syedzayyan/paper_mill_benchmark huggingface dataset:
Risk of drug-induced interstitial lung disease in hospitalised patients: a nested case-control study.

Introduction information on drug-induced interstitial lung disease (dild) is limited due to its low incidence.This study investigated the frequencies of drug categories with potential risk in patients developing dild during hospitalisation and analysed the risk of developing dild associated with each of these drugs.Methods using a japanese national inpatient database, we identified patients without interstitial pneumonia on admission who developed dild and required corticosteroid therapy during hospitalisation from july 2010 to march 2016.We conducted a nested case-control study; four controls from the entire non-dild patient cohort were matched to each dild case on age, sex, main diagnosis, admission year and hospital.We defined 42 classified categories of drugs with 216 generic names as drugs with potential risk of dild, and we identified the use of these drugs during hospitalisation for each patient.We analysed the association between each drug category and dild development using conditional logistic regression analyses.Results we retrospectively identified 2342 patients who developed dild.After one-to-four case-control matching, 1541 case patients were matched with 5677 control patients.Six drug categories were significantly associated with the increased occurrence of dild.These included epidermal growth factor receptor inhibitors (or: 16.84, 95% ci 9.32 to 30.41) and class iii antiarrhythmic drugs (or: 7.01, 95% ci 3.86 to 12.73).Statins were associated with reduced risk of dild (or: 0.68, 95% ci 0.50 to 0.92).Conclusions we demonstrated significant associations between various drug categories and dild.Our findings provide useful information on drug categories with potential risk to help physicians prevent and treat dild.

Journal: Thorax (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
How Coalescing Bubbles Depart from a Wall.

Bubble evolution plays a fundamental role in boiling and gas-evolving electrochemical systems.One key stage is bubble departure, which is traditionally considered to be buoyancy-driven.However, conventional understanding cannot provide the full physical picture, especially for departure events with small bubble sizes commonly observed in water splitting and high heat flux boiling experiments.Here, we report a new regime of bubble departure owing to the coalescence of two bubbles, where the departure diameter can be much smaller than the conventional buoyancy limit.We show the significant reduction of the bubble base area due to the dynamics of the three-phase contact line during coalescence, which promotes bubble departure.More importantly, combining buoyancy-driven and coalescence-induced bubble departure modes, we demonstrate a unified relationship between the departure diameter and nucleation site density.By elucidating how coalescing bubbles depart from a wall, our work provides design guidelines for energy systems which can largely benefit from efficient bubble departure.

Journal: Langmuir : the ACS journal of surfaces and colloids (2022)
Publication types: Journal Article
The Role of Inhibitory Interneurons in Circuit Assembly and Refinement Across Sensory Cortices.

Sensory information is transduced into electrical signals in the periphery by specialized sensory organs, which relay this information to the thalamus and subsequently to cortical primary sensory areas.In the cortex, microcircuits constituted by interconnected pyramidal cells and inhibitory interneurons, distributed throughout the cortical column, form the basic processing units of sensory information underlying sensation.In the mouse, these circuits mature shortly after birth.In the first postnatal week cortical activity is characterized by highly synchronized spontaneous activity.While by the second postnatal week, spontaneous activity desynchronizes and sensory influx increases drastically upon eye opening, as well as with the onset of hearing and active whisking.This influx of sensory stimuli is fundamental for the maturation of functional properties and connectivity in neurons allocated to sensory cortices.In the subsequent developmental period, spanning the first five postnatal weeks, sensory circuits are malleable in response to sensory stimulation in the so-called critical periods.During these critical periods, which vary in timing and duration across sensory areas, perturbations in sensory experience can alter cortical connectivity, leading to long-lasting modifications in sensory processing.The recent advent of intersectional genetics,in vivocalcium imaging and single cell transcriptomics has aided the identification of circuit components in emergent networks.Multiple studies in recent years have sought a better understanding of how genetically-defined neuronal subtypes regulate circuit plasticity and maturation during development.In this review, we discuss the current literature focused on postnatal development and critical periods in the primary auditory (a1), visual (v1), and somatosensory (s1) cortices.We compare the developmental trajectory among the three sensory areas with a particular emphasis on interneuron function and the role of inhibitory circuits in cortical development and function.

Journal: Frontiers in neural circuits (2022)
Publication types: Journal Article;Review;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Extensive diversity of RNA viruses in ticks revealed by metagenomics in northeastern China.

Ticks act as important vectors of infectious agents, and several emerging tick-borne viruses have recently been identified to be associated with human diseases in northeastern china.However, little is known about the tick virome in northeastern china.Methods ticks collected from april 2020 to july 2021 were pooled for metagenomic analysis to investigate the virome diversity in northeastern china.Results in total, 22 rna viruses were identified, including four each in the nairoviridae and phenuiviridae families, three each in the flaviviridae, rhabdoviridae, and solemoviridae families, two in the chuviridae family, and one each in the partitiviridae, tombusviridae families and an unclassified virus.Of these, eight viruses were of novel species, belonging to the nairoviridae (ji'an nairovirus and yichun nairovirus), phenuiviridae (mudanjiang phlebovirus), rhabdoviridae (tahe rhabdovirus 1-3), chuviridae (yichun mivirus), and tombusviridae (yichun tombus-like virus) families, and five members were established human pathogens, including alongshan virus, tick-borne encephalitis virus, songling virus, beiji nairovirus, and nuomin virus.I.Persulcatus ticks had significant higher number of viral species than h.Japonica, h.Concinna, and d.Silvarum ticks.Significant differences in tick viromes were observed among daxing'an, xiaoxing'an and changbai mountains.Conclusions these findings showed an extensive diversity of rna viruses in ticks in northeastern china, revealing potential public health threats from the emerging tick-borne viruses.Further studies are needed to explain the natural circulation and pathogenicity of these viruses.

Journal: PLoS neglected tropical diseases (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Charting roadmaps towards novel and safe synergistic immunotherapy combinations.

Checkpoint inhibitor-based cancer immunotherapy is often combined in the clinic with other immunotherapy strategies, targeted therapies, chemotherapy or standard-of-care treatments to achieve superior therapeutic efficacy.The large number of immunotherapy combinations that are currently undergoing clinical testing necessitate the establishment of faithful criteria to prioritize optimal combinations with evidence of synergy, to determine their safety and optimal sequence of administration and to identify biomarkers of therapy resistance and response.In this review, we focus on recent developments in immunotherapy combinations and reflect on how combinations should be optimized to maximize the impact of immunotherapy in clinical oncology.

Journal: Nature cancer (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Impact of Oxygen Concentration on Metabolic Profile of Human Placenta-Derived Mesenchymal Stem Cells As Determined by Chemical Isotope Labeling LC-MS.

The placenta resides in a physiologically low oxygen microenvironment of the body.Hypoxia induces a wide range of stem cell cellular activities.Here, we report a workflow for exploring the role of physiological (hypoxic, 5% oxygen) and original cell culture (normoxic, 21% oxygen) oxygen concentrations in regulating the metabolic status of human placenta-derived mesenchymal stem cells (h pmscs).The general biological characteristics of h pmscs were assessed via a variety of approaches such as cell counts, flow cytometry and differentiation study.A sensitive13c/12c-dansyl labeling liquid chromatography-mass spectrometry (lc-ms) method targeting the amine/phenol submetabolome was used for metabolic profiling of the cell and corresponding culture supernatant.Multivariate and univariate statistical analyses were used to analyze the metabolomics data.H pmscs cultured in hypoxia display smaller size, higher proliferation, greater differentiation ability and no difference in immunophenotype.Overall, 2987 and 2860 peak pairs or metabolites were detected and quantified in h pmscs and culture supernatant, respectively.Approximately 86.0% of cellular metabolites and 84.3% of culture supernatant peak pairs were identified using a dansyl standard library or matched to metabolite structures using accurate mass search against human metabolome libraries.The orthogonal partial least-squares discriminant analysis (opls-da) showed a clear separation between the hypoxic group and the normoxic group.Ten metabolites from cells and six metabolites from culture supernatant were identified as potential biomarkers of hypoxia.This study demonstrated that chemical isotope labeling lc-ms can be used to reveal the role of oxygen in the regulation of h pmsc metabolism, whereby physiological oxygen concentrations may promote arginine and proline metabolism, pantothenate and coenzyme a (co a) biosynthesis, and alanine, aspartate and glutamate metabolism.

Journal: Journal of proteome research (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19.

On march 23 2020, the uk enacted an intensive, nationwide lockdown to mitigate transmission of covid-19.As restrictions began to ease, more localized interventions were used to target resurgences in transmission.Understanding the spatial scale of networks of human interaction, and how these networks change over time, is critical to targeting interventions at the most at-risk areas without unnecessarily restricting areas at low risk of resurgence.We use detailed human mobility data aggregated from facebook users to determine how the spatially-explicit network of movements changed before and during the lockdown period, in response to the easing of restrictions, and to the introduction of locally-targeted interventions.We also apply community detection techniques to the weighted, directed network of movements to identify geographically-explicit movement communities and measure the evolution of these community structures through time.We found that the mobility network became more sparse and the number of mobility communities decreased under the national lockdown, a change that disproportionately affected long distance connections central to the mobility network.We also found that the community structure of areas in which locally-targeted interventions were implemented following epidemic resurgence did not show reorganization of community structure but did show small decreases in indicators of travel outside of local areas.We propose that communities detected using facebook or other mobility data be used to assess the impact of spatially-targeted restrictions and may inform policymakers about the spatial extent of human movement patterns in the uk.These data are available in near real-time, allowing quantification of changes in the distribution of the population across the uk, as well as changes in travel patterns to inform our understanding of the impact of geographically-targeted interventions.

Journal: PLoS computational biology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Targeting the MITF/APAF-1 axis as salvage therapy for MAPK inhibitors in resistant melanoma.

Melanoma is a deadly form of cancer characterized by remarkable therapy resistance.Analyzing the transcriptome of mapk inhibitor sensitive- and resistant-melanoma, we discovered that apaf-1 is negatively regulated by mitf in resistant tumors.This study identifies the mitf/apaf-1 axis as a molecular driver of mapk inhibitor resistance.A drug-repositioning screen identified quinacrine and methylbenzethonium as potent activators of apoptosis in a context that mimics drug resistance mediated by apaf-1 inactivation.The compounds showed anti-tumor activity in in vitro and in vivo models, linked to suppression of mitf function.Both drugs profoundly sensitize melanoma cells to mapk inhibitors, regulating key signaling networks in melanoma, including the mitf/apaf-1 axis.Significant activity of the two compounds in inhibiting specific epigenetic modulators of mitf/apaf-1 expression, such as histone deacetylases, was observed.In summary, we demonstrate that targeting the mitf/apaf-1 axis may overcome resistance and could be exploited as a potential therapeutic approach to treat resistant melanoma.

Journal: Cell reports (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Stable, reproducible, and binder-free gold/copper core-shell nanostructures for high-sensitive non-enzymatic glucose detection.

The core-shell non-enzymatic glucose sensors are generally fabricated by chemical synthesis approaches followed by a binder-based immobilization process.Here, we have introduced a new approach to directly synthesis the core-shell of au@cu and its au@cux o oxides on an fto electrode for non-enzymatic glucose detection.Physical vapor deposition of au thin film followed by thermal annealing has been used to fabricate au nanocores on the electrode.The cu shells have been deposited selectively on the au cores using an electrodeposition method.Additionally, au@cu2o and au@cu o have been synthesized via post thermal annealing of the au@cu electrode.This binder-free and selective-growing approach has the merit of high electrooxidation activity owing to improving electron transfer ability and providing more active sites on the surface.Electrochemical measurements indicate the superior activity of the au@cu2o electrode for glucose oxidation.The high sensitivity of 1601 μacm-2m m-1and a low detection limit of 0.6 μm are achieved for the superior electrode.Additionally, the sensor indicates remarkable reproducibility and supplies accurate results for glucose detection in human serums.Moreover, this synthesis approach can be used for fast, highly controllable and precise fabrication of many core-shell structures by adjusting the electrochemical deposition and thermal treatment parameters.

Journal: Scientific reports (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Redox-Active Lewis Pairs Yield Diradicaloids and Enable Modular Control of the Diradical Character.

Stable metal-free diradicaloids are fascinating compounds, typically based on covalent polycyclic or nitrogen-containing π-conjugated frameworks.Unfortunately, their preparation and the modulation of their diradical character require substantial synthetic efforts.The present work introduces a synthetic approach to diradicaloids by the ease and modularity of lewis pair formation.Binding redox-active bis(catecholato)silane lewis acids to ditopic tetraoxolene lewis bases yields adducts with varying spin ground states.Computational analyses disclose that the diradical character increases with the electron donor ability of the catechols and the electron accepting ability of the tetraoxolene.Hence, this protocol grants access to diradicaloids with rationally adjustable diradical character of high potential for numerous applications in a single step.

Journal: Chemistry (Weinheim an der Bergstrasse, Germany) (2023)
Publication types: Journal Article
The epidemiology of apnoea of prematurity.

What is known and objective many premature infants less than 37 weeks gestational age (ga), and almost all infants less than 28 weeks ga, will experience apnoea of prematurity (aop)-a cessation of respiration for 20 or more seconds (or less than 20 s if accompanied by other signs).Because the treatment options for aop are so limited, we explore its epidemiology, with the ultimate hope of learning how to decrease its incidence.Comment although aop usually resolves with maturation of the respiratory system, many short- and long-term negative effects are correlated statistically with aop (although direct causality has not been established).The primary risk factor for aop is preterm birth, but delivery technique, genetics, socioeconomic status, racial disparities and other influences are suspected to be involved.Anaemia, asthma and gastric reflux have also been associated with preterm birth, but the relationship with aop is unclear.The postulated associations and the strength of the evidence are briefly reviewed and discussed.What is new and conclusion attempts to elucidate the epidemiology of apnoea of prematurity have been challenging.Studies of aop are hampered in part by challenges in monitoring the condition, the interplay of multiple comorbidities in preterm neonates and lack of expert consensus definitions.However, since the primary risk factor is preterm birth, efforts to decrease the prevalence of preterm birth would have a positive secondary effect on the prevalence of aop.Until then, better pharmacotherapeutic options are needed.

Journal: Journal of clinical pharmacy and therapeutics (2022)
Publication types: Journal Article
Brokerage System for Integration of LrWPAN Technologies.

The prevalent demand for remote data sharing and connectivity has catalysed the development of many wireless network technologies.However, low-power and low-rate wireless network technologies have emerged as the preferred choice (due to cheap procurement and maintenance cost, efficiency, and adaptability).Currently, these groups of wireless networks are adopted in homes, health, and business sectors.The increase in existing wsns has resulted in the incompatibility of wireless network protocols and poses a problem that results in high acquisition or maintenance costs, increased complexity, reliability inadequacies in some instances, lack of uniformity within similar standards, and high energy consumption.To address this problem, we develop a novel machine-to-machine software-based brokerage application (known as jos net) for interoperability and integration between bluetooth le, zigbee, and thread wireless network technologies.Jos net allows one network protocol to exchange data packets or commands with each other.In this paper, we present a novel working network brokerage model for a one-to-one network protocol to communication (e.g., from zigbee to bluetooth) or one-to-many network protocol communication (e.g., from bluetooth to zigbee, thread, etc.) to securely send messages in a large-scale routing process for short or long-range connections.We also present a large-scale implementation of jos net using a routing table for large areas.The results show an industry standard performance for end-to-end latency time and throughput.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Predictive Models of Gas/Particulate Partition Coefficients (KP) for Polycyclic Aromatic Hydrocarbons and Their Oxygen/Nitrogen Derivatives.

Polycyclic aromatic hydrocarbons (pahs) and their oxygen/nitrogen derivatives released into the atmosphere can alternate between a gas phase and a particulate phase, further affecting their environmental behavior and fate.The gas/particulate partition coefficient (kp) is generally used to characterize such partitioning equilibrium.In this study, the correlation between log kp of fifty pah derivatives and their n-octanol/air partition coefficient (log koa) was first analyzed, yielding a strong linear correlation (r2 = 0.801).Then, gaussian 09 software was used to calculate quantum chemical descriptors of all chemicals at m062x/6-311+g (d,p) level.Both stepwise multiple linear regression (mlr) and support vector machine (svm) methods were used to develop the quantitative structure-property relationship (qspr) prediction models of log kp.They yield better statistical performance (r2 > 0.847, rmse < 0.584) than the log koa model.Simulation external validation and cross validation were further used to characterize the fitting performance, predictive ability, and robustness of the models.The mechanism analysis shows intermolecular dispersion interaction and hydrogen bonding as the main factors to dominate the distribution of pah derivatives between the gas phase and particulate phase.The developed models can be used to predict log kp values of other pah derivatives in the application domain, providing basic data for their ecological risk assessment.

Journal: Molecules (Basel, Switzerland) (2022)
Publication types: Journal Article
Bovine serum miR-21 expression affected by mastitis.

The expression levels of circulating micro rnas (mi rnas) can be affected by disease.The mi rna released from cells within exosomes can act as a remote communication tool and can participate in inflammatory response regulation.Therefore, circulating mi rna has the potential to be an indicator of local disease.The objective of this study was to investigate the serum level of bovine mastitis-related mi rnas.We found that mi r-16 expression in serum was affected by hemolysis.The expression levels of mi r-21 in serum were increased significantly in cows with mastitis compared with unaffected controls; however, the expression levels of mi r-146a, mi r-155, mi r-222 and mi r-383 in cows with mastitis were unchanged.We further verified the upregulation of mi r-21 in the serum of cows with mastitis using a digital pcr system.Although the sensitivity and specificity of mi r-21 in the serum to detect bovine mastitis was inferior to mi rna biomarkers in the milk, the significant increase of mi r-21 in serum may reflect the impact of local inflammation on the systemic reaction.

Journal: Research in veterinary science (2021)
Publication types: Journal Article