double-trouble" inherited myopathy; two had an inherited myopathy with coexistent idiopathic myositis; three had an inherited myopathy with coexisting rare neuromuscular disorder of neurogenic type; a female dmd carrier had co-existing distal spinal muscular atrophy, which was featuring the clinical phenotype; and a patient with a myh7 pathogenic variant had sandhoff disease causing motor neuron disease.These cases highlight the relevance of correlating genetic findings, even when diagnostic, with clinical features, to allow precise diagnosis, optimal care, and accurate prognosis.

Journal: Neuromuscular disorders : NMD (2023)
Publication types: Journal Article
Comparing single- and mixed-species groups in fruit flies: differences in group dynamics, but not group formation.

Mixed-species groups describe active associations among individuals of 2 or more species at the same trophic level.Mixed-species groups are important to key ecological and evolutionary processes such as competition and predation, and research that ignores the presence of other species risks ignoring a key aspect of the environment in which social behavior is expressed and selected.Despite the defining emphasis of active formation for mixed-species groups, surprisingly little is known about the mechanisms by which mixed-species groups form.Furthermore, insects have been almost completely ignored in the study of mixed-species groups, despite their taxonomic importance and relative prominence in the study of single-species groups.Here, we measured group formation processes in drosophila melanogaster and its sister species, drosophila simulans.Each species was studied alone, and together, and one population of d.Melanogaster was also studied both alone and with another, phenotypically distinct d.Melanogaster population, in a nested-factorial design.This approach differs from typical methods of studying mixed-species groups in that we could quantitatively compare group formation between single-population, mixed-population, and mixed-species treatments.Surprisingly, we found no differences between treatments in the number, size, or composition of groups that formed, suggesting that single- and mixed-species groups form through similar mechanisms of active attraction.However, we found that mixed-species groups showed elevated interspecies male-male interactions, relative to interpopulation or intergenotype interactions in single-species groups.Our findings expand the conceptual and taxonomic study of mixed-species groups while raising new questions about the mechanisms of group formation broadly.

Journal: The Journal of heredity (2022)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.
The Level of Knowledge about Toxoplasmosis among University Students in Rabat in Morocco.

The aim of this descriptive cross-sectional study is to evaluate the knowledge of toxoplasmosis among medical, biology, and veterinary students in rabat in morocco.The data was collected by using a questionnaire which includes demographic characteristics, epidemiology, diagnosis, and clinical issues related to knowledge of toxoplasmosis.During analysis, the study groups were divided based upon their specialty of students who were medical, biology, and veterinary students.Out of 230 students, 55.2% were female and 44.8% were male.The average age of the study population is 21.7 ± 02 years.Less than half (42.6%) have heard of the disease; most of them have heard from faculty during studies in classrooms with 75.8%, and 3.2% were from the internet.Only 36.5% knew the correct causative agent of toxoplasmosis, and 32.1% were aware of the definitive host.The current study documented that there are gaps in the knowledge of the students regarding toxoplasmosis.Therefore, the present study puts the basis for future studies highlighting the importance of educating students to improve knowledge and attitudes towards toxoplasmosis.

Journal: Journal of parasitology research (2021)
Publication types: Journal Article
Reverse Genetics for Influenza A and B Viruses Driven by Swine Polymerase I Promoter.

Influenza viruses are considered prominent pathogens of humans and animals that are extensively investigated because of public health importance.Plasmid-based reverse genetics is a fundamental tool that facilitates the generation of genetically modified viruses from a c dna copy.The ability to rescue viruses enables researchers to understand different biological characteristics including iv replication, pathogenesis, and transmission.Furthermore, understanding the biology and ability to manipulate different aspects of the virus can aid in providing a better understanding of the mechanisms of antiviral resistance and development of alternative vaccination strategies.This chapter describes the process of cloning c dna copies of iav and ibv rna segments into a swine polymerase-driven reverse genetics plasmid vector, successful generation of recombinant ivs in swine cells, and propagation of virus in cells or eggs.The swine polymerase reverse genetics system was previously shown to be efficient for de novo rescue of human-, swine-, and avian-origin iavs and ibv in swine and human origin cell lines utilizing the same protocols discussed in this chapter.

Journal: Methods in molecular biology (Clifton, N.J.) (2022)
Publication types: Journal Article