syedzayyan/paper_mill_benchmark huggingface dataset:
Discovery of a novel six-long non-coding RNA signature predicting survival of colorectal cancer patients.

Colorectal cancer (crc) is one of the most leading causes of cancer deaths worldwide.In the study, we aimed to identify key long non-coding rnas (lnc rnas) significantly associated with prognosis of crc and develop an expression-based lnc rna signature to provide survival risk prediction for crc patients.Lnc rna expression profiles and clinical information of crc patients were collected from the cancer genome atlas (tcga) database.Six hundred and eighteen differentially expressed lnc rnas were identified between crc and normal tissues.After univariate and multivariate cox regression analysis for these differentially expressed lnc rnas and overall survival of crc patients, six predictive lnc rnas (rp1-170o19.17, rp11-785d18.3, rp11-798k3.2, xxbac-b476c20.9, rp11-481j13.1, and rp11-167h9.4) were finally screened out to construct a six-lnc rna signature, based on which patients in the training dataset were divided into the high-risk and low-risk group with significantly different overall survival.Roc curve analysis demonstrated competitive performance of the six-lnc rna signature.The prognostic power of the six-lnc rna signature was successfully validated in the testing and entire dataset.Multivariate cox regression analysis and stratification analysis further suggested that the six-lnc rna signature was independent of other conventional clinical variables for survival prediction in crc patients.Functional enrichment analysis revealed the possible roles of these predictive lnc rnas in some cancer-related biological processes and pathways.Our study demonstrated the promising potential of the novel six-lnc rna signature as an independent biomarker for survival prediction of crc patients.

Journal: Journal of cellular biochemistry (2018)
Publication types: Journal Article
Redesigning a Healthcare Demand Questionnaire for National Population Survey: Experience of a Developing Country.

Since its inception in 1986, the contents of the national health and morbidity survey (nhms) have been periodically updated to support emerging health data needs for evidence-based policy and program development.In 2018, the healthcare demand questionnaire was redesigned to capture diverse and changing population demand for healthcare services and their utilization pattern.This paper describes the methods and processes undertaken in redesigning the questionnaire.We aim to highlight the systematic and inclusive approach, enabling all potential evidence users to be involved, indirectly encouraging research evidence uptake for policy and program planning.We applied a systematic approach of comprehensive literature search for national-level population survey instruments implemented globally and translated non-english tools to english.The development phases were iterative, conducted in parallel with active stakeholder engagements.Here, we detailed the processes in the planning and exploratory phase as well as a qualitative assessment of the questionnaire.We included instruments from 45 countries.The majority were from the organisation for economic co-operation and development (oecd) countries and focused on perceived health, health-related behavior, and healthcare use.Thirty-four stakeholders from 14 areas of expertise were involved.Stakeholders identified additional content areas required, such as chronic pain, alternative use of healthcare services (community pharmacy, home-visit, and private medical laboratory), family doctor, and informal caregiving.The questionnaire, redesigned based on existing literature with concordant involvement and iterative feedback from stakeholders, improved the choice of health topics through the identification of new topics and modification of existing questions to better meet future evidence needs on health problems, strategy, and program planning towards strengthening the nation's health systems.

Journal: International journal of environmental research and public health (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Detection of hypermethylated BCAT1 and IKZF1 DNA in blood and tissues of colorectal, breast and prostate cancer patients.

Detection of circulating cell-free dna (ccf dna) methylated in bcat1 and ikzf1 is sensitive for detection of colorectal cancer (crc), but it is not known if these biomarkers are present in other common adenocarcinomas.Objective compare methylation levels of bcat1 and ikzf1 in tissue and plasma from breast, prostate, and colorectal cancer patients.Methods blood was collected from 290 crc, 32 breast and 101 prostate cancer patients, and 606 cancer-free controls.Tumor and matched normal tissues were collected at surgery: 26 breast, 9 prostate and 15 crc.Dna methylation in bcat1 and ikzf1 was measured in blood and tissues.Results either biomarker was detected in blood from 175/290 (60.3%) of crc patients.The detection rate was higher than that measured in controls (48/606 (8.1%), or = 18.2, 95%ci: 11.1-29.0).The test positivity rates in breast and prostate cancer patients were 9.4% (3/32) and 6.9% (7/101), respectively, and not significantly different to that measured in gender-matched controls (8.0% (33/382) females (or = 0.84, 95%ci: 0.23-3.1) and 7.6% (26/318) males (or = 0.86, 95%ci: 0.65-2.1).In tumor and non-neoplastic tissues, 93.5% (14/15) of crc tumors were methylated in bcat1 and/or ikzf1 (p< 0.004).Only 11.5% (3/26) and 44.4% (4/9) (p= 0.083) of breast and prostate tumors were hypermethylated in these two genes.Conclusions detection of circulating dna methylated in bcat1 and ikzf1 is sensitive and specific for crc but not breast or prostate cancer.

Journal: Cancer biomarkers : section A of Disease markers (2022)
Publication types: Journal Article
Genetic purity of a rear-edge population of Carex podogyna Franch. et Sav. (Cyperaceae) maintained under interspecific hybridization.

Interspecific hybridization is a critical issue in conservation biology because it may drive small populations to extinction through direct or indirect processes.In this study, to develop a conservation strategy for an endangered rear-edge population of carex podogyna in ashiu, kyoto, japan, we performed a molecular genetic analysis of the wild population and an ex-situ population established from wild seeds.Microsatellite genotypic data revealed a complete loss of genetic diversity in the wild population, suggesting that it has long been prone to genetic drift due to isolation as a small population.In contrast, microsatellite analysis of 13 ex-situ individuals detected multiple alleles that are not harbored in the wild c.Podogyna population.Sequence analysis revealed that these individuals are likely natural hybrids between c.Podogyna and a co-occurring species, c.Curvicollis, although established hybrids have never been found in the natural habitat.Based on our observation of variegated leaves in hybrid individuals, we propose that hybrids have been excluded by natural selection and/or interspecific competition caused by insufficient productivity of photosynthesis, although other genetic and ecological factors may also be influential.Overall, this study indicates that natural mechanisms selectively removing the hybrids have maintained the genetic purity of this rear-edge population of c.Podogyna, and also emphasizes the importance of genetic assessment in ex-situ conservation programs.

Journal: Genes & genetic systems (2022)
Publication types: Journal Article
Sphere-in-fiber hybrid of N-doped carbon/cerium dioxide as an interlayer material with superior electrocatalytic performance for lithium sulfide precipitation and conversion.

The inferior conductivity and infamous "shuttle effect" of lithium-sulfur (li-s) batteries lead to low sulfur utilization and undesired cycle stability, which both seriously affect their practical application.Here, a multifunctional nanofiber material based on cerium dioxide spheres embedded inside nitrogen-doped carbon fibers (denoted as ncf@ce o2) fabricated by electrospinning technology is used as an interlayer for high-performance li-s batteries.The nitrogen-doped carbon fiber skeleton matrix provides a through-conducting grid to accelerate electron transfer at the interface of the nitrogen-doped carbon and the ce o2, and the large specific surface area guarantees a sufficient interfacial fast-redox reaction for sulfur species.Ce o2with a hollow structure provides strong physicochemical adsorption of lithium polysulfides (li pss) to weaken the migration behavior, and abundant oxygen defects as catalytic active sites are conducive to lithium sulfide conversion.The "sphere in fiber" construction minimizes the direct contact between the catalyst and electrolyte, effectively avoiding side reactions.Based on the multiple functions of nitrogen-doped carbon fibers and ce o2, li-s batteries with ncf@ce o2interlayers exhibit superior electrochemical performances, including a high discharge specific capacity of 1072.9 m ah g-1at 0.2 c and a low capacity decay rate of only 0.063% per cycle after 1000 cycles.Moreover, the mechanisms of li pss adsorption-conversion and the quantification of the catalytic ability are elaborately clarified.

Journal: Journal of colloid and interface science (2022)
Publication types: Journal Article
Evolving Concepts on Inflammatory Biomarkers and Malnutrition in Chronic Kidney Disease.

While patient care, kidney replacement therapy, and transplantation techniques for chronic kidney disease (ckd) have continued to progress, the incidence of malnutrition disorders in ckd appears to have remained unchanged over time.However, there is now a better understanding of the underlying pathophysiology according to the disease background, disease stage, and the treatment received.In ckd patients, the increased production of proinflammatory cytokines and oxidative stress lead to a proinflammatory milieu that is at least partially responsible for the increased morbidity and mortality in this patient population.New insights into the pathogenic role of innate immunity and the proinflammatory cytokine profile, characterized, for instance, by higher levels of il-6 and tnf-α, explain some of the clinical and laboratory abnormalities observed in these patients.In this article, we will explore currently available nutritional-inflammatory biomarkers in distinct ckd populations (hemodialysis, peritoneal dialysis, transplantation) with a view to evaluating their efficacy as predictors of malnutrition and their involvement in the common proinflammatory process.Although there is a direct relationship between inflammatory-nutritional status, signs and symptoms [e.g., protein-energy wasting (pew), anorexia], and comorbidities (e.g., atheromatosis, atherosclerosis), we are in need of clearly standardized markers for nutritional-inflammatory assessment to improve their performance and design appropriate bidirectional interventions.

Journal: Nutrients (2022)
Publication types: Journal Article;Review
Dorsal Corporoplasty Techniques in the Management of Chordee Associated with Severe Hypospadias at a Teaching Hospital in Yaoundé, Cameroon: A Retrospective Study.

Introduction the prevalence of hypospadias is 1 in 300 male births, of whom one in four will have some form of chordee.Correction of the chordee is imperative but presents a challenge with complications, including residual chordee, penile nodulations, and shortening.This study aimed at reporting the outcomes and at sharing our experience with the surgical correction of chordee associated with hypospadias at the yaounde gyneco-obstetric and pediatric hospital (ygoph).Patients and methods we carried out a retrospective cross-sectional study covering an eight-year period from 1 january 2010 to december 2017 at the pediatric surgery service of the ygoph.The study included all files of patients with severe hypospadias who underwent chordee correction using dorsal corporoplasty techniques and were reviewed for outcome evaluation.Results a total of 40 patients met the inclusion criteria, of whom 22 (55%) had chordee corrected by the nesbit corporoplasty technique, 13 (32.5%) by the tunica albuginia plication (tap) corporoplasty technique, and five (12.5%) by the yachia corporoplasty technique.The median age at surgery was six (five to seven) years.The median follow-up period for the patients was five (three to six) years.Penile nodules were not observed in our series.Penile shortening was identified in four patients (18.2%) after nesbit corporoplasty.Four patients had a residual chordee that was significant enough, requiring another correction.Conclusion irrespective of the technique of dorsal corporoplasty used in the correction of chordee associated with severe hypospadias, penile nodulation and shortening are not of concern, and residual chordee, if present, is usually mild and does not require any correction.

Journal: Journal of the West African College of Surgeons (2020)
Publication types: Journal Article
Neutralization Titers in Vaccinated Patients with SARS-CoV-2 Delta Breakthrough Infections.

The continuous emergence of sars-co v-2 variants with increased transmission and immune evasion has caused breakthrough infections in the vaccinated population.It is important to determine the threshold of neutralizing antibody titers (nt50) that permit breakthrough infections in humans.Here, we tested the neutralization titers of vaccinated patients who contracted delta variant.All 64 patients with delta breakthrough infections exhibited nt50of less than 70.When the breakthrough sera were tested against usa-wa1/2020 (a strain isolated in late january 2020), 82.8%, 15.6%, and 1.6% of them had the nt50ranges of <20, 20 to 50, and 50 to 69, respectively.When the same breakthrough sera were tested against delta-spike sars-co v-2, 68.7%, 26.6%, and 4.7% of them had the nt50ranges of <20, 20 to 50, and 50 to 69, respectively.Overall, the results suggest nt50of 70 as a potential neutralizing threshold required to prevent delta breakthrough infections.These clinical laboratory results have implications in vaccine strategy and public health policy.importancegiven that neutralizing antibodies play a key role in protection of sars-co v-2 infection, it is important to define the neutralization levels in vaccinated individuals when they contracted breakthrough infections.In this study, we analyzed the neutralization levels from 64 vaccinated patients on days 0 to 5 before they tested positive for delta breakthrough infections.The neutralization titers in these vaccinated individuals were all lower than 70 when they contracted breakthrough infections.The results suggest a neutralization titer of 70 as the potential threshold required to prevent breakthrough infections of delta variant.

Journal: mBio (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Main and Accessory Canal Filling Quality of a Premixed Calcium Silicate Endodontic Sealer According to Different Obturation Techniques.

The present study aimed to investigate the effects of different obturation techniques on the main and accessory canal filling quality of a premixed calcium silicate endodontic sealer (endoseal tcs).We also highlighted the validity of the methods used for evaluating the canal filling quality.Thirty single-rooted premolars were used for the main canal filling and 75 were used for accessory canal filling.The canals were instrumented and randomly divided into three groups according to the filling techniques: (1) single-cone technique (sc), (2) single-cone with ultrasonic activation (su), and (3) warm vertical compaction (wv).Voids in relation to the root canal fillings were assessed using cross-section images from microcomputed tomography (μct) scans or transversely sectioned tooth specimens (n= 10).After demineralization and clearing of the teeth, the incidence, number, and completeness of the accessory canal fillings were evaluated (n= 25).One-way analysis of variance (anova) and tukey's post hoc test was used for the evaluation of the voids in the main root canal and the incidence and number of filled accessory canals.Pearson's chi-squared (χ2) test was used for the evaluation of the filling completeness (α = 0.05).In the stereomicroscopic evaluation of the sectioned specimen, the sc group had significantly higher void occurrence than the other groups (p< 0.05), although there was no difference between groups in the μct evaluation.However, there was no difference between the su and wv.There was no difference between all the groups regarding the incidence, number, and completeness of the accessory canal fillings.When the premixed calcium silicate sealer is used with sc, the ultrasonic activation is recommended to obtain a better main canal filling quality.In contrast, the obturation techniques did not affect the accessory canal filling.We also recommend using the sectioning method when the void formation in the root canal filling materials is evaluated.

Journal: Materials (Basel, Switzerland) (2020)
Publication types: Journal Article
The Prevalence of Elevated Blood Lead Levels in Foreign-Born Refugee Children Upon Arrival to the U.S. and the Adequacy of Follow-up Treatment.

This study sought to evaluate the prevalence of blood lead levels (bll) in refugee children upon arrival to the u.s.And determine whether they received bll screening and follow-up according to cdc guidelines.301 refugee children ages 6 months to 16 years were seen at the international family medicine clinic from 2003 to 2016.Data were collected on bll, treatment, age, gender, english proficiency, native language, anemia, malnutrition, and microcytosis.Bivariate analyses were conducted to determine the association between these variables and bll.The prevalence of elevated blood lead levels (ebll), defined as ≥ 10 μg/d l before june 2012 and ≥ 5 μg/d l from june 2012, was observed in 13% (n = 39).Male sex (p = 0.033), young age (p = 0.003), and microcytosis (p = 0.009) were significantly associated with ebll.Follow-up and treatment for ebll were lower than the recommended cdc guidelines for bll and greater education of healthcare providers is needed.

Journal: Journal of immigrant and minority health (2020)
Publication types: Journal Article
Supervillin Contributes to LPS-induced Inflammatory Response in THP-1 Cell-derived Macrophages.

Supervillin (svil) is an actin-binding and membrane-associated protein, which belongs to villin/gelsolin family.It has been reported that svil was involved in the regulation of macrophages' movement and lipopolysaccharide (lps) increased the svil m rna expression in neutrophils, but the underlying mechanisms remain unknown.This work investigated the underlying molecular mechanisms of lps regulating svil expression in macrophages and hence the possible role of svil in lps-induced inflammation.We found that in thp-1-derived macrophages, lps obviously increased svil m rna and protein expression.Inhibition of tlr4 by resatorvid (res) remarkably reversed the lps-induced svil expression.Additionally, inhibition of erk1/2 signaling pathway (by u0126 or gdc-0994) and nf-κb (by bay) significantly reduced the lps-induced svil expression.Interestingly, down-regulation of svil by svil-specific sh rnas significantly attenuated the expression of il-6, il-1β & tnf-α induced by lps at both m rna and protein levels.Furthermore, we also observed that svil knockdown decreased the proportion of cells in g2/m phase and increased the proportion of cells in s & g0-1phase of thp-1 derived macrophages, but did not influence the cell viability.Taken together, we demonstrated that lps induced the expression of svil via activating tlr4/nf-κb and erk1/2 mapk pathways, and svil participated in the inflammatory response of lps-induced il-6, il-1β and tnf-α upregulation in macrophages.

Journal: Inflammation (2022)
Publication types: Journal Article
Combining EQ-5D-5L items into a level summary score: demonstrating feasibility using non-parametric item response theory using an international dataset.

The eq-5d-5l is a well-established health questionnaire that estimates health utilities by applying preference-based weights.Limited work has been done to examine alternative scoring approaches when utility weights are unavailable or inapplicable.We examined whether the mokken scaling approach can elucidate 1) if the level summary score is appropriate for the eq-5d-5l and 2) an interpretation of such a score.Methods the r package "mokken" was used to assess monotonicity (scaling coefficients h, automated item selection procedure) and manifest invariant item ordering (miio: paired item response functions [irf], ht).We used a rich dataset (the multiple instrument comparison, mic) which includes eq-5d-5l data from six western countries.Results while all eq-5d-5l items demonstrated monotonicity, the anxiety/depression (ad) item had weak scalability (hi= 0.377).Without ad, scalability improved from hs= 0.559 to hs= 0.714.Miio revealed that the 5 items can be ordered, and the ordering is moderately accurate in the mic data (ht= 0.463).Excluding ad, htimproves to 0.743.Results were largely consistent across disease and country subgroups.Discussion the 5 items of the eq-5d-5l form a moderate to strong mokken scale, enabling persons to be ordered using the level summary score.Item ordering suggests that the lower range of the score represents mainly problems with pain and anxiety/depression, the mid-range indicates additional problems with mobility and usual activities, and middle to higher range of scores reveals additional limitations with self-care.Scalability and item ordering are even stronger when the anxiety/depression item is not included in the scale.

Journal: Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation (2022)
Publication types: Journal Article
AFP and eGFR are related to early and late recurrence of HCC following antiviral therapy.

An unexpected recurrence of hepatocellular carcinoma (hcc) sometimes occurs in patients with hepatitis c virus (hcv) after treatment with direct-acting antivirals (daas).However, the characteristics of patients with hcc recurrence may differ depending on time after daa treatment.We aimed to identify risk factors related to hcc recurrence according to time after daa treatment.Methods of 1663 patients with hcv treated with a daa, 199 patients had a previous history of hcc.We defined hcc recurrence within 1 year after daa treatment as 'early recurrence', and recurrence more than 1 year after as 'late recurrence'.The different risk factors between the early and late phases of hcc recurrence after the end of daa therapy were investigated.Results ninety-seven patients experienced hcc recurrence during the study period.Incidences of recurrence were 29.8, 41.0, and 53.4% at 1, 2, and 3 years, respectively, after the end of daa therapy.Multivariate analysis identified post-treatment α-fetoprotein (afp) as an independent factor contributing to hcc recurrence in the early phase (hazard ratio, 1.056; 95% confidence interval, 1.026-1.087, p < 0.001) and post-treatment estimated glomerular filtration rate (e gfr) (hazard ratio, 0.98; 95% confidence interval, 0.96-0.99, p = 0.032) as a predictor of hcc recurrence in the late phase.Conclusion patients with higher post-treatment afp in the early phase and those with lower post-treatment e gfr in the late phase had a high risk of hcc recurrence.The risk factors associated with hcc recurrence after daa treatment were different between the early and late phases.

Journal: BMC cancer (2021)
Publication types: Journal Article