syedzayyan/paper_mill_benchmark huggingface dataset:
Mapping the complex causal mechanisms of drinking and driving behaviors among adolescents and young adults.

The proportion of motor vehicle crash fatalities involving alcohol-impaired drivers declined substantially between 1982 and 1997, but progress stopped after 1997.The systemic complexity of alcohol-impaired driving contributes to the persistence of this problem.This study aims to identify and map key feedback mechanisms that affect alcohol-impaired driving among adolescents and young adults in the u.s.Methods we apply the system dynamics approach to the problem of alcohol-impaired driving and bring a feedback perspective for understanding drivers and inhibitors of the problem.The causal loop diagram (i.e., map of dynamic hypotheses about the structure of the system producing observed behaviors over time) developed in this study is based on the output of two group model building sessions conducted with multidisciplinary subject-matter experts bolstered with extensive literature review.Results the causal loop diagram depicts diverse influences on youth impaired driving including parents, peers, policies, law enforcement, and the alcohol industry.Embedded in these feedback loops are the physical flow of youth between the categories of abstainers, drinkers who do not drive after drinking, and drinkers who drive after drinking.We identify key inertial factors, discuss how delay and feedback processes affect observed behaviors over time, and suggest strategies to reduce youth impaired driving.Conclusion this review presents the first causal loop diagram of alcohol-impaired driving among adolescents and it is a vital first step toward quantitative simulation modeling of the problem.Through continued research, this model could provide a powerful tool for understanding the systemic complexity of impaired driving among adolescents, and identifying effective prevention practices and policies to reduce youth impaired driving.

Journal: Social science & medicine (1982) (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, N.I.H., Intramural;Research Support, U.S. Gov't, P.H.S.;Review
Short-course antidepressant therapy reduces discontinuation syndrome while maintaining treatment efficacy in patients with refractory functional dyspepsia: A randomized controlled trial.

And objective long-course (lc) antidepressants for the treatment of disorders of gut-brain interaction, such as refractory functional dyspepsia (r fd), pose patients at risk of antidepressant discontinuation syndrome (ads).Short-course (sc) therapy of rapid-acting antidepressant may reduce discontinuation syndromes while maintaining efficacy for dyspeptic symptoms.However, the evidence-based research is lacking.This study aims to determine whether sc therapy with antidepressants could decrease the risk of ads with comparable treatment efficacy to lc therapy in r fd.Methods this randomized clinical trial with r fd patients was conducted at a tertiary hospital in china.Participants (n= 240) were randomly allocated to receive flupentixol-melitracen (fm) plus omeprazole therapy for 2 (sc group) or 4 (lc group) weeks, respectively.Scores for leeds dyspepsia questionnaire (ldq), generalized anxiety disorder-7 (gad-7) and patient health questionnaire-9 for depression (phq-9) were assessed at baseline and every 2 weeks, ending at 4 weeks after treatment.Ads was assessed after drug cessation.Medication possession ratio (mpr) for fm was calculated.Results the severity and incidence of ads of patients in sc group were significantly lower than those in lc group (0.60 ± 0.62 vs.1.71 ± 1.58 and 3.64 vs.39.45%; both p< 0.0001).The mpr values for fm were significantly higher in patients of sc group than in lc group (p< 0.0001).Scores for ldq, gad-7 and phq-9 decreased in patients of both groups, and the symptom improvement in sc group was comparable to that in lc group after treatment.Conclusions compared to 4-week fm therapy, the 2-week fm therapy reduces the risk of ads with non-inferior treatment efficacy in patients with r fd.Clinical trial registration clinical trials.gov, identifier nct05099913.

Journal: Frontiers in psychiatry (2022)
Publication types: Journal Article
A comparison of group prediction approaches in longitudinal discriminant analysis.

Longitudinal discriminant analysis (lo da) can be used to classify patients into prognostic groups based on their clinical history, which often involves longitudinal measurements of various clinically relevant markers.Patients' longitudinal data is first modelled using multivariate generalised linear mixed models, allowing markers of different types (e.g.Continuous, binary, counts) to be modelled simultaneously.We describe three approaches to calculating a patient's posterior group membership probabilities which have been outlined in previous studies, based on the marginal distribution of the longitudinal markers, conditional distribution and distribution of the random effects.Here we compare the three approaches, first using data from the mayo primary biliary cirrhosis study and then by way of simulation study to explore in which situations each of the three approaches is expected to give the best prediction.We demonstrate situations in which the marginal or random-effects approach perform well, but find that the conditional approach offers little extra information to the random-effects and marginal approaches.

Journal: Biometrical journal. Biometrische Zeitschrift (2018)
Publication types: Comparative Study;Journal Article;Research Support, Non-U.S. Gov't
TOP1 CAD-seq: A protocol to map catalytically engaged topoisomerase 1 in human cells.

Top1 cad-seq enables mapping of top1 sites of covalent engagement with dna.The procedure depends upon enrichment of dna-covalent adducts using chaotropic salts and immunoprecipitation with an antibody specific for top1.Here, we describe a step-by-step protocol compatible with illumina sequencing and bioinformatic pipeline for preliminary data analysis.Compared to other approaches for the genomic study of topoisomerases, top1 cad-seq provides information about active top1 engaged on the dna, taking advantage of low background due to absence of crosslinking.For complete details on the use and execution of this protocol, please refer to das et al.(2022).

Journal: STAR protocols (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Viable Properties of Natural Rubber/Halloysite Nanotubes Composites Affected by Various Silanes.

Natural rubber (nr) is incompatible with hydrophilic additives like halloysite nanotubes (hnt) due to their different polarity.The silane coupling agent is the ideal component to include in such a compound to solve this problem.Many types of silane are available for polymer composites depending on their functionalities.This work aimed to tune it to the composite based on nr and hnt.Four different silanes, namely bis[3- (triethoxysilyl)propyl]tetrasulfide (tespt), 3-aminopropyl triethoxysilane (aptes), n-[3-(trimethoxysilyl)propyl] ethylenediamine (aeaptms), and vinyltrimethoxysilane (vtms) were used.Here, the mechanical properties were used to assess the properties, paying close attention to how their reinforcement influenced their crystallization behavior after stretching.It was revealed that adding silane coupling agents greatly improved the composites' modulus, tensile strength, and tear strength.From the overall findings, aeaptms was viable for nr/hnt composites.This was in direct agreement with the interactions between nr and hnt that silanes had encouraged.The findings from stress-strain curves describing the crystallization of the composites are in good agreement with the findings from synchrotron wide-angle x-ray scattering (waxs).The corresponding silanes have substantially aided the strain-induced crystallization (sic) of composites.

Journal: Polymers (2022)
Publication types: Journal Article
Nonstoichiometric Cu0.6Ni0.4Co2O4Nanowires as an Anode Material for High Performance Lithium Storage.

Transition metal oxide is one of the most promising anode materials for lithium-ion batteries.Generally, the electrochemical property of transition metal oxides can be improved by optimizing their element components and controlling their nano-architecture.Herein, we designed nonstoichiometric cu0.6ni0.4co2o4nanowires for high performance lithium-ion storage.It is found that the specific capacity of cu0.6ni0.4co2o4nanowires remain 880 m ah g-1after 50 cycles, exhibiting much better electrochemical performance than cu co2o4and ni co2o4.After experiencing a large current charge and discharge state, the discharge capacity of cu0.6ni0.4co2o4nanowires recovers to 780 m ah g-1at 50 m a g-1, which is ca.88% of the initial capacity.The high electrochemical performance of cu0.6ni0.4co2o4nanowires is related to their better electronic conductivity and synergistic effect of metals.This work may provide a new strategy for the design of multicomponent transition metal oxides as anode materials for lithium-ion batteries.

Journal: Nanomaterials (Basel, Switzerland) (2020)
Publication types: Journal Article
DLIN: Deep Ladder Imputation Network.

Many efforts have been dedicated to addressing data loss in various domains.While task-specific solutions may eliminate the respective issue in certain applications, finding a generic method for missing data estimation is rather complex.In this regard, this article proposes a novel missing data imputation algorithm, which has supreme generalization ability for a vast variety of applications.Making use of both complete and incomplete parts of data, the proposed algorithm reduces the effect of missing ratio, which makes it suitable for situations with very high missing ratios.In addition, this feature enables model construction on incomplete training sets, which is rarely addressed in the literature.Moreover, the nonparametric nature of this new algorithm brings about supreme flexibility against all variations of missing values and data distribution.We incorporate the advantages of denoising autoencoders and ladder architecture into a novel formulation based on deep neural networks.To evaluate the proposed algorithm, a comparative study is performed using a number of reputable imputation techniques.In this process, real-world benchmark datasets from different domains are selected.On top of that, a real cyber-physical system is also evaluated to study the generalization ability of the proposed algorithm for distinct applications.To do so, we conduct studies based on three missing data mechanisms, namely: 1) missing completely at random; 2) missing at random; and 3) missing not at random.The attained results indicate the superiority of the proposed method in these experiments.

Journal: IEEE transactions on cybernetics (2022)
Publication types: Journal Article
Phosphodiesterases 5 Inhibitors and Erectile Dysfunction Recovery after Pelvic Surgery: Future Perspectives for New Drugs and New Formulations.

Phosphodiesterase 5 inhibitors (pde5i) represent the first-line treatment in the management of post-operative erectile dysfunction (ed) after pelvic oncological surgery.The aim of our study is to evaluate the available evidence on the efficacy of pde5is, including new formulations and penile rehabilitation post-pelvic surgery.Evidence acquisition a systematic review of the literature was performed until may 2020.The following databases were searched: scopus, medline and web of science.The me sh search was conducted by combining the following terms: 'erectile dysfunction', 'radical prostatectomy' 'pelvic' 'bladder' 'phosphodiesterase' inhibitors' 'avanafil' 'sildenafil' 'tadalafil' 'lodenafil' 'mirodenafil' 'udenafil' 'vardenafil' 'sublingual' 'orodispersible' 'penile' 'rehabilitation'.Evidence synthesis sildenafil, tadalafil, vardenafil and avanafil improve ef compared with placebo in men with all levels of ed severity after radical prostatectomy with good tolerability.No specific recommendations can be suggested regarding the superiority of a drug over the other.The optimal dose, continuous vs.On-demand and duration of treatment, is still under investigation.In vitro and preclinical studies suggest the possible role for lodenafil, mirodenafil and oro-dispersible formulations in patients undergoing oncological pelvic surgery.Few studies demonstrated the efficacy of udenafil in improving ed after rectal surgery or radical prostatectomy.Complete recovery of ef after surgery is still an unmet need in the field of penile rehabilitation after pelvic surgery.Conclusion pde5is have a crucial role in the management of post pelvic surgery of ed.New drugs and new formulations have shown excellent results in patients with ed; however, data in patients after surgery is still scarce.Further well designed rct should clarify the role of these new compounds and oro-dispersible formulations in the management of ed in patients undergoing pelvic surgery.

Journal: Current drug targets (2021)
Publication types: Journal Article;Systematic Review
Uroplakin II as a single marker for luminal versus basal molecular subtypes in muscle invasive urothelial carcinoma.

Bladder cancer is a heterogeneous disease classified into two broad molecular subtype categories, basal and luminal, with critical treatment and prognostic implications.Recent studies have shown the utility of immunohistochemistry in predicting bladder cancer molecular subtypes, with a two-marker approach using gata3 and ck5/6 showing over 80% reliability.In the current study, we calculated the accuracy of uroplakin ii (upii), a marker of urothelial differentiation, with different scores (0: 50%) to predict rna-based luminal versus basal subtypes in a cohort of muscle-invasive bladder cancer-received neoadjuvant chemotherapy followed by radical cystectomy.The 1% cutoff of the upii stain predicts the luminal subtype with the sensitivity and specificity of 95% and 56%, respectively.With a upii cutoff of 10%, the sensitivity and specificity were 93% and 81%, respectively, and with a upii cutoff of 50%, the sensitivity and specificity were 91% and 96%, respectively.The prediction performance of upii was better than either gata3 or ck5/6.There was no significant difference in prognoses between upii 0-2+ and upii 3+ patients in this cohort.The current study shows that evaluating the staining proportion score of upii can accurately predict basal and luminal subtypes of muscle-invasive bladder cancer.

Journal: Virchows Archiv : an international journal of pathology (2022)
Publication types: Journal Article
Discrete space-based route planning for rotary-wing UAV formation in urban environments.

The route planning problem for rotary-wing uav formation is studied in discrete urban environments.First, a discrete-space consensus algorithm (dsca) integrating asynchronous planning and grouping mechanism is developed to make the rotary-wing uavs converge to the desired formation.Then the dsca is combined with the improved rapidly-exploring random tree (irrt) algorithm to enable the rotary-wing uav formation to avoid the obstacles.Finally, the time information of waypoints is complemented by resolving the conflicts among multiple rotary-wing uavs, thus reducing the rotary-wing uavs' time gap of reaching the destinations.The proposed method extends the original consensus theory in the discrete space and for the obstacle avoidance issue.Also, it is valid in the route planning problem for rotary-wing uav formation considering the real urban environments.

Journal: ISA transactions (2022)
Publication types: Journal Article
Safety, efficacy and tumor mutational burden as a biomarker of overall survival benefit in chemo-refractory gastric cancer treated with toripalimab, a PD-1 antibody in phase Ib/II clinical trial NCT02915432.

High tumor mutational burden (tmb-h) is correlated with enhanced objective response rate (orr) and progression-free survival (pfs) for certain cancers receiving immunotherapy.This study aimed to investigate the safety and efficacy of toripalimab, a humanized programmed death-1 (pd-1) antibody, in advanced gastric cancer (agc), and the predictive survival benefit of tmb and pd-l1.Patients and methods we reported on the agc cohort of phase ib/ii trial evaluating the safety and activity of toripalimab in patients with agc, oesophageal squamous cell carcinoma, nasopharyngeal carcinoma and head and neck squamous cell carcinoma.In cohort 1, 58 chemo-refractory agc patients received toripalimab (3 mg/kg d1, q2w) as a monotherapy.In cohort 2, 18 chemotherapy-naive agc patients received toripalimab (360 mg d1, q3w) with oxaliplatin 130 mg/m2 qd, d1, capecitabine 1000 mg/m2 b.i.d., d1-d14, q3w as first-line treatment.Primary end point was orr.Biomarkers such as pd-l1 and tmb were evaluated for correlation with clinical efficacy.Results in cohort 1, the orr was 12.1% and the disease control rate (dcr) was 39.7%.Median pfs was 1.9 months and median os was 4.8 months.The tmb-h group showed significant superior os than the tmb-l group [14.6 versus 4.0 months, hr = 0.48 (96% ci 0.24-0.96), p = 0.038], while pd-l1 overexpression did not correlate with significant survival benefit.A 77.6% of patients experienced at least one treatment-related adverse event (trae), and 22.4% of patients experienced a grade 3 or higher trae.In cohort 2, the orr was 66.7% and the dcr was 88.9%.A 94.4% of patients experienced at least one trae and 38.9% of patients experienced grade 3 or higher traes.Conclusions toripalimab has demonstrated a manageable safety profile and promising antitumor activity in agc patients, especially in combination with xelox.High tmb may be a predictive marker for os of agc patients receiving toripalimab as a single agent.Trial registration clinical trials.gov nct02915432.

Journal: Annals of oncology : official journal of the European Society for Medical Oncology (2019)
Publication types: Clinical Trial, Phase I;Clinical Trial, Phase II;Journal Article;Research Support, Non-U.S. Gov't
Neurodevelopmental Outcomes Associated with Prefrontal Cortical Deoxygenation in Children with Fetal Alcohol Spectrum Disorders.

Relationships between neurodevelopmental functioning and hemodynamic changes in the prefrontal cortex (pfc) were contrasted between children with prenatal alcohol exposure (pae) and children who differed relative to their history of pae and the presence of other neurodevelopmental impairment.For all groups, deoxygenated hemoglobin (hbr) levels in the medial pfc area were negatively related to externalizing problems and levels in the medial and right lateral pfc were positively related to errors on a cognitive inhibition task.Hemodynamic changes in the medial and right lateral pfc of children with pae demonstrated stronger relationships to aspects of executive functioning relative to contrast groups.

Journal: Developmental neuropsychology (2020)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
A generalizable one health framework for the control of zoonotic diseases.

Effectively preventing and controlling zoonotic diseases requires a one health approach that involves collaboration across sectors responsible for human health, animal health (both domestic and wildlife), and the environment, as well as other partners.Here we describe the generalizable one health framework (gohf), a five-step framework that provides structure for using a one health approach in zoonotic disease programs being implemented at the local, sub-national, national, regional, or international level.Part of the framework is a toolkit that compiles existing resources and presents them following a stepwise schematic, allowing users to identify relevant resources as they are required.Coupled with recommendations for implementing a one health approach for zoonotic disease prevention and control in technical domains including laboratory, surveillance, preparedness and response, this framework can mobilize one health and thereby enhance and guide capacity building to combat zoonotic disease threats at the human-animal-environment interface.

Journal: Scientific reports (2022)
Publication types: Journal Article
Genome-Wide Association Mapping of Host-Plant Resistance to Soybean Aphid.

Soybean aphid [ matsumura (hemiptera: aphididae)] is the most damaging insect pest of soybean [ (l.) merr.] in the upper midwest of the united states and is primarily controlled by insecticides.Soybean aphid resistance (i.e., genes) has been documented in some soybean accessions but more sources of resistance are needed.Incorporation of the resistance into marketed varieties has also been slow.Genome-wide association mapping can aid in identifying resistant accessions by correlating phenotypic data with single nucleotide polymorphisms (snps) across a genome.Aphid population measures from 2366 soybean accessions were collected from published studies screening cultivated soybean () and wild soybean ( siebold & zucc.) with aphids exhibiting biotype 1, 2, or 3 characteristics.Genotypic data were obtained from the soy snp50k high-density genotyping array previously used to genotype the usda soybean germplasm collection.Significant associations between snps and soybean aphid counts were found on 18 of the 20 soybean chromosomes.Significant snps were found on chromosomes 7, 8, 13, and 16 with known genes.Snps were also significant on chromosomes 1, 2, 4 to 6, 9 to 12, 14, and 17 to 20 where genes have not yet been mapped, suggesting that many genes remain to be discovered.These snps can be used to determine accessions that are likely to have novel aphid resistance traits of value for breeding programs.

Journal: The plant genome (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Environmental chemicals and metabolic disruption in primary and secondary human parathyroid tumors.

The incidence of primary hyperparathyroidism has increased 300% in the united states in the past 30 years, and secondary hyperparathyroidism is almost universal in patients with end-stage renal disease.We assessed the presence of environmental chemicals in human hyperplastic parathyroid tumors as possible contributing factors to this increase.Methods cryopreserved hyperplastic parathyroid tumors and normal human parathyroids were analyzed by gas chromatography and liquid chromatography coupled to ultra-high-resolution mass spectrometry, bioinformatics, and biostatistics.Results detected environmental chemicals included polychlorinated biphenyls, polybrominated diphenyl ethers, dichloro-diphenyl-trichloroethane derivatives, and other insecticides.A total of 99% had p,p'-dichlorodiphenyldichloroethylene.More than 50% contained other environmental chemicals, and many classified as endocrine disruptors.Polychlorinated biphenyl-28 and polychlorinated biphenyl-49 levels correlated positively with parathyroid tumor mass.Polybrominated diphenyl ether-47 concentrations in tumors were inversely correlated with patients' serum calcium levels.Cellular metabolites in pathways of purine and pyrimidine synthesis and mitochondrial energy production were associated with tumor growth and with p,p'-dichlorodiphenyldichloroethylene in primary hyperparathyroidism tumors.In normal parathyroids, p,p'-dichlorodiphenyldichloroethylene , polychlorinated biphenyl-28, polychlorinated biphenyl-74, and polychlorinated biphenyl-153, but not p,p'-dichlorodiphenyldichloroethylene or polychlorinated biphenyl-49, were detected.Conclusion environmental chemicals are present in human parathyroid tumors and warrant detailed epidemiologic and mechanistic studies to test for causal links to the growth of human parathyroid tumors.

Journal: Surgery (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural