bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive variability to low‐pH river discharges in Acartia tonsa and stress responses to high PCO2 conditions
Authors: Aguilera Victor M. , Vargas Cristian A. , Lardies Marco A. , Poupin María J. 
Published: April 2015

AbstractEnvironmental transitions leading to spatial physical–chemical gradients are of ecological and evolutionary interest because they are able to induce variations in phenotypic plasticity. Thus, the adaptive variability to low‐pH river discharges may drive divergent stress responses [ingestion rates (IR) and expression of stress‐related genes such as Heat shock protein 70 (Hsp70) and Ferritin] in the neritic copepod Acartia tonsa facing changes in the marine chemistry associated to ocean acidification (OA). These responses were tested in copepod populations inhabiting two environments with contrasting carbonate system parameters (an estuarine versus coastal area) in the Southern Pacific Ocean, and assessing an in situ and 96‐h experimental incubation under conditions of high pressure of CO2 (PCO2 1200 ppm). Adaptive variability was a determining factor in driving variability of copepods' responses. Thus, the food‐rich but colder and corrosive estuary induced a traits trade‐off expressed as depressed IR under in situ conditions. However, this experience allowed these copepods to tolerate further exposure to high PCO2 levels better, as their IRs were on average 43% higher than those of the coastal individuals. Indeed, expression of both the Hsp70 and Ferritin genes in coastal copepods was significantly higher after acclimation to high PCO2 conditions. Along with other recent evidence, our findings confirm that adaptation to local fluctuations in seawater pH seems to play a significant role in the response of planktonic populations to OA‐associated conditions. Facing the environmental threat represented by the inter‐play between multiple drivers of climate change, this biological feature should be examined in detail as a potential tool for risk mitigation policies in coastal management arrangements.
Lineage‐specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana
Authors: Bush Stephen J. , Kover Paula X. , Urrutia Araxi O. 
Published: April 2015

AbstractRapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the ‘edges’ of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region. However, the extent to which these regions may be masking indicators of positive selection or account for the relationship between dN/dS and other genomic parameters is unclear. We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana. We also obtain lineage‐specific dN/dS estimates, making use of the recently sequenced genome of Thellungiella parvula, the second closest sequenced relative after the sister species Arabidopsis lyrata. Overall, we find that the effect of exon edge conservation, as well as the use of lineage‐specific substitution estimates, upon dN/dS ratios partly explains the relationship between the rates of protein evolution and expression level. Furthermore, the removal of exon edges shifts dN/dS estimates upwards, increasing the proportion of genes potentially under adaptive selection. We conclude that lineage‐specific substitutions and exon edge conservation have an important effect on dN/dS ratios and should be considered when assessing their relationship with other genomic parameters.
The saccharopine pathway in seed development and stress response of maize
Authors: Kiyota Eduardo , Pena Izabella Agostinho , Arruda Paulo 
Published: April 2015

AbstractLysine is catabolized in developing plant tissues through the saccharopine pathway. In this pathway, lysine is converted into α‐aminoadipic semialdehyde (AASA) by the bifunctional enzyme lysine‐ketoglutarate reductase/saccharopine dehydrogenase (LKR/SDH). AASA is then converted into aminoadipic acid (AAA) by aminoadipic semialdehyde dehydrogenase (AASADH). Here, we show that LKR/SDH and AASADH are co‐expressed in the sub‐aleurone cell layers of the developing endosperm; however, although AASADH protein is produced in reproductive and vegetative tissues, the LKR/SDH protein is detectable only in the developing endosperm. AASADH showed an optimum pH of 7.4 and Kms for AASA and NAD+ in the micromolar range. In the developing endosperm, the saccharopine pathway is induced by exogenous lysine and repressed by salt stress, whereas proline and pipecolic acid synthesis are significantly repressed by lysine. In young coleoptiles, the LKR/SDH and AASADH transcriptions are induced by abiotic stress, but while the AASADH protein accumulates in the stressed tissues, the LKR/SDH protein is not produced. In the developing seeds, the saccharopine pathway is used for pipecolic acid synthesis although proline may play a major role in abiotic stress response. The results indicate that the saccharopine pathway in maize seed development and stress responses significantly differ from that observed for dicot plants.
Effect of breast‐feeding frequency on hyperbilirubinemia in breast‐fed term neonate
Authors: Chen Ying‐Juang , Yeh Tsu‐Fu , Chen Chung‐Ming 
Published: April 2015

AbstractBackgroundHyperbilirubinemic neonates have significantly less bodyweight gain from nursery discharge to outpatient department (OPD) follow up. We tested the hypothesis that discharge instructions encouraging frequent breast‐feeding given in the nursery would increase infant bodyweight gain and decrease the incidence of hyperbilirubinemia.MethodsWe enrolled consecutively live‐born neonates who were discharged from the nursery and who received OPD follow up within the first 2 weeks of birth in 2011. The nursing staff discussed the discharge instructions with the parents at the time of nursery discharge. Parents were asked to fill in a nursing information form to record the frequency of breast‐feeding and diaper change per day.ResultsParents of 98 breast‐fed term neonates provided complete nursing information forms. These 98 neonates were classified into two groups according to breast‐feeding frequency, namely <8 times/day (63 neonates) and ≥8 times/day (35 neonates). A significant positive correlation between breast‐feeding frequency and diaper change frequency per day indicated that the data were highly reliable. The gestational age, Apgar score, birthweight, and bodyweight at nursery discharge and at OPD were similar between the two groups. Neonates who were breast‐fed ≥8 times/day had a significantly lower incidence of hyperbilirubinemia.ConclusionsNursery discharge instructions that encouraged mothers to breast‐feed their newborns frequently decreased the rate of hyperbilirubinemia in exclusively breast‐fed term neonates.
“A Logic of Camps”: French Antiracism as Competitive Nationalism
Authors: Tejani Riaz 
Published: April 2015

As the Charlie Hebdo and Copenhagen attacks starkly remind us, European multicultural policy continues to falter over the growth of public Islam. But long before these events, tension between competing visions of citizenship and nationhood had weakened the very civil society organizations that could shape such policy. In France, where non‐governmental organizations had labored against discrimination for over a century, this conflict led to profound disaffection within the nation's powerful antiracism movement. Drawing from more than two years of ethnographic fieldwork among French antiracist NGOs, this article examines that disaffection among activists whose work in the name of cultural outsiders simultaneously served to rememorialize historic national traumas from the Dreyfus Affair to Algeria. Revealing a new despondency over sociolegal advocacy for Islam, some decried “infiltration” of communitarian voices into their erstwhile republican movement while others, under increasing pressure to adopt an emergent pluralist vision, equated this new model with foreignness itself. The resulting “crisis of antiracism” saw competitive reassertions of nationhood in the face of countervailing state discourses of European postnationalism. If writings on French multiculturalism to date have focused on Islamic piety and urban youth deviance, this article examines the significant impact these have had on France's preeminent social justice movement.
A matching pursuit algorithm for inferring tonic sympathetic arousal from spontaneous skin conductance fluctuations
Authors: Bach Dominik R. , Staib Matthias 
Published: April 2015

AbstractTonic sympathetic arousal is often inferred from spontaneous fluctuations in skin conductance, and this relies on assumptions about the shape of these fluctuations and how they are generated. We have previously furnished a psychophysiological model for this relation, and an efficient and reliable inversion method to estimate tonic arousal from given data in the framework of dynamic causal modeling (DCM). Here, we provide a fast alternative inversion method in the form of a matching pursuit (MP) algorithm. Analyzing simulated data, this algorithm approximates the true underlying arousal up to about 10 spontaneous fluctuations per minute of data. For empirical data, we assess predictive validity as the ability to differentiate two known psychological arousal states. Predictive validity is comparable between the methods for three datasets, and also comparable to visual peak scoring. Computation time of the MP algorithm is 2–3 orders of magnitude faster for the MP than the DCM algorithm. In summary, the new MP algorithm provides a fast and reliable alternative to DCM inversion for SF data, in particular when the expected number of fluctuations is lower than 10 per minute, as in typical experimental situations.
A Marginalized Zero-Inflated Poisson Regression Model with Random Effects
Authors: Leann Long D. , Preisser John S. , Herring Amy H. , Golin Carol E. 
Published: April 2015

SummaryPublic health research often concerns relationships between exposures and correlated count outcomes. When counts exhibit more 0s than expected under Poisson sampling, the zero-inflated Poisson (ZIP) model with random effects may be used. However, the latent class formulation of the ZIP model can make marginal inference on the population sampled challenging. The paper presents a marginalized ZIP model with random effects to model directly the mean of the mixture distribution consisting of ‘susceptible’ individuals and excess 0s, providing straightforward inference for overall exposure effects. Simulations evaluate finite sample properties, and the new methods are applied to a motivational interviewing-based safer sex intervention trial, designed to reduce the number of unprotected sexual acts, to illustrate the new methods.
Heteroscedastic Conditional Auto-Regression Models for Areally Referenced Temporal Processes for Analysing California Asthma Hospitalization Data
Authors: Quick Harrison , Carlin Bradley P. , Banerjee Sudipto 
Published: April 2015

SummaryOften in regionally aggregated spatiotemporal models, a single variance parameter is used to capture variability in the spatial structure of the model, ignoring the effect that spatially varying factors may have on the variability in the underlying process. We extend existing methodologies to allow for region-specific variance components in our analysis of monthly asthma hospitalization rates in California counties, introducing a heteroscedastic conditional auto-regression model that can greatly improve the fit of our spatiotemporal process. After demonstrating the effectiveness of our new model via simulation, we reanalyse the asthma hospitalization data and note some important findings.
Coping Strategies Used by Athletic Training Majors to Manage Clinical and Academic Responsibilities
Authors: Mazerolle Stephanie M. , Bowman Thomas G. , Fister Carrie 
Published: April 2015

Context:Athletic training majors are at risk for experiencing elevated stress, frustrations, and eventual burnout. Evidence suggests that stressors can accumulate over time, but academic standing can plausibly influence experiences with stress.Objective:Gain information related to coping strategies used by athletic training majors to manage their stress and frustrations to prevent burnout.Design:Online qualitative study.Setting:Athletic training programs.Patients or Other Participants:10 sophomores, 9 juniors, and 4 seniors completed the online questionnaire. The athletic training majors were recruited from four institutions with accredited programs.Data Collection and Analysis:Data were collected in March 2013 via asynchronous online interviewing via QuestionPro. All participants responded to the same set of 25 questions and data were analyzed following a general inductive approach. The questionnaire was reviewed by a peer and piloted. Multiple analyst coding was completed.Results:We identified an overarching theme of personal coping strategies, which athletic training majors used to manage and cope with their stressors. These strategies were simply considered outside the confines of the athletic training program itself, and included outside support networks, physical outlets, and time management skills. We acknowledged athletic training majors also employed stress-relieving strategies that were facilitated within or by the athletic training program itself. Specifically, our participants noted that they received support from peer and programmatic personnel (preceptors, faculty).Conclusions:Athletic training majors must develop personal strategies that can help them best alleviate their stressors, but also must have strong support in place especially within their athletic training programs. We recommend that athletic training majors reflect upon what strategies work best for them and to find hobbies and personal interests that help them de-stress and rejuvenate from their demanding workloads.
Intrarater and Interrater Agreement of the Intrinsic Foot Muscle Test
Authors: Facchini Stephanie J. , Hoch Matthew C. , Smith Deanna H. , Hoch Johanna M. 
Published: April 2015

Context:The intrinsic foot muscle test (IFMT) is purported to identify intrinsic foot muscle (IFM) weakness during clinical examination. However, before this test can be used in clinical practice the clinometric properties must be determined. In addition, it is unclear if the IFMT provides information regarding the integrity of the foot arch beyond static foot posture assessments such as the navicular drop test (NDT).Objective:To determine the reliability of the IFMT as well as its correlation with the NDT.Setting:Laboratory.Patients or other Participants:Two novice ATs served as the raters. The NDT was assessed by a third investigator during the first session. Twenty-five participants (16 females, 9 males; age: 22.4 ± 1.7 years; height: 170.8 ± 10.2 cm; mass: 73.5 ± 12.8 kg) completed two data collection sessions separated by one week.Interventions:During each session the IFMT was assessed bilaterally in a counterbalanced order by the raters. Each test was rated simultaneously by both raters during each trial and the raters were blinded to each other’s results during and between test sessions.Main Outcome Measures:The independent variable was time (session one and session two) and the dependent variables included rating on the IFMT and navicular drop height.Results:Intrarater agreement was poor to fair (κ = .03−.41) and interrater agreement was fair to moderate (κ = .25−.60). Post hoc Wilcoxon rank tests demonstrated a significant number of participants improved between sessions for both raters. A weak correlation was observed between the NDT and IFMT for both right (r = −.14 to .04, p < .49) and left (r = −.19 to .07, p < .37) feet.conclusion:The IFMT demonstrated poor to fair intrarater and fair to moderate interrater agreement, suggesting future research is needed to modify this method of measuring IFM function. The improvement between sessions indicates a potential familiarization period within the test. The weak correlation between the IFMT and NDT indicates these tests evaluate different aspects of foot function.
Complete Genome Sequences for 35 Biothreat Assay-Relevant
Bacillus
Species
Authors: Johnson Shannon L. , Daligault Hajnalka E. , Davenport Karen W. , Jaissle James , Frey Kenneth G. , Ladner Jason T. , Broomall Stacey M. , Bishop-Lilly Kimberly A. , Bruce David C. , Gibbons Henry S. , Coyne Susan R. , Lo Chien-Chi , Meincke Linda , Munk A. Christine , Koroleva Galina I. , Rosenzweig C. Nicole , Palacios Gustavo F. , Redden Cassie L. , Minogue Timothy D. , Chain Patrick S. 
Published: April 2015

ABSTRACT

In 2011, the Association of Analytical Communities (AOAC) International released a list of
Bacillus
strains relevant to biothreat molecular detection assays. We present the complete and annotated genome assemblies for the 15 strains listed on the inclusivity panel, as well as the 20 strains listed on the exclusivity panel.
Microbiological and Clinical Studies of Legionellosis in 33 Patients with Cancer
Authors: Han Xiang Y. , Ihegword Andrea , Evans Scott E. , Zhang Jiaqi , Li Li , Cao Hongjing , Tarrand Jeffrey J. , El-Kweifi Omar 
Published: April 2015

ABSTRACTLegionella, a large group of environmental Gram-negative bacteria, represents an occasional cause of pneumonia. We analyzed the microbiological and clinical features of 33 consecutive cases ofLegionellainfections that occurred at the University of Texas MD Anderson Cancer Center, Houston, TX, from 2002 to 2014. TheLegionellastrains were isolated from bronchoscopy specimens (32 strains) and a blood culture (1 strain) and were identified by sequencing analysis of the full-length 16S rRNA gene. The 33 strains involved 12Legionellaspecies or subspecies: 15 strains ofL. pneumophilasubsp.pneumophila, 3 strains ofL. pneumophilasubsp.fraseriorL. pneumophilasubsp.pascullei, 4 strains of “L. donaldsonii,” 3 strains ofL. micdadei, and one each ofL. bozemanae,L. feeleii,L. gormanii,L. longbeachae,L. maceachernii,L. parisiensis,L. sainthelensi, andLegionellasp. strain D5382. All patients except one asymptomatic carrier showed pneumonia, including one with concurrent bacteremia. Nine patients died, with this infection being the immediate cause of death in six. Twenty-seven patients had underlying hematologic malignancies. Twenty-three patients were leukopenic. Six patients were recipients of allogeneic hematopoietic stem cell transplant, with their infections caused by fiveLegionellaspecies. Together, these results suggest that diverseLegionellaspecies infect patients with cancer in the Houston area and its vicinity. The five cases of pneumonia due toL. donaldsoniiandLegionellasp. D5382 are likely the first reports of human infection with these organisms.
Sepsis Due to a Novel Urease-Positive Helicobacter Species in a Young Man
Authors: Mori Nobuaki , Kagawa Narito , Higuchi Akiko , Aoki Yasuko , Ohkusu Kiyofumi 
Published: April 2015

ABSTRACT

We report the first case of sepsis with enterocolitis that was caused by a novel urease-positive
Helicobacter
species in a young man. The isolate was characterized via 16S rRNA gene sequencing and their biochemical properties, and the patient was successfully treated with short-term antimicrobial therapy; no recurrence was observed.
Direct Detection of Influenza A and B Viruses in Less Than 20 Minutes Using a Commercially Available Rapid PCR Assay
Authors: Binnicker Matthew J. , Espy Mark J. , Irish Cole L. , Vetter Emily A. 
Published: April 2015

ABSTRACT

We compared an FDA-cleared rapid (<20 min) PCR assay (Cobas Liat; Roche Diagnostics) to our routine influenza A and B real-time PCR assay (Simplexa Flu A/B & RSV Direct; Focus Diagnostics) using respiratory swabs (
n
= 197). The Cobas Liat influenza A and B assays demonstrated sensitivities of 99.2% (123/124) and 100% (23/23), respectively, while showing a specificity of 100% for each target.
Genome-Based Characterization of Emergent Invasive Neisseria meningitidis Serogroup Y Isolates in Sweden from 1995 to 2012
Authors: Törös Bianca , Hedberg Sara T. , Unemo Magnus , Jacobsson Susanne , Hill Dorothea M. C. , Olcén Per , Fredlund Hans , Bratcher Holly B. , Jolley Keith A. , Maiden Martin C. J. , Mölling Paula 
Published: April 2015

ABSTRACT

Invasive meningococcal disease (IMD) caused by
Neisseria meningitidis
serogroup Y has increased in Europe, especially in Scandinavia. In Sweden, serogroup Y is now the dominating serogroup, and in 2012, the serogroup Y disease incidence was 0.46/100,000 population. We previously showed that a strain type belonging to sequence type 23 was responsible for the increased prevalence of this serogroup in Sweden. The objective of this study was to investigate the serogroup Y emergence by whole-genome sequencing and compare the meningococcal population structure of Swedish invasive serogroup Y strains to those of other countries with different IMD incidence. Whole-genome sequencing was performed on invasive serogroup Y isolates from 1995 to 2012 in Sweden (
n
= 186). These isolates were compared to a collection of serogroup Y isolates from England, Wales, and Northern Ireland from 2010 to 2012 (
n
= 143), which had relatively low serogroup Y incidence, and two isolates obtained in 1999 in the United States, where serogroup Y remains one of the major causes of IMD. The meningococcal population structures were similar in the investigated regions; however, different strain types were prevalent in each geographic region. A number of genes known or hypothesized to have an impact on meningococcal virulence were shown to be associated with different strain types and subtypes. The reasons for the IMD increase are multifactorial and are influenced by increased virulence, host adaptive immunity, and transmission. Future genome-wide association studies are needed to reveal additional genes associated with serogroup Y meningococcal disease, and this work would benefit from a complete serogroup Y meningococcal reference genome.