syedzayyan/paper_mill_benchmark huggingface dataset:
Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data.

Single-cell rna sequencing (sc rna-seq) distinguishes cell types, states and lineages within the context of heterogeneous tissues.However, current single-cell data cannot directly link cell clusters with specific phenotypes.Here we present scissor, a method that identifies cell subpopulations from single-cell data that are associated with a given phenotype.Scissor integrates phenotype-associated bulk expression data and single-cell data by first quantifying the similarity between each single cell and each bulk sample.It then optimizes a regression model on the correlation matrix with the sample phenotype to identify relevant subpopulations.Applied to a lung cancer sc rna-seq dataset, scissor identified subsets of cells associated with worse survival and with tp53 mutations.In melanoma, scissor discerned a t cell subpopulation with low pdcd1/ctla4 and high tcf7 expression associated with an immunotherapy response.Beyond cancer, scissor was effective in interpreting facioscapulohumeral muscular dystrophy and alzheimer's disease datasets.Scissor identifies biologically and clinically relevant cell subpopulations from single-cell assays by leveraging phenotype and bulk-omics datasets.

Journal: Nature biotechnology (2022)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
3D Molecular Imaging of Stratum Corneum by Mass Spectrometry Suggests Distinct Distribution of Cholesteryl Esters Compared to Other Skin Lipids.

The crucial barrier properties of the stratum corneum (sc) depend critically on the design and integrity of its layered molecular structure.However, analysis methods capable of spatially resolved molecular characterization of the sc are scarce and fraught with severe limitations, e.g., regarding molecular specificity or spatial resolution.Here, we used 3d time-of-flight secondary ion mass spectrometry to characterize the spatial distribution of skin lipids in corneocyte multilayer squams obtained by tape stripping.Depth profiles of specific skin lipids display an oscillatory behavior that is consistent with successive monitoring of individual lipid and corneocyte layers of the sc structure.Whereas the most common skin lipids, i.e., ceramides, c24:0 and c26:0 fatty acids and cholesteryl sulfate, are similarly organized, a distinct 3d distribution was observed for cholesteryl oleate, suggesting a different localization of cholesteryl esters compared to the lipid matrix separating the corneocyte layers.The possibility to monitor the composition and spatial distribution of endogenous lipids as well as active drug and cosmetic substances in individual lipid and corneocyte layers has the potential to provide important contributions to the basic understanding of barrier function and penetration in the sc.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article
Ameliorative effect of herbacetin against cyclophosphamide-induced nephrotoxicity in rats via attenuation of oxidative stress, inflammation, apoptosis and mitochondrial dysfunction.

Herbacetin (hbn) is a glycosylated flavonoid, which possesses numerous pharmacological properties.Cyclophosphamide (cyc) is a chemotherapeutic drug that adversely affects the kidneys.The present investigation aimed to evaluate the curative potential of hbn against cyc-induced nephrotoxicity.Sprague dawley rats (n= 48) were randomly divided into four groups: control (0.1% dmso + food), cyc (150 mg/kg b.wt.), cyc+hbn (150 + 40 mg/kg b.wt.), and hbn (40mg/kg b.wt.).Cyc treatment significantly decreased the activities of antioxidant enzymes such as catalase (cat), superoxide dismutase (sod), glutathione peroxidase (gpx), and glutathione reductase (gsr) while elevating the concentration of reactive oxygen species (ros) and malondialdehyde (mda).Treatment with hbn significantly recovered the activity of cat, sod, gpx, and gsr while reducing the concentrations of ros and mda.Moreover, an increase in the level of renal functional markers, including urea, creatinine, kidney injury molecule-1 (kim-1), and neutrophil gelatinase-associated lipocalin (ngal), and a decrease in creatinine clearance after cyc administration was recovered to control values by hbn treatment.Furthermore, hbn treatment normalized the increased levels of inflammatory markers such as nuclear factor kappa-b (nf-κb), tumor necrosis factor-α (tnf-α), interleukin-1β (il-1β), interleukin-6 (il-6), inducible nitric oxide synthase (i nos) and cyclooxygenase-2 (cox-2) after cyc administration.Besides, hbn administration increased the expression of anti-apoptotic markers (bcl-2) while decreasing the apoptotic markers (bax and caspase-3).Furthermore, hbn decreased the activities of tricarboxylic acid (tca) cycle enzymes (icdh, αkgdh, sdh, and mdh) as well as renal mitochondrial respiratory-chain complexes (i-iv) and repolarized mitochondrial membrane potential (δψm).additionally, hbn administration significantly protected against renal histological damage induced by cyc.In conclusion, cyc-induced toxicity was effectively ameliorated by the hbn administration.These results indicate that hbn might be considered as a potential protective agent against nephrotoxicity.The observed protection may be due to its antioxidant, anti-inflammatory, and anti-apoptotic potential.

Journal: Human & experimental toxicology (2022)
Publication types: Journal Article
Why do people with similar levels of internal control differ in their likelihood to commit fraud? Analysis of the moderating effect of perceived opportunity to commit fraud.

This research focuses on one of the three components of the fraud triangle, namely opportunity, and empirically tests the tendency to commit fraud.The perceived opportunity to commit fraud can be considered in terms of temptation and obstacles.This research employs concepts from cognitive psychology, i.e., desire and motivation for action, which affect people's decision-making processes when presented with an opportunity to commit fraud.Questionnaires were used to analyze the tendency to commit fraud.First, dispositional differences among people differing in self-control were observed, which may influence the likelihood of fraudulent behavior.That is, low self-control mediates the relationship between self-regard and fraud tendency.Second, strong relationships of both personal disposition and self-efficacy with the tendency to commit fraud were revealed; high self-efficacy enhances the tendency to commit fraud.This research offers a new psychological perspective on fraud opportunity, and showing for the first time that fraud can be reduced not only by improved internal control and external supervision, as suggested in previous studies, but also by changing people's perceptions of fraud opportunity, given the fallibility of both internal control and external supervision.

Journal: Frontiers in psychology (2022)
Publication types: Journal Article
Physical-stochastic continuous-time identification of a forced Duffing oscillator.

Despite the simplicity of the duffing oscillator, its dynamical behaviour is extremely rich.Hence, the duffing equations are used to describe the dynamic behaviour of many real-world nonlinear systems for a wide range of frequency bands and amplitude of the excitation signal in basic sciences and engineering.For example, the duffing oscillator has been successfully used to model a variety of physical processes such as stiffening springs, beam buckling, nonlinear electronic circuits, superconducting josephson parametric amplifiers, and ionisation waves in plasmas etc.Therefore, the identification of the duffing oscillator model/parameters directly from the measured input-output data is a topic of active research in many scientific fields in this paper, we use the concept of stochastic differential equations (sdes) to identify a model of the duffing oscillator.Sde-based grey-box models allow us to capture the underlying mathematical structure describing the physics of the system (e.g.The original duffing equations) using the drift term and explicitly handling of model uncertainty (or the process noise) using the diffusion term whereas the measurement uncertainty is modelled using the measurement noise term respectively.In this paper, we propose a slight variation of the maximum likelihood estimation framework used for the identification of sdes based grey-box models yielding improved performance for long-term predictions.The proposed framework is combined with an iterative residual analysis to develop a grey-box model of the forced duffing oscillator.The benchmark data from the so-called brussels "silverbox system", which is an electrical circuit mimicking the forced duffing oscillator dynamics is used for the identification purpose.Finally, the identified model performance (the simulation errors) is compared with the existing results available in the literature.

Journal: ISA transactions (2022)
Publication types: Journal Article
Cognitive correlates of autism spectrum disorder symptoms.

Due to the diverse behavioral presentation of autism spectrum disorder (asd), identifying asd subtypes using patterns of cognitive abilities has become an important point of research.Some previous studies on cognitive profiles in asd suggest that the discrepancy between verbal intelligence quotient (viq) and performance iq (piq) is associated with asd symptoms, while others have pointed to viq as the critical predictor.Given that viq is a component of the viq-piq discrepancy, it was unclear which was most driving these associations.This study tested whether viq, piq, or the viq-piq discrepancy was most associated with asd symptoms in children and adults with asd (n = 527).Using data from the autism brain imaging data exchange (abide), we tested the independent contribution of each iq index and their discrepancy to asd symptom severity using multiple linear regressions predicting asd symptoms.Viq was most associated with lower symptom severity as measured by the autism diagnostic observation schedule (ados) total score, and when viq was included in models predicting asd symptoms, associations with piq and iq discrepancy were not significant.An association between viq and asd communication symptoms drove the association with asd symptom severity.These results suggest that associations between asd communication symptoms and iq discrepancy or piq reported in prior studies likely resulted from variance shared with viq.Subtyping asd on the basis of viq should be a point of future research, as it may allow for the development of more personalized approaches to intervention.Lay summary: previous research on links between autism severity and verbal and nonverbal intelligence has produced mixed results.Our study examined whether verbal intelligence, nonverbal intelligence, or the discrepancy between the two was most related to autism symptoms.We found that higher verbal intelligence was most associated with less severe autism communication symptoms.Given the relevance of verbal intelligence in predicting autism symptom severity, subtyping autism on the basis of verbal intelligence could lead to more personalized treatments.

Journal: Autism research : official journal of the International Society for Autism Research (2021)
Publication types: Journal Article
Current and prospective control strategies of influenza A virus in swine.

Influenza a viruses (iav) are endemic pathogens of significant concern in humans and multiple keystone livestock species.Widespread morbidity in swine herds negatively impacts animal welfare standards and economic performance whilst human iav pandemics have emerged from pigs on multiple occasions.To combat the rising prevalence of swine iav there must be effective control strategies available.Main body the most basic form of iav control on swine farms is through good animal husbandry practices and high animal welfare standards.To control inter-herd transmission, biosecurity considerations such as quarantining of pigs and implementing robust health and safety systems for workers help to reduce the likelihood of swine iav becoming endemic.Closely complementing the physical on-farm practices are iav surveillance programs.Epidemiological data is critical in understanding regional distribution and variation to assist in determining an appropriate response to outbreaks and understanding the nature of historical swine iav epidemics and zoonoses.Medical intervention in pigs is restricted to vaccination, a measure fraught with the intrinsic difficulties of mounting an immune response against a highly mutable virus.It is the best available tool for controlling iav in swine but is far from being a perfect solution due to its unreliable efficacy and association with an enhanced respiratory disease.Because iav generally has low mortality rates there is a reticence in the uptake of vaccination.Novel genetic technologies could be a complementary strategy for iav control in pigs that confers broad-acting resistance.Transgenic pigs with iav resistance are useful as models, however the complexity of these reaching the consumer market limits them to research models.More promising are gene-editing approaches to prevent viral exploitation of host proteins and modern vaccine technologies that surpass those currently available.Conclusion using the suite of iav control measures that are available for pigs effectively we can improve the economic productivity of pig farming whilst improving on-farm animal welfare standards and avoid facing the extensive social and financial costs of a pandemic.Fighting 'flu in pigs will help mitigate the very real threat of a human pandemic emerging, increase security of the global food system and lead to healthier pigs.

Journal: Porcine health management (2021)
Publication types: Journal Article;Review
Astaxanthin prevents mitochondrial impairment in the dopaminergic SH-SY5Y cell line exposed to glutamate-mediated excitotoxicity: Role for the Nrf2/HO-1/CO-BR axis.

Mitochondrial dysfunction has been viewed in several diseases, including neurological disorders.In the glutamate (glu)-mediated excitotoxicity, it has been described mitochondrial impairment, disrupted redox environment, and increased rates of cell death in the affected brain areas.Astaxanthin (ast) is a potent antioxidant and anti-inflammatory xanthophyll that also promotes beneficial mitochondria-related effects in brain cells.However, it is not completely clear how ast would be able to promote mitochondrial protection in those cell types.Thus, we investigated here how ast would protect mitochondria in the dopaminergic sh-sy5y cell line exposed to glu.Ast was administrated to the cells at 1-40 μm for 24 h prior to the exposure to glu at 80 m m for additional 24 h.Ast prevented the glu-induced impairment in the activity of the complexes i and v, the loss in mitochondrial membrane potential (mmp), and the decline in the synthesis of atp.Ast also induced an antioxidant effect in the membranes of mitochondria obtained from the glu-treated sh-sy5y cells.Inhibition of the enzyme heme oxygenase-1 (ho-1) or silencing of the transcription factor nuclear factor erythroid 2-related factor 2 (nrf2) suppressed the ast-promoted cellular and mitochondrial protection.Either tricarbonyldichlororuthenium(ii) dimer (corm-2, a source of carbon monoxide - co) or bilirubin (br), that are products of the ho-1-biliverdin reductase (bvr) axis, blocked some of the effects caused by glu in the sh-sy5y cells.Overall, our data demonstrate that ast prevented mitochondrial dysfunction by a mechanism related to the nrf2/ho-1 axis in glu-challenged cells.

Journal: European journal of pharmacology (2021)
Publication types: Journal Article
Airborne particle dispersion by high flow nasal oxygen: An experimental and CFD analysis.

High flow nasal oxygen (hfno) therapy offers a proven means of delivering respiratory support to critically ill patients suffering from viral illness such as covid-19.However, the therapy has the potential to modify aerosol generation and dispersion patterns during exhalation and thereby put healthcare workers at increased risk of disease transmission.Fundamentally, a gap exists in the literature with regards to the effect of the therapy on the fluid dynamics of the exhalation jet which is essential in understanding the dispersion of aerosols and hence quantifying the disease transmission risk posed by the therapy.In this paper, a multi-faceted approach was taken to studying the aerosol-laden exhalation jet.Schlieren imaging was used to visualise the flow field for a range of expiratory activities for three healthy human volunteers receiving hfno therapy at flow rates of 0-60 l/min.A rans turbulence model was implemented using the cfd software open foam and used to perform a parametric study on the influence of exhalation velocity and duration on the dispersion patterns of non-evaporating droplets in a room environment.A dramatic increase in the turbulence of the exhalation jet was observed when hfno was applied.Quantitative analysis indicated that the mean exhalation velocity was increased by 2.2-3.9 and 2.3-3 times that for unassisted breathing and coughing, respectively.A 1-2 second increase was found in the exhalation duration.The cfd model showed that small droplets (10-40 μm) were most greatly affected, where a 1 m/s increase in velocity and 1 s increase in duration caused an 80% increase in axial travel distance.

Journal: PloS one (2022)
Publication types: Journal Article
Energy Status Differentially Modifies Feeding Behavior and POMCARCNeuron Activity After Acute Treadmill Exercise in Untrained Mice.

Emerging evidence identifies a potent role for aerobic exercise to modulate activity of neurons involved in regulating appetite; however, these studies produce conflicting results.These discrepancies may be, in part, due to methodological differences, including differences in exercise intensity and pre-exercise energy status.Consequently, the current study utilized a translational, well-controlled, within-subject, treadmill exercise protocol to investigate the differential effects of energy status and exercise intensity on post-exercise feeding behavior and appetite-controlling neurons in the hypothalamus.Mature, untrained male mice were exposed to acute sedentary, low (10m/min), moderate (14m/min), and high (18m/min) intensity treadmill exercise in a randomized crossover design.Fed and 10-hour-fasted mice were used, and food intake was monitored 48h.Post-exercise.Immunohistochemical detection of c fos was performed 1-hour post-exercise to determine changes in hypothalamic npy/ag rp, pomc, tyrosine hydroxylase, and sim1-expressing neuron activity concurrent with changes in food intake.Additionally, stains for p stat3tyr705and p erkthr202/tyr204were performed to detect exercise-mediated changes in intracellular signaling.Results demonstrated that fasted high intensity exercise suppressed food intake compared to sedentary trials, which was concurrent with increased anorexigenic pomc neuron activity.Conversely, fed mice experienced augmented post-exercise food intake, with no effects on pomc neuron activity.Regardless of pre-exercise energy status, tyrosine hydroxylase and sim1 neuron activity in the paraventricular nucleus was elevated, as well as npy/ag rp neuron activity in the arcuate nucleus.Notably, these neuronal changes were independent from changes in p stat3tyr705and p erkthr202/tyr204signaling.Overall, these results suggest fasted high intensity exercise may be beneficial for suppressing food intake, possibly due to hypothalamic pomc neuron excitation.Furthermore, this study identifies a novel role for pre-exercise energy status to differentially modify post-exercise feeding behavior and hypothalamic neuron activity, which may explain the inconsistent results from studies investigating exercise as a weight loss intervention.

Journal: Frontiers in endocrinology (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Lower Motor Neuron Abnormality in Chronic Cervical Spinal Cord Injury: Implications for Nerve Transfer Surgery.

Nerve transfer surgery (nt) constitutes an exciting option to improve upper limb functions in chronic spinal cord injury (sci), but requires intact sublesional lower motor neuron (lmn) health.The purpose of this study was to characterize patterns of lmn abnormality in nerve-muscle groups that are the potential recipients of nt, using a standardized electrodiagnostic examination, in individuals with chronic sci (injury duration >2 years, injury levels c4-t1).The lmn abnormality was determined using a semihierarchical approach, combining the amplitude compound muscle action potential (cmap) and abnormal spontaneous activity on needle electromyography (emg).Ten participants (46 potential recipient muscles) were included (median age, 42.5 years; six males and four females; median duration from injury, 15.5 years).A high frequency of lmn abnormality was observed (87%), although there was substantial variation within and between individuals.No statistically significant discordance was observed between lmn abnormality on cmap and emg (p= 0.24), however, 50% of muscles with normal cmap demonstrated abnormal spontaneous activity.The high frequency of lmn abnormality in recipient nerve-muscle groups has implications to candidate selection for nt surgery in chronic sci and supports the important role of the pre-operative electrodiagnostic examination.Our results further support the inclusion of both cmap and needle emg parameters for characterization of lmn health.Although the number of nerve-muscle groups with normal lmn health was small (13%), this underscores the neurophysiological potential of some patients with chronic injuries to benefit from nt surgery.

Journal: Journal of neurotrauma (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Survey of parental awareness of obstructive sleep apnea among children in Guangdong province, South China.

S childhood obstructive sleep apnea (osa) is underdiagnosed.The aim of this study was to assess the awareness level of osa among parents in the general population of guangdong province of south china.Methods this descriptive epidemiological study was conducted from july to november 2019 using an anonymous questionnaire that evaluated the knowledge of osa-related symptoms and complications.Exclusion criteria included age under 18 years, refusal to fill out the questionnaire, and a linguistic barrier.Results a total of 1123 respondents participated in the survey.Among them, 530 (47.2%) respondents were aware of childhood osa.The most common source of information about childhood osa was the internet (49.9%).On multivariate analysis, the respondents obtained higher scores if they were mothers (b: -0.105, 95% confidence interval [ci]: -0.153,-0.057), lived in an urban area (b: -0.077, 95% ci: -0.125,-0.28), and knew about childhood osa previously (b: -0.55, 95% ci:-0.598,-0.502).Conclusion parents demonstrated limited awareness of osa complications.Innovative educational campaigns must be organized to inform medical practitioners and the general public about this disease and raise awareness about its complications.The effectiveness of the ongoing health education campaigns to increase awareness should be monitored by examining the temporal trends in public knowledge of childhood sleep apnea.

Journal: Auris, nasus, larynx (2021)
Publication types: Journal Article