syedzayyan/paper_mill_benchmark huggingface dataset:
Implementation and challenges of portable blood gas measurements in air medical transport.

S ventilator management in prehospital settings using end-tidal co2can lead to inappropriate ventilation in the absence of point of care blood gas (pocbg) measurements.Implementation of pocbg testing in helicopter emergency medical services (hems) is limited in part because of concern for preanalytical and analytical errors due to altitude, vibration, and other associated environmental factors and due to insufficient documentation of implementation challenges.Methods we performed accuracy and precision verification studies using standard materials tested pre-, in-, and post-flight (n=10) in a large hems agency.Quality assurance error log data were extracted and summarized for common pocbg errors during the first 31 months of use and air medical transport personnel were surveyed regarding pocbg use (n=63).Results no clinically significant differences were found between pre-, in-, and post-flight blood gas measurements.Error log data demonstrated a reduction in device errors over time.Survey participants found troubleshooting device errors and learning new clinical processes to be the largest barriers to implementation.Continued challenges for participants coincided with error log data including temperature and sampling difficulties.Survey participants indicated that pocbg testing improved patient management.Conclusions pocbg testing does not appear to be compromised by the hems environment.Temperature excursions can be reduced by use of insulated transport bags with heating and cooling packs.Availability of pocbg results in air medical transport appeared to improve ventilator management, increase recognition of ventilation-perfusion mismatch, and improve patient tolerance of ventilation.

Journal: Clinical chemistry and laboratory medicine (2022)
Publication types: Journal Article
Effects of shuxuetong injection for cerebral infarction: A protocol for systematic review and meta-analysis.

Cerebral infarction (ci) is a common disease with high morbidity and disability.Shuxuetong (sxt) injection is a chinese materia medica standardized product used in the treatment of ci.Currently, there is a lack of high-quality evidence to support the effectiveness and safety of sxt on patients with ci.This systematic review protocol aims at describing a meta-analysis to evaluate the efficacy of sxt for the treatment of ci.Methods we will search the databases of pub med, medline, embase, cochrane library central register of controlled trials, china national knowledge infrastructure database (cnki), wan fang database, chongqing vip information, and sino med from their inception to jun 2020.Two reviewers will independently screen randomized controlled trials of sxt for the treatment of ci.The meta-analysis will be conducted using rev man v.5.3 software.Results the results of this study will be published in a peer-reviewed journal.Conclusion the conclusion of our systematic review will provide evidence to judge whether sxt is an effective intervention for patients with ci.Trial registration number .

Journal: Medicine (2020)
Publication types: Journal Article
Clopidogrel versus Ticagrelor in CYP2C19 Loss-of-Function Allele Noncarriers: A Real-World Study in China.

This article compares the clinical outcomes of clopidogrel and ticagrelor in patients with acute coronary syndrome (acs) without cytochrome p450 (cyp)2c19 loss-of-function (lof) alleles and investigates whether clopidogrel could be an alternative p2y12 inhibitor without increasing the risk of ischemic events.Methods patients were divided into the clopidogrel-treated group and the ticagrelor-treated group.Inverse probability of treatment weighting (iptw) calculated by propensity scores was used to adjust confounding covariates.The primary outcome was major adverse cardiovascular or cerebrovascular events (macces) within 12 months.The secondary outcomes were macces plus unstable angina, and clinically significant bleeding events.Results finally, 2,199 patients were included.Of them, 1,606 were treated with clopidogrel, and 593 were treated with ticagrelor.The mean age of the original cohort was 59.92 ± 9.81 years.During the 12-month follow-up period, macces occurred in 89 patients (4.0%).No significant differences were observed in macces (iptw-adjusted hazard ratio [hr], 0.87; 95% confidence interval [ci], 0.65-1.18), macces plus unstable angina (iptw-adjusted hr, 1.20; 95% ci, 0.91-1.59), or clinically significant bleeding events (iptw-adjusted hr, 0.81; 95% ci, 0.53-1.23) between the clopidogrel- and ticagrelor-treated groups.Conclusion in patients with acs without cyp2c19 lof alleles, clopidogrel was not associated with a higher risk of macces when compared with ticagrelor.The main findings of this study support use of clopidogrel in cyp2c19 lof noncarriers as an alternative p2y12 inhibitor, which may reduce medical expenses and adverse reactions caused by more potent p2y12 inhibitors in these patients.

Journal: Thrombosis and haemostasis (2022)
Publication types: Journal Article
Love in a time of anti-Blackness: social rank, attachment, and race in psychotherapy.

This paper draws on critical race theory and research on attachment, social rank and dehumanization to theorize the implications of addressing anti-blackness in psychotherapy with both black and non-black clients in the context of white supremacy.Drawing on and critiquing a recent review of attachment theory and race, the author draws on historical and empirical research outlining the contours of a racial capitalist world.Recontextualizing attachment theory through this critical race theory lens, it will be argued psychotherapy must address anti-blackness with both black and non-black clients, redefining therapeutic action not only as the provision of repair of interpersonal ruptures, but also as the capacity to mentalize about socio-historical ruptures, allowing space to clarify and pursue one's values despite an anti-black, capitalist and white supremacist world.This paper will provide case examples illustrating these principles with black and non-black clients and conclude with their clinical and political implications.

Journal: Attachment & human development (2022)
Publication types: Journal Article
Establishment of a diagnostic model of coronary heart disease for patients with diabetic foot.

This study aims to establish a diagnostic model of coronary heart disease (chd) for diabetic foot (df) patients.the clinical data of 489 hospitalized patients with df were retrospectively analyzed in this case-control study.The patients were divided into the chd group (df with chd, n = 212) and the control group (df without chd, n = 277).Univariate analysis was performed to screen for chd-related risk factors, and multivariate logistic regression analysis was conducted to determine significant chd risk factors.Scores were assigned according to the ratio of risk factors (or) to establish a diagnostic model of chd for patients with df.The area under the roc curve was used to test the application value of the diagnostic model.the logistic regression analysis showed that the risk factors for chd in df patients were age, duration of diabetes, toe-brachial index, hyperuricemia, and chronic renal insufficiency.The area under the roc curve of the diagnostic model was 0.798 (0.759-0.837), the diagnostic point of chd was 6 points, the diagnostic sensitivity was 69.3%, and the specificity was 76.5%.the established model has good diagnostic value and provides the basis for preliminary screening for chd in patients with df.

Journal: Medicine (2020)
Publication types: Journal Article
Encephaloduroarteriosynangiosis with Dural Inversion for Moyamoya Disease in a Pediatric and Adult Population-a Single-Center 20-Year Experience.

Moyamoya disease refers to a progressive vasostenotic or vaso-occlusive disease that puts patients at risk for ischemic and/or hemorrhagic events.Surgical revascularization procedures aim to restore cerebral blood flow to mitigate stroke risk and functional decline.Direct and indirect bypass procedures have been proposed.Encephaloduroarteriosynangiosis (edas) with dural inversion is a well-accepted indirect procedure.Methods patients with moyamoya disease undergoing edas with dural inversion between 2000 and 2019 were retrospectively reviewed.Clinical data including short-term and long-term outcome were measured using the modified rankin scale.Patient satisfaction was assessed in patients with a minimum of 3 years of clinical follow-up.Results over a 20-year period, 54 patients underwent 88 edas with dural inversion procedures.Most patients underwent bilateral surgery (34/54 patients, 63.0%).Median age at surgery was 19 years (range, 1-63 years) with a median follow-up of 6 years (range, 1-20 years).Periprocedural complications occurred in 4 of 54 patients (7.4%).Periprocedural infarction occurred in 3 of 88 operations (3.4%).Functional outcome at 90 days was favorable (modified rankin scale score 0-2) in 92.6% of cases.On long-term follow-up, 3 patients experienced ischemic infarction (5.6%), and 1 patient (1.9%) experienced hemorrhagic infarction.Patients' overall satisfaction with the surgical procedure at last follow-up was determined in 36 of 45 patients with at least 3 years of follow-up (response rate 80.0%).Median satisfaction was very good (score 5; range, 3-5).Conclusions edas with dural inversion is a safe and effective indirect revascularization procedure for pediatric and adult moyamoya disease that is associated with favorable long-term outcomes and high patient satisfaction.

Journal: World neurosurgery (2021)
Publication types: Journal Article
Androgen-deprivation therapy, dementia, and cognitive dysfunction in men with prostate cancer: How much smoke and how much fire?

Androgen-deprivation therapy (adt) remains the cornerstone of management for patients with metastatic prostate cancer.Although the toxicities of adt are well established, there is increasing controversy surrounding the association between cognitive dysfunction and the receipt of adt, with some evidence suggesting an increased risk of dementia.The authors conducted a literature search to identify pertinent clinical studies in this field.This general review outlines the key findings and discusses the relative strengths and weaknesses when drawing conclusions about the risk of cognitive dysfunction or dementia with adt use.Cancer 2018;124:1326-34.© 2018 american cancer society.

Journal: Cancer (2018)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Review
Bioprospecting Fluorescent Plant Growth Regulators from Arabidopsis to Vegetable Crops.

The phytohormone auxin is involved in almost every process of a plant's life, from germination to plant development.Nowadays, auxin research connects synthetic chemistry, plant biology and computational chemistry in order to develop innovative and safe compounds to be used in sustainable agricultural practice.In this framework, we developed new fluorescent compounds, ethanolammoniump-aminobenzoate (hea-p aba) andp-nitrobenzoate (hea-p nba), and investigated their auxin-like behavior on two main commercial vegetables cultivated in europe, cucumber (cucumis sativus) and tomato (solanumlycopersicum), in comparison to the model plant arabidopsis (arabidopsis thaliana).Moreover, the binding modes and affinities of two organic salts in relation to the natural auxin indole-3-acetic acid (iaa) into tir1 auxin receptor were investigated by computational approaches (homology modeling and molecular docking).Both experimental and theoretical results highlight hea-p aba as a fluorescent compound with auxin-like activity both in arabidopsis and the commercial cucumber and tomato.Therefore, alkanolammonium benzoates have a great potential as promising sustainable plant growth stimulators to be efficiently used in vegetable crops.

Journal: International journal of molecular sciences (2021)
Publication types: Journal Article
How do drying-wetting cycles influence availability of heavy metals in sediment? A perspective from DOM molecular composition.

Investigating the influence mechanism of drying-wetting cycles on the availability and mobility of heavy metals in sediment from the perspective of the molecular composition of dissolved organic matter (dom) may gain a new understanding, but little current information exists.Here, we used spectral technologies, high-resolution mass spectrometry, and elemental stoichiometry method to trace the change rules of the molecular composition of dom in the riparian sediment of the river.Results showed that the drying-wetting cycles could benefit the degradation of labile fractions (e.g., proteins, aliphatics, and lipids) of dom and retain the fractions with high aromaticity and molecular size (e.g., lignin).The decrease in the availability of cd after drying-wetting alternation processes was highly related to these changes in dom composition.However, the availability of zn and cu remained almost unchanged, which probably resulted from the release and depletion of n and s in sediment-derived dom under drying-wetting alternation conditions.As for cr, its exchangeable fraction was unchanged during the drying-wetting alternation process, likely due to its high stability in the sediment.These results have implications on the environmental geochemical cycling of heavy metals in the riparian sediment with frequent drying-wetting alternation.

Journal: Water research (2022)
Publication types: Journal Article
Dynamic N6-methyladenosine modification of lncRNA modulated by METTL3 during bacterial disease development in an echinoderm.

Long non-coding rnas (lnc rnas) are novel functional non-coding rnas which engaged in many aspects of biological processes.N6-methyladenosine (m6a) as a kind of abundant epitranscriptomic modification in eukaryotes, plays important roles in regulation of gene expression for various physiological functions.Our previous study demonstrated that sea cucumber lnc rnas were differentially expressed during bacterial infection.However, whether the post-transcriptional regulation of lnc rnas influenced by m6a modification in sea cucumbers with different stages of skin ulceration syndrome (sus) are largely unknown.Here, we generated the genome-wide map of m6a lnc rnas in sus-diseased and sus-resistant sea cucumbers for the first time, revealed that m6a levels in lnc rnas were mainly upregulated in sus-resistant group.Intriguingly, most of the m6a lnc rnas showed a positive correlation between the expression levels and m6a levels based on conjoint analysis, suggesting that m6a modification on a lnc rna may contribute to its rna stability.Furthermore, the host genes of lnc rnas with dysregulated m6a peaks were enriched in immune pathway.More importantly, methyltransferase mettl3 was required for m6a methylation modification and played positive roles in lnc rna expression.Collectively, this study presents the comprehensive characters of m6a lnc rnas in marine invertebrate.These m6a modified lnc rnas may be served as potential regulators associated with sus and provide a promising avenue for disease therapy through targeting mettl3.

Journal: Fish & shellfish immunology (2022)
Publication types: Journal Article
Clinical impact of a targeted next-generation sequencing gene panel for autoinflammation and vasculitis.

Monogenic autoinflammatory diseases (aid) are a rapidly expanding group of genetically diverse but phenotypically overlapping systemic inflammatory disorders associated with dysregulated innate immunity.They cause significant morbidity, mortality and economic burden.Here, we aimed to develop and evaluate the clinical impact of a ngs targeted gene panel, the "vasculitis and inflammation panel" (vip) for aid and vasculitis.Methods the agilent sure design tool was used to design 2 versions of vip; vip1 targeting 113 genes, and a later version, vip2, targeting 166 genes.Captured and indexed libraries (qxt target enrichment system) prepared for 72 patients were sequenced as a multiplex of 16 samples on an illumina mi seq sequencer in 150bp paired-end mode.The cohort comprised 22 positive control dna samples from patients with previously validated mutations in a variety of the genes; and 50 prospective samples from patients with suspected aid in whom previous sanger based genetic screening had been non-diagnostic.Results vip was sensitive and specific at detecting all the different types of known mutations in 22 positive controls, including gene deletion, small indels, and somatic mosaicism with allele fraction as low as 3%.Six/50 patients (12%) with unclassified aid had at least one class 5 (clearly pathogenic) variant; and 11/50 (22%) had at least one likely pathogenic variant (class 4).Overall, testing with vip resulted in a firm or strongly suspected molecular diagnosis in 16/50 patients (32%).Conclusions the high diagnostic yield and accuracy of this comprehensive targeted gene panel validate the use of broad ngs-based testing for patients with suspected aid.

Journal: PloS one (2017)
Publication types: Journal Article
Ibaraki virus enters host cells by macropinocytosis.

Ibaraki virus (ibav) is the pathogen associated with ibaraki disease.In a previous study, we suggested that ibav enters hamster lung (hm lu-1) cells via endocytosis and subsequently escapes into the cytoplasm upon endosomal acidification.However, it is unclear which of the endocytic pathways ibav utilizes.In this study, we aimed to further elucidate the pathway of ibav entry into host cells.We found that ibav replication was not suppressed by inhibitors of clathrin-mediated or caveolin-mediated endocytosis but was markedly suppressed by 5-(n-ethyl-n-isopropyl) amiloride (eipa) and cytochalasin d, both of which inhibit macropinocytosis.Monensin, which inhibits endosomal acidification, also suppressed ibav replication.To assess the inhibitory effects of these reagents on endocytosis, dextran and transferrin were used as indicators of macropinocytosis and clathrin-mediated endocytic activity, respectively.Our data confirmed that eipa and monensin inhibited dextran uptake, and cytochalasin d inhibited the uptake of both.Additionally, we confirmed that endosomal/lysosomal acidification was inhibited by monensin.These results suggest that the macropinocytosis pathway is the major route of ibav entry and confirm that ibav infection of hm lu-1 cells is dependent on endosomal acidification.

Journal: Virus research (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Schrödinger's Cat Meets Occam's Razor.

We discuss v.p.Belavkin's approach to the schrödinger cat problem and show its close relation to ideas based on superselection and interaction with the environment developed by n.p.Landsman.The purpose of the paper is to explain these ideas in the most simple possible context, namely: discrete time and separable hilbert spaces, in order to make them accessible to those coming from the philosophy of science and not too happy with idiosyncratic notation and terminology and sophisticated mathematical tools.Conventional elementary mathematical descriptions of quantum mechanics take "measurement" to be a primitive concept.Paradoxes arise when we choose to consider smaller or larger systems as measurement devices in their own right, by making different and apparently arbitrary choices of location of the "heisenberg cut".Various quantum interpretations have different resolutions of the paradox.In belavkin's approach, the classical world around us does really exist, and it evolves stochastically and dynamically in time according to probability laws following from successive applications of the born law.It is a collapse theory.The quantum/classical distinction is determined by the arrow of time.The underlying unitary evolution of the wave-function of the universe enables the designation of a collection of beables which grows as time evolves, and which therefore can be assigned random, classical trajectories.In a slogan: the past is particles, the future is a wave.We, living in the now, are located on the cutting edge between past and future.

Journal: Entropy (Basel, Switzerland) (2022)
Publication types: Journal Article
A preliminary study of KAT2A on cGAS-related immunity in inflammation amplification of systemic lupus erythematosus.

Previous studies demonstrated that c gas pathway is related to the inflammation amplification in a variety of autoimmune diseases.Lysine acetyltransferase family (kats) can regulate the nuclear transcription or cytoplasmic activation of c gas through different mechanisms.However, its role and related immunity patterns in systemic lupus erythematosus (sle) have not been explored.In this study, rna-seq and sc rna-seq profiling were performed for peripheral blood mononuclear cells (pbmcs) from patients with sle.R packages were used for bioinformatic analysis.Cell culture, rt-pcr, western blotting, immunofluorescence, immunohistochemistry, and elisa were used to explore gene expression in vitro or clinical specimens.Plasmid transfection and mass spectrometry were used to detect protein modifications.Eight acetyltransferase and deacetylase family members with significantly differential expression in sle were found.Among them, kat2a was abnormally upregulated and positively correlated with disease activity index.Further, kat2a-c gas pathway was aberrantly expressed in specific immune cell subsets in sle.In vitro studies showed kat2a modulated c gas through increasing expression and post-translational modification.Our research provides novel insights for accurately positioning specific immune-cell subgroups in which kat2a-c gas reaction mainly works and kat2a regulation patterns.

Journal: Cell death & disease (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Inflammatory myofibroblastic tumour of the urinary bladder: the role of immunoglobulin G4 and the comparison of two immunohistochemical antibodies and fluorescence in-situ hybridization for the detection of anaplastic lymphoma kinase alterations.

S we examined gene rearrangement and the expression of anaplastic lymphoma kinase (alk) in urinary bladder inflammatory myofibroblastic tumour (imt) using fluorescence in-situ hybridization (fish) and two immunohistochemical antibodies to alk.We also investigated whether imt represents an immunoglobulin (ig)g4-related disease.Methods and results the performance of the dako flex alk monoclonal antibody (cd246) and the cell signaling technology alk (d5f3) xp monoclonal antibody were compared.Overall, 11 of 16 tumours showed alk expression by immunohistochemistry (69%).Ten demonstrated alk expression with both stains and one was positive with d5f3 but not cd246 (91% correlation).The d5f3 antibody yielded a stronger staining intensity and a higher sensitivity.Nine tumours demonstrated alk rearrangements (56%) by fish.Three were alk(+) by immunohistochemistry but negative for rearrangement by fish, whereas one showed rearrangement by fish but was negative by immunohistochemistry.In total, 12 tumours were positive for alk abnormalities (75%).Using current criteria, no cases were classified as an ig g4-related disease.Conclusions the alk d5f3 immunohistochemical stain showed superior staining characteristics compared with alk cd246.Discrepancies in the results between fish and immunohistochemistry for alk abnormalities may have causes that are multifactorial.By current criteria, imt does not represent an ig g4-related disease.

Journal: Histopathology (2015)
Publication types: Comparative Study;Journal Article