syedzayyan/paper_mill_benchmark huggingface dataset:
Modelling the mechanics of exploration in larval Drosophila.

The drosophila larva executes a stereotypical exploratory routine that appears to consist of stochastic alternation between straight peristaltic crawling and reorientation events through lateral bending.We present a model of larval mechanics for axial and transverse motion over a planar substrate, and use it to develop a simple, reflexive neuromuscular model from physical principles.The mechanical model represents the midline of the larva as a set of point masses which interact with each other via damped translational and torsional springs, and with the environment via sliding friction forces.The neuromuscular model consists of: 1.Segmentally localised reflexes that amplify axial compression in order to counteract frictive energy losses, and 2.Long-range mutual inhibition between reflexes in distant segments, enabling overall motion of the model larva relative to its substrate.In the absence of damping and driving, the mechanical model produces axial travelling waves, lateral oscillations, and unpredictable, chaotic deformations.The neuromuscular model counteracts friction to recover these motion patterns, giving rise to forward and backward peristalsis in addition to turning.Our model produces spontaneous exploration, even though the nervous system has no intrinsic pattern generating or decision making ability, and neither senses nor drives bending motions.Ultimately, our model suggests a novel view of larval exploration as a deterministic superdiffusion process which is mechanistically grounded in the chaotic mechanics of the body.We discuss how this may provide new interpretations for existing observations at the level of tissue-scale activity patterns and neural circuitry, and provide some experimental predictions that would test the extent to which the mechanisms we present translate to the real larva.

Journal: PLoS computational biology (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Clopidogrel plus aspirin prevents early neurologic deterioration and improves 6-month outcome in patients with acute large artery atherosclerosis stroke.

S to evaluate the effects of treatments with clopidogrel plus aspirin (dual therapy) on early neurological deterioration (end) and outcomes at 6 months in patients with acute large artery atherosclerosis (laa) stroke.Methods a total of 574 patients with laa stroke were randomly assigned to receive either dual therapy or aspirin alone (monotherapy).The primary outcome was end.Secondary outcomes included recurrent ischemic stroke (ris) and outcomes at 6 months.Results the prevalence of end and ris was lower in patients on dual therapy than in those on monotherapy during the 30 days.At 6 months, dual therapy improved outcomes among older patients and those with symptomatic stenosis in the posterior circulation and basilar artery.Conclusion clopidogrel plus aspirin is superior to aspirin alone for reducing end and ris within 30 days and improves outcomes in certain subgroups at 6 months.

Journal: Clinical and applied thrombosis/hemostasis : official journal of the International Academy of Clinical and Applied Thrombosis/Hemostasis (2015)
Publication types: Journal Article;Randomized Controlled Trial
Ecological efficiency evaluation and driving factor analysis of the coupling coordination of the logistics industry and manufacturing industry.

The coupling coordination of the logistics industry and manufacturing industry is conducive to the sustainable development of logistics and manufacturing and the stability of sustainable supply chain.The logistics and manufacturing industries are not only the basic industries that support social development, but also the industries with high carbon emissions.This paper constructs the measurement system of coupling coordinating ecological efficiency of two industries based on carbon emission constraints and finds out the driving factors affecting ecological efficiency, which is of great significance to the low-carbon coordinated development of the two industries in the future.Firstly, this paper classifies the carbon emissions from the logistics industry and manufacturing industry as undesirable outputs and evaluates the ecological efficiency of the logistics industry (lee) and manufacturing industry (mee) in the three urban agglomerations from 2006 to 2019 by using the unexpected slacks-based measure (sbm) model.Secondly, the coupling coordination method is used to analyze the coupling coordination scheduling of industrial ecological efficiency (mlcc).Finally, the spatial econometric model is used to analyze the driving factors of the mlcc.The results show that during the study period, the coupling coordination of the three urban agglomerations continued to grow, the pearl river delta coupling coordination is the highest, the yangtze river delta coupling coordination grew the fastest, and the beijing-tianjin-hebei coupling coordination grew slightly slower.The development during the 13th five-year plan period is obviously faster than that during the 11th and 12th five-year plan.The empirical analysis results of spatial econometrics show that the driving factors have an impact on the coupling coordination degree of the three urban agglomerations, but the significance of each factor is different.The driving factors have significant spatial heterogeneity.The three urban agglomerations should formulate low-carbon industry development policies in line with local development according to the actual situation of each region and local conditions.

Journal: Environmental science and pollution research international (2022)
Publication types: Journal Article
#RheumTwitter - the Rise of Social Media in Rheumatology: Research, Collaboration, Education, and Engagement.

Social media broadly refers to an internet-based platform that allows for the online publication of content that is shared across a virtual community or network.Over recent years, there has been growing utilization of social media in the medical community.The field of rheumatology is no different.Social media allows for the sharing of information among rheumatologists, which can be useful in online education, disseminating research findings, forming new networks of collaborators, and discussing the latest advances in the field.However, there are several challenges facing clinicians using social media.As such, regulatory bodies have produced advisory codes of conduct to ensure better awareness concerning the appropriate use of social media among clinicians.In addition, clinicians (even those who do not use social media) need to be mindful of the fact that many patients will use these online platforms to find information, and with this comes the risk of false information.In this review, we highlight the benefits and challenges facing rheumatologists in relation to the world of social media.

Journal: Rheumatology and immunology research (2022)
Publication types: Journal Article
Correlation of Anti-SalmonellaAntibodies Between Serum and Saliva Samples Collected From Finisher Pigs.

Saliva samples obtained by using absorptive devices, can provide an alternative diagnostic matrix to serum for monitoring disease status in pigs.The aim of this study was to investigate the correlation of anti-salmonellaantibodies between serum and saliva samples collected from pigs.Twenty individual paired serum and saliva samples were collected from a single farm.Anti-salmonella ig g was detected in individual serum samples using a commercial salmonella elisa kit, validated for sera.The same kit was used with a protocol modified by extending incubation time and increasing temperature to test individual saliva samples.Anti-salmonella ig g antibodies in pig saliva were always detected at a lower level than in the matching serum samples.A correlation (rho= 0.66;p= 0.002) and a moderate agreement (k> 0.62p= 0.003) was found between individual salmonella ig g in serum and saliva samples.Both correlation and the agreement levels are moderate.The size of this investigation was small, and further studies are necessary to further confirm these findings.The results of this work provide some evidence that saliva samples have the potential to be used for the diagnosis of salmonellainfection in pig farms.

Journal: Frontiers in veterinary science (2019)
Publication types: Journal Article
Autophagy Induced by Toll-like Receptor Ligands Regulates Antigen Extraction and Presentation by B Cells.

The engagement of b cells with surface-tethered antigens triggers the formation of an immune synapse (is), where the local secretion of lysosomes can facilitate antigen uptake.Lysosomes intersect with other intracellular processes, such as toll-like receptor (tlr) signaling and autophagy coordinating immune responses.However, the crosstalk between these processes and antigen presentation remains unclear.Here, we show that tlr stimulation induces autophagy in b cells and decreases their capacity to extract and present immobilized antigens.We reveal that tlr stimulation restricts lysosome repositioning to the is by triggering autophagy-dependent degradation of gef-h1, a rho gtp exchange factor required for stable lysosome recruitment at the synaptic membrane.Gef-h1 degradation is not observed in b cells that lack αv integrins and are deficient in tlr-induced autophagy.Accordingly, these cells show efficient antigen extraction in the presence of tlr stimulation, confirming the role of tlr-induced autophagy in limiting antigen extraction.Overall, our results suggest that resources associated with autophagy regulate tlr and bcr-dependent functions, which can finetune antigen uptake by b cells.This work helps to understand the mechanisms by which b cells are activated by surface-tethered antigens in contexts of subjacent inflammation before antigen recognition, such as sepsis.

Journal: Cells (2022)
Publication types: Journal Article
Increase and Change in the Pattern of Antibiotic Use in Serbia (2010-2019).

The aim of this study was to determine and describe trends in antibiotics utilization in serbia over a ten-year period.Data were retrieved from publicly available annual reports (2010-2019).The results were expressed as defined daily dose (ddd) per 1000 inhabitants per day (did).All calculations were performed using the ddd values for the 2020 anatomical therapeutic chemical/defined daily dose (atc/ddd) version for each year of the study, to account for the ddd changes during the study period.Antibiotics were classified using the who access, watch, reserve (awa re) classification.Total utilization of antibacterials for systemic use increased from 17.25 did in 2010 to 28.65 did in 2019.A statistically significant increasing trend in the use of the watch category antibiotics was observed.A tendency towards use of broad-spectrum antibiotics, apparent by a statistically significant increase in the rate of utilization of broad-spectrum macrolides, quinolones and third-generation cephalosporins vs.Narrow-spectrum ones, as well as a significant increasing trend in the use of quinolones was identified.Total antibiotic utilization was found to be well above the european average.Several specific problem areas were identified, which requires further efforts to improve antibiotic prescribing.The present study provides the information needed to facilitate antibiotic stewardship in serbia further and proposes specific interventions to optimize antibiotic use in serbia.

Journal: Antibiotics (Basel, Switzerland) (2021)
Publication types: Journal Article
circ_0001821 Contributes to the Development of Cutaneous Squamous Cell Carcinoma by Regulating MicroRNA-148a-3p/EGFR Axis and Activating Phosphatidylinositol 3-Kinase/Akt Pathway.

Circular rnas (circ rnas) are implicated in diverse human cancers.However, the effects of circ rnas on cutaneous squamous cell carcinoma (cscc) are barely known.We focused on the function of circ_0001821 in cscc.Quantitative reverse transcription pcr was performed for the expression of circ_0001821, mi r-148a-3p, and epidermal growth factor receptor (egfr).Cell counting kit-8 assay and colony formation assay were conducted to evaluate cell viability and colony formation ability.Flow cytometry analysis was adopted to analyze cell cycle and apoptosis.A transwell assay was employed to detect cell motility.Dual-luciferase reporter assay, rna immunoprecipitation assay, and rna pulldown assay were utilized to verify the interaction between mi r-148a-3p and circ_0001821 or egfr.A western blot assay was conducted for protein levels.Murine xenograft model assay was used to explore the function of circ_0001821in vivo.Circ_0001821 level was increased in cscc tissues and cells.Circ_0001821 knockdown restrained cell viability, colony formation, cell cycle processes, and metastasis, and facilitated cell apoptosisin vitro, and restrained tumor growthin vivo.For mechanism analysis, circ_0001821 directly targeted mi r-148a-3p to elevate egfr expression.Downregulation of mi r-148a-3p weakened the impacts of circ_0001821 deficiency on cscc malignant phenotypes.Moreover, mi r-148a-3p overexpression inhibited the malignant phenotypes of cscc cells, with egfr elevation abrogating the effects.In addition, circ_0001821 knockdown blocked the activation of the phosphatidylinositol 3-kinase (pi3k)/akt pathway.Circ_0001821 functioned as a tumor promoter in cscc via regulating the mi r-148a-3p/egfr axis and pi3k/akt pathway.

Journal: Molecular and cellular biology (2022)
Publication types: Journal Article
The effects of Lombard perturbation on speech intelligibility in noise for normal hearing and cochlear implant listeners.

Natural compensation of speech production in challenging listening environments is referred to as the lombard effect (le).The resulting acoustic differences between neutral and lombard speech have been shown to provide intelligibility benefits for normal hearing (nh) and cochlear implant (ci) listeners alike.Motivated by this outcome, three le perturbation approaches consisting of pitch, duration, formant, intensity, and spectral contour modifications were designed specifically for ci listeners to combat speech-in-noise performance deficits.Experiment 1 analyzed the effects of loudness, quality, and distortion of approaches on speech intelligibility with and without formant-shifting.Significant improvements of +9.4% were observed in ci listeners without the formant-shifting approach at +5 d b signal-to-noise ratio (snr) large-crowd-noise (lcn) when loudness was controlled, however, performance was found to be significantly lower for nh listeners.Experiment 2 evaluated the non-formant-shifting approach with additional spectral contour and high pass filtering to reduce spectral smearing and decrease distortion observed in experiment 1.This resulted in significant intelligibility benefits of +30.2% for nh and +21.2% for ci listeners at 0 and +5 d b snr lcn, respectively.These results suggest that le perturbation may be useful as front-end speech modification approaches to improve intelligibility for ci users in noise.

Journal: The Journal of the Acoustical Society of America (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Risk Factors Predicting Cellulitis Diagnosis in a Prospective Cohort Undergoing Dermatology Consultation in the Emergency Department.

Cellulitis is an infection of the skin and skin-associated structures with many clinical mimickers known collectively as pseudocellulitis.Dermatology or infectious disease consultation is considered the gold standard for diagnosis.We evaluated a prospective cohort of adult patients presenting to the emergency department (ed) with concern for lower extremity cellulitis who received dermatology consultation with conferral of a final diagnosis.Possible risk factors independently associated with cellulitis diagnosis (p<.1) were included in a logistic regression model for prediction of cellulitis diagnosis.Factors having odds ratios with a confidence interval excluding 1 were identified as significant independent predictors.The study identified factors that should be considered in evaluation of patients with suspected uncomplicated lower extremity cellulitis.

Journal: Cutis (2022)
Publication types: Journal Article
Visible and near-infrared spectroscopy and deep learning application for the qualitative and quantitative investigation of nitrogen status in cotton leaves.

Leaf nitrogen concentration (lnc) is a critical indicator of crop nutrient status.In this study, the feasibility of using visible and near-infrared spectroscopy combined with deep learning to estimate lnc in cotton leaves was explored.The samples were collected from cotton's whole growth cycle, and the spectra were from different measurement environments.The random frog (rf), weighted partial least squares regression (wpls), and saliency map were used for characteristic wavelength selection.Qualitative models (partial least squares discriminant analysis (pls-da), support vector machine for classification (svc), convolutional neural network classification (cnnc) and quantitative models (partial least squares regression (plsr), support vector machine for regression (svr), convolutional neural network regression (cnnr)) were established based on the full spectra and characteristic wavelengths.Satisfactory results were obtained by models based on cnn.The classification accuracy of leaves in three different lnc ranges was up to 83.34%, and the root mean square error of prediction (rmsep) of quantitative prediction models of cotton leaves was as low as 3.36.In addition, the identification of cotton leaves based on the predicted lnc also achieved good results.These results indicated that the nitrogen content of cotton leaves could be effectively detected by deep learning and visible and near-infrared spectroscopy, which has great potential for real-world application.

Journal: Frontiers in plant science (2022)
Publication types: Journal Article
Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments.

As sequencing technology improves and the cost of metagenome sequencing decreases, the number of sequenced environments increases.These metagenomes provide a wealth of data in the form of annotated and unannotated genes.The role of multidrug resistance efflux pumps (mdreps) is the removal of antibiotics, biocides and toxic metabolites created during aromatic hydrocarbon metabolism.Due to their naturally occurring role in hydrocarbon metabolism and their role in biocide tolerance, mdrep genes are of particular importance for the protection of pipeline assets.However, the heterogeneity of mdrep genes creates a challenge during annotation and detection.Here we use a selection of primers designed to target mdreps in six pure species and apply them to publicly available metagenomes associated with oil and gas environments.Usingin silico pcr with relaxed primer binding conditions we probed the metagenomes of a shale reservoir, a heavy oil tailings pond, a civil wastewater treatment, two marine sediments exposed to hydrocarbons following the deepwater horizon oil spill and a non-exposed marine sediment to assess the presence and abundance of mdrep genes.Through relaxed primer binding conditions duringin silico pcr, the prevalence of mdreps was determined.The percentage of nucleotide sequences identified by the mdrep primers was partially augmented by exposure to hydrocarbons in marine sediment and in shale reservoir compared to hydrocarbon-free marine sediments while tailings ponds and wastewater had the highest percentages.We believe this approach lays the groundwork for a supervised method of identifying poorly conserved genes within metagenomes.

Journal: Microbiology (Reading, England) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Engaging with EPIO, a digital pain self-management program: a qualitative study.

Chronic pain conditions entail significant personal and societal burdens and improved outreach of evidence-based pain self-management programs are needed.Digital cognitive-behavioral self-management interventions have shown promise.However, evidence is still scarce and several challenges with such interventions for chronic pain exist.Exploring patients' experiences and engagement with digital interventions may be an essential step towards developing meaningful digital self-management interventions for those living with chronic pain.Objectives this study aimed to gain insight into the experiences of people with chronic pain when engaging with epio, an application (app)-based cognitive-behavioral pain self-management intervention program.Methods participants (n = 50) living with chronic pain received access to the epio intervention in a feasibility pilot-study for 3 months.During this time, all participants received a follow-up phone call at 2-3 weeks, and a subsample (n = 15) also participated in individual semi-structured interviews after 3 months.A qualitative design was used and thematic analysis was employed aiming to capture participants' experiences when engaging with the epio intervention program.Results findings identifying program-related experiences and engagement were organized into three main topics, each with three sub-themes: (1) engaging with epio; motivation to learn, fostering joy and enthusiasm, and helpful reminders and personalization, (2) coping with pain in everyday life; awareness, practice and using epio in everyday life, and (3) the value of engaging with the epio program; epio - a friend, making peace with the presence of pain, and fostering communication and social support.Conclusions this qualitative study explored participants' experiences and engagement with epio, a digital self-management intervention program for people living with chronic pain.Findings identified valued aspects related to motivation for engagement, and showed how such a program may be incorporated into daily life, and encourage a sense of acceptance, social support and relatedness.The findings highlight vital components for facilitating digital program engagement and use in support of self-management for people living with chronic pain.Trial registration clinical trials.gov nct03705104 .

Journal: BMC health services research (2022)
Publication types: Journal Article
CYP1A1, VEGFA and Adipokine Responses of Human Adipocytes Co-exposed to PCB126 and Hypoxia.

It is increasingly recognized that hypoxia may develop in adipose tissue as its mass expands.Adipose tissue is also the main reservoir of lipophilic pollutants, including polychlorinated biphenyls (pcbs).Both hypoxia and pcbs have been shown to alter adipose tissue functions.The signaling pathways induced by hypoxia and pollutants may crosstalk, as they share a common transcription factor: aryl hydrocarbon receptor nuclear translocator (arnt).Whether hypoxia and pcbs crosstalk and affect adipokine secretion in human adipocytes remains to be explored.Using primary human adipocytes acutely co-exposed to different levels of hypoxia (24 h) and pcb126 (48 h), we observed that hypoxia significantly inhibits the pcb126 induction of cytochrome p450 (cyp1a1) transcription in a dose-response manner, and that acriflavine (acf)-an hif1α inhibitor-partially restores the pcb126 induction of cyp1a1 under hypoxia.On the other hand, exposure to pcb126 did not affect the transcription of the vascular endothelial growth factor-a (vegfa) under hypoxia.Exposure to hypoxia increased leptin and interleukin-6 (il-6), and decreased adiponectin levels dose-dependently, while pcb126 increased il-6 and il-8 secretion in a dose-dependent manner.Co-exposure to pcb126 and hypoxia did not alter the adipokine secretion pattern observed under hypoxia and pcb126 exposure alone.In conclusion, our results indicate that (1) hypoxia inhibits pcb126-induced cyp1a1 expression at least partly through arnt-dependent means, suggesting that hypoxia could affect pcb metabolism and toxicity in adipose tissue, and (2) hypoxia and pcb126 affect leptin, adiponectin, il-6 and il-8 secretion differently, with no apparent crosstalk between the two factors.

Journal: Cells (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't