bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global analysis of mRNA decay intermediates in Bacillus subtilis wild‐type and polynucleotide phosphorylase‐deletion strains
Authors: Liu Bo , Deikus Gintaras , Bree Anna , Durand Sylvain , Kearns Daniel B. , Bechhofer David H. 
Published: August 2014

SummaryMessenger RNA decay in Bacillus subtilis is accomplished by a combination of exoribonucleases and endoribonucleases. Intermediates in the decay process have not been readily detectable, and previous studies on mRNA decay have used a handful of highly expressed transcripts as models. Here, we use RNA‐Seq analysis to probe mRNA turnover globally. A significant fraction of messages showed differential accumulation of RNA fragments that mapped near the 5′ or 3′ end of the coding sequence, consistent with initiation of decay from either the 5′ end or from an internal cleavage site. Patterns of mRNA decay in the wild type were compared with patterns in a mutant strain lacking polynucleotide phosphorylase (PNPase), which is considered the major 3′ exonuclease activity in mRNA decay and which is one of four known 3′ exonucleases in B. subtilis. The results showed a striking dependence on PNPase for mRNA turnover in many cases, suggesting specificity in the ability of 3′ exonucleases to degrade from 3′‐hydroxyl termini. RNA‐Seq data demonstrated a sharp decrease in expression of Sigma D in the PNPase‐deletion strain. Reduction in sigD regulon expression explained the chain growth phenotype of the PNPase mutant and also predicted a defect in swarming motility.
Advanced glycation end products increase expression of S100A8 and A9 via RAGE–MAPK in rat dental pulp cells
Authors: Nakajima Y , Inagaki Y , Kido J , Nagata T 
Published: August 2014

ObjectiveAdvanced glycation end products (AGE) are involved in the progression of diabetic complications. Although our previous reports show that AGE increased dental pulp calcification, AGE accumulation is also associated with inflammation. This study examined AGE effect on the expression of inflammation factors using rat dental pulp tissues and cell cultures.Materials and MethodsReceptor for AGE (RAGE), S100A8, S100A9, and interleukin (IL)‐1β were selected as inflammation parameters. Rat dental pulp cells were cultured and treated with AGE, and the effects were determined by real‐time PCR. An anti‐RAGE antibody or MAPK pathway inhibitors (PD98059, SB203580, and SP60012) were used to investigate AGE signaling pathway.ResultsThe mRNA levels of RAGE, S100A8, S100A9, and IL‐1β were higher in diabetic pulp tissues. AGE increased mRNA expressions of S100A8, S100A9, and IL‐1β in cultured dental pulp cells. In the presence of anti‐RAGE antibody, AGE did not increase in S100A8 or S100A9 expressions. The AGE‐induced increases in S100A8 and S100A9 were inhibited by PD98059 and SB203580, respectively.ConclusionsAdvanced glycation end products increased mRNA expression of S100A8, S100A9, and IL‐1β under diabetic pulp conditions, and AGE‐induced increases in S100A8 and S100A9 expressions may be associated with the RAGE–MAPK signaling pathway.
Charity and Error‐Theoretic Nominalism
Authors: Båve Arvid 
Published: August 2014

AbstractI here investigate whether there is any version of the principle of charity both strong enough to conflict with an error‐theoretic version of nominalism about abstract objects (EN), and supported by the considerations adduced in favour of interpretive charity in the literature. I argue that in order to be strong enough, the principle, which I call “(Charity)”, would have to read, “For all expressions e, an acceptable interpretation must make true a sufficiently high ratio of accepted sentences containing e”. I next consider arguments based on (i) Davidson's intuitive cases for interpretive charity, (ii) the reliability of perceptual beliefs, and (iii) the reliability of “non‐abstractive inference modes”, and conclude that none support (Charity). I then propose a diagnosis of the view that there must be some universal principle of charity ruling out (EN). Finally, I present a reason to think (Charity) is false, namely, that it seems to exclude the possibility of such disagreements as that between nominalists and realists.
Unilateral microphthalmia or anophthalmia in eight pythons (Pythonidae)
Authors: Da Silva Mari‐Ann O. , Bertelsen Mads F. , Wang Tobias , Pedersen Michael , Lauridsen Henrik , Heegaard Steffen 
Published: August 2014

AbstractObjectiveTo provide morphological descriptions of microphthalmia or anophthalmia in eight pythons using microcomputerized tomography (μCT), magnetic resonance imaging (MRI), and histopathology.Animals studiedSeven Burmese pythons (Python bivittatus) and one ball python (P. regius) with clinically normal right eyes and an abnormal or missing left eye.ProcedureAt the time of euthanasia, four of the eight snakes underwent necropsy. Hereafter, the heads of two Burmese pythons and one ball python were examined using μCT, and another Burmese python was subjected to MRI. Following these procedures, the heads of these four pythons along with the heads of an additional three Burmese pythons were prepared for histology.ResultsAll eight snakes had left ocular openings seen as dermal invaginations between 0.2 and 2.0 mm in diameter. They also had varying degrees of malformations of the orbital bones and a limited presence of nervous, glandular, and muscle tissue in the posterior orbit. Two individuals had small but identifiable eyes. Furthermore, remnants of the pigmented embryonic framework of the hyaloid vessels were found in the anophthalmic snakes. Necropsies revealed no other macroscopic anomalies.ConclusionsEight pythons with unilateral left‐sided microphthalmia or anophthalmia had one normal eye and a left orbit with malformed or incompletely developed ocular structures along with remnants of fetal structures. These cases lend further information to a condition that is often seen in snakes, but infrequently described.
Histopathologic insights into the mechanism of anti‐non‐Gal antibody‐mediated pig cardiac xenograft rejection
Authors: Byrne Guerard W. , Azimzadeh Agnes M. , Ezzelarab Mohamed , Tazelaar Henry D. , Ekser Burcin , Pierson Richard N. , Robson Simon C. , Cooper David K. C. , McGregor Christopher G. A. 
Published: August 2014

AbstractThe histopathology of cardiac xenograft rejection has evolved over the last 20 yr with the development of new modalities for limiting antibody‐mediated injury, advancing regimens for immune suppression, and an ever‐widening variety of new donor genetics. These new technologies have helped us progress from what was once an overwhelming anti‐Gal‐mediated hyperacute rejection to a more protracted anti‐Gal‐mediated vascular rejection to what is now a more complex manifestation of non‐Gal humoral rejection and coagulation dysregulation. This review summarizes the changing histopathology of Gal‐ and non‐Gal‐mediated cardiac xenograft rejection and discusses the contributions of immune‐mediated injury, species‐specific immune‐independent factors, transplant and therapeutic procedures, and donor genetics to the overall mechanism(s) of cardiac xenograft rejection.
Prevalence, Characterization and Antibiotic Resistance of Salmonella Isolates in Large Corvid Species of Europe and North America Between 2010 and 2013
Authors: Janecko N. , Čížek A. , Halová D. , Karpíšková R. , Myšková P. , Literák I. 
Published: August 2014

SummaryIt is well understood that Salmonella is carried by animals and in majority of cases as asymptomatic hosts. Surveillance efforts have focused on the role of agriculture and contamination points along the food chain as the main source of human infection; however, very little attention has been paid to the contribution of wildlife in the dissemination of Salmonella and what effect anthropogenic sources have on the circulation of antibiotic resistant Salmonella serovars in wildlife species. A purposive survey was taken of large corvids roosting yearly between November and March in Europe and North America. Two thousand and seven hundred and seventy‐eight corvid faecal specimens from 11 countries were submitted for Salmonella spp. culture testing. Presumptive positive isolates were further serotyped, susceptibility tested and analysed for antibiotic resistance genes. Overall, 1.40% (39/2778) (CI = 1.01, 1.90) of samples were positive for Salmonella spp. Salmonella Enteritidis was the most prevalent serovar followed by S. Infantis, S. Montevideo and S. Typhimurium. No significant difference (P > 0.05) was found in the proportion of Salmonella recovered in Europe versus North America. The most variability of serovars within a site was in Kansas, USA with five different serovars recovered. European sites were significantly more likely to yield Salmonella resistant to more than one antibiotic (OR 71.5, P < 0.001, CI = 3.77, 1358) than North American sites, where no resistance was found. Resistance to nalidixic acid, a quinolone, was recovered in nine isolates from four serovars in four different sites across Europe. Large corvids contribute to the transmission and dissemination of Salmonella and resistance genes between human and animal populations and across great distances. This information adds to the knowledge base of zoonotic pathogen prevalence and antibiotic resistance ecology in wild birds.
Is the Provision of Physical Education to Senior-Years Students Associated With Greater Physical Activity Levels? Insight Into a Province-Wide Policy
Authors: Comte Melisa , Hobin Erin , Manske Steve , Casey Catherine , Griffith Jane , Leggett Carly , Veugelers Paul , Murnaghan Donna , McGavock Jonathan 
Published: August 2014

Objectives:The purpose of this study was to determine if participation in physical education (PE) was associated with increased moderate-to-vigorous physical activity (MVPA) levels in adolescents.Methods:This was a cross sectional study comparing MVPA levels in senior-years students—grade 11 and 12—enrolled in high school PE during the semester data were collected compared with those not enrolled in PE in that same semester. The primary outcome measure was daily MVPA measured by accelerometry. The primary exposure was participation in PE.Results:Among the 508 adolescents (16.9 ± 0.8 yrs, 49% female, n = 338 exposed to PE) studied, no differences in MVPA (47.0 ± 25.8 vs. 43.9 ± 25.0 mins/day, P = .25) or sedentary time (540.2 ± 94.7 vs. 550.2 ± 79.4 mins/day, P = .79) were noted between students enrolled in PE compared with students not enrolled in PE. Participation in PE was associated with a greater odds of achieving >60 minutes of MVPA daily (OR: 1.69; 95% CI: 1.04−2.75). This association was stronger among boys (OR: 2.4; 95% CI: 1.2−4.8) than girls (OR: 1.17; 95% CI: 5−2.7).Conclusion:Enrollment in PE in grade 11 or 12 is associated with modestly higher levels of MVPA and an increased likelihood of meeting PA guidelines among students in grades 11 and 12, particularly among boys.
Contextual Influences on Weight Status Among Impoverished Adolescents: Neighborhood Amenities for Physical Activity and State Laws for Physical Education Time Requirements
Authors: Oh April Y. , Hennessy Erin , McSpadden Kate E. , Perna Frank M. 
Published: August 2014

Purpose:This study examines the relationship between state laws for physical education and neighborhood amenities for physical activity on weight status in adolescents of low socioeconomic status.Methods:Data from 2 national data sources: Classification of Laws Associated with School Students (CLASS) and the National Survey of Children’s Health (NSCH) were combined and analyzed.Results:Multinomial regression models found that adolescents in states with strong PE law were associated with a lower odds of being obese [OR = 0.63 (0.41, 0.97)]; however, when PE law and neighborhood amenities were included, only neighborhood amenities were associated with lower odds of obesity, but also greater odds of overweight status.Conclusion:This study emphasizes the potential significance of state laws on low SES groups to combat obesity; as well as the potential differential effects of local level factors, and alignment with policy goals for healthy weight.
Measuring the Ability to Tolerate Activity-Related Discomfort: Initial Validation of the Physical Activity Acceptance Questionnaire (PAAQ)
Authors: Butryn Meghan L. , Arigo Danielle , Raggio Greer A. , Kaufman Alison Infield , Kerrigan Stephanie G. , Forman Evan M. 
Published: August 2014

Background:Physical activity (PA) is essential for health, but many adults find PA adherence challenging. Acceptance of discomfort related to PA may influence an individual’s ability to begin and sustain a program of exercise. The aim of this study was to evaluate the psychometric properties of the Physical Activity Acceptance Questionnaire (PAAQ).Methods:The PAAQ was administered to 3 distinct samples (N = 418). Each sample completed additional self-report measures; 1 sample also wore accelerometers for 7 days (at baseline and 6 months later).Results:The PAAQ demonstrated high internal validity for its total score (α = .89) and 2 subscales (Cognitive Acceptance α = .86, Behavioral Commitment α = .85). The PAAQ also showed convergent validity with measures of mindfulness, self-reported physical activity levels, and accelerometer-verified levels of moderate-to-vigorous PA (MVPA; P-values < .05). The Cognitive Acceptance subscale showed predictive validity for objectively-verified PA levels among individuals attempting to increase PA over 6 months (P = .05). Test-retest reliability for a subset of participants (n = 46) demonstrated high consistency over 1 week (P < .0001).Conclusions:The PAAQ demonstrates sound psychometric properties, and shows promise for improving the current understanding of PA facilitators and barriers among adults.
Total Activity Counts and Bouted Minutes of Moderate-To-Vigorous Physical Activity: Relationships With Cardiometabolic Biomarkers Using 2003–2006 NHANES
Authors: Wolff-Hughes Dana L. , Fitzhugh Eugene C. , Bassett David R. , Churilla James R. 
Published: August 2014

Purpose:To contrast associations of accelerometer-measured moderate-to-vigorous physical activity (MVPA) accumulated in bouts and total activity counts (TAC) with cardiometabolic biomarkers in U.S. adults.Methods:Using 2003–2006 National Health and Nutrition Examination Survey (NHANES) data, the sample was comprised of adults ≥ 20 years, not pregnant or lactating, with self-reported PA and at least 4 days of ≥ 10 hours accelerometer wear time (N = 5668). Bouted MVPA represented the minutes/day with ≥ 2020 counts/minute in bouts of 10 minutes or longer and TAC represented the total activity counts per day. Biomarkers included: cholesterol, triglyceride, glycohemoglobin, plasma glucose, C-peptide, insulin, C-reactive protein, homocysteine, blood pressure, body mass index (BMI), waist circumference, and skinfolds. Nested regression models were conducted which regressed each biomarker on bouted MVPA and TAC simultaneously, while adjusting for relevant covariates.Results:Results indicated TAC was more strongly associated with 11 biomarkers: HDL-C, triglyceride, plasma glucose, C-peptide, insulin, C-reactive protein, homocysteine, systolic blood pressure, waist circumference, triceps skinfold, and subscapular skinfold. Bouted MVPA, however, only displayed stronger associations with BMI.Conclusions:The total volume of physical activity, represented by TAC, appears to have stronger associations with cardiometabolic biomarkers than MVPA accumulated in bouts.
Physical and Sedentary Activity Levels Among Preschoolers in Home-Based Childcare: A Systematic Review
Authors: Vanderloo Leigh M. , Martyniuk Olivia J. M. , Tucker Patricia 
Published: August 2014

Background:Although preschoolers’ physical activity in center-based childcare has received considerable attention, less is known regarding this group’s activity levels within home-based childcare. This review aimed to explore and synthesize the literature on preschoolers’ physical and sedentary activity levels in home-based childcare. Outdoor playtime was also examined to contribute to the understanding of preschoolers’ activity levels within this particular setting.Methods:Nine online databases were searched for peer-reviewed, English-language, primary studies that quantitatively measured physical and sedentary activity levels of preschoolers attending home-based childcare. Studies were excluded if they were nonprimary research, if they lacked a preschool-aged sample, if they did not quantitatively measure physical or sedentary activity, or if they took place in an ineligible environment.Results:Seven articles were included in this review; 3 had objective measures of activity levels, and 4 relied on nonobjective measures. Accelerometry data suggest that preschoolers’ average sedentary, moderate-to-vigorous, and total physical activity levels in home-based childcare ranged from 39.5 to 49.6, 1.8 to 9.7, and 10.4 to 33.8 min/hr, respectively. Outdoor playtime appears to be inconsistent in home-based childcare.Conclusion:Physical activity among preschoolers attending home-based childcare appears to be relatively low and widely varied. Sedentary time has received less attention in home-based childcare settings. Future research examining activity levels in this unique environment is warranted.
Reliability and Validity of 2 Self-Report Measures to Assess Sedentary Behavior in Older Adults
Authors: Gennuso Keith P. , Matthews Charles E. , Colbert Lisa H. 
Published: August 2014

Background:The purpose of this study was to examine the reliability and validity of 2 currently available physical activity surveys for assessing time spent in sedentary behavior (SB) in older adults.Methods:Fifty-eight adults (≥65 years) completed the Yale Physical Activity Survey for Older Adults (YPAS) and Community Health Activities Model Program for Seniors (CHAMPS) before and after a 10-day period during which they wore an ActiGraph accelerometer (ACC). Intraclass correlation coefficients (ICC) examined test-retest reliability. Overall percent agreement and a kappa statistic examined YPAS validity. Lin’s concordance correlation, Pearson correlation, and Bland-Altman analysis examined CHAMPS validity.Results:Both surveys had moderate test-retest reliability (ICC: YPAS = 0.59 (P < .001), CHAMPS = 0.64 (P < .001)) and significantly underestimated SB time. Agreement between YPAS and ACC was low (κ = −0.0003); however, there was a linear increase (P < .01) in ACC-derived SB time across YPAS response categories. There was poor agreement between ACC-derived SB and CHAMPS (Lin’s r = .005; 95% CI, −0.010 to 0.020), and no linear trend across CHAMPS quartiles (P = .53).Conclusions:Neither of the surveys should be used as the sole measure of SB in a study; though the YPAS has the ability to rank individuals, providing it with some merit for use in correlational SB research.
Water droplets in oil are microhabitats for microbial life
Authors: Meckenstock Rainer U. , von Netzer Frederick , Stumpp Christine , Lueders Tillmann , Himmelberg Anne M. , Hertkorn Norbert , Schmitt-Kopplin Philipp , Harir Mourad , Hosein Riad , Haque Shirin , Schulze-Makuch Dirk 
Published: August 2014

Microbial life thrives in an oily bubbleMicroorganisms can break down hydrocarbons in oil reservoirs. Microbes grow primarily at the interface between oil and water, where they can find nutrients and dispose of metabolites. Meckenstocket al.now show that tiny water droplets can also provide a suitable home for hydrocarbon-degrading microorganisms. The authors examined oil from Pitch Lake, Trinidad and Tobago, and found that diverse microorganisms thrived in these tiny isolated microhabitats.Science, this issue p.673
Performance Comparison of the Versant HCV Genotype 2.0 Assay (LiPA) and the Abbott Realtime HCV Genotype II Assay for Detecting Hepatitis C Virus Genotype 6
Authors: Yang Ruifeng , Cong Xu , Du Shaocai , Fei Ran , Rao Huiying , Wei Lai 
Published: August 2014

ABSTRACTThe Versant HCV genotype 2.0 assay (line probe assay [LiPA] 2.0), based on reverse hybridization, and the Abbott Realtime HCV genotype II assay (Realtime II), based on genotype-specific real-time PCR, have been widely used to analyze hepatitis C virus (HCV) genotypes. However, their performances for detecting HCV genotype 6 infections have not been well studied. Here, we analyzed genotype 6 in 63 samples from the China HCV Genotyping Study that were originally identified as genotype 6 using the LiPA 2.0. The genotyping results were confirmed by nonstructural 5B (NS5B) or core sequence phylogenetic analysis. A total of 57 samples were confirmed to be genotype 6 (51 genotype 6a, 5 genotype 6n, and 1 genotype 6e). Four samples identified as a mixture of genotypes 6 and 4 by the LiPA 2.0 were confirmed to be genotype 3b. The remaining two samples classified as genotype 6 by the LiPA 2.0 were confirmed to be genotype 1b, which were intergenotypic recombinants and excluded from further comparison. In 57 genotype 6 samples detected using the Realtime II version 2.00 assay, 47 genotype 6a samples were identified as genotype 6, one 6e sample was misclassified as genotype 1, and four 6a and five 6n samples yielded indeterminate results. Nine nucleotide profiles in the 5′ untranslated region affected the performances of both assays. Therefore, our analysis shows that both assays have limitations in identifying HCV genotype 6. The LiPA 2.0 cannot distinguish some 3b samples from genotype 6 samples. The Realtime II assay fails to identify some 6a and all non-6a subtypes, and it misclassifies genotype 6e as genotype 1.
Rapid Detection of Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae from Urine Samples by Use of the ESBL NDP Test
Authors: Dortet Laurent , Poirel Laurent , Nordmann Patrice 
Published: August 2014

ABSTRACT

From June to September 2012, 500 urine samples were recovered from patients with urinary tract infections (UTI) due to Gram-negative bacilli (≥10
4
leukocytes/ml and ≥10
5
Gram-negative isolates/ml) who visited the University hospital Bicêtre (France). They were challenged with extended-spectrum-β-lactamase (ESBL)-producing
Enterobacteriaceae
(ESBL-E) using the rapid diagnostic ESBL NDP test. Results of the ESBL NDP test were compared to the results of the double-disc susceptibility test (DDST) performed on solid-agar plates and molecular identification of the β-lactamase genes. Among the 450 nonduplicate urine samples, 11.3% were positive for ESBL-E by using the DDST, the ESBL determinants being mostly of the CTX-M type (CTX-M-15) according to molecular testing. Results of the ESBL NDP test were obtained within 15 min. The sensitivity and specificity of the ESBL NDP test were 98% and 99.8%, respectively, whereas the positive and negative predictive values of this test were 98% and 99.8%, respectively. A perfect correlation between cefotaxime resistance and positivity of the ESBL NDP test was observed. Therefore, the ESBL NDP test offers a powerful tool for a rapid identification of ESBL-E and associated resistance to expanded-spectrum cephalosporins. It may be useful in particular for guiding first-line antibiotic therapy.