syedzayyan/paper_mill_benchmark huggingface dataset:
Selected topics in diffraction with protons and nuclei: past, present, and future.

We review a broad range of phenomena in diffraction in the context of hadron-hadron, hadron-nucleus collisions and deep inelastic lepton-proton/nucleus scattering focusing on the interplay between the perturbative qcd and non-perturbative models.We discuss inclusive diffraction in dis, phenomenology of dipole models, resummation and parton saturation at lowx, hard diffractive production of vector mesons, inelastic diffraction in hadron-hadron scattering, formalism of color fluctuations, inclusive coherent and incoherent diffraction as well as soft and hard diffraction phenomena in hadron-hadron/nucleus and photon-nucleus collisions.For each topic we review key results from the past and present experiments including hera and the lhc.Finally, we identify the remaining open questions, which could be addressed in the continuing experiments, in particular in photon-induced reactions at the lhc and the future electron-ion collider in the us, large hadron electron collider and future circular collider at cern.

Journal: Reports on progress in physics. Physical Society (Great Britain) (2022)
Publication types: Journal Article;Review
Evaluation of sediment and137Cs redistribution in the Oginosawa River catchment near the Fukushima Dai-ichi Nuclear Power Plant using integrated watershed modeling.

The oginosawa river catchment lies 15 km south-west of the fukushima dai-ichi nuclear plant and covers 7.7 km2.Parts of the catchment were decontaminated between fall 2012 and march 2014 in preparation for the return of the evacuated population.The general-purpose terrestrial fluid-flow simulator (getflows) code was used to study sediment and137cs redistribution within the catchment, including the effect of decontamination on redistribution.Fine resolution grid cells were used to model local features of the catchment, such as paddy fields adjacent to the oginosawa river.The simulation was verified using monitoring data for river water discharge rates (r = 0.92), suspended sediment concentrations, and particulate137cs concentrations (r = 0.40).Cesium-137 input to watercourses came predominantly from land adjacent to river channels and forest gullies, e.g.The paddy fields in the ogi and kainosaka districts, as the ground in these areas saturates during heavy rain and is easily eroded.A discrepancy between the simulation and monitoring results on the sediment discharge rate following decontamination may be explained by fast erosion occurring after decontamination.Forested areas far from the channels only made a minor contribution to137cs input to watercourses, total erosion of between 0.001 and 0.1 mm from may 2011 to december 2015, as ground saturation is infrequent in these areas.The 2.3-6.9% y-1decrease in the amount of137cs in forest topsoil over the study period can be explained by radioactive decay (approximately 2.3% y-1), along with a migration downwards into subsoil and a small amount of export.The amount of137cs available for release from land adjacent to rivers is expected to be lower in future than compared to this study period, as the simulations indicate a high depletion of inventory from these areas by the end of 2015.However continued monitoring of137cs concentrations in river water over future years is advised, as recultivation of paddy fields by returnees may again lead to fast erosion rates and release of the remaining inventory.

Journal: Journal of environmental radioactivity (2018)
Publication types: Journal Article
Comparing Phylogenetic Approaches to Reconstructing Cell Lineage From Microsatellites With Missing Data.

Due to the imperfect fidelity of dna replication, somatic cells acquire dna mutations at each division which record their lineage history.Microsatellites, tandem repeats of dna nucleotide motifs, mutate more frequently than other genomic regions and by observing microsatellite lengths in single cells and implementing suitable inference procedures, the cell lineage tree of an organism can be reconstructed.Due to recent advances in single cell next generation sequencing (ngs) and the phylogenetic methods used to infer lineage trees, this work investigates which computational approaches best exploit the lineage information found in single cell ngs data.We simulated trees representing cell division with mutating microsatellites, and tested a range of available phylogenetic algorithms to reconstruct cell lineage.We found that distance-based approaches are fast and accurate with fully observed data.However, maximum parsimony and the computationally intensive probabilistic methods are more robust to missing data and therefore better suited to reconstructing cell lineage from ngs datasets.We also investigated how robust reconstruction algorithms are to different tree topologies and mutation generation models.Our results show that the flexibility of maximum parsimony and the probabilistic approaches mean they can be adapted to allow good reconstruction across a range of biologically relevant scenarios.

Journal: IEEE/ACM transactions on computational biology and bioinformatics (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Crafting a blueprint for single-cell RNA sequencing.

Droplet-based single-cell rna sequencing (sc rna-seq) has moved rapidly from a technology with great potential to a method applied to ever-broader questions.The detailed information that sc rna-seq offers has proven incredibly powerful in resolving cell responses to developmental and environmental cues.However, to maximize the potential of this technology, a panoply of upstream, practical points require consideration.Principal among these are the optimization of cell-isolation procedures, accommodating biotic/abiotic stress responses, and discerning the number of cells and sequencing reads needed.To complement excellent reviews outlining applications and data analysis tools for sc rna-seq, we here discuss these considerations and provide practical tips to tailor experimental design and ensure the best possible outcome.

Journal: Trends in plant science (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Evidence of potential pro-haemorrhagic drug interactions between CYP3A4 inhibitors and direct oral anticoagulants: Analysis of the FAERS database.

S there is no consensus on the haemorrhagic risk associated with potential interactions between commonly used cyp3a4 inhibitors and direct oral anticoagulants (doacs).Methods macrolide antibiotics and azole antimycotics were investigated in this study.Data from food and drug administration adverse event reporting system were retrieved from july 2010 to september 2021.Haemorrhagic signals were expressed by reporting odds ratios (rors) and 95% confidence intervals (cis) based on the interaction/noninteraction methodology as (a/c) / (b/d) and considered significant when the lower limit of 95% ci was >1 and the case number of interaction group was ≥3.Subgroup analyses and logistic regression were conducted by adjusting associated factors in haemorrhagic events.Results from the third quarter of 2010 to the first quarter of 2021, we retrieved 382 853 distinct cases of adverse events associated with doacs, in which 1128 cases of bleeding were associated with coadministration of cyp3a4 inhibitors and doacs.The haemorrhagic signal was significant for apixaban when coadministered with clarithromycin (ror 1.60, 95% ci 1.16-2.20) and posaconazole (ror 2.69, 95% ci 1.37-5.28).For dabigatran, coadministration with azithromycin (ror 4.06, 95% ci 2.77-5.95), fluconazole (ror 2.26, 95% ci 1.52-3.37), itraconazole (ror 7.52, 95% ci 1.51-37.46) and ketoconazole (ror 2.06, 95% ci 1.25-3.41) was associated with significantly higher risks of haemorrhages.At the same time, addition of itraconazole to rivaroxaban also indicated significant haemorrhagic signal (ror 3.58, 95% ci 1.30-9.85).Conclusions macrolide antibiotics and azole antimycotics have potential but different effects on the bleeding risk of doacs.Close attention is needed when using these drugs together.Such precautions have already been included in some drug labels.

Journal: British journal of clinical pharmacology (2023)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Perinatal stress and epigenetics.

Animal and humans exposed to stress early in life are more likely to suffer from long-term behavioral, mental health, metabolic, immune, and cardiovascular health consequences.The hypothalamus plays a nodal role in programming, controlling, and regulating stress responses throughout the life course.Epigenetic reprogramming in the hippocampus and the hypothalamus play an important role in adapting genome function to experiences and exposures during the perinatal and early life periods and setting up stable phenotypic outcomes.Epigenetic programming during development enables one genome to express multiple cell type identities.The most proximal epigenetic mark to dna is a covalent modification of the dna itself by enzymatic addition of methyl moieties.Cell-type-specific dna methylation profiles are generated during gestational development and define cell and tissue specific phenotypes.Programming of neuronal phenotypes and sex differences in the hypothalamus is achieved by developmentally timed rearrangement of dna methylation profiles.Similarly, other stations in the life trajectory such as puberty and aging involve predictable and scheduled reorganization of dna methylation profiles.Dna methylation and other epigenetic marks are critical for maintaining cell-type identity in the brain, across the body, and throughout life.Data that have emerged in the last 15 years suggest that like its role in defining cell-specific phenotype during development, dna methylation might be involved in defining experiential identities, programming similar genes to perform differently in response to diverse experiential histories.Early life stress impact on lifelong phenotypes is proposed to be mediated by dna methylation and other epigenetic marks.Epigenetic marks, as opposed to genetic mutations, are reversible by either pharmacological or behavioral strategies and therefore offer the potential for reversing or preventing disease including behavioral and mental health disorders.This chapter discusses data testing the hypothesis that dna methylation modulations of the hpa axis mediate the impact of early life stress on lifelong behavioral and physical phenotypes.

Journal: Handbook of clinical neurology (2021)
Publication types: Journal Article;Review
Distinct Gene Expression Profiles Define Anaplastic Grade in Retinoblastoma.

Morbidity and mortality associated with retinoblastoma have decreased drastically in recent decades, in large part owing to better prediction of high-risk disease and appropriate treatment stratification.High-risk histopathologic features and severe anaplasia both predict the need for more aggressive treatment; however, not all centers are able to assess tumor samples easily for the degree of anaplasia.Instead, identification of genetic signatures that are able to distinguish among anaplastic grades and thus predict high- versus low-risk retinoblastoma would facilitate appropriate risk stratification in a wider patient population.A better understanding of genes dysregulated in anaplasia also would yield valuable insights into pathways underlying the development of more severe retinoblastoma.Here, we present the histopathologic and gene expression analysis of 28 retinoblastoma cases using microarray analysis.Tumors of differing anaplastic grade show clear differential gene expression, with significant dysregulation of unique genes and pathways in severe anaplasia.Photoreceptor and nucleoporin expression in particular are identified as highly dysregulated in severe anaplasia and suggest particular cellular processes contributing to the development of increased retinoblastoma severity.A limited set of highly differentially expressed genes also are able to predict severe anaplasia accurately in our data set.Together, these data contribute to the understanding of the development of anaplasia and facilitate the identification of genetic markers of high-risk retinoblastoma.

Journal: The American journal of pathology (2018)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Impact of adaptive gastric electrical stimulation on weight, food intake, and food intake rate in dogs.

Gastric electrical stimulation (ges) has been studied for decades as a promising treatment for obesity.Stimulation pulses with fixed amplitude and pulse width are usually applied, but these have limitations with regard to overcoming habituation to ges and inter-subject variation.This study aims to analyze the efficacy of an adaptive ges protocol for reducing food intake and maintaining lean weight in dogs.Methods six beagle dogs were implanted with a remotely programmable gastric stimulator.An adaptive protocol was designed to increase the stimulation energy proportionally to the excess of food consumption, with respect to the dogs' maintenance energy requirements.After surgery and habituation to experimental conditions, the dogs went through both a control and a stimulation period of 4 weeks each, in a randomized order.The stimulation parameters were adapted daily.Body weight, food intake, food intake rate, and postprandial cutaneous electrogastrograms (egg) were recorded to assess the effect of adaptive ges.Results adaptive ges decreased food intake and food intake rate (p < 0.05) resulting in weight maintenance.In the absence of ges, the dogs gained weight (p < 0.05).Postprandial egg dominant frequency was accelerated by ges (p < 0.05).The strategy of adapting the stimulation energy was effective in causing significant mid-term changes.Conclusion adaptive ges is effective for reducing food intake and maintaining lean weight.The proposed adaptive strategy may offer benefits to counter habituation and adapt to inter-subject variation in clinical use of ges for obesity.

Journal: Artificial organs (2022)
Publication types: Journal Article
Quality of life in people with epidermolysis bullosa: a systematic review.

Individuals with epidermolysis bullosa (eb) present with various clinical manifestations of different severities that affect quality of life (qo l).This systematic review synthesizes the current evidence about the qo l of individuals with eb.Methods we included observational studies with people of all age groups, both sexes, and any eb type.Studies with qualitative methodology, chapters of books, meeting proceedings, and abstracts were excluded.Results in this study, 12 articles comprising 745 individuals were included.More than half of the articles observed lower qo l in individuals with recessive dystrophic eb (rdeb) or junctional eb (jeb).Three articles indicated that eb affected qo l more in women than in men, and one article identified that children with eb suffered more than adults with the disease.Pain was frequently reported.Seven articles identified difficulty in sports, two identified a need for bathing assistance, and three identified eating difficulties.Additionally, participants reported that family relationships and friendships were affected, and they experienced feelings of anxiety and depression.Some of the instruments used evaluated qo l in general dermatologic conditions, and one was specific to eb.Conclusion qo l is more affected in people who have rdeb and jeb.Regarding sex and age, women and children need special care in their monitoring.It is necessary that guidelines on pain management be more disseminated and put into practice.Future studies should use standardized specific instruments to assess the qo l in eb individuals, while considering the particularities of the different age groups.

Journal: Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation (2020)
Publication types: Journal Article;Systematic Review
A physical wiring diagram for the human immune system.

The human immune system is composed of a distributed network of cells circulating throughout the body, which must dynamically form physical associations and communicate using interactions between their cell-surface proteomes1.Despite their therapeutic potential2, our map of these surface interactions remains incomplete3,4.Here, using a high-throughput surface receptor screening method, we systematically mapped the direct protein interactions across a recombinant library that encompasses most of the surface proteins that are detectable on human leukocytes.We independently validated and determined the biophysical parameters of each novel interaction, resulting in a high-confidence and quantitative view of the receptor wiring that connects human immune cells.By integrating our interactome with expression data, we identified trends in the dynamics of immune interactions and constructed a reductionist mathematical model that predicts cellular connectivity from basic principles.We also developed an interactive multi-tissue single-cell atlas that infers immune interactions throughout the body, revealing potential functional contexts for new interactions and hubs in multicellular networks.Finally, we combined targeted protein stimulation of human leukocytes with multiplex high-content microscopy to link our receptor interactions to functional roles, in terms of both modulating immune responses and maintaining normal patterns of intercellular associations.Together, our work provides a systematic perspective on the intercellular wiring of the human immune system that extends from systems-level principles of immune cell connectivity down to mechanistic characterization of individual receptors, which could offer opportunities for therapeutic intervention.

Journal: Nature (2022)
Publication types: Journal Article
CRISPR/Cas13a combined with hybridization chain reaction for visual detection of influenza A (H1N1) virus.

This study provides proof of concept of a colorimetric biosensor for influenza h1n1 virus assay based on the crispr/cas13a system and hybridization chain reaction (hcr).Target rna of influenza h1n1 virus activated the trans-cleavage activity of cas13a, which cleaved the special rna sequence (-uuu-) of the probe, further initiating hcr to copiously generate g-rich dna.Abundant g-quadruplex/hemin was formed in the presence of hemin, thus catalyzing a colorimetric reaction.The colorimetric biosensor exhibited a linear relationship from 10 p m to 100 n m.The detection limit was 0.152 p m.The biosensor specificity was excellent.This new and sensitive detection method for influenza virus is a promising rapid influenza diagnostic test.

Journal: Analytical and bioanalytical chemistry (2022)
Publication types: Journal Article
Sacroiliac Joint Interventions.

The sacroiliac joint complex (sijc) is composed of complex anatomy of numerous potential pain generators that demonstrate varying pathophysiology and differing innervations.This heterogeneity has been a challenge to advancing research and clinical care.Moving forward, individualized approaches taking these factors into account may be a path forward to improved outcomes.Thus, as we move toward precision medicine in interventional spine care, it is imperative to investigate more targeted diagnostic and therapeutic approaches to the sijc.

Journal: Physical medicine and rehabilitation clinics of North America (2022)
Publication types: Journal Article;Review
Psychophysiological Reactivity, Postures and Movements among Academic Staff: A Comparison between Teleworking Days and Office Days.

The aim of this study was to determine if psychophysiological activity, postures and movements differ during telework (i.e., work performed at home) and work performed at the conventional office.We performed twenty-four-hour pulse recordings and accelerometry measurements on 23 academic teaching and research staff during five consecutive workdays, with at least one day of telework.Additionally, we conducted salivary sampling during one day of telework, and one day of office work.Heart rate and heart rate variability indices, postural exposure and cortisol concentration were analyzed using repeated measures analysis of variance with workplace and time (i.e., before, during and after workhours) as within-subject effects.We found a significant interaction effect of workplace and time in heart rate variability indices and in the number of transitions between seated and standing postures.This shows more parasympathetic activity among academic teleworkers during telework than office work, which may indicate more relaxation during telework.They had an overall sedentary behavior at both workplaces but switched between sitting and standing more often during telework, which may be beneficial for their health.

Journal: International journal of environmental research and public health (2021)
Publication types: Journal Article
Factors influencing perceived communication quality for successful fertility preservation counseling for adolescent and young adult cancer patients and their caregivers in Korea.

Although relatively new in asian countries, fertility preservation (fp) discussions are crucial for adolescent and young adult (aya) cancer patients.This study highlights patients' and their caregivers' perceptions of communications quality during fp discussions in korea.Methods participants were aya patients and their caregivers (each: n = 34).The study examined the clinical pathways for fp and used surveys to collect details on discussion characteristics and satisfaction levels during fp discussions at the yonsei cancer center, seoul, korea.Quality and degree of satisfaction with fp discussions were measured on a scale ranging from 1 to 7.Results two caregivers did not complete the survey.All respondents reported high overall satisfaction; however, several factors were related to low satisfaction with information quality.Caregivers who received both verbal communication and nonverbal communication tools (e.g., pamphlets, internet resources) were more satisfied with the information quality than those who only received verbal communication.Regarding provider type, both respondent groups reported high overall satisfaction with physicians, rather than other types of care providers.Regarding the number of discussion sessions, respondents reported an improved understanding of fp and better communication and information quality if they participated in more than one discussion session.Conclusion the fp process for aya cancer patients can be improved by adjusting the type of provider, number of discussion sessions, and types of information.This will form the cornerstone of effective fp communication in korea.

Journal: Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer (2022)
Publication types: Journal Article