syedzayyan/paper_mill_benchmark huggingface dataset:
Testing of four-sample pools offers resource optimization without compromising diagnostic performance of real time reverse transcriptase-PCR assay for COVID-19.

Quick identification and isolation of sars-co v-2 infected individuals is central to managing the covid-19 pandemic.Real time reverse transcriptase pcr (r rt-pcr) is the gold standard for covid-19 diagnosis.However, this resource-intensive and relatively lengthy technique is not ideally suited for mass testing.While pooled testing offers substantial savings in cost and time, the size of the optimum pool that offers complete concordance with results of individualized testing remains elusive.To determine the optimum pool size, we first evaluated the utility of pool testing using simulated 5-sample pools with varying proportions of positive and negative samples.We observed that 5-sample pool testing resulted in false negativity rate of 5% when the pools contained one positive sample.We then examined the diagnostic performance of 4-sample pools in the operational setting of a diagnostic laboratory using 500 consecutive samples in 125 pools.With background prevalence of 2.4%, this 4-sample pool testing showed 100% concordance with individualized testing and resulted in 66% and 59% reduction in resource and turnaround time, respectively.Since the negative predictive value of a diagnostic test varies inversely with prevalence, we re-tested the 4-sample pooling strategy using a fresh batch of 500 samples in 125 pools when the prevalence rose to 12.7% and recorded 100% concordance and reduction in cost and turnaround time by 36% and 30%, respectively.These observations led us to conclude that 4-sample pool testing offers the optimal blend of resource optimization and diagnostic performance across difference disease prevalence settings.

Journal: PloS one (2021)
Publication types: Journal Article
An IoT-Based Motion Tracking System for Next-Generation Foot-Related Sports Training and Talent Selection.

Motion tracking in different fields (medical, military, film, etc.) based on microelectromechanical systems (mems) sensing technology has been attracted by world's leading researchers and engineers in recent years; however, there is still a lack of research covering the sports field.In this study, we propose a new aio t (ai + io t) paradigm for next-generation foot-driven sports (soccer, football, takraw, etc.) training and talent selection.The system built is cost-effective and easy-to-use and requires much fewer computational resources than traditional video-based analysis on monitoring motions of players during training.The system built includes a customized wireless wearable sensing device (wwsds), a mobile application, and a data processing interface-based cloud with an ankle attitude angle analysis model.Eleven right-foot male participators wore the wwsd on their ankle while each performed 20 instances of different actions in a formal soccer field.The experimental outcome demonstrates the proposed motion tracking system based on aio t and mems sensing technologies capable of recognizing different motions and assessing the players' skills.The talent selection function can partition the elite and amateur players at an accuracy of 93%.This intelligent system can be an emerging technology based on wearable sensors and attain the experience-driven to data-driven transition in the field of sports training and talent selection and can be easily extended to analyze other foot-related sports motions (e.g., taekwondo, tumble, and gymnastics) and skill levels.

Journal: Journal of healthcare engineering (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Milk metabolites, proteins and oxidative stress markers in dairy cows suffering fromStaphylococcus aureussubclinical mastitis with or without spontaneous cure.

Our objective was to evaluate relationships between milk components (acute phase proteins, enzymes, metabolic parameters and oxidative indices) and the spontaneous cure outcome of staphylococcus aureus subclinical mastitis in dairy cows.The values of haptoglobin, serum amyloid a (saa), malondialdehyde (mda), total antioxidant capacity, milk urea nitrogen (mun), lactate dehydrogenase (ldh), alkaline phosphatase (alp), electrolytes (cl and k), total protein, albumin, α-lactalbumin, β-lactoglobulin, and immunoglobulin were measured in milk samples of s.Aureus subclinical mastitis cows with spontaneous cure (n = 23), s.Aureus subclinical mastitis cows without spontaneous cure (n = 29) and healthy cows (n = 23).The comparison of measured parameters revealed that subclinical mastitis cows with spontaneous cure had lower alp and haptoglobin concentrations both at diagnosis and after cure (p < 0.05).In contrast, total antioxidant capacity and mda concentration in subclinical mastitis cows without spontaneous cure significantly increased with time (p < 0.05).We can suggest that elevated haptoglobin concentration and higher alp activity indicative of enhanced oxidative stress could potentially serve as early diagnostic indicators of chronic disease and the persistence of s.Aureus subclinical mastitis in dairy cows.

Journal: The Journal of dairy research (2021)
Publication types: Journal Article
Blindfolded adults use mental transformation strategies for spatial scaling of tactile maps.

The current study tested strategies of spatial scaling in the haptic domain.Blindfolded adults (n = 31, aged 20-24 years) were presented with an embossed graphic including a target and asked to encode a target location on this map, imagine this map at a given scale, and to localize a target at the same spot on an empty referent space.Maps varied in three different sizes whereas the referent space had a constant size, resulting in three different scaling factors (1:1, 1:2, 1:4).Participants' response times and localization errors were measured.Analyses indicated that both response times and errors increased with higher scaling factors, suggesting the usage of mental transformation stratergies for spatial scaling.Overall, the present study provides a suitable, novel methodology to assess spatial scaling in the haptic domain.

Journal: Scientific reports (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Development of novel clinical examination scales for the measurement of disease severity in Creutzfeldt-Jakob disease.

To use a robust statistical methodology to develop and validate clinical rating scales quantifying longitudinal motor and cognitive dysfunction in sporadic creutzfeldt-jakob disease (s cjd) at the bedside.Methods rasch analysis was used to iteratively construct interval scales measuring composite cognitive and motor dysfunction from pooled bedside neurocognitive examinations collected as part of the prospective national prion monitoring cohort study, october 2008-december 2016.a longitudinal clinical examination dataset constructed from 528 patients with s cjd, comprising 1030 motor scale and 757 cognitive scale scores over 130 patient-years of study, was used to demonstrate scale utility.Results the rasch-derived motor scale consists of 8 items, including assessments reliant on pyramidal, extrapyramidal and cerebellar systems.The cognitive scale comprises 6 items, and includes measures of executive function, language, visual perception and memory.Both scales are unidimensional, perform independently of age or gender and have excellent inter-rater reliability.They can be completed in minutes at the bedside, as part of a normal neurocognitive examination.A composite examination scale can be derived by averaging both scores.Several scale uses, in measuring longitudinal change, prognosis and phenotypic heterogeneity are illustrated.Conclusions these two novel s cjd motor and cognitive scales and the composite examination scale should prove useful to objectively measure phenotypic and clinical change in future clinical trials and for patient stratification.This statistical approach can help to overcome obstacles to assessing clinical change in rapidly progressive, multisystem conditions with limited longitudinal follow-up.

Journal: Journal of neurology, neurosurgery, and psychiatry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Measurement of Digital Literacy Among Older Adults: Systematic Review.

Numerous instruments are designed to measure digital literacy among the general population.However, few studies have assessed the use and appropriateness of these measurements for older populations.Objective this systematic review aims to identify and critically appraise studies assessing digital literacy among older adults and to evaluate how digital literacy instruments used in existing studies address the elements of age-appropriate digital literacy using the european commission's digital competence (dig comp) framework.Methods electronic databases were searched for studies using validated instruments to assess digital literacy among older adults.The quality of all included studies was evaluated using the crowe critical appraisal tool (ccat).Instruments were assessed according to their ability to incorporate the competence areas of digital literacy as defined by the dig comp framework: (1) information and data literacy, (2) communication and collaboration, (3) digital content creation, (4) safety, and (5) problem-solving ability, or attitudes toward information and communication technology use.Results searches yielded 1561 studies, of which 27 studies (17 cross-sectional, 2 before and after, 2 randomized controlled trials, 1 longitudinal, and 1 mixed methods) were included in the final analysis.Studies were conducted in the united states (18/27), germany (3/27), china (1/27), italy (1/27), sweden (1/27), canada (1/27), iran (1/27), and bangladesh (1/27).Studies mostly defined older adults as aged ≥50 years (10/27) or ≥60 years (8/27).Overall, the e health literacy scale (e heals) was the most frequently used instrument measuring digital literacy among older adults (16/27, 59%).Scores on the ccat ranged from 34 (34/40, 85%) to 40 (40/40, 100%).Most instruments measured 1 or 2 of the dig comp framework's elements, but the mobile device proficiency questionnaire (mdpq) measured all 5 elements, including "digital content creation" and "safety." conclusions the current digital literacy assessment instruments targeting older adults have both strengths and weaknesses, relative to their study design, administration method, and ease of use.Certain instrument modalities like the mdpq are more generalizable and inclusive and thus, favorable for measuring the digital literacy of older adults.More studies focusing on the suitability of such instruments for older populations are warranted, especially for areas like "digital content creation" and "safety" that currently lack assessment.Evidence-based discussions regarding the implications of digitalization for the treatment of older adults and how health care professionals may benefit from this phenomenon are encouraged.

Journal: Journal of medical Internet research (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Systematic Review
Comparison of homogeneous and heterogeneous catalysts in dye-sensitised photoelectrochemical cells for alcohol oxidation coupled to dihydrogen formation.

This study examines two strategies-homo- and heterogeneous approaches for the light-driven oxidation of benzyl alcohol in dye-sensitised photoelectrochemical cells (dspecs).The dspec consists of a mesoporous anatase ti o2film on fto (fluorine-doped tin oxide), sensitised with the thienopyrroledione-based dye ap11as the photoanode and an fto-pt cathode combined with a redox-mediating catalyst.The homogeneous catalyst approach entails the addition of the soluble 2,2,6,6-tetramethylpiperidine-1-oxyl (tempo) to the dspec anolyte, while the heterogeneous strategy employs immobilisation of a tempoanalogue with a silatrane anchor (s-tempo) onto the photoanode.Irradiation of the photoanode oxidises the tempo-moiety to tempo+, both in the homogeneous and the heterogeneous system, which is a chemical oxidant for benzyl alcohol oxidation.Photoanodes containing the heterogeneous s-tempo+demonstrate decreased photocurrent, attributed to introducing alternative pathways for electron recombination.Moreover, the immobilised s-tempodemonstrates an insufficient ability to mediate electron transfer from the organic substrate to the photooxidised dye, resulting in device instability.In contrast, the homogeneous approach with tempoas a redox-mediating catalyst in the anolyte is efficient in the light-driven oxidation of benzyl alcohol to benzaldehyde over 32 hours, promoted by the efficient electron mediation of tempobetween ap11and the organic substrate.Our work demonstrates that operational limitations in dspecs can be solved by rational device design using diffusion-mediated electron transfer steps.

Journal: Sustainable energy & fuels (2021)
Publication types: Journal Article
The sesquiterpene lactone eupatolide induces apoptosis in non-small cell lung cancer cells by suppressing STAT3 signaling.

We aimed to evaluate the role of a natural sesquiterpene lactone, eupatolide, in non-small-cell lung cancer (nsclc) and further explore its underlying mechanism on regulating the activation of signal transducer and activator of transcription 3 (stat3), which is thought to have carcinogenic function in a variety of malignancies including lung cancer.Cell survival was measured by cell counting kit-8 assay.In vivo experiments were performed by inoculating nsclc cells into nude mice.Western blot and q rt-pcr were applied to detect the activation level of stat3 and the m rna levels of anti-apoptotic markers.The cell apoptosis was measured by annexin v-fitc/pi apoptosis detection kit.Our results showed that eupatolide suppressed the survival of nsclc cells in a dose and time dependent manner.Furthermore, eupatolide increased the anti-tumor activity of the chemotherapeutic drugs cisplatin and 5-fluoracil (5-fu).The xenograft study revealed that eupatolide suppressed tumor growth of nsclc cells in vivo.Furthermore, eupatolide induced apoptosis by suppressing the activation of stat3 in nsclc cells.Sustained activation or knockdown of stat3 suppressed and enhanced the activity of eupatolide, respectively.This paper is the first to report that eupatolide could effectively inhibit nsclc progression, suggesting that eupatolide might be utilized as a novel stat3 inhibitor for treating nsclc.

Journal: Environmental toxicology and pharmacology (2021)
Publication types: Journal Article
Mild inflammation persists in the glenohumeral joint of patients with shoulder instability: Cross-sectional study.

Approximately two-thirds of patients with history of shoulder dislocation may develop osteoarthritis (oa) of the glenohumeral joint.However, the biochemical mechanisms underlying the association between dislocation and oa are largely unknown.This study aimed to investigate macrophage markers and inflammatory cytokine expression associated with shoulder instability (si) in comparison to rotator cuff tears (rcts).Design this study included 30 patients with si and 30 patients with rcts.Synovial membrane samples were harvested from the rotator interval during the arthroscopic anatomical repair for both groups.The localization of tumor necrosis factor-α (tnf-α), interleukin (il)-1β, and cluster of differentiation (cd) 68 in synovial membranes was determined by immunohistochemistry.Transcript-level expressions of the inflammatory cytokines (tnfaand il1b) and macrophage markers pan-cd68and -m1 (cd80and cd86) were quantified.Cd80 and cd86 expression in macrophages from the si group was confirmed using flow cytometry.Results tnf-α, il-1β, and cd68 were expressed in the synovial lining layer of the synovial tissue in both groups.In addition, the m rna expressions of tnfa,il1b,cd68, and cd80were significantly higher in the si group compared to the rct group (p ​= ​0.012, 0.014, 0.022, 0.003, respectively).In samples from the si group, 96.3% of cd68+/cd14+ macrophages were cd86-positive, whereas 2.5% of cd68+/cd14+/cd86+ cells were cd80-positive.Conclusions patients with si had higher m rna levels of tnfa,il1b,cd68, and cd80than those with rcts.These findings may partially explain the biochemical mechanism underlying the frequent development and progression of osteoarthritis in patients with si.

Journal: Osteoarthritis and cartilage open (2022)
Publication types: Journal Article
Analysis of radical formation by EPR in complex starch-protein-lipid model systems and corn extrudates.

The formation of short-lived and stable radicals was investigated using electron paramagnetic resonance (epr) spectroscopy and compared with hydroperoxides and hexanal in complex starch-protein-lipid model systems, as well as in corn extrudates.Stable radicals were detected directly in ground samples.Short-lived lipid radicals were measured ex situ in ethyl acetate extracts of model systems and extrudates by the use of the spin trap pbn.Significant adduct formation was found after 30 min at 50 °c.During storage, lipid radicals (pbn adducts) increased in model systems.Simulation of epr spectra from bulk oil demonstrated that mainly alkoxyl radical adducts were detected, to which rapidly decomposing peroxyl radical adducts also contributed.Stable radicals in extrudates were attributed to protein radicals based on g-value of 2.00467 compared with 2.00474 found in model system prepared with zein.The signal intensity of the stable radical remained constant during storage, but increased during extrusion.

Journal: Food chemistry (2020)
Publication types: Journal Article
Postoperative adjuvant radiation for cervix cancer: reflections on the evidence and a peep into the future.

Early stage cervical cancer, stages ib1-2 and iia1, can be treated with (chemo)radiation and brachytherapy or radical hysterectomy with or without further adjuvant (chemo)radiation.In a carefully selected cohort for surgery, traditionally a small proportion of patients would need adjuvant (chemo)radiation so that the therapeutic ratio is maximized.However, advances in radiation technology, specifically intensity modulated radiotherapy, have led to a reduction in treatment related adverse events.Also, recent developments in risk stratification suggest using a lower threshold to offer adjuvant treatment to minimize pelvic relapse.These developments together present opportunities of not only re-examining the therapeutic ratio but also of further evolving postoperative risk stratification.This review article summarizes the current evidence on adjuvant treatment strategies and summarizes the key areas where research should be focused.

Journal: International journal of gynecological cancer : official journal of the International Gynecological Cancer Society (2022)
Publication types: Journal Article;Review
The incidence of reintervention and reoperation following Heller myotomy across multiple indications.

Introduction achalasia is a debilitating primary esophageal motility disorder.Heller myotomy (hm) is a first-line therapy for the treatment of achalasia patients who have failed other modalities.Other indications for hm include diverticulum, diffuse esophageal spasm, and esophageal strictures.However, long-term outcomes of hm are unclear.This study aims to assess incidence of reintervention, either endoscopically or through minimally invasive or resectional procedures, in patients who underwent hm in new york state.Methods the statewide planning and research cooperative system (sparcs) administrative longitudinal database identified 1817 adult patients who underwent hm between 2000 and 2008 for achalasia, esophageal diverticulum, diffuse esophageal spasm, and esophageal strictures, based on icd-9 and cpt codes.Through the use of unique identifiers, patients requiring reintervention were tracked up to 2016 (for at least 8 years follow-up).Primary outcome was incidence of subsequent procedures following hm.Secondary outcomes were time to reintervention and risk factors for reintervention.Results of the 1817 patients who underwent hm, 320 (17.6%) required subsequent intervention.Of the 320 patients, 234 (73.1%) underwent endoscopic reinterventions, 54 (16.9%) underwent minimally invasive procedures, and 32 (10%) underwent resectional procedures as their initial revisional intervention.Of the 234 patients who underwent endoscopic reintervention as their initial revisional procedure, only 40 (16.8%) required subsequent surgical procedures.Over a mean follow-up of 7.0 years, the mean time to a subsequent procedure was 4.3 ± 3.74 years.Reintervention rates after 10 years following hm for achalasia, diverticulum ,and other indication were 24.4%, 12.6%, and 37%, respectively.Conclusion the majority of hm reinterventions were managed solely by endoscopic procedures (60.6%).Heller myotomy remains an excellent procedure to prevent surgical reintervention for achalasia and diverticulum.

Journal: Surgical endoscopy (2022)
Publication types: Journal Article
Leigh syndrome associated with TRMU gene mutations.

T rna 5-methylaminomethyl-2-thiouridylate methyltransferase (trmu) deficiency causes an early onset potentially reversible acute liver failure, so far reported in less than 30 patients.We describe two new unrelated patients with an acute liver failure and a neuroimaging compatible with leigh syndrome (ls) due to trmu deficiency, a combination not previously reported.Our report enlarges the phenotypical spectrum of trmu disease.

Journal: Molecular genetics and metabolism reports (2021)
Publication types: Journal Article
Multilevel interactions between native and ectopic isoprenoid pathways affect global metabolism in rice.

Isoprenoids are natural products derived from isopentenyl diphosphate (ipp) and dimethylallyl diphosphate (dmapp).In plants, these precursors are synthesized via the cytosolic mevalonate (mva) and plastidial methylerythritol phosphate (mep) pathways.The regulation of these pathways must therefore be understood in detail to develop effective strategies for isoprenoid metabolic engineering.We hypothesized that the strict regulation of the native mva pathway could be circumvented by expressing an ectopic plastidial mva pathway that increases the accumulation of ipp and dmapp in plastids.We therefore introduced genes encoding the plastid-targeted enzymes hmgs, t hmgr, mk, pmk and mvd and the nuclear-targeted transcription factor wr1 into rice and evaluated the impact of their endosperm-specific expression on (1) endogenous metabolism at the transcriptomic and metabolomic levels, (2) the synthesis of phytohormones, carbohydrates and fatty acids, and (3) the macroscopic phenotype including seed morphology.We found that the ectopic plastidial mva pathway enhanced the expression of endogenous cytosolic mva pathway genes while suppressing the native plastidial mep pathway, increasing the production of certain sterols and tocopherols.Plants carrying the ectopic mva pathway only survived if wr1 was also expressed to replenish the plastid acetyl-co a pool.The transgenic plants produced higher levels of fatty acids, abscisic acid, gibberellins and lutein, reflecting crosstalk between phytohormones and secondary metabolism.

Journal: Transgenic research (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't