bluuebunny/crossref_metadata_2025_split huggingface dataset:
Degree of Perceived Accent in Finnish as a Second Language for Turkish Children Born in Finland
Authors: Uzal Melike , Peltonen Teemu , Huotilainen Minna , Aaltonen Olli 
Published: July 2015

This study investigated whether children born in a second language (L2) environment pronounce their L2 with foreign accents and, if so, when foreign accents first emerge. This study also examined the latest age of onset (AO) of extensive L2 experience at which native L2 pronunciation is possible and explored several factors that affect the degree of perceived accent for child L2 learners. Participants included 20 native Finnish children and 19 Finnish‐born Turkish children 7–17 years of age (mean AO = 3) as well as 61 native Finnish raters who evaluated the speech samples for foreign accent using a 9‐point scale. Only 4 of the 19 Turkish children spoke Finnish without foreign accents, which were first detectable at an AO of 2.5 years. AO was the main determiner of perceived accent, followed by home use of first language (L1), and the amount of L2 and L1 use. These findings suggest that there is an interplay between AO and language use factors in determining child L2 learners’ accent.
Toward an experimental synthesis of the chondritic insoluble organic matter
Authors: Biron Kasia , Derenne Sylvie , Robert François , Rouzaud Jean‐Noël 
Published: July 2015

AbstractBased on the statistical model proposed for the molecular structure of the insoluble organic matter (IOM) isolated from the Murchison meteorite, it was recently proposed that, in the solar T‐Tauri disk regions where (photo)dissociation of gaseous molecules takes place, aromatics result from the cyclization/aromatization of short aliphatics. This hypothesis is tested in this study, with n‐alkanes being submitted to high‐frequency discharge at low pressure. The contamination issue was eliminated using deuterated precursor. IOM was formed and studied using solid‐state nuclear magnetic resonance, pyrolysis coupled to gas chromatography and mass spectrometry, RuO4 oxidation, and high‐resolution transmission electron microscopy. It exhibits numerous similarities at the molecular level with the hydrocarbon backbone of the natural IOM, reinforcing the idea that the initial precursors of the IOM were originally chains in the gas. Moreover, a fine comparison between the chemical structure of several meteorite IOM suggests either that (i) the meteorite IOMs share a common precursor standing for the synthetic IOM or that (ii) the slight differences between the meteorite IOMs reflect differences in their environment at the time of their formation i.e., related to plasma temperature that, in turn, dictates the dissociation–recombination rates of organic fragments.
Genome‐wide association and genome partitioning reveal novel genomic regions underlying variation in gastrointestinal nematode burden in a wild bird
Authors: Wenzel Marius A. , James Marianne C. , Douglas Alex , Piertney Stuart B. 
Published: July 2015

AbstractIdentifying the genetic architecture underlying complex phenotypes is a notoriously difficult problem that often impedes progress in understanding adaptive eco‐evolutionary processes in natural populations. Host–parasite interactions are fundamentally important drivers of evolutionary processes, but a lack of understanding of the genes involved in the host's response to chronic parasite insult makes it particularly difficult to understand the mechanisms of host life history trade‐offs and the adaptive dynamics involved. Here, we examine the genetic basis of gastrointestinal nematode (Trichostrongylus tenuis) burden in 695 red grouse (Lagopus lagopus scotica) individuals genotyped at 384 genome‐wide SNPs. We first use genome‐wide association to identify individual SNPs associated with nematode burden. We then partition genome‐wide heritability to identify chromosomes with greater heritability than expected from gene content, due to harbouring a multitude of additive SNPs with individually undetectable effects. We identified five SNPs on five chromosomes that accounted for differences of up to 556 worms per bird, but together explained at best 4.9% of the phenotypic variance. These SNPs were closely linked to genes representing a range of physiological processes including the immune system, protein degradation and energy metabolism. Genome partitioning indicated genome‐wide heritability of up to 29% and three chromosomes with excess heritability of up to 4.3% (total 8.9%). These results implicate SNPs and novel genomic regions underlying nematode burden in this system and suggest that this phenotype is somewhere between being based on few large‐effect genes (oligogenic) and based on a large number of genes with small individual but large combined effects (polygenic).
Molecular biology research to benefit patients with Entamoeba histolytica infection
Authors: Watanabe Koji , Petri William A. 
Published: July 2015

SummaryThe development of molecular microbiology has made it possible for us to deepen our understanding of the pathogenesis of amebiasis. Research using the trophozoite form of Entamoeba histolytica has clearly shown us the importance of the interface between the parasite and host cells in vitro. Immuno‐pathogenesis after excystation was similarly well advanced by the use of a novel murine model of amebic colitis. However, it is still challenging to apply these findings to clinical and epidemiological settings. This is mainly because of the lack of a complete infection animal model of amebiasis by oral–fecal infection. Moreover, in vitro experiments have predominantly been performed using the same axenic cultured strain HM‐1: IMSS isolated about 50 years ago, whereas highly diverse strains are prevalent all over the world. Translational research informed by clinical observations has the greatest potential for the development of effective interventions. Here, we highlight discoveries of the experiments designed from cohort observation and discuss remaining problems to be solved.
Hydrogen peroxide produced by NADPH oxidases increases proline accumulation during salt or mannitol stress in Arabidopsis thaliana
Authors: Ben Rejeb Kilani , Lefebvre‐De Vos Delphine , Le Disquet Isabel , Leprince Anne‐Sophie , Bordenave Marianne , Maldiney Régis , Jdey Asma , Abdelly Chedly , Savouré Arnould 
Published: July 2015

Summary

Many plants accumulate proline, a compatible osmolyte, in response to various environmental stresses such as water deficit and salinity. In some stress responses, plants generate hydrogen peroxide (H2O2) that mediates numerous physiological and biochemical processes. The aim was to study the relationship between stress‐induced proline accumulation and H2O2 production.

Using pharmacological and reverse genetic approaches in Arabidopsis thaliana, we investigated the role of NADPH oxidases, Respiratory burst oxidase homologues (Rboh), in the induction of proline accumulation was investigated in response to stress induced by either 200 mM NaCl or 400 mM mannitol.

Stress from NaCl or mannitol resulted in a transient increase in H2O2 content accompanied by accumulation of proline. Dimethylthiourea, a scavenger of H2O2, and diphenylene iodonium (DPI), an inhibitor of H2O2 production by NADPH oxidase, were found to significantly inhibit proline accumulation in these stress conditions. DPI also reduced the expression level of Δ1‐pyrroline‐5‐carboxylate synthetase, the key enzyme involved in the biosynthesis of proline. Similarly, less proline accumulated in knockout mutants lacking either AtRbohD or AtRbohF than in wild‐type plants in response to the same stresses.

Our data demonstrate that AtRbohs (A. thaliana Rbohs) contribute to H2O2 production in response to NaCl or mannitol stress to increase proline accumulation in this plant.
Molecular mechanisms underlying the entrance in secondary dormancy of Arabidopsis seeds
Authors: Ibarra Silvia E. , Tognacca Rocío S. , Dave Anuja , Graham Ian A. , Sánchez Rodolfo A. , Botto Javier F. 
Published: July 2015

AbstractAs seasons change, dormant seeds cycle through dormant states until the environmental conditions are favourable for seedling establishment. Dormancy cycle is widespread in the plant kingdom allowing the seeds to display primary and secondary dormancy. Several reports in the last decade have focused on understanding the molecular mechanisms of primary dormancy, but our knowledge regarding secondary dormancy is limited. Here, we studied secondary dormancy induced in Arabidopsis thaliana by incubating seeds at 25 °C in darkness for 4 d. By physiological, pharmacological, expression and genetics approaches, we demonstrate that (1) the entrance in secondary dormancy involves changes in the content and sensitivity to GA, but the content and sensitivity to ABA do not change, albeit ABA is required; (2) RGL2 promotes the entrance in secondary dormancy through ABI5 action; and (3) multivariate analysis with 18 geographical and environmental parameters of accession collection place suggests that temperature is an important variable influencing the induction of secondary dormancy in nature.
Lung abscess caused by Mycoplasma pneumoniae
Authors: Omae Takashi , Matsubayashi Tadashi 
Published: July 2015

AbstractA 10‐year‐old boy with West syndrome was referred to hospital because of high fever and cough. Chest X‐ray and computed tomography showed consolidation with an abscess in the right upper lobe. Laboratory data indicated cytokine storm. Various antibacterial agents and additional corticosteroid were unable to control the hypercytokinemia, which was suppressed after cyclosporine A was started. The lung abscess remained, however, and right upper lobectomy was performed. Culture from the abscess showed no growth, while polymerase chain reaction assay indicated Mycoplasma pneumoniae DNA. Serum passive agglutinin titer for M. pneumoniae was significantly elevated in the convalescent phase. These findings are strong evidence that the lung abscess was caused by M. pneumoniae infection.
The Effect of pH Values on the Synthesis, Microstructure and Photocatalytic Activity of Ce‐Bi2O3 by a Two‐Step Hydrothermal Method
Authors: Zhang Fengjun , Lu Wei , Xiao Guosheng , Liu Zhuojing , Xing Fanwei , Lyu Cong 
Published: July 2015

AbstractIn this study, the effect of pH values on the microstructure and photocatalytic activity of Ce‐Bi2O3 under visible light irradiation was investigated in detail. In alkaline condition (e.g. pH = 9), the as‐prepared Ce‐Bi2O3 exhibited an agglomerated status and mesoporous structures without a long‐range order. While in weak acid condition (e.g. pH = 5), the Ce‐Bi2O3 exhibited a best morphology with irregular nanosheets. Correspondingly, it possessed largest surface area (24.641 m2 g−1) and pore volume (9.825E‐02 cm3 g−1). These unique nanosheets can offer an attachment for pollutant molecules and reduce the distance of electron immigration from inner to surface, thus facilitating the separation of photoelectron and hole pairs. Compared with the pure Bi2O3, the band gap of Ce‐Bi2O3 prepared at different pH was much lower. Among them, the band gap of Ce‐Bi2O3 (pH of 5) was lowest (2.61 eV). Ce‐Bi2O3 (pH of 5) exhibited as tetragonal crystal with the bismuth oxide in the form of the composites, which could reduce the band gap width or suppress the charge‐carrier recombination, subsequently possessing great photocatalytic activity for acid orange II under visible light irradiation. After 2 h degradation under visible light, the degradation rate of acid Orange II was up to 96.44% by Ce‐Bi2O3 prepared at pH 5. Overall, it can be concluded that the pH values had effects on the microstructure and photocatalytic activity of Ce‐Bi2O3 catalysts.
What is regulation? An interdisciplinary concept analysis
Authors: Koop Christel , Lodge Martin 
Published: July 2015

AbstractThe concept of regulation is believed to suffer from a lack of shared understanding. Yet the maturation of the field raises the question whether this conclusion is still valid. By taking a new methodological approach toward this question of conceptual consolidation, this study assesses how regulation is conceived in the most cited articles in six social science disciplines. Four main conclusions are drawn. First, there is a remarkable absence of explicit definitions. Second, the scope of the concept is vast, which requires us to talk about regulation in rather abstract terms. Third, scholars largely agree that “prototype regulation” is characterized by interventions that are intentional and direct – involving binding standard‐setting, monitoring, and sanctioning – and exercised by public‐sector actors on the economic activities of private‐sector actors. Fourth, while there is considerable variation in research concerns, this variation cannot be attributed to disciplinary differences. Instead, our findings support the portrayal of the field as interdisciplinary, including a shared conception of regulation.
Natural history of COPD: Focusing on change in FEV1
Authors: Vestbo Jørgen , Lange Peter 
Published: July 2015

AbstractThe natural history of chronic obstructive pulmonary disease (COPD) is usually described with a focus on change in forced expiratory volume in 1 s (FEV1) over time as this allows for exploration of risk factors for an accelerated decline—and thus of developing COPD. From epidemiological studies we have recognized important risk factors such as smoking, exposure to biomass and occupational exposures, but we have also learnt about features such as chronic bronchitis, airway hyper‐responsiveness and asthma that seem to accelerate decline in FEV1 independent of exposures. In addition we are gradually beginning to better link early life events to subsequent risk of disease in adulthood. Although more complicated, our current understanding of COPD has come a long way from being a simple image of smoking leading to poor lungs.
Management of the Dialysis Patient with Sickle Cell Disease
Authors: Boyle Suzanne M. , Jacobs Benjamin , Sayani Farzana A. , Hoffman Brenda 
Published: July 2015

AbstractWhile patients with sickle cell disease currently constitute a very small minority of the US dialysis population (0.1%), there is anticipated growth of this group as the life expectancy of those with sickle cell disease (SCD) increases. SCD patients suffer a high burden of morbidity, which is enhanced by the presence of end‐stage renal disease (ESRD). In this review, we discuss the pathophysiology of SCD and the basic tenets of its management with focus on the dialysis patient with SCD. Anemia in dialysis patients with SCD is a unique challenge. The hemoglobin target in SCD dialysis patients with ESRD should not exceed 10 g/dl. SCD patients, and particularly those on dialysis, are likely to be poorly responsive to erythropoietin‐stimulating agent (ESA) therapy and might be at increased risk for vaso‐occlusive crisis (VOC) with ESA. Iron chelation and hydroyxurea therapy require special considerations and modifications in dialysis patients with SCD. There are theoretical advantages to both hemodialysis (HD) and peritoneal dialysis (PD) in SCD patients. With HD, there is a secure vascular access available for both standard and exchange blood transfusion in patients who need them. With PD, the absence of an acute rise in hematocrit with ultrafiltration (UF) might offer lower risk of VOC. During VOC, reduction in UF goals should be considered but administration of intravenous fluids should be reserved only for clear cases of volume depletion. Finally, renal transplantation appears to confer a survival advantage to dialysis in SCD patients and should be pursued when possible.
Virological analysis of inherited chromosomally integrated human herpesvirus‐6 in three hematopoietic stem cell transplant patients
Authors: Miura H. , Kawamura Y. , Kudo K. , Ihira M. , Ohye T. , Kurahashi H. , Kawashima N. , Miyamura K. , Yoshida N. , Kato K. , Takahashi Y. , Kojima S. , Yoshikawa T. 
Published: July 2015

AbstractWe analyzed 3 hematopoietic stem cell transplant (HSCT) recipients with inherited chromosomally integrated human herpesvirus‐6 (inherited CIHHV‐6). Cases 1 (inherited CIHHV‐6A) and 2 (inherited CIHHV‐6B) were inherited CIHHV‐6 recipients. Case 3 received bone marrow from a donor with inherited CIHHV‐6B. Following HSCT, HHV‐6B was isolated from Case 1. HHV‐6A and ‐6B messenger RNAs were detected in Cases 1 and 3.
Evaluation of an individual‐donation nucleic acid amplification testing algorithm for detecting hepatitis B virus infection in Chinese blood donors
Authors: Gou Hongna , Pan Yang , Ge Hongwei , Zheng Yourong , Wu Yaling , Zeng Jinfeng , Yang Zhongsi , Pan Tong , Cun Wei , Zhou Guoping , Fang Gen , Zhang Jiahong , Zhang Kuo , Zhang Rui , Sun Yu , Xie Jiehong , Li Jinming , Wang Lunan 
Published: July 2015

BACKGROUNDThis multicenter study was performed to evaluate the efficiency of a multiplex individual‐donation nucleic acid amplification technology (ID‐NAT) and discriminatory testing algorithm for detecting hepatitis B virus (HBV) infection in Chinese blood donors.STUDY DESIGN AND METHODSA total of 1,205,796 hepatitis B surface antigen (HBsAg)‐nonreactive donations from 10 blood centers were tested by ID‐NAT using the Ultrio assay. Multiplex Ultrio‐reactive donations were tested in the discriminatory tests as well as in quantitative polymerase chain reaction (qPCR) and in supplemental electrochemiluminescence immunoassays for HBsAg, hepatitis B surface antibody (anti‐HBs), hepatitis B e antigen, and antibody to hepatitis B core antigen (anti‐HBc). Meanwhile, a control group of 4317 Ultrio‐nonreactive donations was tested for anti‐HBc and anti‐HBs.RESULTSOf all donations, 2033 (0.17%) were reactive in the multiplex Ultrio assay. Among 1776 further tested samples, 548 (30.9%) were HBV discriminatory assay (dHBV)‐reactive, while 1214 (68.4%) were nonreactive. Of 472 Ultrio+ and dHBV+ samples 86.2% were qPCR positive compared to 15.0% in 1046 Ultrio+ and dHBV– samples. The proportion of anti‐HBc+ and anti‐HBs– (potentially infectious) donations was higher in 409 Ultrio+ and dHBV+ than in 1028 Ultrio+ and dHBV– samples (51.3% vs. 31.1%, p < 0.001). The yield rate of Ultrio+, dHBV+, and qPCR+ donations was estimated at 1 in 2500, but at 1 in 1100 when all supplemental tests were taken into account assuming that 44% of detected donations by Ultrio were false reactive.CONCLUSIONSA quarter of HBsAg‐negative Ultrio+ and dHBV– donations in China are likely given by potentially infectious low‐viral‐load occult carriers. Although this has no implication for blood safety, the testing algorithm needs to be redesigned to more efficiently discriminate between true and false NAT reactivity.
Age of blood and adverse outcomes in a maternity population
Authors: Patterson Jillian A. , Irving David O. , Isbister James P. , Morris Jonathan M. , Mayson Eleni , Roberts Christine L. , Ford Jane B. 
Published: July 2015

BACKGROUNDIn recent times there has been debate around whether longer storage time of blood is associated with increased rates of adverse outcomes after transfusion. It is unclear whether results focused on cardiac or critically ill patients apply to a maternity population. This study investigates whether older blood is associated with increased morbidity and readmission in women undergoing obstetric transfusion.STUDY DESIGN AND METHODSWomen giving birth in hospitals in New South Wales, Australia, between July 2006 and December 2010 were included in the study population if they had received between 1 and 4 red blood cell units during the birth admission. Information on women's characteristics, transfusions, and outcomes were obtained from five routinely collected data sets including blood collection, birth, and hospitalization data. Generalized propensity score methods were used to determine the effect of age of blood on rates of severe morbidity and readmission, independent of confounding factors.RESULTSTransfusion data were available for 2990 women, with a median age of blood transfused of 20 days (interquartile range, 14‐27 days). There were no differences in the maximum age of blood transfused between women with and without severe morbidity (21 [14‐28] days vs. 22 [15‐30] days) and in women readmitted or not (22 [14‐28] days vs. 22 [16‐30] days). After potential confounding factors were considered, no relationship was found between the age of blood transfused and rates of severe morbidity and readmission.CONCLUSIONAmong women receiving low‐volume transfusions during a birth admission, there was no evidence of increased rates of adverse outcomes after transfusion with older blood.
IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites
Authors: Hadjithomas Michalis , Chen I-Min Amy , Chu Ken , Ratner Anna , Palaniappan Krishna , Szeto Ernest , Huang Jinghua , Reddy T. B. K. , Cimermančič Peter , Fischbach Michael A. , Ivanova Natalia N. , Markowitz Victor M. , Kyrpides Nikos C. , Pati Amrita 
Published: July 2015

ABSTRACT

In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In this work, we present IMG-ABC (
https://img.jgi.doe.gov/abc
), an atlas of biosynthetic gene clusters within the Integrated Microbial Genomes (IMG) system, which is aimed at harnessing the power of “big” genomic data for discovering small molecules. IMG-ABC relies on IMG's comprehensive integrated structural and functional genomic data for the analysis of biosynthetic gene clusters (BCs) and associated secondary metabolites (SMs). SMs and BCs serve as the two main classes of objects in IMG-ABC, each with a rich collection of attributes. A unique feature of IMG-ABC is the incorporation of both experimentally validated and computationally predicted BCs in genomes as well as metagenomes, thus identifying BCs in uncultured populations and rare taxa. We demonstrate the strength of IMG-ABC's focused integrated analysis tools in enabling the exploration of microbial secondary metabolism on a global scale, through the discovery of phenazine-producing clusters for the first time in
Alphaproteobacteria
. IMG-ABC strives to fill the long-existent void of resources for computational exploration of the secondary metabolism universe; its underlying scalable framework enables traversal of uncovered phylogenetic and chemical structure space, serving as a doorway to a new era in the discovery of novel molecules.

IMPORTANCE
IMG-ABC is the largest publicly available database of predicted and experimental biosynthetic gene clusters and the secondary metabolites they produce. The system also includes powerful search and analysis tools that are integrated with IMG's extensive genomic/metagenomic data and analysis tool kits. As new research on biosynthetic gene clusters and secondary metabolites is published and more genomes are sequenced, IMG-ABC will continue to expand, with the goal of becoming an essential component of any bioinformatic exploration of the secondary metabolism world.