syedzayyan/paper_mill_benchmark huggingface dataset:
Cancer Health Economics Research: The Future Is Now.

The goals of the "future of cancer health economics research" virtual conference were to identify challenges, gaps, and unmet needs for conducting cancer health economics research; and develop suggestions and ideas to address these challenges and to support the development of this field.The conference involved multiple presentations and panels featuring several key themes, including data limitations and fragmentation; improving research methods; role and impacts of structural and policy factors; and the transdisciplinary nature of this field.The conference also highlighted emerging areas such as communicating results with nonresearchers; balancing data accessibility and data security; emphasizing the needs of trainees; and including health equity as a focus in cancer health economics research.From this conference, it is clear that cancer health economics research can have substantial impacts on how cancer care is delivered and how related health-care policies are developed and implemented.To support further growth and development, this field should continue to welcome individuals from multiple disciplines and enhance opportunities for training in economics and in analytic methods and perspectives from across the social and clinical sciences.Researchers should continue to engage with diverse stakeholders throughout the cancer community, building collaborations and focusing on the goal of improving health and well-being.

Journal: Journal of the National Cancer Institute. Monographs (2022)
Publication types: Journal Article
A risk signature of three autophagy-related genes for predicting lower grade glioma survival is associated with tumor immune microenvironment.

Treatment for lower-grade gliomas (lgg) has been challenging.Though emerging approaches such as immunotherapy is promising, it is still faced with immune tolerance, an obstacle that may be overcome by targeting autophagy-related (atg) genes.After identifying three differentially expressed atg genes (ripk2, mul1 and cxcr4), we constructed an atg gene risk signature by kaplan-meier, univariate cox regression, least absolute shrinkage and selection operator regression and multivariate cox regression, followed by internal and external validation using k-m and roc analysis.Since gene set enrichment analysis (gsea) suggested that the signature was strongly associated with immune cell functions, cibersort, lm22 matrix and pearson correlation were further performed, showing that the risk signature was significantly correlated with immune cell infiltration and immune checkpoint genes.In conclusion, we identified and independently validated an atg gene risk signature for lgg patients, as well as discovering its significant association with lgg immune microenvironment.

Journal: Genomics (2021)
Publication types: Journal Article
Selected Spatiotemporal and Joint Angle Parameters in Normal Gait and Nordic Walking with Classical and Mechatronic Poles in Aspects of Sex Differences.

Introduction the aim of this study was to compare selected spatiotemporal parameters and changes in the range of motion in the joints of lower and upper limbs during normal gait and during nordic walking performed with classical and mechatronic poles of females and males.Methods the study involved 19 physical education students (11 males and 8 females).The myo motion research motion analysis system was used to collect gait kinematic variables.The subject task was to cover a 100 m distance in a straight line with three types of gait: gait without poles, gait with classical poles, and gait with mechatronic poles at preferred velocity.Parameters were measured both on the right (rt) and on the left side (lt) of the body.The data was analyzed using two-way repeated measures anova with the between-subject factor "sex." friedman's test was used when necessary.Results the most significant differences in spatiotemporal parameters between males and females were revealed in gait with the classical and mechatronic pole (stance phase lt and rt, load response lt and rt, single support lt and rt, preswing lt and rt, swing phase lt and rt, double stance lt and rt, and step length lt), the least in gait without a pole (stance phase rt, load response lt, single support lt, preswing rt, and swing phase rt); whereas, the most significant differences in kinematic parameters were revealed in gait without poles (shoulder rotation rt, wrist radial-ulnar lt, hip flexion-extension lt and rt, knee flexion-extension lt and rt, ankle inversion-eversion lt, and ankle abduction-adduction lt and rt), the least in gait with mechatronic poles (knee flexion-extension lt and rt, ankle dorsiflexion-plantarflexion lt, ankle inversion-eversion lt, and ankle abduction-adduction lt and rt).Conclusion statistical analysis revealed many differences in spatiotemporal and kinematic parameters in normal gait, as well as in gait with the classical and mechatronic poles, which allows the conclusion that the gait of females and males should be analyzed separately.

Journal: BioMed research international (2022)
Publication types: Journal Article
Hybrid_DBP: Prediction of DNA-binding proteins using hybrid features and convolutional neural networks.

Dna-binding proteins (dbp) play an essential role in the genetics and evolution of organisms.A particular dna sequence could provide underlying therapeutic benefits for hereditary diseases and cancers.Studying these proteins can timely and effectively understand their mechanistic analysis and play a particular function in disease prevention and treatment.The limitation of identifying dna-binding protein members from the sequence database is time-consuming, costly, and ineffective.Therefore, efficient methods for improving dbp classification are crucial to disease research.In this paper, we developed a novel predictor hybrid _dbp, which identified potential dbp by using hybrid features and convolutional neural networks.The method combines two feature selection methods, mono di kgap and kmer, and then used mrmd2.0 to remove redundant features.According to the results, 94% of dbp were correctly recognized, and the accuracy of the independent test set reached 91.2%.This means hybrid_ dbp can become a useful prediction tool for predicting dbp.

Journal: Frontiers in pharmacology (2022)
Publication types: Journal Article
Lateral double magnetic tunnel junction device with orthogonal polarizer for high-performance magnetoresistive memory.

Magnetic tunnel junction (mtj)-based memory devices have larger switching delay and energy consumption, compared to cache or dynamic random access memory.In order to broaden the applications of the magnetoresistive random access memory, reducing the switching time and energy consumption of the mtj is required.Here, a novel lateral double mtj with an orthogonal polarizer is proposed.The proposed device consists of three ferromagnetic regions: the first pinned region (pr1) with perpendicular magnetic anisotropy (pma), a free region (fr) with pma, and the second pinned region (pr2) with in-plane magnetic anisotropy (ima).Pr1 and pr2 are placed on top of the oxide barrier, which separates them from the fr, comprising a lateral double mtj structure.The current pulse through pr2 helps to perturb the magnetization of the fr.Since the angle between pr2 and fr is 90°, the initial torque increases significantly, decreasing switching delay by 4.02 times and energy-delay product by 7.23 times.It is also shown, that the area of the access transistor can be reduced by approximately 10%, while maintaining the same energy-delay product and reducing gate rc delay.

Journal: Scientific reports (2022)
Publication types: Journal Article
Brain injuries: health care capacity and policy in Georgia.

Over 90% of morbidity and mortality associated with traumatic brain injury (tbi) occurs in low- and middle-income countries.Lack of reliable, high-quality data regarding tbi prevention and care hinders the ability to reduce tbi burden.We sought to identify current tbi data collection practices and capacity in georgia, focusing on pre-hospital, hospital, and rehabilitation treatment.Methods the eight level i and two level ii trauma hospitals in georgia with the highest number of tbi admissions in 2017 were selected for study.A semi-structured survey about various aspects of tbi care was designed and semi-structured interviews of healthcare providers treating tbi patients (e.g.Neurologists, neurosurgeons) were conducted based on this survey.Results pre-hospital triage protocols were not routinely used to match patient treatment needs with hospital capacity.All hospitals provided specialist care for tbi 24 hours/day.Mri was available at only three (30%) centers, and in-hospital rehabilitation units were available in only one (10%).No center used a defined protocol for treating tbi patients and no national protocol exists.Conclusions even among the largest, most highly specialized hospitals in georgia, tbi care varies in terms of diagnostic and treatment protocols.While tbi specialists are available, diagnostic equipment often is not.Gaps in pre-hospital coordination and access to rehabilitation services exist and provide areas of focus for future investment in reducing tbi burden.

Journal: Journal of injury & violence research (2021)
Publication types: Journal Article
Complex Relation Between Diet and Phospholipid Fatty Acids in Children With Cystic Fibrosis.

S altered total plasma n-6 and n-3 fatty acids are common in cystic fibrosis (cf).Whether alterations extend to plasma phosphatidylcholine (pc) and phosphatidylethanolamine (pe) and are explained by diet is unclear.The present study was to describe the dietary intake of a large group of children with cf and to determine whether dietary fat composition explains differences in plasma pc and pe fatty acids between children with and without cf.Methods dietary intake was assessed using a food frequency questionnaire.Venous blood was collected.Plasma pc and pe were separately analyzed for fatty acids.Results children with cf, n = 74, consumed more calories and fat (g/day and % energy), with significantly more saturates mainly from dairy foods and less polyunsaturates including linoleic acid (la), arachidonic acid (ara), eicosapentaenoic acid (epa), and docosahexaenoic acid (dha) (% fat) than reference children, n = 71.A subset of children with cf, not differing in dietary intake from the larger group, had significantly lower la and dha, but higher epa in plasma pc and had higher la and lower ara and dha in plasma pe, compared to a subset of reference children.In both groups, la intake and la in plasma pc and pe were not associated.Epa and dha intakes were positively associated with epa and dha, respectively, in plasma pc, but not pe, in reference children only.Conclusions the fatty acid composition of plasma pc and pe is altered in cf.Fatty acid differences between children with and without cf are inconsistent between pc and pe and are not explained by dietary fat.

Journal: Journal of pediatric gastroenterology and nutrition (2017)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
In vitro multi-enzymatic cascades using recombinant lysates of E. coli: an emerging biocatalysis platform.

In recent years, cell-free extracts (or lysates) have (re-)emerged as a third route to the traditional options of isolated or whole-cell biocatalysts.Advances in molecular biology and genetic engineering enable facile production of recombinant cell-free extracts, where endogenous enzymes are enriched with heterologous activities.These inexpensive preparations may be used to catalyse multistep enzymatic reactions without the constraints of cell toxicity and the cell membrane or the cost and complexity associated with production of isolated biocatalysts.Herein, we present an overview of the key advancements in cell-free synthetic biology that have led to the emergence of cell-free extracts as a promising biocatalysis platform.

Journal: Biophysical reviews (2020)
Publication types: Journal Article;Review
Cross-regulatory circuits linking inflammation, high-fat diet, and the circadian clock.

Mammalian physiology resonates with the daily changes in the external environment, allowing processes such as rest-activity cycles, metabolism, and body temperature to synchronize with daily changes in the surroundings.Studies have identified the molecular underpinnings of robust oscillations in gene expression occurring over the 24-h day, but how acute or chronic perturbations modulate gene expression rhythms, physiology, and behavior is still relatively unknown.In this issue of genes & development, hong and colleagues (pp.1367-1379) studied how acute and chronic inflammation interacts with the circadian clock.They found that nf-κb signaling can modify chromatin states and modulate expression of genes in the core clock network as well as circadian locomotor behavior.Interestingly, a high-fat diet (hfd) fed to mice also triggers this inflammation pathway, suggesting that cross-regulatory circuits link inflammation, hfd, and the circadian clock.

Journal: Genes & development (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review;Comment
Steric and Electronic Effects in Gold N-Heterocyclic Carbene Complexes Revealed by Computational Analysis.

A computational analysis of a series of cationic and neutral gold imidazolylidene and benzimidizolylidene complexes is reported.The bond dissociation energies of the various ligands in the complexes calculated at the pbe0-d3/def2-tzvp level of theory increase with increasing ligand volume, except for those of complexes containing t-butyl-substituted ligands, which are anomalously low particularly for the benzimidazolylidene species.Atoms in molecules studies show the presence of a variety of weak intramolecular interactions, characterised by the presence of bond critical points with a range of different properties.Energy decomposition analysis and calculation of electrostatic surface potentials indicate that some interactions are weakly attractive dispersion-type interactions, while others are repulsive.The octanol/water partition coefficients (log p values) were calculated as a measure of the lipophilicities of the complexes and were found to increase with increasing volume.

Journal: ChemistryOpen (2019)
Publication types: Journal Article
How Old Do I Look? Exploring the Facial Cues of Age in a Tasked Eye-Tracking Study.

Importance:this is the first eye-tracking study to use a tasked age estimation paradigm to explore the facial cues of age as seen by casual observers.objectives:determine where observers gaze on faces when tasked with estimating an individual's age.design, setting, and participants:this was a prospective controlled experiment, which took place at an academic tertiary referral center.In total, 220 casual observers (80 untasked, 140 tasked) viewed frontal facial images of women while an infrared eye-tracking monitor recorded their eye movements and fixations in real time.main outcomes and measures:multivariate hotelling's analysis followed by planned posthypothesis testing was used to compare fixation durations for predefined regions of interest, including the central triangle, upper face, midface, lower face, and neck between tasked and untasked observers.results:a total of 80 observers (mean age 23.6 years, 53% female) successfully completed the first untasked eye-tracking experiment.A total of 140 observers (mean age 26.1 years, 60% female) successfully completed the second age estimation experiment.On multivariate analysis, there were significant differences in the distribution of attention between observers in the two experiments (t2= 99.70;f(5,2084) = 19.9012,p< 0.0001).On planned posthypothesis testing, observers attended significantly more to the lower third of the face (0.20 s,p< 0.0001, 95% confidence interval (ci) 0.14-0.27 s) and neck (0.05 s,p= 0.0074, 95% ci 0.01-0.08 s) and less to the upper third of the face (-0.27 s,p< 0.0001, 95% ci -0.40 to -0.14 s) when tasked.There was no significant difference in time spent on the whole face in the two experiments, suggesting that peripheral elements such as hair color or jewelry did not significantly influence gaze patterns.conclusions and relevance:humans form judgments about others every day of their lives, and age perception colors their every interaction.To our knowledge, this study is the first to use eye tracking to investigate facial cues of age.The results showed that when tasked with estimating age, casual observer visual attention was shifted toward the lower face when compared with those who were untasked.These data inform our understanding of facial age perception and potential areas to target for facial rejuvenation.level of evidence:na.

Journal: Facial plastic surgery & aesthetic medicine (2020)
Publication types: Journal Article
Design, development and deployment of a web-based patient registry for rare genetic lipid disorders.

Rare genetic lipid disorders comprise all the monogenic disorders of lipoprotein metabolism with the exception of heterozygous familial hypercholesterolaemia (fh).The creation and maintenance of patient registries is critical for disease monitoring, improving clinical best practice, facilitating research and enabling the development of novel therapeutics, but very few disease-specific rare genetic lipid disorder registries currently exist.Our aim was to design, develop and deploy a web-based patient registry for rare genetic lipid disorders.The rare genetic lipid disorders registry is based on the fh australasia network (fhan) registry, which has been operating since 2015.The rare genetic lipid disorders registry was deployed utilising the open-source rare disease registry framework (rdrf), which enables the efficient customisation and sustainable deployment of web-based registries.The registry has been designed to capture longitudinal data on 13 rare genetic lipid disorders, with the ability to add more if required in the future.Recruitment of volunteers into the registry is currently through the royal perth hospital lipid disorders clinic in western australia.Although in essence a clinic-based patient registry, the web-based design allows for expansion and distribution across australia and beyond.Data collated by the registry may ultimately improve the diagnosis, management and treatment of these conditions.

Journal: Pathology (2020)
Publication types: Journal Article
Machine learning predicts live-birth occurrence before in-vitro fertilization treatment.

In-vitro fertilization (ivf) is a popular method of resolving complications such as endometriosis, poor egg quality, a genetic disease of mother or father, problems with ovulation, antibody problems that harm sperm or eggs, the inability of sperm to penetrate or survive in the cervical mucus and low sperm counts, resulting human infertility.Nevertheless, ivf does not guarantee success in the fertilization.Choosing ivf is burdensome for the reason of high cost and uncertainty in the result.As the complications and fertilization factors are numerous in the ivf process, it is a cumbersome task for fertility doctors to give an accurate prediction of a successful birth.Artificial intelligence (ai) has been employed in this study for predicting the live-birth occurrence.This work mainly focuses on making predictions of live-birth occurrence when an embryo forms from a couple and not a donor.Here, we compare various ai algorithms, including both classical machine learning, deep learning architecture, and an ensemble of algorithms on the publicly available dataset provided by human fertilisation and embryology authority (hfea).Insights on data and metrics such as confusion matrices, f1-score, precision, recall, receiver operating characteristic (roc) curves are demonstrated in the subsequent sections.The training process has two settings without feature selection and with feature selection to train classifier models.Machine learning, deep learning, ensemble models classification paradigms have been trained in both settings.The random forest model achieves the highest f1-score of 76.49% in without feature selection setting.For the same model, the precision, recall, and area under the roc curve (roc auc) scores are 77%, 76%, and 84.60%, respectively.The success of the pregnancy depends on both male and female traits and living conditions.This study predicts a successful pregnancy through the clinically relevant parameters in in-vitro fertilization.Thus artificial intelligence plays a promising role in decision making process to support the diagnosis, prognosis, treatment etc.

Journal: Scientific reports (2020)
Publication types: Journal Article
Coexpression network analysis of human candida infection reveals key modules and hub genes responsible for host-pathogen interactions.

Invasive fungal infections are a significant reason for morbidity and mortality among organ transplant recipients.Therefore, it is critical to investigate the host and candida niches to understand the epidemiology of fungal infections in transplantation.candida albicansis an opportunistic fungal pathogen that causes fatal invasive mucosal infections, particularly in solid organ transplant patients.Therefore, identifying and characterizing these genes would play a vital role in understanding the complex regulation of host-pathogen interactions.Using 32 rna-sequencing samples of human cells infected with c.Albicans, we developed wgcna coexpression networks and performed deseq2 differential gene expression analysis to identify the genes that positively correlate with human candida infection.Using hierarchical clustering, we identified 5 distinct modules.We studied the inter- and intramodular gene network properties in the context of sample status traits and identified the highly enriched genes in the correlated modules.We identified 52 genes that were common in the most significant wgcna turquoise module and differentially expressed genes in human endothelial cells (huvec) infection vs.Control samples.As a validation step, we identified the differentially expressed genes from the independent candida-infected human oral keratinocytes (okf6) samples and validated 30 of the 52 common genes.We then performed the functional enrichment analysis using kegg and go.Finally, we performed protein-protein interaction (ppi) analysis using string and cyto hubba from 30 validated genes.We identified 8 hub genes (jun, atf3, vegfa, slc2a1, hk2, ptgs2, pfkfb3, and klf6) that were enriched in response to hypoxia, angiogenesis, vasculogenesis, hypoxia-induced signaling, cancer, diabetes, and transplant-related disease pathways.The discovery of genes and functional pathways related to the immune system and gene coexpression and differential gene expression analyses may serve as novel diagnostic markers and potential therapeutic targets.

Journal: Frontiers in genetics (2022)
Publication types: Journal Article