syedzayyan/paper_mill_benchmark huggingface dataset:
Lessons learned from the investigation and management of an outbreak of Shigella flexneri associated with a restaurant in London, 2019-2020.

Foodborne outbreaks of shigella flexneri infection are uncommon in the uk.In november 2019, the united kingdom health security agency investigated an outbreak of s.Flexneri associated with a fast-food restaurant in london.Methods epidemiological investigations included case ascertainment and interviewing suspected cases using enhanced surveillance questionnaires.Whole-genome sequencing (wgs) was used for characterisation of human isolates.Environmental investigations included a review of food safety processes at the implicated restaurant, administration of exposure questionnaires and stool sampling of staff.Results between november 2019 and february 2020, 17 cases were confirmed as part of the outbreak by wgs in london.Among these, 15 were linked to the implicated restaurant.A review of the food safety processes at the restaurant was satisfactory.Despite initial suboptimal coverage of stool screening of staff, all staff members working at the restaurant during the sampling period were screened and an asymptomatic food handler tested positive for s.flexneri with the outbreak wgs profile.The individual underwent microbiological clearance, and no further cases were reported.It was not possible to confirm the direction of transmission for the community cases or the staff member.Conclusion we report an outbreak of s.Flexneri in a fast-food restaurant in london with previous inspection ratings indicating good compliance with food safety and hygiene standards.Wgs was crucial in identifying cases linked to the outbreak.This outbreak highlights the importance of prompt testing of food handlers in outbreaks suspected to be associated with food businesses.

Journal: Public health (2022)
Publication types: Journal Article
Melatonin induces apoptotic cell death through Bim stabilization by Sp1-mediated OTUD1 upregulation.

Melatonin, secreted by the pineal gland, regulates the circadian rhythms and also plays an oncostatic role in cancer cells.Previously, we showed that melatonin induces the expression of bim, a pro-apoptotic bcl-2 protein, at both the transcriptional and post-translational levels.In the present study, we investigated the molecular mechanisms underlying the melatonin-mediated bim upregulation through post-translational regulation.We found that ovarian tumor domain-containing protein 1 (otud1), a deubiquitinase belonging to the otu protein family, is upregulated by melatonin at the m rna and protein levels.Otud1 knockdown inhibited melatonin-induced bim upregulation and apoptosis in cancer cells.Otud1 directly interacted with bim and inhibited its ubiquitination.Melatonin-induced otud1 upregulation caused deubiquitination at the lysine 3 residue of bim, resulting in its stabilization.In addition, melatonin-induced activation of sp1 was found to be involved in otud1 upregulation at the transcriptional level, and pharmacological inhibition and genetic ablation of sp1 (si rna) interrupted melatonin-induced otud1-mediated bim upregulation.Furthermore, melatonin reduced tumor growth and induced upregulation of otud1 and bim in a mouse xenograft model.Notably, bim expression levels correlated with otud1 levels in patients with renal clear cell carcinoma.Thus, our results demonstrated that melatonin induces apoptosis by stabilizing bim via sp1-mediated otud1 upregulation.

Journal: Journal of pineal research (2022)
Publication types: Journal Article
Liquid-repellent and self-repairing lubricant-grafted surfaces constructed by thiol-ene click chemistry using activated hollow silica as the lubricant reservoir.

The development of robust, stain-resistant, and self-healing liquid-repellent surfaces is a common aspiration of both consumer and industrial applications, but the existing methods suffer from limitations, such as complicated procedures, weak mechanical durability and substrate dependency.In this work, a lubricant-grafted slippery surface (lgss) was prepared by grafting vinyl-terminated polydimethylsiloxane (vi-pdms) onto various substrates coated with sulfhydryl-modified hollow mesoporous silica (sh-hms) through a thiol-ene click reaction.The uniform and intact lubricant layer can effectively decrease the absorption of the polysaccharide and protein, exhibiting superior antifouling properties.Notably, the hollow structure of sh-hms could significantly increase the oil grafting capacity of the slippery surface from 0.013 g/cm2to 0.027 g/cm2compared with the surface constructed by solid silica.By virtue of the strong covalent bond forces between the lubricant oil and surfaces, the obtained lgss exhibited robust liquid repellency when subjected to high/low temperature, ultraviolet irradiation and water impact.Moreover, the liquid-repellent lgss exhibited good self-repairing performance owing to the directional migration of the vi-pdms chain segment from the hollow capsule to the surface through the mesoporous channels under heating treatment.Therefore, such a newly developed strategy for constructing liquid-repellent coatings on various substrates with self-repairing properties has the potential to promote the advancement of interfacial antifouling materials and exhibit tremendous potential for consumer and industrial applications.

Journal: Journal of colloid and interface science (2021)
Publication types: Journal Article
Hyperactivation of P2X7 receptors as a culprit of COVID-19 neuropathology.

Scientists and health professionals are exhaustively trying to contain the coronavirus disease 2019 (covid-19) pandemic by elucidating viral invasion mechanisms, possible drugs to prevent viral infection/replication, and health cares to minimize individual exposure.Although neurological symptoms are being reported worldwide, neural acute and long-term consequences of sars-co v-2 are still unknown.Covid-19 complications are associated with exacerbated immunoinflammatory responses to sars-co v-2 invasion.In this scenario, pro-inflammatory factors are intensely released into the bloodstream, causing the so-called "cytokine storm".Both pro-inflammatory factors and viruses may cross the blood-brain barrier and enter the central nervous system, activating neuroinflammatory responses accompanied by hemorrhagic lesions and neuronal impairment, which are largely described processes in psychiatric disorders and neurodegenerative diseases.Therefore, sars-co v-2 infection could trigger and/or worse brain diseases.Moreover, patients with central nervous system disorders associated to neuroimmune activation (e.g.Depression, parkinson's and alzheimer's disease) may present increased susceptibility to sars-co v-2 infection and/or achieve severe conditions.Elevated levels of extracellular atp induced by sars-co v-2 infection may trigger hyperactivation of p2x7 receptors leading to nlrp3 inflammasome stimulation as a key mediator of neuroinvasion and consequent neuroinflammatory processes, as observed in psychiatric disorders and neurodegenerative diseases.In this context, p2x7 receptor antagonism could be a promising strategy to prevent or treat neurological complications in covid-19 patients.

Journal: Molecular psychiatry (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Studying the Biotransformation of Phosphorothioate-Containing Oligonucleotide Drugs by LC-MS.

Across the pharmaceutical industry, there is increasing interest and need to investigate the biotransformation of oligonucleotide drugs.The method of choice is high-resolution mass spectrometry due to its unmet sensitivity and specificity.here, we describe a method developed and applied in our laboratory studying the biotransformation of phosphorothioate-containing oligonucleotide drugs.This method is based on capillary flow liquid chromatography with column switching coupled to high-resolution mass spectrometry.

Journal: Methods in molecular biology (Clifton, N.J.) (2019)
Publication types: Journal Article
Dataset describing the development, optimization and application of SRM/MRM based targeted proteomics strategy for quantification of potential biomarkers of EGFR TKI sensitivity.

The data presented here describes the use of targeted proteomic assays to quantify potential biomarkers of epidermal growth factor receptor (egfr) tyrosine kinase inhibitor (tki) sensitivity in lung adenocarcinoma and is related to the research article: "quantitative targeted proteomic analysis of potential markers of tyrosine kinase inhibitor (tki) sensitivity in egfr mutated lung adenocarcinoma" [1].This article describes the data associated with liquid chromatography coupled to multiple reaction monitoring (lc-mrm) method development which includes selection of an optimal transition list, retention time prediction and building of reverse calibration curves.Sample preparation and optimization which includes phosphotyrosine peptide enrichment via a combination of pan-phosphotyrosine antibodies is described.The dataset also consists of figures, tables and excel files describing the quantitative results of testing these optimized methods in two lung adenocarcinoma cell lines with egfr mutations.

Journal: Data in brief (2018)
Publication types: Journal Article
Biomineralization-inspired synthesis of amorphous manganese phosphates for GLUT5-targeted drug-free catalytic therapy of osteosarcoma.

Osteosarcoma, occurring most frequently in children, teens, and young adults, is a lethal bone cancer with a high incidence of distant metastases and drug resistance.Developing a therapeutic platform that integrates targeting, curing and imaging is highly desirable for enhanced osteosarcoma therapy, yet quite challenging.In this work, we demonstrate a novel biomineralization-inspired strategy for the synthesis of a fructose incorporated manganese phosphate (fru-mn p) nanoplatform for tumour targeting, drug-free therapy, and mri imaging.Benefitting from the glucose transporter 5 (glut5)-mediated endocytosis, our fru-mn p nanoplatform produces a high level of reactive oxygen species (ros)viathe mn2+-driven fenton reaction within osteosarcoma cells, leading to efficient cancer cell killing due to caspase-mediated apoptosis.By virtue of the t1 signal enhancement of mn2+, our fru-mn p nanoplatform also acts as an effective tumour-specific mri contrast agent, realizing the mri-monitored chemodynamic therapy.The proposed synergistic therapeutic platform opens new possibilities for high efficacy therapy for osteosarcoma.

Journal: Nanoscale (2022)
Publication types: Journal Article
Respiratory outcomes of late preterm infants of mothers with early and late onset preeclampsia.

To study the effect of early and late onset preeclampsia (eope, lope, respectively) on outcomes of late preterm infants.Study design cohort study of late preterm infants admitted to a tertiary care nicu from january 2014-july 2015.Outcomes of late preterm infants of eope mothers were compared with the next late preterm infant of a lope mother and the next two late preterm infants of normotensive non-pe mothers.Primary outcome comprised use of continuous positive airway pressure, mechanical ventilation and/or surfactant in the 24 h after birth.Results compared to normotensives (n = 131), adjusted odds ratio (aors) of the primary outcome was higher in the eope (n = 64) and lope (n = 65) groups but reached statistical significance only in the eope group, aors 12.9, 95% ci 3.5-37 and 2.7, 95% ci 0.95-8.1, respectively.Conclusions compared to late preterm infants of normotensive and lope mothers, infants of mothers with eope have significantly higher respiratory morbidity.

Journal: Journal of perinatology : official journal of the California Perinatal Association (2020)
Publication types: Comparative Study;Journal Article;Research Support, Non-U.S. Gov't
Phytoplankton community organization and succession by sea warming: A case study in thermal discharge area of the northern coastal seawater of China.

Thermal discharges from power plants elevate temperatures in the surrounding waters, and this warming of the marine environment inevitably influences phytoplankton communities.In this study, we conducted seasonal sampling in coastal waters of the bohai sea off qinhuangdao, china.The results revealed that the coastal waters are notably affected by thermal discharge, with unseasonably-high water temperatures, particularly during winter.The change of phytoplankton community structure has been detected in the warmer coastal seawater.Although diatoms were the dominant species during field investigations, there were no significant seasonal changes in diatom abundance.In contrast, the density of dinoflagellates was low in all seasons due to the effects of thermal discharge.Consequently, the general trend in phytoplankton succession was interrupted.In general, the findings of this study may provide further insights into the warmer environmental impacts on phytoplankton communities in temperate regions.

Journal: Marine pollution bulletin (2021)
Publication types: Journal Article
S100A9 Drives the Chronification of Psoriasiform Inflammation by Inducing IL-23/Type 3 Immunity.

Psoriasis is a chronic inflammatory skin disorder driven by the il-23/type 3 immune response.However, molecular mechanisms sustaining the chronicity of inflammation and psoriatic lesions remain elusive.Combining systematic analyses of several transcriptomic datasets, we delineated gene signatures across human psoriatic skin, identifying s100a9 as one of the most up-regulated genes, which was confirmed in lesioned skin from patients with psoriasis and preclinical psoriasiform skin inflammation models.Genetic ablation or pharmacologic inhibition of s100a9 alleviated aldara-induced skin inflammation.By single-cell mapping of human psoriatic skin and bone marrow chimeric mice experiments, we identified keratinocytes as the major source of s100a9.Mechanistically, s100a9 induced il-23 production by dendritic cells, driving the il-23/type 3 immunity in psoriasiform skin inflammation.In addition, the cutaneous il-23/il-17 axis induced epidermal s100a9 expression in human and experimental psoriasis.Thus, we showed an autoregulatory circuit between keratinocyte-derived s100a9 and il-23/type 3 immunity during psoriasiform inflammation, identifying a crucial function of s100a9 in the chronification of psoriasis.

Journal: The Journal of investigative dermatology (2023)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Novel brachytherapy drainage tube loaded with double125I strands for hilar cholangiocarcinoma: A case report.

Hilar cholangiocarcinoma (cc) is a common malignant tumor with high malignancy and poor prognosis.Most patients have lost the opportunity to undergo radical surgery when diagnosed.Although palliative drainage or biliary stent placement is a preferable choice, the tumor cannot be controlled.This study aimed to develop a novel brachytherapy drainage tube for low-dose-rate brachytherapy with an effective drainage, thereby prolonging the survival time of patients.Case summary a 54-year-old male patient had undergone choledochal stent implantation due to obstructive jaundice.He was admitted to the hospital because of the recurrence of jaundice.Preoperative imaging and pathological biopsy revealed hilar cc (bismuth-corlette type iiia).First, the patient underwent percutaneous transhepatic cholangial drainage and the symptoms of jaundice gradually relieved.To further treat hilar cc and remove the biliary drainage tube as far as possible, the patient chose to use the novel brachytherapy drainage tube after a multi-disciplinary consultation.After 1 mo of brachytherapy, the re-examination revealed that the obstructive lesions disappeared, and the drainage tube was finally removed.During the following 10 mo of follow-up, the patient's hilar cc did not recur.Conclusion the novel brachytherapy drainage tube may be a new choice for patients with unresectable hilar cc.

Journal: World journal of clinical cases (2020)
Publication types: Case Reports;Journal Article
Design of advanced separators for high performance Li-S batteries using natural minerals with 1D to 3D microstructures.

Lithium-sulfur (li-s) batteries are of great interest due to their high energy density.However, polysulfides shuttle and low s loading severely impede their practical applications.Here, we report design of advanced separators for li-s batteries using natural minerals with 1d to 3d microstructures.Four natural minerals with different microstructures including 1d halloysite nanotubes, 1d attapulgite nanorods, 2d li+-montmorillonite (mmt) nanosheets and 3d porous diatomite were used together with carbon black (cb) for preparation of the mineral/cb-celgard separators.The si-oh groups of the minerals act as lewis acid sites, which could effectively absorb polysulfides by forming li o and os bonds with polysulfides.Among all the separators, the mmt/cb-celgard separator endowed the li-s battery with the highest upper plateau discharge capacity (369 m a h g-1), initial reversible capacity (1496 m a h g-1at 0.1 c), rate performance and cycling stability (666 m a h g-1after 500 cycles at 1.0 c with 0.046% capacity decay per cycle).The mmt/cb-celgard separator also enabled stable cycling of the li-s battery with high s loading (8.3 mg cm-2) cathode.This work will provide inspiration for future development of advanced separators for high-energy-density li-s batteries.

Journal: Journal of colloid and interface science (2022)
Publication types: Journal Article
The association between serum zinc levels and subjective symptoms in zinc deficiency patients with chronic liver disease.

This study aimed to analyze the association between serum zinc levels and major subjective symptoms in zinc deficiency patients with chronic liver disease.578 patients with chronic liver disease were enrolled.The patients, whose serum zinc level of <80 μg/dl, completed a questionnaire to determine whether they had subjective symptoms of the five conditions (taste disorder, aphthous stomatitis, dermatitis, alopecia, and anorexia).Then, the association between these subjective symptoms and serum zinc levels was analyzed.In total, 193 patients (33.4%) experienced any subjective symptoms.The prevalence of each symptom was as follows: 36 patients with taste disorder (6.2%), 46 with aphthous stomatitis (8.0%), 77 with dermatitis (13.3%), 46 with alopecia (8.0%), and 53 with anorexia (9.2%).In total, 70.8%, 34.1%, and 26.1% patients with serum zinc levels of <40, ≥40 to <60, and ≥60 to <80 μg/dl, respectively, had these symptoms.When zinc deficiency was defined as a serum zinc level of <80 μg/dl, approximately one-third of patients displayed symptoms presumably originating from zinc deficiency.As serum zinc levels decreased, the prevalence of these symptoms increased.Dermatitis, especially, was relevant to zinc.

Journal: Journal of clinical biochemistry and nutrition (2020)
Publication types: Journal Article
Derivation of combined species sensitivity distributions for acute toxicity of pyrethroids to aquatic animals.

The aquatic toxicity profiles of synthetic pyrethroid insecticides are remarkably similar, and results for a large number of species can be combined across compounds in species sensitivity distributions (ssds).Normalizing acute toxicity values (median lethal concentrations, lc50s) for each species and each pyrethroid to the lc50 of the same pyrethroid to the freshwater amphipod hyalella azteca (the most sensitive species to all pyrethroids tested) enabled expression of lc50s as hyalella equivalents that can be pooled across pyrethroids.The resulting normalized lc50s (geometric means for each species across pyrethroids) were analyzed using ssds.Based on tests with measured exposure concentrations, the fifth percentiles (hazard concentrations, hc5s) of the ssds were 4.8 hyalella equivalents for arthropods (36 species) and 256 hyalella equivalents for fish (24 species).Hc5 values are useful as effects metrics for screening-level risk assessments, and the full ssds can be integrated with estimated exposure distributions for higher-level risk characterization.The combined pyrethroid ssds provide a more taxonomically representative and statistically robust basis for risk characterization than data for the most sensitive single species or ssds based on data for a single pyrethroid alone, and are especially useful for pyrethroids that have been tested with smaller numbers of species.

Journal: Ecotoxicology (London, England) (2019)
Publication types: Journal Article
Case 301.

History a 38-year-old man who had been in a motor vehicle collision was referred to our institute.He was suspected of having left-sided pneumothorax.This necessitated intercostal drainage with a chest tube, which had been placed elsewhere prior to his arrival.Paraparesis was noted on the initial clinical examination, with adequately maintained vital signs, while the blood work-up revealed a mildly reduced hemoglobin level of 10.1 mg/d l (normal range, 13.8-17.2 mg/d l); however, the rest of the laboratory values were within normal limits (figs 1-5).The patient was then immediately referred for further evaluation with ct of the brain, cervical spine, and thorax.Thereafter, serial chest radiography was performed for follow-up.

Journal: Radiology (2022)
Publication types: Journal Article
The effect of a school-based fruit and vegetable promotion program on adolescents' fruit and vegetable consumption behavior in Turkey.

The aim of this study was to analyze the effect of a school-based f&v promotion program developed in line with the transtheoretical model (ttm) on the consumption behavior of middle school students.Design and methods the study was designed as semi-experimental research with pre-/post- and follow-up tests and a control group.It was conducted at a total of six middle schools in the district of fethiye/muğla, turkey.Three of the schools were selected with the random clustering method as an intervention group and the others as the control group.The f&v promotion program was executed in the intervention group for a period of 24 weeks.Results it was found in the 6th and 12th months after the intervention that the daily number of portions of fruits (p<.01) and vegetables (p<.01) consumed by the students in the intervention group was significantly more compared to the control group.The perception of the pros of f&v consumption and self-efficacy in the intervention group were higher than in the controls (p<.01).Conclusions the school-based f&v consumption promotion program was effective in increasing the number of portions of fruits and vegetables students consumed and in improving their behaviors in this regard.Application to practice the study indicates that the interventions described may be recommended to school nurses for use in their efforts to increase levels of f&v consumption.

Journal: Journal of pediatric nursing (2022)
Publication types: Journal Article