Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Papillomavirus (HPV) DNA Triage of Women with Atypical Squamous Cells of Undetermined Significance with cobas 4800 HPV and Hybrid Capture 2 Tests for Detection of High-Grade Lesions of the Uterine Cervix

ABSTRACT The triage of women with high-risk (HR) human papillomavirus (HPV)-positive smears for atypical squamous cells of undetermined significance (ASC-US) to colposcopy is now an integrated option in clinical guidelines. The performance of cobas 4800 HPV and that of Hybrid Capture 2 (HC2) for HR HPV DNA detection in cervical samples in PreservCyt were compared in 396 women referred to colposcopy for ASC-US. Of these, 316 did not have cervical intraepithelial neoplasia (CIN), 47 had CIN1, 29 had CIN2 or CIN3 (CIN2+), and 4 had CIN of unknown grade. HR HPV was detected in 129 (32.6%) and 149 (37.6%) samples with HC2 and cobas 4800 HPV, respectively (P = 0.15). The clinical sensitivities and specificities for detecting CIN2+ were 89.7% (95% confidence interval [CI], 72.8 to 97.2%) and 66.7% (95% CI, 61.7 to 71.3%) with cobas 4800 HPV and 93.1% (95% CI, 77.0 to 99.2%) and 72.2% (95% CI 67.4 to 76.5%) with HC2. The performance of cobas 4800 HPV was similar to that of HC2 for identifying women with ASC-US who would benefit the most from colposcopy.
Large firms and heterogeneity : the structure of trade and industry under oligopoly ∗

We develop a model with endogeneity in key features of industry structure linked to cross-firm variations in costs under Cournot competition. In contrast to the literature with cost heterogeneity and atomistic firms, our approach allows us to explore firm heterogeneity in international trade in a setting with strategic interaction between potentially large firms. Entry/exit dynamics are therefore more complex but also richer. The market exhibits churn in key variables, meaning variables like market price and total sales vary over time as firms enter and exit. We also offer a solution for the integer problem inherent in small group models, based on stochastic dominance. We examine both free entry and limited entry (free exit) cases. The model generates testable predictions on the probability of zero trade flows and the pattern of export prices and is consistent with endogenous moves between zero and non-zero trade flows due to entry and exit. In a two country setting, moving from autarky to free trade means market prices fall, though along the path from autarky to free trade market prices might increase at certain points. Also with lower trade costs the least productive firms get squeezed out of the market, exporting firms gain market share, and more firms become trade oriented.
What makes a non-native accent?: a study of Korean English

We report a set of results in the second language (L2) acquisition of English phonology by first language (L1) speakers of Korean. Specifically, we focus on significant differences isolated between L2 speakers‟ production of isolated words in English and their production of the same words in sentence and phrasal contexts. Results indicate significantly more accurate production of words in isolation than in the production of the same words in phrasal contexts. The particular phonological phenomena focused on concern both stress reduction and placement. We also consider several other aspects of segmental phonology. We argue that the discrepancy in results observed between tasks may account for many of the seemingly disparate results indicated in other studies of L2 phonology. We discuss several possible explanations for these data in terms of which production task most closely provides a measurement of developing linguistic competence and which might reflect the role of either general learning strategies (overgeneralization) or reversion back to the L1 grammar under conditions of stress or when the L2 grammar is not fully developed.
Hepatobiliary alterations in patients with inflammatory bowel disease: a multicenter study. Caprilli & Gruppo Italiano Studio Colon-Retto.

BACKGROUND AND METHODS Four hundred and eighty-four patients with inflammatory bowel disease underwent clinical examination, ultrasonography, and biochemical liver function tests, to estimate the prevalence of hepatobiliary alterations. The patient group included patients without a history of liver disease. Controls were recruited from patients with functional symptoms. RESULTS More patients with ulcerative colitis than controls had liver steatosis and increased alkaline phosphatase levels. Factors increasing the probability of liver damage were long-standing disease, the presence of moderate/severe disease activity, and treatment with steroids and mesalazine. A significant association was found between biliary disease and long-standing colitis and also therapy with steroids and mesalazine. Alkaline phosphatase and aminotransferase levels were significantly higher in Crohn's disease patients than in controls. Hepatic and biliary damage was found more commonly in the 1st year after diagnosis. CONCLUSIONS The monitoring of hepatobiliary function is suggested for patients with inflammatory bowel disease, even in the absence of symptoms and history.
Changes in fat mitochondrial DNA and function in subjects randomized to abacavir-lamivudine or tenofovir DF-emtricitabine with atazanavir-ritonavir or efavirenz: AIDS Clinical Trials Group study A5224s, substudy of A5202.

BACKGROUND The effect of nonthymidine nucleoside reverse-transcriptase inhibitors (NRTIs) on fat mitochondrial DNA (mtDNA) content and function is unclear. METHODS A5202 randomized antiretroviral therapy-naive human immunodeficiency virus-infected subjects to abacavir-lamivudine (ABC/3TC) versus tenofovir DF-emtricitabine (TDF/FTC) with efavirenz (EFV) or atazanavir-ritonavir (ATV/r). A5224s, substudy of A5202, enrolled 269 subjects with fat measurements by dual-energy x-ray absorptiometry and computed tomography. A subset of subjects underwent fat biopsies at baseline and week 96 for mtDNA content (real-time polymerase chain reaction) and oxidative phosphorylation nicotinamide adenine dinucleotide (reduced) dehydrogenase (complex I) and cytochrome c oxidase (complex IV) activity levels (immunoassays). Intent-to-treat analyses were performed using analysis of variance and paired t tests. RESULTS Fifty-six subjects (87% male; median age, 39 years) were included; their median body mass index, CD4 cell count, and fat mtDNA level were 26 kg/m(2), 227 cells/μL, and 1197 copies/cell, respectively. Fat mtDNA content decreased within the ABC/3TC and TDF/FTC groups (combining EFV and ATV/r arms; median change, -341 [interquartile range, -848 to 190; P = .03] and -400 [-661 to -221; P < .001] copies/cell, respectively), but these changes did not differ significantly between the 2 groups (P = .57). Complex I and IV activity decreased significantly in the TDF/FTC group (median change, -12.45 [interquartile range, -24.70 to 2.90; P = .003] and -8.25 [-13.90 to -1.30; P < .001], optical density × 10(3)/µg, respectively) but not the ABC/3TC group. Differences between the ABC/3TC and TDF/FTC groups were significant for complex I (P = .03). CONCLUSIONS ABC/3TC and TDF/FTC significantly and similarly decreased fat mtDNA content, but only TDF/FTC decreased complex I and complex IV activity levels. CLINICAL TRIALS REGISTRATION NCT00118898.
Rpl12p affects the transcription of the PHO pathway high‐affinity inorganic phosphate transporters and repressible phosphatases

The ribosomal protein Rpl12p of Saccharomyces cerevisiae is encoded by duplicated genes, RPL12A and RPL12B. The gene products possess an identical amino acid sequence. Yeast strain 6EA1, which lacks both genes, is viable but exhibits a very slow‐growth phenotype. In this study, 6EA1 cells were transformed with plasmids carrying either RPL12A or RPL12B, and the transcriptional profiles of wild‐type W303, 6EA1 and the transformed cells grown in synthetic complete medium were examined by microarray analysis. Transcription of PHO84, a gene encoding a high‐affinity phosphate transporter, was drastically suppressed in 6EA1. PHO84 expression is induced under phosphate‐limiting conditions. Therefore, cells were grown in low‐phosphate medium and transcripts encoding the PHO pathway proteins were quantified by qRT–PCR. The high‐affinity phosphate transporters and repressible phosphatases were suppressed, while PHO4, a PHO pathway transcription activator, was upregulated in 6EA1. Accordingly, phosphate transport and acidic phosphatase activities were significantly decreased in 6EA1. Addition of RPL12A or RPL12B to 6EA1 largely lessens these effects. We postulate that RPL12 has an extra‐ribosomal function in modulating the transcription of genes that need Pho4p activation. Copyright © 2011 John Wiley & Sons, Ltd.
Educational Data Mining / Learning Analytics: Methods, Tasks and Current Trends

The 1 st international conference on "Educational Data Mining" (EDM) took place in Montreal in 2008 while the 1 st international conference on "Learning Analytics and Knowledge" (LAK) took place in Banff in 2011. Since then the fields have grown and established themselves with an annual international conference, a journal and an association each, and gradually increase their overlapping. This paper begins with some considerations on big data in education. Then the principal analysis methods used with educational data are reviewed and are illustrated with some of the tasks they solve. Current emerging trends are presented. Analysis of educational data on a routine basis to understand learning and teaching better and to improve them is not a reality yet. The paper concludes with challenges on the way.
Multiple Imputation of Covariates by Substantive-model Compatible Fully Conditional Specification

Multiple imputation is a practical, principled approach to handling missing data. When used to impute missing values in covariates of regression models, imputation models may be misspecified if they are not compatible with the substantive model of interest for the outcome. In this article, we introduce the smcfcs command, which imputes covariates by substantive-model compatible fully conditional specification. This modifies the popular fully conditional specification or chained-equations approach to multiple imputation by imputing each covariate compatibly with a user-specified substantive model. We compare the smcfcs command with standard fully conditional specification imputation using mi impute chained in a simulation study and illustrative analysis of data from a study investigating time to tumor recurrence in breast cancer.
On the Relationship Between Probabilistic and Deterministic Skills in Dynamical Seasonal Climate Prediction

Despite the gradually increasing emphasis on assessing the skill of dynamical seasonal climate predictions from the probabilistic perspective, there is a lack of in‐depth understanding that an inherent relationship may exist between the probabilistic and deterministic seasonal forecast skills. In this study, we focus on investigating this relationship, through theoretical consideration based on an analytical approach and diagnostic analysis of the historical forecasts produced by multiple dynamical models. The probabilistic forecast skill is gauged in terms of its two different attributes: resolution and reliability, while the deterministic forecast skill is measured in terms of anomaly correlation (AC). Through the theoretical consideration under certain simplified assumptions, a nonlinear, monotonic relationship is analytically derived between the resolution and the AC. Subsequent diagnostic analysis shows that the resolution and AC skills of both the multimodel ensemble and its member single models indeed appear to be approximately monotonically and nonlinearly related, specifically when they are calculated in a zonally aggregated manner by which the impact of finite sample size is reduced. This observed relationship has a specific form that is consistent with what the theory predicts. In short, the theoretical result is well verified by the dynamical model forecasts. Diagnostic analysis also shows that no good relationship exists between the reliability and the AC, signifying the difference of reliability and resolution in nature. A specific application of the proven resolution‐AC coherence is also demonstrated. The proved resolution‐AC relationship can facilitate comparisons among various assessments of seasonal climate prediction skill from the deterministic or probabilistic perspective alone.
Decline in NRF2-regulated antioxidants in chronic obstructive pulmonary disease lungs due to loss of its positive regulator, DJ-1.

RATIONALE Oxidative stress is a key contributor in chronic obstructive pulmonary disease (COPD) pathogenesis caused by cigarette smoking. NRF2, a redox-sensitive transcription factor, dissociates from its inhibitor, KEAP1, to induce antioxidant expression that inhibits oxidative stress. OBJECTIVES To determine the link between severity of COPD, oxidative stress, and NRF2-dependent antioxidant levels in the peripheral lung tissue of patients with COPD. METHODS We assessed the expression of NRF2, NRF2-dependent antioxidants, regulators of NRF2 activity, and oxidative damage in non-COPD (smokers and former smokers) and smoker COPD lungs (mild and advanced). Cigarette smoke-exposed human lung epithelial cells (Beas2B) and mice were used to understand the mechanisms. MEASUREMENTS AND MAIN RESULTS When compared with non-COPD lungs, the COPD patient lungs showed (1) marked decline in NRF2-dependent antioxidants and glutathione levels, (2) increased oxidative stress markers, (3) significant decrease in NRF2 protein with no change in NRF2 mRNA levels, and (4) similar KEAP1 but significantly decreased DJ-1 levels (a protein that stabilizes NRF2 protein by impairing KEAP1-dependent proteasomal degradation of NRF2). Exposure of Bea2B cells to cigarette smoke caused oxidative modification and enhanced proteasomal degradation of DJ-1 protein. Disruption of DJ-1 in mouse lungs, mouse embryonic fibroblasts, and Beas2B cells lowered NRF2 protein stability and impaired antioxidant induction in response to cigarette smoke. Interestingly, targeting KEAP1 by siRNA or the small-molecule activator sulforaphane restored induction of NRF2-dependent antioxidants in DJ-1-disrupted cells in response to cigarette smoke. CONCLUSIONS NRF2-dependent antioxidants and DJ-1 expression was negatively associated with severity of COPD. Therapy directed toward enhancing NRF2-regulated antioxidants may be a novel strategy for attenuating the effects of oxidative stress in the pathogenesis of COPD.
Biological and Biochemical Characterization of Sheep Scrapie in Japan

ABSTRACT Due to the apparent absence of an agent-specific nucleic acid genome, scrapie strains cannot be classified by genome characterization, which is commonly used for the classification of many viruses. However, scrapie strains can be distinguished to some extent by biological properties such as transmissibility to experimental animals and distribution of neuropathological lesions and by biochemical properties such as the molecular mass and relative protease-resistance of the disease-specific isoform of prion protein (PrPSc). In order to preliminarily characterize the scrapie strains that are prevalent in Japan, we analyzed the transmissibility of sheep scrapie isolates to mice and the relative proteinase K (PK) resistance of the corresponding PrPSc. The results indicate that Japanese scrapie strains can be divided into at least three groups based on biological and biochemical properties. The first group includes isolates which cause disease in mice with an incubation period of ∼400 days and possess PrPSc with relatively high PK resistance. Isolates of the second group contain PrPSc that is highly resistant to PK digestion but transmit poorly to mice. The final group consists of isolates that cause disease in mice with an incubation period of less than 300 days and are associated with PrPSc with reduced PK resistance. Sheep scrapie has occurred sporadically in Japan since1982, with only ∼60 officially reported cases so far. However, the diversity of scrapie strains in the field suggested by our data raises the concern that a scrapie strain similar to the parental agent of bovine spongiform encephalopathy could exist or emerge in Japan. Thus, continuous surveillance for scrapie will be required to prevent the further spread of scrapie, not only among the sheep population but also to other species, and to eliminate any potential risk of sheep scrapie to public health.
The importance of environment on respiratory genotype/phenotype relationships in the Inuit

To cite this article: Candelaria PV, Backer V, Khoo S‐K, Bizzintino JA, Hayden CM, Baynam G, Laing IA, Zhang G, Porsbjerg C, Goldblatt J, LeSouëf PN, The Greenlandic Study Population Group. The importance of environment on respiratory genotype/phenotype relationships in the Inuit. Allergy 2010; 65: 229–237.
Abundance of Antibiotic Resistance Genes in Two Municipal Wastewater Treatment Plants and Receiving Water in Atlantic Canada

Wastewater treatment plants (WWTPs) constitute a reservoir for high levels of antibiotic resistance genes (ARGs), creating public health concerns due to their presence and possible transfer between bacteria. Therefore, WWTPs may represent a critical control point in reducing the release of antibiotic resistance into the environment. The objective of this study was to investigate how the abundance of ARGs is affected by individual treatment steps in two different municipal WWTPs, located in Atlantic Canada, which use two different biological treatment technologies namely aerated lagoons (ALs) versus biological nutrient removal (BNR) reactors. Quantitative real-time PCR (qPCR) was used to quantify the absolute (copies/mL) and relative abundances (copies/copies 16S rRNA) for 9 ARGs as well as one indicator integron gene (int1) to assess ARG cassette presence and ARG mobility potential. Water quality assessment revealed both plants were meeting provincial effluent regulations, however eight out of ten genes (int1, sul1, sul2, tetO, ermB, blaCTX-M, blaTEM, qnrS) were detected in all samples at both plants (vanA was not detected in any samples, and mecA was only detected above the limit of detection in winter samples at AL plant). Although absolute ARG abundances were significantly (p<0.05) decreased from influent to effluent water samples at both plants, the relative abundance remained unchanged at the AL plant and decreased slightly at the BNR plant, suggesting that the BNR system may be better equipped to decrease relative ARG
A Comparative Study of Dual Enrollment Student Achievement in Various Learning Environments and Non-Dual Enrollment Student Achievement

A Comparative Study of Dual Enrollment Student Achievement in Various Learning Environments and Non-Dual Enrollment Student Achievement by Bethany Kaye Hall Arnold The purpose of this study was to examine whether variations in student achievement in college courses exist between high school students who took the courses as dual enrollment (DE) courses and academically comparable high school students (AIMS scholars) who took the courses upon matriculation to college. Additionally, the researcher explored whether differences exist in DE course grade for students by course environment (online, face-to-face at a high school, or faceto-face at a college.) The researcher used final course grades as determinants of student achievement. The study focused on DE student and AIMS scholar grades in English 111, Biology 101, Math 163, and History 101 courses that were taken between the 2009-2010 and 2013-2014 school years at a community college in Southwest Virginia. The population consisted of 429 AIMS scholars and 2,015 DE students. For this study 3,639 DE student grades and 706 AIMS student grades were used in calculations. The dependent variables in this study were final course grades; the independent variables were DE participation and course delivery environment. Welch’s t tests were used to examine the variations in final grades for DE and non-DE students; ANOVA procedures were used to examine variations in final course grades for DE courses based on delivery environment. The quantitative findings revealed that students who took English 111, Biology 101, Math 163, and History 101 as DE courses performed significantly better than academically comparable
Reliable shortest path finding in stochastic networks with spatial correlated link travel times

This article proposes an efficient solution algorithm to aid travelers' route choice decisions in road network with travel time uncertainty, in the context of advanced traveler information systems (ATIS). In this article, the travel time of a link is assumed to be spatially correlated only to the neighboring links within a local ‘impact area. ’ Based on this assumption, the spatially dependent reliable shortest path problem (SD-RSPP) is formulated as a multicriteria shortest path-finding problem. The dominant conditions for the SD-RSPP are established in this article. A new multicriteria A* algorithm is proposed to solve the SD-RSPP in an equivalent two-level hierarchical network. A case study using real-world data shows that link travel times are, indeed, only strongly correlated within the local impact areas; and the proposed limited spatial dependence assumption can well approximate path travel time variance when the size of the impact area is sufficiently large. Computational results demonstrate that the size of the impact area would have a significant impact on both accuracy and computational performance of the proposed solution algorithm.
Cross-Protective Efficacy of Influenza Virus M2e Containing Virus-Like Particles Is Superior to Hemagglutinin Vaccines and Variable Depending on the Genetic Backgrounds of Mice

Influenza virus M2 extracellular domain (M2e) has been a target for developing cross-protective vaccines. However, the efficacy and immune correlates of M2e vaccination are poorly understood in the different host genetic backgrounds in comparison with influenza vaccines. We previously reported the cross-protective efficacy of virus-like particle (M2e5x VLP) vaccines containing heterologous tandem M2e repeats (M2e5x) derived from human, swine, and avian influenza viruses. In this study to gain better understanding of cross-protective influenza vaccines, we compared immunogenicity and efficacy of M2e5x VLP, H5 hemagglutinin VLP (HA VLP), and inactivated H3N2 virus (H3N2i) in wild-type strains of BALB/c and C57BL/6 mice, and CD4 and CD8 knockout (KO) mice. M2e5x VLP was superior to HA VLP in conferring cross-protection whereas H3N2i inactivated virus vaccine provided high efficacy of homologous protection. After M2e5x VLP vaccination and challenge, BALB/c mice induced higher IgG responses, lower lung viral loads, and less body weight loss when compared with those in C57BL/6 mice. M2e5x VLP but not H3N2i immune mice after primary challenges developed strong immunity against a secondary heterosubtypic virus as a model of future pandemics. M2e5x VLP and HA VLP vaccines were able to raise IgG isotypes in CD4 KO mice. T cells were found to contribute to cross-protection by playing a role in reducing lung viral loads. In conclusion, M2e5x VLP vaccination induced better cross-protection than HA VLP, and its efficacy varied depending on the genetic backgrounds of mice, supporting the important roles of T cells.