syedzayyan/paper_mill_benchmark huggingface dataset:
DietaryAronia melanocarpaPomace Supplementation Enhances the Expression of ZO-1 and Occludin and Promotes Intestinal Development in Pigs.

A fruit juice production byproduct,aronia melanocarpapomace (amp) is rich in natural polyphenol antioxidant components.The objectives of this study were to study the effects of dietary amp supplementation on the feeding outcome and intestinal barrier function of pigs.In total, 27 growing pigs (duroc × landrace × yorkshire, ~60 days, average weight of 27.77 ± 2.87 kg, males and females included at random) were randomly allotted to 3 treatment groups, with 3 repetitions per group and 3 pigs per repetition.At the experiment completion, 2 pigs (close to the average body weight of all experimental pigs) per replicate were slaughtered.The control group (con group) was fed a basic diet, and the experimental groups were fed 4% (4% amp group) and 8% (8% amp group) amp in the basic diet.These pigs were prefed for 3 days, and the formal experiments were performed for 7 weeks.The results showed that compared with the con diet, the 4% amp supplementation significantly increased the average daily gain of pigs (p< 0.05).Regarding intestinal development, 4% amp significantly increased the jejunal villus height/crypt depth ratio (p< 0.05), and different amp levels had no significant effect on the pig cecum morphology.Different amp levels significantly decreased the relative abundance of proteobacteria (p< 0.05).Regarding other microbial genera, 4% amp supplementation significantly increased the levels of lachnospira, solobacterium, romboutsiaand other beneficial microorganisms (p< 0.05).Different amp levels significantly decreased the relative abundances of the opportunistic pathogens escherichia-shigellaand pseudoscardovia(p< 0.05) and increased the contents of acetic acid and butyric acid in the pig cecal contents (p< 0.05).Compared with the con treatment, 4% amp supplementation significantly downregulated the jejunal gene expression of porcine proinflammatory factors (il-1β, il-6, il-8 and tnf-α) and significantly upregulated the jejunal gene expression of zo-1, occludin and claudin-1 (p< 0.05).In conclusion, 4% amp supplementation in feed is beneficial to overall pig health and growth.

Journal: Frontiers in veterinary science (2022)
Publication types: Journal Article
A pilot feasibility study of a behavioral intervention for nicotine vaping cessation among young adults delivered via telehealth.

Nicotine vaping among youth has increased, warranting concern from tobacco control proponents.Many youth who vape indicate interest in quitting; however, few empirically supported vaping cessation interventions exist.This pilot feasibility study adapted an established behavioral intervention, contingency management (cm), delivered via telehealth to promote vaping cessation among young adults.Methods participants (n = 27; ages 17-21) vaping nicotine regularly were recruited via social media and digital advertisements from across the us (june 2020-january 2021).Participants were randomized at approximately 4:1 to cm or monitoring control (22:5).Cm was delivered through dynami care health's smartphone app for 4 weeks, in which financial incentives were delivered contingent on abstinent cotinine samples after the quit day until the end of treatment (eot; days 7-28; 10 expected submissions).Control participants earned incentives for submitting cotinine, regardless of abstinence.Feasibility, acceptability, and abstinence was collected throughout treatment, at eot, and at 1-month follow-up.Results the majority of enrolled participants completed treatment (monitoring: 5/5; cm: 20/22), and intervention components were rated favorably overall (> 80%).Cm participants submitted 112/220 (55%) abstinent cotinine samples throughout the quit attempt, while the monitoring group submitted 4/50 (8%) negative samples.There were no differences in abstinence between groups at eot or follow-up.Conclusion this pilot study of a telehealth-based youth vaping cessation intervention demonstrated preliminary feasibility and acceptability.These results suggest that cm for young adult vaping cessation, delivered remotely, is a promising direction for future work and fully powered trials are warranted to assess intervention efficacy.

Journal: Drug and alcohol dependence (2022)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
The combination of aerobic digestion and bioleaching for heavy metal removal from excess sludge.

In this study, bioleaching is employed for removing heavy metals from excess sludge generated during municipal wastewater treatment.To avoid organic matter impact on bioleaching, aerobic digestion was performed as pretreatment of the bioleaching or accompanied with the bioleaching.The results showed that the leaching amounts of heavy metals from the process of aerobic digestion accompanied with bioleaching was 2.3 times more than that of the process of aerobic digestion followed by bioleaching.The stable-state proportions of zn, cu, ni and mn increased by 83%, 94%, 96% and 91%, respectively, in the process of aerobic digestion accompanied with bioleaching, and moreover, the reduction rate of mlss increased by 22.7%.Although the content of ammonia nitrogen and total phosphorus in sludge decreased after bioleaching treatment, they were still much higher than the soil background value.It indicates that the treated sludge still has agricultural value.High throughput sequencing analysis showed that the relative abundance of acid-producing bacteria (romboutsia, clostridium, tricibacter, and intestinibacter) significantly increased from 0% to 28.6%, 6.9%, 3.9%, and 2.4%.The enrichment of these acidogenic bacteria was the main reason for the p h decrease, which was conducive to the removal of heavy metals from sludge.

Journal: Chemosphere (2022)
Publication types: Journal Article
Postoperative C-reactive protein-to-albumin ratio predicts poor prognosis in patients with bladder cancer undergoing radial cystectomy.

The purpose of the present study was to investigate the prognostic value of the postoperative c-reactive protein/albumin ratio (car) in patients with bladder cancer undergoing radial cystectomy.The present study retrospectively reviewed 102 patients who underwent radical cystectomy and were followed for ≥6 months postoperatively at our institution, and evaluated clinicopathological factors and laboratory parameters for cancer-specific survival (css) and extraurothelial recurrence-free survival (erfs).Multivariate analysis using the cox proportional hazards model revealed that only postoperative car ≥0.27 [hazard ratio (hr), 3.368; 95% confidence interval (ci), 1.674-6.731; p<0.001] was an independent factor for poor css rate.Higher postoperative car was also the only significant factor for shortened erfs time (hr, 2.401; 95% ci, 1.196-4.684; p=0.015).No significant association was identified between postoperative car ≥0.27 and any pathological factors or postoperative laboratory markers besides postoperative neutrophil-to-lymphocyte ratio.Furthermore, postoperative car (≥0.27) was an independent factor for poor css and erfs rates in 48 patients with advanced p t stage (≥p t3) in the multivariate analysis (p=0.026 and p=0.036, respectively).A higher postoperative car value can provide additional information about the possibility of poor css and erfs rates in patients with bladder cancer undergoing radical cystectomy.

Journal: Molecular and clinical oncology (2021)
Publication types: Journal Article
A community perspective of COVID-19 and obesity in children: Causes and consequences.

The pandemic of childhood obesity that has been increasing over the last decade has collided with the current pandemic of covid-19.Enforced behavioural changes have resulted in a myriad of problems for children particularly in weight management.Restricted activity is the most obvious but many other aspects of life have exacerbated biological, psychosocial, and behavioral factors identified as risks for childhood obesity.Significant effort is required to turn around the prevailing tide of weight gain necessitating changes in personal and family behavior and diet, as well as high-level governmental and educational policy.Evidence-based, focused, long-term interventions which are adequately funded are required.Enthusiasm and optimism for change coupled with public engagement by utilization of new technology as well as traditional methods offers hope for change.Public health interventions in isolation are inadequate and bolder changes to central policies and social structure are needed for sustained change.This will allow some mitigation of the affects of covid-19 but also reduce negative outcomes in future comparable situations.

Journal: Obesity medicine (2021)
Publication types: Journal Article;Review
Comparison of Survival After In-Hospital Cardiac Arrest in Patients With Versus Without Diabetes Mellitus.

Diabetes mellitus (dm) increases the risk of sudden cardiac death, but the extent to which it influences survival after an in-hospital cardiac arrest (ihca) remains unclear.We assessed the association of dm and survival after ihca.The study included 1,009,073 patients aged ≥18 years who underwent cardiopulmonary resuscitation for ihca between january 2003 and december 2013, recorded in the nationwide inpatient sample database.The outcomes were survival to hospital discharge and discharge disposition assessed using multivariable logistic regression accounting for relevant covariates and clustering.Of the patients with ihca, 30.8% (310,825) had dm and were more likely to be older and to have a higher prevalence of co-morbidities including hypertension, dyslipidemia, chronic kidney disease, and previous cardiovascular disease (all p <0.001).The rates of survival to hospital discharge after ihca were 27.0% and 25.1% in patients with and without dm, respectively.After multivariable adjustment, dm was associated with a modestly lower risk-adjusted survival to hospital discharge (adjusted or [a or] 0.96, 95% confidence interval [95% ci] 0.95 to 0.97, p <0.001).This association was influenced by a number of factors (all interaction p <0.001), including a lower risk of survival among patients with dm who were younger (a or 0.93, 95% ci 0.92 to 0.94 among those aged <75 years), those with a primary cardiovascular diagnosis (a or 0.88, 95% ci 0.86 to 0.89), and those with ventricular fibrillation/ventricular tachycardia as the cardiac arrest rhythm (a or 0.88, 95% ci 0.79 to 0.82).Patients with dm had lower odds of being discharged home with self-care after surviving an ihca (p <0.001).In conclusion, preexisting dm was associated with a modestly lower risk-adjusted chance of survival after an ihca.

Journal: The American journal of cardiology (2018)
Publication types: Comparative Study;Journal Article;Research Support, N.I.H., Extramural
Genetic Variations of Ultraconserved Elements in the Human Genome.

Ultraconserved elements (uces) are among the most popular dna markers for phylogenomic analysis.In at least three of five placental mammalian genomes (human, dog, cow, mouse, and rat), 2189 uces of at least 200 bp in length that are identical have been identified.Most of these regions have not yet been functionally annotated, and their associations with diseases remain largely unknown.This is an important knowledge gap in human genomics with regard to uce roles in physiologically critical functions, and by extension, their relevance for shared susceptibilities to common complex diseases across several mammalian organisms in the event of their polymorphic variations.In the present study, we remapped the genomic locations of these uces to the latest human genome assembly, and examined them for documented polymorphisms in sequenced human genomes.We identified 29,983 polymorphisms within analyzed uces, but revealed that a vast majority exhibits very low minor allele frequencies.Notably, only 112 of the identified polymorphisms are associated with a phenotype in the ensembl genome browser.Through literature analyses, we confirmed associations of 37 (i.e., out of the 112) polymorphisms within 23 uces with 25 diseases and phenotypic traits, including, muscular dystrophies, eye diseases, and cancers (e.g., familial adenomatous polyposis).Most reports of uce polymorphism-disease associations appeared to be not cognizant that their candidate polymorphisms were actually within uces.The present study offers strategic directions and knowledge gaps for future computational and experimental work so as to better understand the thus far intriguing and puzzling role(s) of uces in mammalian genomes.

Journal: Omics : a journal of integrative biology (2019)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Agnes Rimando, a Pioneer in the Fate of Glyphosate and Its Primary Metabolite in Plants.

Glyphosate is the most used herbicide on the planet because of its excellent efficacy on almost all weed species and due to the large-scale adoption of transgenic, glyphosate-resistant (gr) crops.Agnes rimando became an expert in glyphosate analysis almost 20 years ago to support research on gr crop safety and on mechanisms of evolved glyphosate resistance by weeds.Her work was the first to show that the amount of glyphosate and its primary metabolite aminomethylphosphonic acid (ampa) that accumulates in gr soybean seed from plants treated with approved glyphosate doses can approach their legal limits.However, she later found that only trace amounts of these compounds accumulate in the seed of gr maize treated with recommended glyphosate doses.She showed that gr canola, the only transgenic crop with a transgene encoding an enzyme for degradation of glyphosate, metabolizes glyphosate to ampa very rapidly.Her work was instrumental in providing support for the view that "yellow flash" symptoms sometimes observed in field-grown gr soybeans are due to accumulation of enough ampa to cause mild phytotoxicity.She did the chemical analyses in the only paper to survey the capacity of an array of plant species to metabolize glyphosate to ampa.She found a wide range in this capacity, with grasses with little or no metabolism of glyphosate to ampa and with legumes readily metabolizing glyphosate.Lastly, she found no evidence of enhanced degradation of glyphosate to be a mechanism of evolved resistance to glyphosate by two weed species but that it might be involved in natural tolerance to glyphosate of some weeds.

Journal: Journal of agricultural and food chemistry (2020)
Publication types: Biography;Historical Article;Journal Article;Portrait
Backers Beware: Characteristics and Detection of Fraudulent Crowdfunding Campaigns.

Crowdfunding has seen an enormous rise, becoming a new alternative funding source for emerging companies or new startups in recent years.As crowdfunding prevails, it is also under substantial risk of the occurrence of fraud.Though a growing number of articles indicate that crowdfunding scams are a new imminent threat to investors, little is known about them primarily due to the lack of measurement data collected from real scam cases.This paper fills the gap by collecting, labeling, and analyzing publicly available data of a hundred fraudulent campaigns on a crowdfunding platform.In order to find and understand distinguishing characteristics of crowdfunding scams, we propose to use a broad range of traits including project-based traits, project creator-based ones, and content-based ones such as linguistic cues and named entity recognition features, etc.We then propose to use the feature selection method called forward stepwise logistic regression, through which 17 key discriminating features (including six original and hitherto unused ones) of scam campaigns are discovered.Based on the selected 17 key features, we present and discuss our findings and insights on distinguishing characteristics of crowdfunding scams, and build our scam detection model with 87.3% accuracy.We also explore the feasibility of early scam detection, building a model with 70.2% of classification accuracy right at the time of project launch.We discuss what features from which sections are more helpful for early scam detection on day 0 and thereafter.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Imaging the penetration and distribution of zinc and zinc species after topical application of zinc pyrithione to human skin.

Zinc pyrithione is an active component incorporated in an extensive range of topically applied commercial products that are used worldwide.Despite its prevalence, no published study has investigated the penetration of zinc from the zinc pyrithione complex into human skin.Zinc is crucial for healthy skin function however an elevated concentration of labile zinc is toxic outside a narrow concentration range.Synchrotron x-ray fluorescence microscopy in conjunction with x-ray absorption near edge structure spectroscopy was used to map the deposition of zinc, quantitate the amount of zinc within the skin and to identify a change in the chemical form of zinc after application.This study has demonstrated a ~3.8 fold increase in zinc concentration within the viable epidermis (ve) after 24 h topical application of zinc pyrithione that increased significantly by ~250 fold after 48 h when compared to control skin.Confocal microscopy using a labile zinc specific dye, zin pyr-1, showed that zinc pyrithione disrupted the skin cells zinc homeostasis and significantly increased the intracellular zinc concentration leading to cell toxicity.Overall, this study demonstrates that topical application of zinc pyrithione formulations leads to an increase in zinc penetration in human skin, consequently, raising concerns for potential localised toxicity to occur.

Journal: Toxicology and applied pharmacology (2018)
Publication types: Journal Article
Oscillatory Neural Signatures of Visual Perception Across Developmental Stages in Individuals With 22q11.2 Deletion Syndrome.

Numerous behavioral studies have highlighted the contribution of visual perceptual deficits to the nonverbal cognitive profile of individuals with 22q11.2 deletion syndrome.However, the neurobiological processes underlying these widespread behavioral alterations are yet to be fully understood.Thus, in this paper, we investigated the role of neural oscillations toward visuoperceptual deficits to elucidate the neurobiology of sensory impairments in deletion carriers.Methods we acquired 125 high-density electroencephalography recordings during a visual grating task in a group of 62 deletion carriers and 63 control subjects.Stimulus-elicited oscillatory responses were analyzed with 1) time-frequency analysis using wavelets decomposition at sensor and source level, 2) intertrial phase coherence, and 3) granger causality connectivity in source space.Additional analyses examined the development of neural oscillations across age bins.Results deletion carriers had decreased theta-band (4-8 hz) and gamma-band (58-68 hz) spectral power compared with control subjects in response to the visual stimuli, with an absence of age-related increase of theta- and gamma-band responses.Moreover, adult deletion carriers had decreased gamma- and theta-band responses but increased alpha/beta desynchronization (10-25 hz) that correlated with behavioral performance.Granger causality estimates reflected an increased frontal-occipital connectivity in the beta range (22-40 hz).Conclusions deletion carriers exhibited decreased theta- and gamma-band responses to visual stimuli, while alpha/beta desynchronization was preserved.Overall, the lack of age-related changes in deletion carriers implicates developmental impairments in circuit mechanisms underlying neural oscillations.The dissociation between the maturation of theta/gamma- and alpha/beta-band responses may indicate a selective impairment in supragranular cortical layers, leading to compensatory top-down connectivity.

Journal: Biological psychiatry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Class comparison enabled mass spectrum purification for comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry.

Tile-based fisher ratio (f-ratio) analysis is emerging as a versatile data analysis tool for supervised discovery-based experimentation using comprehensive two-dimensional (2d) gas chromatography coupled with time-of-flight mass spectrometry (gc × gc-tofms).None the less, analyte identification can often be marred by poor 2d resolution and low analyte abundance relative to overlapping compounds.Linear algebra-based chemometric methods, in particular multivariate curve resolution alternating least squares (mcr-als), parallel factor analysis (parafac) and parafac2, are often applied in an effort to address this situation.However, these chemometric methods can fail to produce an accurate spectrum when the analyte is at low 2d resolution and/or in low relative abundance.To address this challenge, we introduce class comparison enabled mass spectrum purification (cce-msp), a method that utilizes the underlying requirement for signal consistency of the background interference compounds between the two classes in the f-ratio analysis to purify the mass spectrum of the analyte hits.Cce-msp is validated using a dataset obtained for a neat jp-8 jet fuel spiked with 14 sulfur containing compounds at two levels (15 ppm and 30 ppm), using the p-value and lack-of-fit (lof) for each analyte hit as consistency metrics.A purified mass spectrum was produced for each spiked analyte hit and their mass spectrum match value (mv) was compared to the mv obtained by mcr-als, parafac, and parafac2.The resulting mv for cce-msp were found to be as good or better than these chemometric methods, eg., for 2-butyl-5-ethylthiophene with an analyte-to-interference relative signal abundance of 1:87 and a 2d resolution of 0.2, cce-msp produced a mv of 831, compared to 476 for mcr-als, 403 for parafac, and 336 for parafac2.Cce-msp is also extended to obtain the purified spectrum for more than one analyte, eg., two analyte hits in overlapping hit locations.The spectra produced by cce-msp can also be utilized as estimates to facilitate quantitative signal decomposition using mcr-als.

Journal: Talanta (2022)
Publication types: Journal Article