syedzayyan/paper_mill_benchmark huggingface dataset:
Enrichment of genes associated with squamous differentiation in cancer initiating cells isolated from urothelial cells transformed by the environmental toxicant arsenite.

Arsenic is an environmental toxicant with long-term exposure associated with the development of urothelial carcinomas.Our lab has developed an in-vitro model of urothelial carcinoma by exposing the immortal, but non-tumorigenic bladder cell line, the urotsa, to arsenite (as3+).These transformed cells form tumors in immune-compromised mice, which resemble urothelial carcinomas with components of the tumor exhibiting squamous differentiation.The goal of the present study was to determine the differences in global gene expression patterns between the as3+-transformed urotsa cells and the urospheres (spheroids containing putative cancer initiating cells) isolated from these cell lines and to determine if the genes involved in the development of squamous differentiation were enriched in the urospheres.The results obtained in this study show an enrichment of genes such as krt1, krt5, krt6a, krt6b, krt6c, krt14 and krt16 associated with squamous differentiation, a characteristic feature seen in aggressive basal subtypes of urothelial cell carcinoma (ucc) in the urospheres isolated from as3+-transformed urotsa cells.In addition, there is increased expression of several of the small proline-rich proteins (sprr) in the urospheres and overexpression of these genes occur in ucc's displaying squamous differentiation.In conclusion, the cancer initiating cells present in the urospheres are enriched with genes associated with squamous differentiation.

Journal: Toxicology and applied pharmacology (2019)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Immunosuppressive regimens for adult liver transplant recipients in real-life practice: consensus recommendations from an Italian Working Group.

It is a well-recognized fact that implementing new guidelines in clinical practice may be difficult; therefore the italian society for organ and tissue transplantation (sito) set out to define practical immunosuppression tools for the management of liver transplantation patients.In 2017, an italian working group of liver transplant experts and hepatologists issued a set of consensus statements along with evidence-based recommendations on the use of everolimus after liver transplantation.This article presents the evidence- and consensus-based algorithms developed within the italian working group, which are aimed towards guiding clinicians in the selection of immunosuppressive regimens for the management of adult liver transplant recipients in real-life practice.The liver transplant recipient population, typically managed in clinical practice, was divided into the following categories: (1) standard patients; (2) critically ill patients; (3) patients with a specific etiology; (4) patients with hepatocellular carcinoma; (5) and patients with de novo malignancies.The algorithms are divided into two parts, according to the time from transplantation (0-3 months and > 3 months) and are discussed here along with relevant supporting literature, when available.Ultimately, it is hoped that the evidence- and consensus-based algorithms developed within the italian working group, and presented here, contribute to simplify, personalize, and optimize immunosuppression of liver transplantation recipients in clinical practice.

Journal: Hepatology international (2020)
Publication types: Journal Article;Review
Bayesian inference in based-kernel regression: comparison of count data of condition factor of fish in pond systems.

The discrete kernel-based regression approach generally provides pointwise estimates of count data that do not account for uncertainty about both parameters and resulting estimates.This work aims to provide probabilistic kernel estimates of count regression function by using bayesian approach and then allows for a readily quantification of uncertainty.Bayesian approach enables to incorporate prior knowledge of parameters used in discrete kernel-based regression.An application was proposed on count data of condition factor of fish (k) provided from an experimental project that analyzed various pond management strategies.The probabilistic distribution of estimates were contrasted by discrete kernels, as a support to theoretical results on the performance of kernels.More practically, bayesian credibility intervals of k-estimates were evaluated to compare pond management strategies.Thus, similarities were found between performances of semi-intensive and coupled fishponds, with formulated feed, in comparison with extensive fishponds, without formulated feed.In particular, the fish development was less predictable in extensive fishpond, dependent on natural resources, than in the two other fishponds, supplied in formulated feed.

Journal: Journal of applied statistics (2022)
Publication types: Journal Article
Potential Pathogenic Genes and Mechanism of Ankylosing Spondylitis: A Study Based on WGCNA and Bioinformatics Analysis.

The purpose of this study is to explore the high-risk pathogenic driver genes for the occurrence and development of ankylosing spondylitis (as) based on the bioinformatics method at the molecular level, to further elaborate the molecular mechanism of the pathogenesis of as, and to provide potential biological targets for the diagnosis and treatment of clinical as.Methods the gene expression profile data gse16879 were downloaded from the geo (gene expression omnibus) database, and weighted gene coexpression network analysis was performed.Highly correlated genes were divided into 14 modules, and 582 genes contained in the yellow (classic module) and 59 genes contained in grey60 (hematologic module) modules had the strongest correlation with as.After protein-protein interaction (ppi) analysis, the top 20 genes with the highest scores were obtained from classic module and hematologic module, respectively.The david (database for annotation, visualization, and integrated discovery) database was used for gene ontology analysis and kyoto encyclopedia of genes and genomes analysis to analyze the biological functions of high-risk genes related to as.Results the results showed that the process of signal recognition particle-dependent cotranslational protein targeting to membrane, ribosome, nicotinamide adenine diphosphate hydride dehydrogenase (ubiquinone) activity, platelet activation, integrin complex, and extracellular matrix binding were enriched.Conclusions in this study, weighted gene coexpression network analysis, an efficient system biology algorithm, was used to analyze the high-risk pathogenic driver gene of as.We provide new targets for the diagnosis and treatment of clinical as and new ideas for further study.

Journal: World neurosurgery (2022)
Publication types: Journal Article
Effects of depot-medroxyprogesterone acetate on the immune microenvironment of the human cervix and endometrium: implications for HIV susceptibility.

Depot-medroxyprogesterone acetate is a commonly used injectable contraceptive that has been associated with an increased risk of hiv acquisition.This study compares effects of depot-medroxyprogesterone acetate on immune parameters from several upper reproductive tract compartments relevant to hiv-1 susceptibility in repetitive samples from 15 depot-medroxyprogesterone acetate users and 27 women not on hormonal contraceptives.Compared with samples from unexposed women in the mid-luteal phase, depot-medroxyprogesterone acetate use was associated with: increased endocervical concentrations of mcp1 and ifnalpha2; decreased endocervical concentrations of il1beta and il6; increased proportions of endometrial cd4+ and cd8+ cells expressing the activation marker hladr; increased density of endometrial macrophages; and decreased density of endometrial regulatory t cells.Unlike previous reports with samples from the vagina, we did not observe increased expression of the hiv co-receptor ccr5 on cd4+ t cells in the endocervix or endometrium.Our results indicate important differences in anatomic compartments regarding mechanisms by which depot-medroxyprogesterone acetate could be associated with increased risk of hiv acquisition, including increased recruitment of macrophages to the endometrium, decreased levels of pro-inflammatory cytokines in the endocervix possibly leading to enhanced susceptibility to viral infection, and activation of endometrial t cells.

Journal: Mucosal immunology (2017)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Liposarcoma of Probable Medullary Bone Origin in a Lovebird (Agapornis roseicollis).

A 15-year-old female peach-faced lovebird (agapornis roseicollis) was presented to the hospital for a possible left wing injury and an inability to fly after falling in its cage.On physical examination the left elbow was swollen and painful.Radiographic images revealed left wing soft tissue swelling surrounding the elbow and lysis of the distal humerus with extensive cortical thinning.Subsequent high-definition volumetric-imaging 3-dimensional computed tomography (hdvi 3d ct) revealed a pathological fracture, cortical lysis, periosteal reaction, and abnormal intraosseous soft tissue of the left humerus with associated soft tissue swelling, suggestive of neoplasia.No evidence of metastatic disease was identified.Surgical amputation of the left wing was elected.A liposarcoma and pathologic fracture of the humerus were diagnosed histologically and by oil red o staining for lipids in the neoplastic cells.The morphologic features of the tumor suggested that it developed within the adipocyte component of the medullary bone.The incision at the amputation site healed without complication.A follow-up hdvi 3d ct performed 4 months postsurgery showed no evidence of metastatic disease.To the authors' knowledge, this is the first report of a primary liposarcoma of medullary bone origin in an avian species.

Journal: Journal of avian medicine and surgery (2022)
Publication types: Case Reports;Journal Article
Daturataturin A, a withanolide in Datura metel L., induces HaCaT autophagy through the PI3K-Akt-mTOR signaling pathway.

Daturataturin a (dta), a withanolide compound in datura metel l., exhibits excellent anti-inflammatory and anti-proliferative activities.Here, we report the study of dta-induced proliferation and inflammation in human immortalized keratinocytes (ha ca ts) and the associated molecular mechanisms.Ha ca ts are a model of the epidermal proliferative state of cells.The pharmacodynamics and mechanism of dta were studied by western blot, immunofluorescence, apoptosis and proliferation detection, and real-time quantitative polymerase chain reaction.We confirmed that dta induced ha ca t autophagy, which, in turn, induced ha ca t senescence and, ultimately, led to cell cycle arrest.Dta also negatively regulated inflammation through the activation of autophagy.This may be one of the mechanisms underlying the action of datura metel l.Preparation used for the treatment of psoriasis.

Journal: Phytotherapy research : PTR (2021)
Publication types: Journal Article
An update on the advancements in the treatment of agitation in Alzheimer's disease.

Neuropsychiatric symptoms (nps) in alzheimer's disease (ad) are associated with significant negative outcomes for patients and their caregivers.Agitation, one of the most distressing nps, lacks safe and effective long term interventions.Nonpharmacological interventions are suggested as first-line treatment, but aren't effective for every patient, resulting in pharmacological interventions for some patients, consisting of off-label use of antipsychotics, sedative/hypnotics, anxiolytics, acetylcholinesterase inhibitors, memantine, and antidepressants; where efficacy doesn't necessarily outweigh associated risks.Areas covered: gains in understanding neurobiological mechanisms underlying agitation have fueled several recent clinical trials.This article updates our review published in 2014.Comprehensive literature search for published articles from january 2014 to december 2016 evaluating pharmacologic interventions for agitation in ad was done.A review of several clinical trials was completed: dextromethorphan/quinidine, scyllo-inositol, brexpiprazole, prazosin, cannabinoids, citalopram, escitalopram, pimavanserin, iti-007, orm-12741 show promise in treating agitation.Expert opinion: neurobiological findings, innovative trials designs, statistical approaches, and preliminary paths for regulatory agency acceptance have re-ignited the area of pharmacological treatment of nps.Though further research is needed to fully determine the safety, tolerability and efficacy of these treatments, the mission to find effective treatments for neuropsychiatric symptoms such as agitation in patients with dementia is well underway.

Journal: Expert opinion on pharmacotherapy (2017)
Publication types: Journal Article;Review
Siniperca chuatsiRhabdovirus (SCRV)-Induced Key Pathways and Major Antiviral Genes in Fish Cells.

Fish rhabdoviruses, including siniperca chuatsirhabdovirus (scrv), are epidemic pathogens that harm fish aquaculture.To clarify the interactions between scrv and its host and explore antiviral targets, the present study performed transcriptome analysis in a cultured s.Chuatsiskin cell line (scsc) after scrv infection at 3, 12, 24, and 36 h post-infection (hpi).Comparison with control obtained 38, 353, 896, and 1452 differentially expressed genes (degs) in the detected time points, respectively.Further analysis of the go terms and kegg pathways revealed the key pathways "cytokine-cytokine receptor interaction" and "interferon related pathways" in scsc cells responding to scrv infection.The significantly up-regulated genes in the pathways were also verified by q pcr.Furthermore, gene cloning and overexpression revealed that five interferon-stimulated genes (isgs) ifi4407, ifi35, viperin, ifit1, and ifit5 had the ability to inhibit scrv replication in fhm (fathead minnow) cells, especially an inhibition efficiency more than 50% was observed in ifi35 overexpressed cells.In summary, current study revealed the main innate immune pathways in s.Chuatsicells induced by scrv infection and the major isgs of s.Chuatsiin controlling scrv replication.

Journal: Microorganisms (2022)
Publication types: Journal Article
A Pragmatic Comparison Between Aerobic Exercise and Suryanamaskar in Stress Management in Medical Professionals: A Quasi-experimental Study.

Stress is an episodic process in an individual's life that depends upon the circumstances that elicit this process, later jeopardizing an individual's mental balance and leading to depression and anxiety.Yoga is a traditional component of physical activity that contains three main domains, namely, maintaining the correct posture (asanas), control over one's breath (pranayama) and meditation with complete concentration (dhyana), which are proven to be effective in enhancing the psychological, physical, and spiritual wellbeing of an individual along with mindfulness.The purpose of the present study was to compare aerobic exercise (ae) and suryanamaskar (sn) in terms of the best intervention in lowering the level of stress in medical professionals (mps).Methods a quasi-experimental study including a pragmatic comparison was conducted involving 30 participants who were divided into two groups a and b.The participants in group a did treadmill walking and the participants in group b were made to perform the complete cycle of sn with all the 12 asanas for four weeks.Results the outcomes demonstrated that both ae and sn had significant statistical values in terms of pre- and post-intervention perceived stress scale (pss) scores, resting heart rate, and systolic and diastolic blood pressure.Also, when post-intervention mean values of both the groups were compared for all the parameters, only mean pss values were found to be statistically significant.Conclusion the current study concluded that both ae and sn were beneficial in decreasing the level of stress in mps with sn being statistically more significant in reducing stress levels than ae.Both interventions are safe to perform.

Journal: Cureus (2022)
Publication types: Journal Article
Impact of the COVID-19 Pandemic on Chronic Disease Care in India, China, Hong Kong, Korea, and Vietnam.

This study aims to provide evidence on how the covid-19 pandemic has impacted chronic disease care in diverse settings across asia.Cross-sectional surveys were conducted to assess the health, social, and economic consequences of the pandemic in india, china, hong kong, korea, and vietnam using standardized questionnaires.Overall, 5672 participants with chronic conditions were recruited from five countries.The mean age of the participants ranged from 55.9 to 69.3 years.A worsened economic status during the covid-19 pandemic was reported by 19% to 59% of the study participants.Increased difficulty in accessing care was reported by 8% to 24% of participants, except vietnam: 1.6%.The worsening of diabetes symptoms was reported by 5.6% to 14.6% of participants, except vietnam: 3%.In multivariable regression analyses, increasing age, female participants, and worsened economic status were suggestive of increased difficulty in access to care, but these associations mostly did not reach statistical significance.In india and china, rural residence, worsened economic status and self-reported hypertension were statistically significantly associated with increased difficulty in access to care or worsening of diabetes symptoms.These findings suggest that the pandemic disproportionately affected marginalized and rural populations in asia, negatively affecting population health beyond those directly suffering from covid-19.

Journal: Asia-Pacific journal of public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Ultrafast Dynamics of Photochemical Nitrile Imine Formation.

The chemical reactivity of nitrile imines is of great utility in organic synthesis with applications rapidly expanding into the materials and life sciences.Yet, our understanding of the electronic and molecular structures of nitrile imines remains incomplete and the elementary mechanism of their photoinduced generation is entirely unknown.Here, femtosecond infrared spectroscopy after 266 nm-excitation of 2,5-diphenyltetrazole has been carried out to temporally resolve the formation and structural relaxation dynamics of the nascent diphenylnitrile imine in liquid solution under ambient conditions.The infrared-spectroscopic evolution is interpreted by an initial sequence of intersystem crossings within 250 fs followed by the cleavage of n2with formation of a structurally relaxed nitrile imine on the adiabatic ground-state singlet surface within a few tens of picoseconds.The infrared spectrum supports the notion of a "floppy" nitrile imine molecule whose equilibrium character ranges from fully propargylic to fully allenic in the room temperature liquid solution.

Journal: Angewandte Chemie (International ed. in English) (2022)
Publication types: Journal Article
Feasibility of a patient-centered method to determine meaningful change in pain intensity on a survey of patients with a history of cancer.

Introduction current methods of determining minimally important differences (mids) in patient-reported outcomes (pros) do not incorporate individual patient values.Objectives this study tested the feasibility of having cancer patients define a personally meaningful change in pain intensity, a method we have termed precision pros.Methods adults with cancer and pain (n = 231) completed an electronic questionnaire twice over 2 weeks.Participants were then given their pain intensity scores with an explanation of score meaning.Participants then defined their own mids for an increase and decrease in pain intensity.Participants also answered 3 questions testing their understanding of the mid concept.Results the majority of participants could define an individually meaningful increase (97% [n = 223]) and individually meaningful decrease (98% [n = 226]) in pain intensity.Seventy-two percent of participants (n = 166) answered all test questions correctly and 26% (n = 60) answered 2 of 3 correctly.Using the individual mid, 32% (95% ci: 25.3, 40.0) of the sample experienced a meaningful change between the 2 surveys, more than other methods (z-test: 14%, 95% ci: 9.4, 20.6; distribution-based method: 24%, 95% ci: 17.7, 31.1).Conclusions this study showed the feasibility of the precision pro individual mid, which could be used in clinical care or clinical trials.Further studies are needed to compare the individual mid to current methods.

Journal: Pain reports (2022)
Publication types: Journal Article
Metformin induces mitochondrial remodeling and differentiation of pancreatic progenitor cells into beta-cells by a potential mechanism including suppression of the T1R3, PLCβ2, cytoplasmic Ca+2, and AKT.

The main goal of this study was to investigate the molecular changes in pancreatic progenitor cells subject to high glucose, aspartame, and metformin in vitro.This scope of work glucose, aspartame, and metformin were exposed to pancreatic islet derived progenitor cells (pid-pcs) for 10 days.Glut1's role in beta-cell differentiation was examined by using glut1 inhibitor wzb117.Insulin+cell ratio was measured by flow cytometry; the expression of beta-cell differentiation related genes was shown by rt-pcr; mitochondrial mass, mitochondrial ros level, cytoplasmic ca2+, glucose uptake, and metabolite analysis were made fluorometrically and spectrophotometrically; and proteins involved in related molecular pathways were determined by western blotting.Findings showed that glucose or aspartame exposed cells had similar metabolic and gene expression profile to control pid-pcs.Furthermore, relatively few insulin+cells in aspartame treated cells were determined.Aspartame signal is transmitted through plcβ2, camkk2 and lkb1 in pid-pcs.The most obvious finding of this study is that metformin significantly increased beta-cell differentiation.The mechanism involves suppression of the sweet taste signal's molecules t1r3, plcβ2, cytoplasmic ca+2, and akt in addition to the direct effect of metformin on mitochondria and ampk, and the energy metabolism of pid-pcs is remodelled in the direction of oxidative phosphorylation.These findings are very important in terms of determining that metformin stimulates the mitochondrial remodeling and the differentiation of pid-pcs to beta-cells and thus it may contribute to the compensation step, which is the first stage of diabetes development.

Journal: Journal of physiology and biochemistry (2022)
Publication types: Journal Article