syedzayyan/paper_mill_benchmark huggingface dataset:
H-ferritin suppression and pronounced mitochondrial respiration make Hepatocellular Carcinoma cells sensitive to RSL3-induced ferroptosis.

Ferroptosis is a form of regulated cell death dependent on iron, reactive oxygen species and characterized by the accumulation of lipid peroxides.It can be experimentally initiated by chemicals, such as erastin and rsl3, that modulate gpx4 activity, the cellular antioxidant machinery that avert lipid peroxidation.The study aimed to investigate mitochondrial respiration and ferritin function as biomarkers of ferroptosis sensitivity of hep g2 and ha22t/vgh, two hepatocellular carcinoma (hcc) cell line models.Cell viability was determined by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyltetrazolium bromide (mtt) assay, labile iron levels were determined using calcein-am fluorescence microscopy, ferritin, glutathione and lipid peroxidation were assayed with commercially available kits.The seahorse assay was used to investigate mitochondrial function in the cells.The study shows that highly differentiated hep g2 cells were more sensitive to rsl3-induced ferroptosis than the poorly differentiated ha22t/vgh (hcc) cell line (rsl3 ic500.07 μm in hep g2 vs 0.3 μm in ha22t/vgh).Interestingly, hep g2 exhibited higher mitochondrial respiration and lower glycolytic activity than ha22t/vgh and were more sensitive to rsl3-induced ferroptosis, indicating a mitochondrial-specific mechanism of action of rsl3.Interestingly, iron metabolism seems to be involved in this different sensitivity, specifically, the downregulation of h-ferritin (but not of l-subunit), makes ha22t/vgh more sensitive toward both rsl3-and iron-induced ferroptosis.Hence only the h-ferritin seems involved in the protection from this cell death process.

Journal: Free radical biology & medicine (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Menstrual Factors, Reproductive History and Liver Cancer Risk: Findings from a Prospective Cohort Study in Chinese Women.

Many studies suggested that menstrual and reproductive factors affected the gender disparity in liver carcinogenesis, but the results were inconsistent.Moreover, there are few studies in asian populations.Therefore, our study was to explore the association of menstrual and reproductive factors on liver cancer risk in chinese women.Methods 72,807 women were recruited in 1996 to 2000 and followed until the end of 2016 in shanghai, china.Cox regression models were used to estimate hrs and 95% confidence intervals (cis) for the association of menstrual and reproductive factors with liver cancer.Results 258 liver cancer cases were identified during 1,269,531 person-years of follow-up.In premenopausal and postmenopausal women, hormone replacement therapy (hrt) and injective contraceptives were positively associated with liver cancer risk respectively (hr, 1.23, 95% ci, 1.15-1.30; hr, 1.23, 95% ci, 1.17-1.30; hr, 1.07, 95% ci, 1.05-1.10; hr, 1.08, 95% ci, 1.05-1.11), while older age at menopause, longer reproductive period and fewer live births were associated with reduced risk, especially among postmenopausal women (ptrend &lt; 0.05).In addition, liver cancer risk was elevated in postmenopausal women who received hysterectomy (hr, 1.07; 95% ci, 1.04-1.11), oophorectomy (hr, 1.05; 95% ci, 1.01-1.10) or oral contraceptives (hr, 1.06; 95% ci, 1.03-1.08).No association was found between age at menarche and liver cancer risk.Similar results were observed when excluding participants with less than 2 follow-up years.Conclusions the findings suggested that female sex hormones could play significant roles in liver carcinogenesis.Impact our study was the first population-based cohort to provide epidemiology evidence of menstrual and reproductive factors on liver cancer risk in chinese women.

Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Differential regional perfusion of the human anterior cruciate ligament: quantitative magnetic resonance imaging assessment.

Surgical reconstruction is the current standard for acl rupture treatment in active individuals.Recently, there is renewed interest in primary repair of proximal acl tears.Despite this, acl biology and healing potential are currently not well understood.Vascularity is paramount in acl healing; however, previous acl vascularity studies have been limited to qualitative histological and dissection-based techniques.The study objective was to use contrast-enhanced quantitative-mri to compare relative perfusion of proximal, middle, and distal thirds of the in situ acl.We hypothesized perfusion would be greatest in the proximal third.Methods fourteen cadaveric knees were studied (8 females, 6 males), age 25-61 years.Superficial femoral, anterior tibial, and posterior tibial arteries were cannulated; without intraarticular dissection.Contrast-enhanced quantitative-mri was performed using a previously established protocol.Acl regions corresponding to proximal, middle, and distal thirds were identified on sagittal-oblique pre-contrast images.Signal enhancement (normalized to tibial plateau cartilage) was quantified to represent regional perfusion as a percentage of total acl perfusion.Comparative statistics were computed using repeated measures anova, and pairwise comparisons performed using the bonferroni method.Results relative perfusion to proximal, middle, and distal acl zones were 56.0% ±17.4%, 28.2% ±14.6%, and 15.8% ±16.3%, respectively (p = 0.002).Relative perfusion to the proximal third was significantly greater than middle (p = 0.007) and distal (p = 0.001).No statistically relevant difference in relative perfusion was found to middle and distal thirds (p = 0.281).Post-hoc subgroup analysis demonstrated greater proximal perfusion in males (66.9% ± 17.3%) than females (47.8% ± 13.0%), p = 0.036.Conclusion using quantitative-mri, in situ adult acl demonstrated greatest relative perfusion to the proximal third, nearly 2 times greater than the middle third and 3 times greater than the distal third.Knowledge of differential acl vascular supply is important for understanding pathogenesis of acl injury and the process of biological healing following various forms of surgical treatment.

Journal: Journal of experimental orthopaedics (2022)
Publication types: Journal Article
Improving lifestyles sustainability through community gardening: results and lessons learnt from the JArDinS quasi-experimental study.

Despite an increasing number of studies highlighting the health benefits of community gardening, the literature is limited by cross-sectional designs.The "jar din s" quasi-experimental study aimed to assess the impact of community garden participation on the adoption of more sustainable lifestyles among french adults.Methods individuals entering a community garden in montpellier (france) in 2018 (n = 66) were compared with pairwise matched individuals with no experience in community gardening (n = 66).Nutritional quality, environmental impact and cost of monthly household food supplies, level of physical activity measured by accelerometers, as well as mental and social well-being, sensitivity to food waste, and connection with nature were evaluated at baseline (t0) and 12 months later (t1) to explore sustainability of lifestyles in social/health, environmental and economic dimensions.Linear mixed models were used to determine the independent effect of community gardening on investigated lifestyles components.In-depth interviews were conducted at t1 with 15 gardeners to better understand changes that may have occurred in gardeners' lives during the first year of gardening.Results at t0, gardeners had lower education level, lower bmi and their household reported lower percentage of meals consumed outside of the home compared to non-gardeners (p < 0.05).Participating in the community garden had no significant impact, in spite of sufficient statistical power, on fruit and vegetables supplies (main outcome), nor on physical activity parameters, nor on others of the social/health, environmental and economic lifestyles components investigated.Qualitative interviews suggested the existence of pre-established health and environmental consciousness in some gardeners and revealed several barriers to the participation such as lack of time, lack of gardening knowledge, physical difficulty of gardening, health problems and conflicts with other gardeners.Conclusions the health benefits of community gardening previously reported by cross-sectional studies might be confounded by selection bias.The jar din s study highlights the need to identify solutions to overcome barriers related to community garden participation when designing relevant public health interventions for the promotion of sustainable lifestyles.Trial registration the study was registered at clinicaltrials.gov as nct03694782 .Date of registration: 3rd october 2018, retrospectively registered.

Journal: BMC public health (2020)
Publication types: Journal Article;Observational Study
The association of new-onset diabetes mellitus and medical therapy for benign prostatic hyperplasia: A population-based study.

Introduction benign prostatic hyperplasia (bph) and associated lower urinary tract symptoms are highly prevalent in the aging male.Similarly, the prevalence of metabolic syndrome is increasing worldwide, with mounting evidence that these two common conditions share more than age as a predisposing factor.The objective of this study was to determine if medical management of bph is associated with an increased risk of new-onset diabetes mellitus (dm) in routine care.Methods this population-based, retrospective cohort study expands on a parent study of linked administrative databases identifying patients diagnosed and treated for bph between 2005 and 2015.The primary outcome of this secondary analysis was a new diagnosis of dm after the index date of bph diagnosis.Covariates included age, dyslipidemia, hypertension, and vascular diseases.A cox proportional hazards regression model was used for inferential statistical analysis.Results a total 129 223 men were identified with a bph diagnosis and no prior history of dm.Of those men, 6390 (5%) were exposed to 5-alpha-reductase inhibitor (5-ari), 39 592 (31%) exposed to alpha-blocker (ab), and 30 545 (24%) exposed to combination therapy.Compared to those men with no bph medication use, those exposed to drugs had an increased risk of new dm.Men treated with combination therapy of 5-ari and ab (hazard ratio [hr] 1.30, 95% confidence interval [ci] 1.25-1.35), 5-ari monotherapy (hr 1.25, 95% ci 1.17-1.34), or ab monotherapy (hr 1.17, 95% ci 1.13-1.22) all were at higher risk of new dm diagnosis after adjusting for important covariates.When calculating the risk of a new diabetes diagnosis measured from the start of drug exposure, men treated with 5-aris had an increased risk of dm compared to ab monotherapy as the reference, with hr 1.12 (95% ci 1.03-1.21) for 5-ari monotherapy and hr 1.20 (95% ci 1.14-1.25) for combination therapy.Conclusions in this large, long-term, retrospective study of men with a bph diagnosis in routine practice, the risk of a new diagnosis of dm was greater in patients receiving medical management compared to controls.This modest but significant increased risk was highest in men treated with any 5-aris, in combination as well as monotherapy, compared to the abs.

Journal: Canadian Urological Association journal = Journal de l'Association des urologues du Canada (2021)
Publication types: Journal Article
Convergence of Kirkwood-Buff Integrals of Ideal and Nonideal Aqueous Solutions Using Molecular Dynamics Simulations.

The computation of kirkwood-buff integrals (kbis) using molecular simulations of closed systems is challenging due to finite system-size effects.One of the problems involves the incorrect asymptotic behavior of the radial distribution function.Corrections to rectify such effects have been proposed in the literature.This study reports a systematic comparison of the proposed corrections (as given by ganguly et al.J.Chem.Theory comput.2013, 9, 1347-1355 and krüger et al.J.Phys.Chem.Lett.2013, 4, 4-7) to assess the asymptotic behavior of the rdfs, the kbis, as well as the estimation of thermodynamic quantities for ideal urea-water and nonideal modified-urea-water mixtures using molecular dynamics simulations.The results show that applying the kbi correction suggested by krüger et al.On the rdf corrected with the ganguly et al.Correction (denoted as b-kbi) yields improved kbi convergence for the ideal and nonideal aqueous mixtures.Different averaging regions in the running kbis (correlated or long-range) are assessed, and averaging over the correlated region for large system sizes is found to be robust toward the change in the degree of solvent nonideality and concentration, providing good estimates of thermodynamic quantities.The study provides new insights into improving the kbi convergence, the suitability of different averaging regions in kbis to estimate thermodynamic properties, as well as the applicability of correction methods to achieve kbi convergence for nonideal aqueous binary mixtures.

Journal: The journal of physical chemistry. B (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The contribution of super typhoons to tropical cyclone activity in response to ENSO.

Western north pacific tropical cyclone (tc) activity is known to have a significant response to el niño and southern oscillation (enso).Among the tc intensity classifications, "super typhoon", is widely used as a symbolic word for warning people about the potential for experiencing the most severe typhoon.This study quantifies the contribution of super typhoons to tc activity in response to enso, where the southern oscillation index (soi) is used to indicate the internal variation of enso.It is found that the number and the genesis location of non-super typhoons are little influenced by enso, and the changes are mostly by the addition of super typhoons.Historical levels of el niño and la niña span from -2σ to +2σ of the soi.Over this range of soi values, the mean response is 5.6 super typhoons (7.1 for el niño and 1.5 for la niña) which nearly matches the mean response overall of 6 storms (24.6 for el niño and 18.6 for la niña).The spatial distribution of tc genesis locations for different enso conditions does not completely explain these results.

Journal: Scientific reports (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Novel management indications for conservative treatment of chylous ascites after gastric cancer surgery.

Chylous ascites (ca) presents a challenge as a relatively common postoperative complication in gastric cancer (gc).Primary conservative therapy involved total parenteral nutrition, continuous low-pressure drainage, somatostatin, and a low-fat diet.Drainage tube (dt) clamping has been presented as a potential alternative conservative treatment for gc patients with ca.Aim to propose novel conservative treatment strategies for ca following gc surgery.Methods the data of patients with ca after gc surgery performed at the fudan university shanghai cancer center between 2006 and 2021 were evaluated retrospectively.Results 53 patients underwent surgery for gc and exhibited postoperative ca during the study period.Postoperative hospitalization and time of dt removal showed a significant positive association (r2= 0.979,p< 0.001).We further observed that delayed dt removal significantly extended the total and postoperative hospitalization, antibiotic usage duration, and hospitalization cost (postoperative hospitalization: 25.8 dvs15.5 d,p< 0.001; total hospitalization: 33.2 dvs24.7 d,p< 0.01; antibiotic usage duration: 10.8 dvs6.2 d,p< 0.01; hospitalization cost: ¥9.2 × 104vs¥6.5 × 104,p< 0.01).Multivariate analysis demonstrated that postoperative infection and antibiotic usage were independent factors for delayed dt removal.Furthermore, dt removal times were shorter in seven patients who underwent dt clamping (clamped dtvsnormal group, 11.8 dvs13.6 d,p= 0.047; clamped dtvsdelayed group, 13.6 dvs27.4 d,p< 0.001).In addition, our results indicated that removal of the dt may be possible after three consecutive days of drainage volumes less than 300 m l in gc patients with ca.Conclusion infection and antibiotic usage were vital independent factors that influenced delayed dt removal in patients with ca.Appropriate standards for dt removal can significantly reduce the duration of hospitalization.Furthermore, dt clamping might be a recommended option for conservative treatment of postoperative ca.

Journal: World journal of gastroenterology (2022)
Publication types: Journal Article
A one-dimensional collagen-based biomechanical model of passive soft tissue with viscoelasticity and failure.

Introduction strains and sprains of soft tissues, including tendons and ligaments, are frequently occurring injuries.Musculoskeletal models show great promise in prediction and prevention of these injuries.However, these models rarely account for the viscoelastic properties of ligaments and tendons, much less their failure properties.The purpose of this project was to develop, simplify, and analyze a collagen-distribution model to address these limitations.Model development a distribution-moment approximation was applied to an existing partial differential equation model to reduce its computational complexity.The resulting model was equipped with a voigt model in series, which endowed it with viscoelastic properties in addition to failure properties.Results the model was able to reproduce the characteristic toe, linear, and failure regions ubiquitous throughout in-vitro tests on tissue specimens.In addition, it was able to reproduce a tri-phasic creep test consisting of an initial deformation, a steady-state, and failure.Stress-relaxation and hysteresis were also reproducible by the model.Discussion and conclusion the ability to reproduce so many characteristics of biological tissues suggests more bio-fidelity was achieved by the reduced model was other currently available models.Future work to further improve its bio-fidelity is proposed for specific tendons and ligaments.

Journal: Journal of theoretical biology (2021)
Publication types: Journal Article
Patients with suspected allergic reactions to COVID-19 vaccines can be safely revaccinated after diagnostic work-up.

When initiating the danish vaccination program against covid-19, the incidence of anaphylaxis was estimated to be 10 times higher compared to other virus-based vaccines.In this study, we present data on patients referred with suspected allergic reactions to covid-19 vaccines.The main purpose of the study is to investigate the incidence and severity of the allergic reactions, and to evaluate the safety of revaccination.Methods all patients in the region of southern denmark with case histories of allergic reactions to covid-19 vaccines in a defined period are included in this study.Diagnostic work up consisted of a detailed case history, evaluation of brighton level of diagnostic certainty and world allergy organization grade of anaphylaxis and skin prick testing- and basophil histamine release testing with covid-19 vaccines and relevant drug excipients.Patients were revaccinated at the allergy center when possible.Results sixty-one patients are included in this study.In 199,377 doses administered, nine patients fulfilled the criteria of anaphylaxis when using the brighton criteria (incidence being 45 per million).Of 55 patients with reactions to the first dose, 52 patients were revaccinated without adverse reactions.We found no proven cases of immediate anaphylaxis due to covid-19 vaccines.By skin prick test, we diagnosed three patients with drug excipient allergy and further a patient with mastocytosis was found.Conclusions anaphylactic reactions to covid-19 vaccines are rare and the incidence is similar to what is seen with other virus-based vaccines.Revaccination is safe in the majority of patients; however, allergological evaluation is important since some prove to have drug excipient allergy.

Journal: Clinical and translational allergy (2021)
Publication types: Journal Article
Evaluation of the Consumption of Fruits and Vegetables by Phenylketonurics in the Metabolic Control of Phenylalanine: An Integrative Review.

Phenylketonuria (pku) is an autosomal recessive disease caused by variants in the gene that encodes phenylalanine hydroxylase (pah), limiting the metabolism of phenylalanine (phe).When pah activity is absent or hindered, phe is not converted to tyrosine, leading to an accumulation of phe in the blood, which can cause serious neurological complications.Once pku is diagnosed, treatment should be started immediately, and the basis for this is dietary restriction of foods with high levels of phe, associated with the use of protein substitutes and intake of foods with low protein content.This restriction accompanies patients throughout their lives, making their diets unpalatable and monotonous, which represents a major challenge for health professionals and patients, considering that these factors favor food transgression.In this context, the objective of this work was to carry out an integrative review based on evidence regarding the intake of fruits and vegetables, by phenylketonurics, taking into account the greater or lesser tolerance to phe.Since, some researchers have dedicated themselves to evaluating the biochemical effect of unrestricted consumption of fruits and vegetables at pku, unifying the information in this regard.It was observed that the intake of vegetable protein by patients with pku has shown to be promising since the studies indicate that the intake of these proteins does not present adverse effects to the metabolic control of the phe.

Journal: Journal of medicinal food (2022)
Publication types: Journal Article;Review
Diversity and paleoenvironmental implications of an elasmobranch assemblage from the Oligocene-Miocene boundary of Ecuador.

The occurrence and diversity of elasmobranchs from the oligocene-miocene boundary from tropical america is poorly known in comparison with the paleodiversity from younger neogene intervals of the region.Here we describe a new elasmobranch assemblage from the rich fossil site of montañita-olón (dos bocas formation, santa elena, ecuador), where other vertebrates have already been described: for example, sea turtles and cetaceans.We report a total of 27 elasmobranch taxa, 19 of which are new fossil records for ecuador, 10 new records for the central eastern pacific and four new records for south america.Additionally, in order to reconstruct the environment where these marine remains were deposited, we performed abundance, paleobathymetric and habitat preference analyses, concluding that they were likely deposited in an outer neritic (open shelf) environment.The study of oligocene and early miocene marine elasmobranchs faunas in tropical america is key to addressing the issues in the evolutionary history of this group.

Journal: PeerJ (2020)
Publication types: Journal Article