syedzayyan/paper_mill_benchmark huggingface dataset:
Complex IV - The regulatory center of mitochondrial oxidative phosphorylation.

Atp, the universal energy currency in all living cells, is mainly synthesized in mitochondria by oxidative phosphorylation (oxphos).The final and rate limiting step of the respiratory chain is cytochrome c oxidase (cox) which represents the regulatory center of oxphos.Cox is regulated through binding of various effectors to its "supernumerary" subunits, by reversible phosphorylation, and by expression of subunit isoforms.Of particular interest is its feedback inhibition by atp, the final product of oxphos.This "allosteric atp-inhibition" of phosphorylated and dimeric cox maintains a low and healthy mitochondrial membrane potential (relaxed state), and prevents the formation of ros (reactive oxygen species) which are known to cause numerous diseases.Excessive work and stress abolish this feedback inhibition of cox by ca2+-activated dephosphorylation which leads to monomerization and movement of ndufa4 from complex i to cox with higher rates of cox activity and atp synthesis (active state) but increased ros formation and decreased efficiency.

Journal: Mitochondrion (2021)
Publication types: Journal Article;Review
Practices and Patterns of Hourly Neurochecks: Analysis of 8,936 Patients With Neurological Injury.

Patients experiencing acute neurological injury often receive hourly neurological assessments ("neurochecks") to capture signs of deterioration.While commonly utilized in the intensive care unit (icu) setting, little is known regarding practices (i.e., variations by age and ordering services) and patterns (i.e., duration and post-discontinuation plans) of hourly neurochecks.To inform future quality improvement intervention efforts, we performed an analysis of hourly neurochecks using an electronic health record-based dataset.Study design and methods our 75-month retrospective dataset consisted of all health system icu patients who received hourly neurochecks.Variables included age, admission diagnosis category, ordering provider, post-discontinuation order, and discharge destination.Multivariable cox regression was used to evaluate factors associated with hourly neurocheck duration.Results we evaluated 9,513 first admission hourly neurocheck orders in 8,936 patients.The trauma, neurosurgery, and neurocritical care services were responsible for 4,067 (43%), 2,071 (22%) and 1,697 (18%) hourly neurocheck orders, respectively.Median (interquartile range) hourly neurocheck duration was 1.09 (0.69, 2.35) days, and was greater than 3 and 7 days, respectively, for 1,773 (19%) and 640 (7%) patients.Median hourly neurocheck duration ranged from 0.87 (0.65, 1.68) to 1.60 (0.83, 2.97) days for neurosurgical and non-neurological icu services, respectively.Upon discontinuation, 2,225 (23%) of hourly neurochecks were transitioned to no neurochecks.Conclusion substantial differences exist between icu services and practice patterns surrounding hourly neurochecks.Understanding these differences will help inform intervention efforts aimed at streamlining hourly neurocheck practices and outcomes for patients with acute neurological injury.

Journal: Journal of intensive care medicine (2022)
Publication types: Journal Article
Stunting as a Risk Factor of Soil-Transmitted Helminthiasis in Children: A Literature Review.

As a high-burden neglected tropical disease, soil-transmitted helminth (sth) infections remain a major problem in the world, especially among children under five years of age.Since young children are at high risk of being infected, sth infection can have a long-term negative impact on their life, including impaired growth and development.Stunting, a form of malnutrition in young children, has been long assumed as one of the risk factors in acquiring the sth infections.However, the studies on sth infection in children under five with stunting have been lacking, resulting in poor identification of the risk.Accordingly, we collected and reviewed existing related research articles to provide an overview of sth infection in a susceptible population of stunted children under five years of age in terms of prevalence and risk factors.There were 17 studies included in this review related to infection with ascaris lumbricoides,trichuris trichiura, hookworm, and strongyloides stercoralisfrom various countries.The prevalence of sth infection in stunted children ranged from 12.5% to 56.5%.Increased inflammatory markers and intestinal microbiota dysbiosis might have increased the intensity of sth infection in stunted children that caused impairment in the immune system.While the age from 2 to 5 years along with poor hygiene and sanitation has shown to be the most common risk factors of sth infections in stunted children; currently there are no studies that show direct results of stunting as a risk factor for sth infection.While stunting itself may affect the pathogenesis of sth infection, further research on stunting as a risk factor for sth infection is encouraged.

Journal: Interdisciplinary perspectives on infectious diseases (2022)
Publication types: Journal Article;Review
Dietary iron to total energy intake ratio and type 2 diabetes incidence in a longitudinal 12-year analysis of the Korean Genome and Epidemiology Cohort Study.

Recent study found iron consumption has been associated with an increased risk of type 2 diabetes (t2dm).Even though, high iron intake is correlated with total caloric intake, most studies have evaluated the individual effect of iron and total caloric intake.The aim of this study was to investigate the effect of iron intake, in conjunction with total energy intake, on developing t2dm.We also investigated the interactions between dietary iron and energy ratios (iers) and iron-related single nucleotide polymorphisms (snps) in the development of t2dm.Methods the study was carried out in ansan and ansung, korea, between march 2001 and december 2014.A total of 6413 participants (3073 men and 3340 women), aged 40-69 years, were enrolled in this study.The mean follow-up period was 8.4 years.The study population was divided into quartiles based on iers with cut-off points at 4.54, 5.41, and 6.29.The odds ratios (ors) for new-onset t2dm were calculated across each quartile of iers and a random forest model was constructed using the default settings to predict new-onset t2dm.To confirm the interaction among iers, snps, and the incidence of t2dm, we measured the predictive power of new-onset t2dm using ier and six snps in genes related to iron metabolism [rs855791 (tpmrss6), rs38116479 (tf), rs1799852 (tf), rs2280673, rs1799945 (hft), rs180562 (hfe)].Results the prevalence of t2dm was 762 (11.8%).Iers showed a positive association with t2dm.The ors were 1.30 (95% ci 1.02-1.67), 1.20 (95% ci 0.94-1.56), and 1.43 (95% ci 1.11-1.86) across the ier quartiles after adjusting for non-dietary and dietary metabolic risk factors.When the ier was 1.89-fold higher than the reference group, the risk of developing t2dm increased by 43% (or 1.43; 95% ci 1.11-1.86).Conclusion a higher ier was positively associated with developing t2dm independent of dietary or non-dietary risk factors.We also found the possible interactions between the identified snps and iron intake in relations to t2dm.

Journal: European journal of nutrition (2021)
Publication types: Journal Article
Virtual vs in-person otolaryngology evaluation: The patient perspective.

To compare patient responses to validated satisfaction surveys for in-person vs virtual otolaryngology ambulatory evaluation.Methods national research corporation (nrc) health patient survey answers between april 2020 and february 2021 were divided into in-person and virtual visit modalities.Responses were compared with two group t-tests or wilcoxon rank sum tests.Relationships between visit modality by gender, age, race, and sub-specialty visit type and satisfaction scores were examined by testing interactions with separate anova models.Results 1242 in-person and 216 virtual patient satisfaction survey responses were highly favorable for all themes (communication, comprehension of treatment plan, and likelihood of future referral) with both visit modalities.Higher satisfaction for in-person evaluation was seen with communication ("care providers listened" 3.68 (0.67)-on a scale of 1-no to 4-yes, definitely) vs 3.57 (0.78), p = 0.0426; "courtesy/respect" 3.75 (0.62) vs 3.66 (0.69), p = 0.0265)), and comprehension of treatment plan ("enough info about treatment" 3.53 (0.79) vs 3.37 (0.92), p = 0.0120; "know what to do" 3.62 (0.76) vs 3.46 (0.88), p = 0.0023)).No differences were detected for future referral of clinic or provider.There was no association between visit modality and patient sociodemographic factors or sub-specialty visit types.Main effects were observed with respect to race, gender, and sub-specialty visit type.Conclusion patient satisfaction scores for virtual visit evaluation were high and comparable to in-person evaluation, with a slight preference for in-person.Future studies are needed to identify which patients and conditions are particularly suited for virtual vs in-person delivery of otolaryngology services.

Journal: American journal of otolaryngology (2022)
Publication types: Journal Article
Epidemiology of bone metastases.

This study evaluated the incidence of de novo bone metastasis across all primary cancer sites and their impact on survival by primary cancer site, age, race, and sex.Questions/purposes our objectives were (i) characterize the epidemiology of de novo bone metastasis with respect to patient demographics, (ii) characterize the incidence by primary site, age, and sex (2010-2015), and (iii) compare survival of de novo metastatic cancer patients with and without bone metastasis.Methods this is a retrospective, population-based study using nationally representative data from the surveillance, epidemiology, and end results program, 2010-2015.Incidence rates by year of diagnosis, annual percentage changes, kaplan-meier, univariate and multiple cox regression models are included in the analysis.Results of patients with cancer in the seer database, 5.1% were diagnosed with metastasis to bone, equaling ~18.8 per 100,000 bone metastasis diagnoses in the us per year (2010-2015).For adults >25, lung cancer is the most common primary site (2015 rate: 8.7 per 100,000) with de novo bone metastases, then prostate and breast primaries (2015 rates: 3.19 and 2.38 per 100,000, respectively).For patients <20 years old, endocrine cancers and soft tissue sarcomas are the most common primaries.Incidence is increasing for prostate (annual percentage change (apc) = 4.6%, p < 0.001) and stomach (apc = 5.0%, p = 0.001) cancers.The presence of de novo bone metastasis was associated with a limited reduction in overall survival (hr = 1.02, 95%, ci = [1.01-1.03], p < 0.001) when compared to patients with other non-bone metastases.Conclusion the presence of bone metastasis versus metastasis to other sites has disease site-specific impact on survival.The incidence of de novo bone metastasis varies by age, sex, and primary disease site.

Journal: Bone (2022)
Publication types: Journal Article
Single-use microfluidic device for purification and concentration of environmental DNA from river water.

Purification and concentration of dna is a critical step on dna-based analysis, which should ensure efficient dna isolation and effective removal of contaminants that may interfere with downstream dna amplification.Complexity of samples, minute content of target analyte, or high dna fragmentation greatly entangles the success of this step.To overcome this issue, we designed and fabricated a novel miniaturized disposable device for a highly efficient dna purification.The microfluidic device showed binding efficiency and elution yield of 90.1% and 86.7%, respectively.Moreover, the effect of dna fragmentation, a parameter that has not been previously addressed, showed a great impact in the recovery step.The microfluidic system integrated micropillars with chitosan being used as the solid-phase for a p h-dependent dna capture and release.We have showed the potential of the device in the successful purification of environmental dna (e dna) from river water samples contaminated with dreissena polymorpha, an invasive alien species responsible for unquestionable economic and environmental consequences in river water basins.Additionally, the device was also able to concentrate the dna extract from highly diluted samples, showing promising results for the early detection of such invasive species, which may allow prompt measures for a more efficient control in affected areas.Suitability for integration with downstream dna analysis was also demonstrated through q pcr analysis of the samples purified with the microfluidic device, allowing detection of the target species even if highly diluted.

Journal: Talanta (2021)
Publication types: Journal Article
A Historical Perspective of the Evolution of Laparoscopic Surgeries in Urology.

Recent decades have seen the rapid progression of minimally invasive surgery in urology with continuing developments in robotic technology paving ways into a new era.In addition to these technological innovations, interests from urologists in developing and embracing new techniques have become a forefront in the ongoing evolution of the field allowing for improvement in intraoperative experience as well as morbidity and mortality outcomes.This article aims to provide an overview of the historical development of laparoscopic surgery in urology while also providing a brief look into its future.

Journal: Journal of endourology (2022)
Publication types: Journal Article
Characteristics, Management, and Outcomes of Patients with Atrial Fibrillation Experiencing a Major Bleeding Event While on Rivaroxaban.

Rivaroxaban, the first oral direct factor xa inhibitor, was approved for stroke prevention in nonvalvular atrial fibrillation in 2011.Limited data are available regarding major bleeding in a clinical practice setting.The purpose of this study is to describe the patient characteristics, management, and outcomes of major bleeding events in patients receiving rivaroxaban for atrial fibrillation.This retrospective, single health system study identified patients with rivaroxaban having a major bleeding event between july 2011 and june 2014.Patients were identified through adverse event reporting or by cross-referencing rivaroxaban with international classification of diseases, ninth revision diagnosis codes for atrial fibrillation and hemorrhage, with and without transfusion.A total of 60 patients were identified.The mean age of patients was 80.3 ± 7.4 years.The most common bleed sites were gastrointestinal (63.3%) and intracranial (26.7%).Higher dose than recommended based on renal function was present in 35% of patients and concurrent antiplatelet therapy occurred in 70%.Activated prothrombin complex concentrate was utilized in 30% of patients and recombinant factor viia in 6.7%.A procedure or surgery was performed for bleed management in 10 patients.Anticoagulation was held at discharge in 76% of patients.A total of 6 patients died during hospital admission, 5 of whom experienced an intracranial hemorrhage.In conclusion, patients experiencing a rivaroxaban major bleeding event were elderly, often renally impaired, and receiving concurrent antiplatelet therapy.In-hospital mortality was 10%.The majority of patients (76%) had anticoagulation therapy held at discharge.

Journal: Clinical and applied thrombosis/hemostasis : official journal of the International Academy of Clinical and Applied Thrombosis/Hemostasis (2018)
Publication types: Journal Article
Associations between Vitamin D, Omega 6:Omega 3 Ratio, and Biomarkers of Aging in Individuals Living with and without Chronic Pain.

Elevated inflammatory cytokines and chronic pain are associated with shorter leukocyte telomere length (ltl), a measure of cellular aging.Micronutrients, such as 25-hydroxyvitamin d (vitamin d) and omega 3, have anti-inflammatory properties.Little is known regarding the relationships between vitamin d, omega 6:3 ratio, ltl, inflammation, and chronic pain.We investigate associations between vitamin d, omega 6:3 ratio, ltl, and c-reactive protein (crp) in people living with/without chronic pain overall and stratified by chronic pain status.A cross-sectional analysis of 402 individuals (63% women, 79.5% with chronic pain) was completed.Demographic and health information was collected.Chronic pain was assessed as pain experienced for at least three months.Ltl was measured in genomic dna isolated from blood leukocytes, and micronutrients and crp were measured in serum samples.Data were analyzed with general linear regression.Although an association between the continuous micronutrients and ltl was not observed, a positive association between omega 6:3 ratio and crp was detected.In individuals with chronic pain, based on clinical categories, significant associations between vitamin d, omega 6:3 ratio, and crp were observed.Findings highlight the complex relationships between anti-inflammatory micronutrients, inflammation, cellular aging, and chronic pain.

Journal: Nutrients (2022)
Publication types: Journal Article
Data on the Impact of Epidemic on Nursing Staff's Mental Health in the Context of Wireless Network.

The research was aimed to analyze the impact of epidemic pneumonia on nursing personnel's mental health under wireless network background and to improve the selection of random forest classification (rfc) algorithm parameters by the whale optimization algorithm (woa).Besides, a total of 148 in-service nursing personnel were selected as the research objects, and 148 questionnaires were recycled effectively.The collected data were analyzed by the improved rfc algorithm.In addition, the research investigated the impacts of demographic factors on nursing personnel's mental health by the one-way variance method.The results demonstrated that the accuracy of the improved algorithm in training samples and test samples reached 83.3% and 81.6%, respectively, both of which were obviously higher than those of support vector machine (svm) (80.1% and 79.3%, respectively) and back-propagation neural network (bpnn) (78.23% and 77.9%, respectively), and the differences showed statistical meanings (p< 0.05).The patient health questionnaire-9(phq-9) showed that the depression levels of 9.46% of the included personnel were above moderate.The generalized anxiety disorder(gad-7) demonstrated that the anxiety levels of 3.38% of the included personnel were above moderate.The insomnia severity index (isi) indicated that the insomnia levels of 3.38% of the included personnel were above moderate.The average score of male personnel (3.65) was obviously lower than that of female personnel (3.71).Besides, the average scale score of married personnel (3.78) was significantly higher than that of unmarried personnel (3.65).The average scale scores of personnel with bachelor's (3.66) and master's degrees (3.62) were obviously lower than those of personnel with junior college (3.77) and technical secondary school (3.75) diplomas.The average scale score of personnel with over 5-year work experience (3.68) was significantly lower than that of personnel working for less than five years (3.72).The average scale score of personnel with experience in responding to public emergencies (3.65) was obviously lower than that of personnel without related experience (3.74).The differences all showed statistical meaning (p< 0.05).The results of this research revealed that the accuracy of the improved rfc algorithm was remarkably higher than that of the svm and bpnn algorithms.Furthermore, many nursing personnel suffered from mental diseases at different levels with the impact of the epidemic.Gender, marital status, education level, and experience in responding to public emergencies were the main factors affecting nursing personnel's mental health.

Journal: Journal of healthcare engineering (2022)
Publication types: Journal Article;Retracted Publication
Improving galegine production in transformed hairy roots of Galega officinalis L. via elicitation.

Galega officinalis l.Is an herbaceous legume used to treat symptoms associated with hyperglycemia or diabetes mellitus because of its dominant alkaloid, galegine.In this study, we induced hairy roots in this plant using rhizobium rhizogenes strain a4, and investigated the effect of type, concentration, and duration of elicitor application on galegine content and some phytochemical characteristics in the hairy roots.Hence, the best growing hairy root line in terms of growth rate was selected and subcultured for treatment with elicitors.Then, at the end of the log phase of growth, chitosan (100, 200, and 400 mg/l), salicylic acid (100, 200, and 300 m m), and ultrasound (1, 2, and 4 min) were applied to hairy roots culture medium.High-performance liquid chromatography (hplc) showed that the content of galegine was significantly increased after elicitation compared with the control.Thus, the highest content of galegine (14.55 mg/g fw) was obtained 2 days after elicitation when ultrasonic waves were applied to the hairy root culture medium for 4 min.Also, elicitation resulted in a significant increase in the content of total phenol, flavonoid, h2o2and mda compared with the control.So that the highest total flavonoid content was obtained in hairy roots that were treated with ultrasonic waves for 4 min and harvested 2 days after elicitation; while, application of 400 mg/l chitosan for 4 days resulted in the highest total phenol (16.84 mg/g fw).

Journal: AMB Express (2022)
Publication types: Journal Article
Selection of a surrogate matrix for the quantification of an endogenous analyte in dried whole blood.

A surrogate matrix is needed to quantify 25-hydroxyvitamin d3in dried whole blood (dwb).To date, there has been limited guidance on approaches for quantification of endogenous analytes in atypical matrices, such as dwb.methods:different surrogate matrices were investigated in a systematic process using an lc-ms/ms assay.Performance assessment was made using quality controls of dwb with different hematocrits.results & conclusion:suitability of both phosphate-buffered saline containing bovine serum albumin and washed red blood cells recombined with phosphate-buffered saline containing bovine serum albumin as a surrogate matrix was demonstrated across a range of concentrations and hematocrits representative of expected endogenous analyte samples.

Journal: Bioanalysis (2020)
Publication types: Journal Article
Arsenic in the top predators sailfish (Istiophorus platypterus) and dolphinfish (Coryphaena hippurus) off the southeastern Gulf of California.

Distribution of arsenic (as) in tissues and gonads of the indo-pacific sailfish istiophorus platypterus and the dolphinfish coryphaena hippurus from the se gulf of california was evaluated.The bioaccumulation patterns of as were the same in the two species.In i.Platypterus, as levels (mg kg-1, wet weight) were gonads (7.4 ± 1.1) > liver (3.1 ± 0.1) > kidney (2.7 ± 0.1) > muscle (1.6 ± 0.1); in c.Hippurus, as (mg kg-1) levels were gonads (4.3 ± 0.6) > liver (3.2 ± 0.2) > kidney (2.3 ± 0.1) > muscle (1.2 ± 0.1).Differences in as distribution could be attributed to the biological functions of tissues.The hypothesis was confirmed that biomagnification was evidenced by the fact that as levels were lower in prey species than in predators.Intake of muscle from either fish did not represent a risk to humans if recommended portions a week are not exceeded, adults as much as 1802.4 g and 2454.1 g and children 257.5 and 350.6 g, for sailfish and dolphinfish, respectively.In addition, the likelihood of developing cancer due to consumption of edible tissues from either of these top predators was in the acceptable range (6.4 × 10-5to 27.3 × 10-6for a population that consumes 50 g of muscle in a week) but if a conservative combined slope factor is used the probabilities to develop bladder and lung cancer increments from 1.1 × 10-3to 9.1 × 10-5.

Journal: Environmental geochemistry and health (2021)
Publication types: Journal Article