syedzayyan/paper_mill_benchmark huggingface dataset:
Job Retention Among Individuals With Multiple Sclerosis: Relationship With Prediagnostic Employment and Education; Demographic Characteristics; and Disease Course, Severity, and Complications.

To identify how prediagnosis employment, education, demographic statuses, and disease factors relate to job retention among people with multiple sclerosis (ms).Design cross-sectional logit model.Setting data were collected at an academic medical university and a specialty hospital, both in the southeastern us.Participants people with ms (n=1126) who were employed at the time of ms diagnosis.Interventions not applicable.Main outcome measures job retention was measured by employment status at the time of follow-up assessment.Results prediagnostic educational attainment was predictive of job retention.Among several prediagnostic employment characteristics, only working in production, transportation, and material moving was significantly related to a lower odds of job retention compared with those working in professional/managerial occupations.Aging factors were strongly related to job retention, with declines in job retention observed with increasing age and years since diagnosis.Non-hispanic black and hispanic participants reported lower odds of job retention than non-hispanic white participants, although there were no observed effects of sex.A significantly lower job retention rate was observed among those with progressive ms, compared with relapsing-remitting.Job retention was also less likely among people with greater ms severity and fatigue.Conclusions job retention strategies and interventions should target people with greater ms complications and severity, as well as non-hispanic black and hispanic persons, because these characteristics are more highly related to job retention than our prediagnostic employment and vocational history.

Journal: Archives of physical medicine and rehabilitation (2022)
Publication types: Journal Article;Research Support, U.S. Gov't, P.H.S.
Surgical management of "Twiddler syndrome" in patients with deep brain stimulation: a technical note and review of the literature.

The twiddler syndrome (ts) describes a situation in which the implanted impulse generator (ipg) rotates several times around its own axis in the subcutaneous pocket.This can lead to severe mechanical damage of the leads and extensions and to dislocations.Method hereby, we report on a technique for revision surgery in patients diagnosed with twiddler syndrome after undergoing previous deep brain stimulation (dbs) surgery.For revision surgery, the tyrx tm absorbable antibacterial envelope was used.Conclusion the ts can be treated well with the envelope tyrx tm absorbable antibacterial envelope tyrx tm.

Journal: Acta neurochirurgica (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Aspirin Use and Common Cancer Risk: A Meta-Analysis of Cohort Studies and Randomized Controlled Trials.

Whether aspirin use can decrease or increase cancer risk remains controversial.In this study, a meta-analysis of cohort studies and randomized controlled trials (rcts) were conducted to evaluate the effect of aspirin use on common cancer risk.Method medline and embase databases were searched to identify relevant studies.Meta-analyses of cohort studies and rcts were performed to assess the effect of aspirin use on the risk of colorectal, gastric, breast, prostate and lung cancer.Cochran q test and the i square metric were calculated to detect potential heterogeneity among studies.Subgroup meta-analyses according to exposure categories (frequency and duration) and timing of aspirin use (whether aspirin was used before and after cancer diagnosis) were also performed.A dose-response analysis was carried out to evaluate and quantify the association between aspirin dose and cancer risk.Results a total of 88 cohort studies and seven rcts were included in the final analysis.Meta-analyses of cohort studies revealed that regular aspirin use reduced the risk of colorectal cancer (crc) (rr=0.85, 95%ci: 0.78-0.92), gastric cancer (rr=0.67, 95%ci: 0.52-0.87), breast cancer (rr=0.93, 95%ci: 0.87-0.99) and prostate cancer (rr=0.92, 95%ci: 0.86-0.98), but showed no association with lung cancer risk.Additionally, meta-analyses of rcts showed that aspirin use had a protective effect on crc risk (or=0.74, 95%ci: 0.56-0.97).When combining evidence from meta-analyses of cohorts and rcts, consistent evidence was found for the protective effect of aspirin use on crc risk.Subgroup analysis showed that high frequency aspirin use was associated with increased lung cancer risk (rr=1.05, 95%ci: 1.01-1.09).Dose-response analysis revealed that high-dose aspirin use may increase prostate cancer risk.Conclusions this study provides evidence for low-dose aspirin use for the prevention of crc, but not other common cancers.High frequency or high dose use of aspirin should be prescribed with caution because of their associations with increased lung and prostate cancer risk, respectively.Further studies are warranted to validate these findings and to find the minimum effective dose required for cancer prevention.

Journal: Frontiers in oncology (2021)
Publication types: Systematic Review;Journal Article
When there's a will, there's a way: Disentangling the effects of goals and means in emotion regulation.

Emotion regulation involves activating an emotion goal (e.g., decrease negative emotions) and using an emotion regulation strategy (e.g., cognitive reappraisal) to pursue it.We propose that activating emotion goals and implementing means can independently affect emotion regulation.People are not always motivated to regulate emotions or to regulate them in a prohedonic manner.Therefore, activating prohedonic emotion goals is consequential.Furthermore, merely activating an emotion goal may trigger accessible means, leading to emotional changes.We tested these ideas by disentangling effects of pursuing prohedonic emotion goals and implementing cognitive reappraisal.First, we show that individuals perceive measures and manipulations of cognitive reappraisal as signaling the activation of specific emotion goals (i.e., decrease unpleasant or increase pleasant emotions) and the implementation of specific means (i.e., think differently about emotion-eliciting events).Second, we decomposed a classic measure of cognitive reappraisal to show that previously documented benefits of reappraisal might be because of the frequency of either pursuing prohedonic goals or using cognitive reappraisal.Third, in 2 empirical studies, we separately manipulated prohedonic goals (without specifying the means), cognitive reappraisal (without specifying the goal), and gave classic reappraisal instructions (specifying both the goal and the means).In both studies, activating prohedonic goals was as effective in decreasing negative emotions as was activating prohedonic goals with reappraisal instructions.Thus, activating emotion goals is essential, and sometimes even sufficient, for successful regulation.Finally, we demonstrate that the confound between goals and means is pervasive in the cognitive reappraisal literature, and offer recommendations for avoiding it.(psyc info database record (c) 2019 apa, all rights reserved).

Journal: Journal of personality and social psychology (2019)
Publication types: Journal Article
Automated Cancer Diagnostics via Analysis of Optical and Chemical Images by Deep and Shallow Learning.

Optical microscopy has long been the gold standard to analyse tissue samples for the diagnostics of various diseases, such as cancer.The current diagnostic workflow is time-consuming and labour-intensive, and manual annotation by a qualified pathologist is needed.With the ever-increasing number of tissue blocks and the complexity of molecular diagnostics, new approaches have been developed as complimentary or alternative solutions for the current workflow, such as digital pathology and mass spectrometry imaging (msi).This study compares the performance of a digital pathology workflow using deep learning for tissue recognition and an msi approach utilising shallow learning to annotate formalin-fixed and paraffin-embedded (ffpe) breast cancer tissue microarrays (tmas).Results show that both deep learning algorithms based on conventional optical images and msi-based shallow learning can provide automated diagnostics with f1-scores higher than 90%, with the latter intrinsically built on biochemical information that can be used for further analysis.

Journal: Metabolites (2022)
Publication types: Journal Article
Multiplexed mobilization and expression of biosynthetic gene clusters.

Bacterial genomes contain large reservoirs of biosynthetic gene clusters (bgcs) that are predicted to encode unexplored natural products.Heterologous expression of previously unstudied bgcs should facilitate the discovery of additional therapeutically relevant bioactive molecules from bacterial culture collections, but the large-scale manipulation of bgcs remains cumbersome.Here, we describe a method to parallelize the identification, mobilization and heterologous expression of bgcs.Our solution simultaneously captures large numbers of bgcs by cloning the genomes of a strain collection in a large-insert library and uses the conkat-seq (co-occurrence network analysis of targeted sequences) sequencing pipeline to efficiently localize clones carrying intact bgcs which represent candidates for heterologous expression.Our discovery of several natural products, including an antibiotic that is active against multi-drug resistant staphylococcus aureus, demonstrates the potential of leveraging economies of scale with this approach to systematically interrogate cryptic bgcs contained in strain collections.

Journal: Nature communications (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Identification and validation of a novel tumor driver gene signature for diagnosis and prognosis of head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (hnscc) is a common heterogeneous cancer with complex carcinogenic factors.However, the current tnm staging criteria to judge its severity to formulate treatment plans and evaluate the prognosis are particularly weak.Therefore, a robust diagnostic model capable of accurately diagnosing and predicting hnscc should be established.methods:gene expression and clinical data were retrieved from the cancer genome atlas and gene expression omnibus databases.Key prognostic genes associated with hnscc were screened with the weighted gene co-expression network analysis and least absolute shrinkage and selection operator (lasso) cox regression model analysis.We used the time roc and survival r packages to conduct time-dependent receiver operating characteristic curve analyses and calculated the area under the curve at different time points of model prediction.Patients in the training and validation groups were divided into high- and low-risk subgroups, and kaplan-meier (k-m) survival curves were plotted for all subgroups.Subsequently, lasso and support vector machine algorithms were used to screen genes to construct diagnostic model.Furthermore, we used the wilcoxon signed-rank test to compare the half-maximal inhibitory concentrations of common chemotherapy drugs among patients in different risk groups.Finally, the expression levels of eight genes were measured using quantitative real-time polymerase chain reaction and immunohistochemistry.results:ten genes (ssb,pfkp,nat10,pcdh9,shank2,pax8,celsr3,dclre1c,map2k7, and odf4) with prognostic potential were identified, and a risk score was derived accordingly.Patients were divided into high- and low-risk groups based on the median risk score.The k-m survival curves confirmed that patients with high scores had significantly worse overall survival.Receiver operating characteristic curves proved that the prognostic signature had good sensitivity and specificity for predicting the prognosis of patients with hnscc.Univariate and multivariate cox regression analyses confirmed that the gene signature was an independent prognostic risk factor for hnscc.Diagnostic model was built by identifying eight genes (ssb,pfkp,nat10,pcdh9,celsr3,dclre1c,map2k7, and odf4).The high-risk group showed higher sensitivity to various common chemotherapeutic drugs.dclre1cexpression was higher in normal tissues than in hnscc tissues.conclusion:our study identified the important role of tumor-driver genes in hnscc and their potential clinical diagnostic and prognostic values to facilitate individualized management of patients with hnscc.

Journal: Frontiers in molecular biosciences (2022)
Publication types: Journal Article
Disruption of TWIST1 translation by 5' UTR variants in Saethre-Chotzen syndrome.

Saethre-chotzen syndrome (scs), one of the most common forms of syndromic craniosynostosis (premature fusion of the cranial sutures), results from haploinsufficiency of twist1, caused by deletions of the entire gene or loss-of-function variants within the coding region.To determine whether non-coding variants also contribute to scs, we screened 14 genetically undiagnosed scs patients using targeted capture sequencing, and identified novel single nucleotide variants (snvs) in the 5' untranslated region (utr) of twist1 in two unrelated scs cases.We show experimentally that these variants, which create translation start sites in the twist1 leader sequence, reduce translation from the main open reading frame (m orf).This is the first demonstration that non-coding snvs of twist1 can cause scs, and highlights the importance of screening the 5' utr in clinically diagnosed scs patients without a coding mutation.Similar 5' utr variants, particularly of haploinsufficient genes, may represent an under-ascertained cause of monogenic disease.

Journal: Human mutation (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Effects of Long-Term Vagus Nerve Electrical Stimulation Therapy on Acute Cerebral Infarction and Neurological Function Recovery in Post MCAO Mice.

Vagus nerve stimulation therapy is proven to produce neuroprotective effects against central nervous system diseases and reduce neurological injury, having a positive effect on the recovery of neurological functions in mouse model of stroke.Objective this study was aimed at exploring a wider time window for vns treatment, investigating the long-term behavioral improvement of long-term vns in mice after p mcao, and exploring the antiapoptotic properties of vns and its role in autophagy, all of which may be a permanent deficiency potential mechanism of neuroprotection in hemorrhagic stroke.Methods permanent focal cerebral ischemia and implantation of vagus nerve stimulator were performed through intracavitary occlusion of the right middle cerebral artery (mca).The vagus nerve stimulation group received five times vagus nerve stimulation from 6 h after surgery for 5 days.Adhesive removal test and nss neurological score were used to evaluate the neurological deficit of mice.Ttc staining of mouse brain tissue was performed one week after surgery in order to assess the area of cerebral infarction.Additionally, frozen sections were stained with fluoro-jade b to observe the apoptotic cells in the ischemic penumbra of brain tissue.Finally, western blot was used to detect the changes in the levels of apoptosis-related proteins such as cleaved-caspase3 and bcl-2 and autophagy-related proteins such as m tor, beclin-1, and lc3-ii in brain tissue.Results vns can effectively reduce the behavioral score of p mcao mice; ttc results showed that vns could effectively reduce the infarct area after p mcao (p< 0.05).After vns intervention of the p mcao group compared with the p mcao+vni group, the fjb-positive cells in the vns group were significantly decreased (p< 0.05); western blot analysis showed that the expression of cleaved-caspase3 in the brain tissue of mice increased after p mcao (p< 0.05), and the expression of bcl-2 decreased (p< 0.05).This change could be effectively reversed after vns intervention (p< 0.05).Conclusion vns could effectively improve the behavioral performance of mice after permanent stroke in addition to significantly reducing the infarct size of the brain tissue.The mechanism may be related to the effective reduction of cell apoptosis and excessive autophagy after p mcao by vns.

Journal: Oxidative medicine and cellular longevity (2022)
Publication types: Journal Article
Highly degraded RNA can still provide molecular information: An in vitro approach.

The long-term survival of rna in postmortem tissues is a tricky topic.Many aged/forensic specimens show, in fact, high rates of null/inconclusive pcr-based results, while reliable outcomes were sometimes achieved from archaeological samples.On the other hand, several data show that the rna is a molecule that survives even to several physical-chemical stresses.In the present study, a simple protocol, which was already developed for the prolonged hydrolysis of dna, was applied to a rna sample extracted from blood.This protocol is based on the heat-mediated (70°c) hydrolysis for up to 36 h using ultrapure water and di-ethyl-pyro-carbonate-water as hydrolysis medium.Measurable levels of depurination were not found even if microfluidic devices showed a progressive pattern of degradation.The reverse transcription/quantitative pcr analysis of two (60 bp long) housekeeping targets (glyceraldehyde-3-phosphate dehydrogenase and porphobilinogen deaminase) showed that the percentage of amplifiable target (%at) decreased in relation to the duration of the damaging treatment (r2> 0.973).The comparison of the %at in the degraded rna and in the dna samples that underwent the same damaging treatment showed that the %at is always higher in rna, reaching up to three orders of magnitude.Lastly, even the end-point pcr of blood-specific markers gave reliable results, which is in agreement with the body fluid origin of the sample.In conclusion, all the pcr-based results show that rna maintains the ability to be retro-transcribed in short c dna fragments even after 36 h of incubation at 70°c in mildly acidic buffers.It is therefore likely that the long-term survival of rna samples depends mainly on the protection against rnaase attacks rather than on environmental factors (such as humidity and acidity) that are instead of great importance for the stability of dna.As a final remark, our results suggest that the rna analysis can be successfully performed even when dna profiling failed.

Journal: Electrophoresis (2020)
Publication types: Journal Article
Contagious Antibiotic Resistance: Plasmid Transfer among Bacterial Residents of the Zebrafish Gut.

By characterizing the trajectories of antibiotic resistance gene transfer in bacterial communities such as the gut microbiome, we will better understand the factors that influence this spread of resistance.Our aim was to investigate the host network of a multidrug resistance broad-host-range plasmid in the culturable gut microbiome of zebrafish.This was done throughin vitroandin vivoconjugation experiments with escherichia colias the donor of the plasmid p b10::gfp when this donor was mixed with the extracted gut microbiome, only transconjugants of aeromonas veroniiwere detected.In separate matings between the same donor and four prominent isolates from the gut microbiome, the plasmid transferred to two of these four isolates,a.Veroniiand plesiomonas shigelloides, but not to shewanella putrefaciensand vibrio mimicus when these a.Veroniiand p.Shigelloidestransconjugants were the donors in matings with the same four isolates, the plasmid now also transferred from a.Veroniito s.Putrefaciens p.Shigelloideswas unable to donate the plasmid, and v.Mimicuswas unable to acquire it.Finally, when the e.Colidonor was addedin vivoto zebrafish through their food, plasmid transfer was observed in the gut, but only to achromobacter, a rare member of the gut microbiome.This work shows that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome depends on the donor-recipient species combinations and therefore their spatial arrangement.It also suggests that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.importanceto understand how antibiotic resistance plasmids end up in human pathogens, it is crucial to learn how, where, and when they are transferred and maintained in members of bacterial communities such as the gut microbiome.To gain insight into the network of plasmid-mediated antibiotic resistance sharing in the gut microbiome, we investigated the transferability and maintenance of a multidrug resistance plasmid among the culturable bacteria of the zebrafish gut.We show that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome can depend on which species are involved, as some are important nodes in the plasmid-host network and others are dead ends.Our findings also suggest that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.

Journal: Applied and environmental microbiology (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Respiratory system findings in pediatric patients with primary immunodeficiency.

Pulmonary involvement which can be infectious or noninfectious is one of the most frequent complications in patients with primary immunodeficiency (pid).Objective the aim of this study is to assess the pulmonary system of the pediatric patients with pid and report the demographical, clinical, and radiological findings regarding the underlying pid.Methods the present study included pediatric patients who were receiving immunoglobulin replacement therapy (igrt) for pid (combined immunodeficiency [cvid] (23), common variable immunodeficiency (15), and agamaglobulinemia [10]) so far or newly diagnosed and started igrt at hacettepe university immunology department, between january 2015 and january 2018.Results a total of 48 patients (60.4% male), aged 9.9 (6.1-14) years were included.Time of delay in the diagnosis of immundeficiency was 2.27 (interquartile range: 1.0-6.75) years.Cvid patients exhibited higher respiratory system symptoms, as well as a history of recurrent lung infection and hospitalization.Hilar and mediastinal lymphadenopathies, peribronchial thickening, and bronchiectasis were the most common pulmonary complications and more than three lung lobes were affected in 69%.Among the newly diagnosed patients, bronchiectasis was present in 25% and more than three lobes were affected in 62.5%.Although pulmonary nodules and mediastinal lymphadenopathy were frequently computed tomography findings in our patients, only two patients (4.16%) were diagnosed with interstitial lung disease.Conclusion although bronchiectasis is predominantly reported as a long-term complication in adult patients with pid, half of our pediatric patient cohort with pid had bronchiectasis, even the newly diagnosed patients.Long-term follow-up is needed to assess the extent to which these pulmonary complications that develop in the natural course of the disease can be prevented by igrt.

Journal: Pediatric pulmonology (2021)
Publication types: Journal Article