bluuebunny/crossref_metadata_2025 huggingface dataset:
Which emotional regulatory strategy makes Chinese adolescents happier? A longitudinal study
Authors: Sang Biao , Deng Xinmei , Luan Ziyan
Published: April 2014

Growing interest in emotion regulation is reflected in the studies of cognitive and social development. However, the extant studies mainly highlight how emotion regulation develops based on a western value system. This study utilised a longitudinal design to examine the development of emotion regulation and explored the contributions of different regulatory strategies to emotion experience regarding the early adolescent development period in a Chinese population. A total of 303 Chinese adolescents (age range = 10–14 years) were followed up in a three‐phase longitudinal study for 3 years. In each phase of the study, participants completed Adolescents Emotion Regulation Questionnaire and Daily Emotion Scale. Results of hierarchical linear regressions revealed that Chinese adolescents reported more down‐regulation. Down‐regulation is more effective than up‐regulation in enhancing desirable emotion experience and reducing undesirable emotion experience during adolescents' development. Also, the adaptive functions of emotional regulatory strategies in Chinese background were discussed.
Visible‐light photocatalytic degradation of methyl orange over spherical activated carbon‐supported and Er3+:YAlO3‐doped TiO2 in a fluidized bed
Authors: Dong Shanshan , Zhang Xueying , He Furong , Dong Shuangshi , Zhou Dandan , Wang Bo
Published: April 2014

BACKGROUND

Powdered photocatalyst by doping TiO2 with upconversion luminescence agents achieved visible light induced photocatalysis. However, slurry photocatalysts are difficult to recover from the treated liquor. In the present study, spherical activated carbon (SAC)‐supported and Er3+:YAlO3‐doped visible‐light responsive photocatalyst (Er3+:YAlO3/TiO2‐SAC) was synthesized and characterized. The photocatalytic performance of photocatalyst was examined for degradation of methyl orange (MO) in a liquid–solid fluidized bed photoreactor under visible‐light irradiation.

RESULTS

Two notable UV emission peaks at 320 and 360 nm were observed for Er3+:YAlO3 by visible light excitation, which were assigned to the transition of 2P3/2→4I15/2 and 4D5/2→4I11/2, respectively. An optimum 8 h photodecolorization efficiency of 65.3% was obtained from the fluidized bed with reaction rate constant 22.17 mg L−1 h−1. The degradation rate first increased and then decreased with the increasing expansion ratio, and the optimum expansion ratio was found to be 130%.

CONCLUSION

Optical characterization revealed that Er3+:YAlO3 could convert incident visible‐light to UV, which can then be utilized by TiO2 for photocatalysis. The visible light generated by Er3+:YAlO3 emissions were not used by TiO2 because of its high band gap. The photocatalytic degradation of MO in the fluidized bed photoreactor followed the Langmuir–Hinshelwood kinetics model. © 2014 Society of Chemical Industry
The quality of carp (Cyprinus carpio L.) cultured in various Polish regions
Authors: Tkaczewska Joanna , Migdał Władysław , Kulawik Piotr
Published: April 2014

BACKGROUND

Although environmental factors greatly affect the quality of carp meat, no regulations impose labelling the place of cultivation of freshwater fish. That is why the purpose of this study was to determine the quality of carp meat cultivated in several regions of Poland as well as to assess the necessity of implementing such regulations.

RESULTS

The influence of the cultivation region on colour, nutrition value, health safety and sensory quality of carp meat was assessed. The analysis included colour measurement, determination of fatty acid profile and sensory evaluation of carp muscle. Moreover, microbiological analysis of the fish surface was performed. The results show that the place of cultivation does not influence the lightness (L*) of fillet, but has an impact on other colour parameters (a*, b*). The microbiological quality of fish from all studied farms was satisfactory, since no pathogenic microorganisms were observed on the fish surface. The fatty acid profile was fairly varied (P < 0.01), depending on the place of cultivation.

CONCLUSION

Since final results seem ambiguous, further analyses of quality features of carp from various regions and cultures should be performed, before any recommendation for the necessity of labelling the place and method of cultivation should be suggested. © 2014 Society of Chemical Industry
Human placental extract reduces allergic inflammation in a murine allergic rhinitis model
Authors: Kim Boo‐Young , Park Hyang Rim , Shin Ji‐Hyeon , Kim Sung Won , Kim Soo Whan
Published: April 2014

Objectives/Hypothesis

In this study, we addressed the immunotherapeutic potential of human placental extract (HPE) in a murine allergic rhinitis (AR) model and explored its immunological mechanisms.

Study Design

In vivo study using an animal model.

Methods

HPE was administered to BALB/c mice before sensitization with allergen (Dermatophagoides farinae [Derf]) (pre‐S group) or after allergen challenge (post‐C group). The groups were compared with Derf‐treated mice that received no HPE (Derf group) and phosphate buffered saline (PBS)‐treated mice (control). Allergic symptom scores, eosinophil counts, and serum Derf‐specific IgE levels were measured. mRNA expression levels of interferon (IFN)‐γ, T‐bet, interleukin (IL)‐4, GATA‐3, and Foxp3 in nasal mucosa were determined by real‐time polymerase chain reaction. IFN‐γ, T‐bet, IL‐4, and GATA‐3 were confirmed by Western blotting analysis. Spleen CD4+CD25+Foxp3+ T cells were detected using flow cytometry.

Results

Rubbing motions, serum Derf‐specific IgE, GATA‐3 mRNA levels, IL‐4 mRNA levels, and tissue eosinophil counts were decreased in both pre‐S and post‐C groups (all P < 0.05). Western blots showed decreased expression of GATA‐3 and IL‐4 in both pre‐S and post‐C groups as compared to the Derf group. An increased percentage of CD4+CD25+Foxp3+ T cells and an increased level of Foxp3 mRNA were found in pre‐S and post‐C groups as compared to those in the Derf group (all P < 0.05).

Conclusion

Both prophylactic and therapeutic treatments with HPE significantly reduced allergic inflammation in nasal mucosa and had the potential to induce regulatory T cells in a murine model of AR.

Level of Evidence

N/A. Laryngoscope 124:E399–E404, 2014
The homozygous VHLD126N missense mutation is associated with dramatically elevated erythropoietin levels, consequent polycythemia, and early onset severe pulmonary hypertension
Authors: Sarangi Susmita , Lanikova Lucie , Kapralova Katarina , Acharya Suchitra , Swierczek Sabina , Lipton Jeffrey M. , Wolfe Lawrence , Prchal Josef T.
Published: April 2014

von Hippel‐Lindau (VHL) protein is the principal negative regulator of hypoxia sensing mediated by transcription factors. Mutations in exon 3 of the VHL gene lead to Chuvash (VHLR200W) and Croatian (VHLH191D) polycythemias. Here, we describe an infant of Bangladesh ethnicity with a novel homozygous VHLD126N mutation with congenital polycythemia and dramatically elevated erythropoietin (EPO) levels, who developed severe fatal pulmonary hypertension. In contrast to Chuvash polycythemia, erythroid progenitors (BFU‐Es) did not reveal a marked EPO hypersensitivity. Further, NF‐E2 and RUNX1 transcripts that correlate with BFU‐Es EPO hypersensitivity in polycythemic mutations were not elevated. Pediatr Blood Cancer 2014;61:2104–2106. © 2014 Wiley Periodicals, Inc.
Gene silencing of two acetylcholinesterases reveals their cholinergic and non‐cholinergic functions in Rhopalosiphum padi and Sitobion avenae
Authors: Xiao Da , Lu Yan‐Hui , Shang Qing‐Li , Song Dun‐Lun , Gao Xi‐Wu
Published: April 2014

BACKGROUD

The function of acetylcholinesterase (AChE) is to terminate synaptic transmission by hydrolysing the neurotransmitter acetylcholine (ACh) in the synaptic cleft, and thus it is an effective target for organophosphate (OP) and carbamate (CB) insecticides.

RESULTS

The transcript levels of the four Ace genes were dramatically suppressed by injection of their respective dsRNA in Rhopalosiphum padi and Sitobion avenae. However, the AChE activity changes in the Ace1 knockdown aphids were consistent with the significant transcript level changes of Ace1 genes in these aphids, but not for Ace2. Bioassay results indicated that the suppression of RpAce1 increased its susceptibilities to pirimicarb and malathion, and SaAce1 silencing also increased susceptibility to pirimicarb in S. avenae, whereas the knockdowns of RpAce2 and SaAce2 had a slight effect on their susceptibilities. The knockdown of Ace1 genes also caused significant reductions in fecundity in the aphids of their parental generation.

CONCLUSIONS

These results suggest that AChE1 is a predominant cholinergic enzyme and is the target of anticholinesterase insecticides in both R. padi and S. avenae. It also plays a non‐cholinergic role in fecundity of these aphids. AChE2 may also be important for the toxicological function, although its importance appeared to be lower than that of AChE1. © 2014 Society of Chemical Industry
Use of an OSSE to evaluate background‐error covariances estimated by the NMC method
Authors: Errico Ronald M. , Privé Nikki C. , Gu Wei
Published: April 2014

The NMC method has proven utility for prescribing approximate background‐error covariances required by variational data assimilation systems. Here, untuned NMC method estimates are compared with explicitly determined error covariances produced within an OSSE context by exploiting availability of the true simulated states. Such a comparison provides insights into what kind of rescaling is required to render the NMC method estimates usable. It is shown that rescaling of variances and directional correlation lengths depends greatly on both pressure and latitude. In particular, some scaling coefficients appropriate in the Tropics are the reciprocal of those in the Extratropics. Also, the degree of dynamic balance is grossly overestimated by the NMC method. These results agree with previous examinations of the NMC method which used ensembles as an alternative for estimating background‐error statistics.
Global radiative and climate effect of the water vapour continuum at visible and near‐infrared wavelengths
Authors: Rädel Gaby , Shine Keith P. , Ptashnik Igor V.
Published: April 2014

Recent laboratory measurements show that absorption by the water vapour continuum in near‐infrared windows may be about an order of magnitude higher than assumed in many radiation codes. The radiative impact of the continuum at visible and near‐infrared wavelengths is examined for the present day and for a possible future warmer climate (with a global‐mean total column water increase of 33%). The calculations use a continuum model frequently used in climate models (‘CKD’) and a continuum model where absorption is enhanced at wavelengths greater than 1 µm based on recent measurements (‘CAVIAR’). The continuum predominantly changes the partitioning between solar radiation absorbed by the surface and the atmosphere; changes in top‐of‐atmosphere net irradiances are smaller. The global‐mean clear‐sky atmospheric absorption is enhanced by 1.5 W m−2 (about 2%) and 2.8 W m−2 (about 3.5%) for CKD and CAVIAR respectively, relative to a hypothetical no‐continuum case, with all‐sky enhancements about 80% of these values. The continuum is, in relative terms, more important for radiation budget changes between the present day and a possible future climate. Relative to the no‐continuum case, the increase in global‐mean clear‐sky absorption is 8% higher using CKD and almost 20% higher using CAVIAR; all‐sky enhancements are about half these values. The effect of the continuum is estimated for the solar component of the water vapour feedback, the reduction in downward surface irradiance and precipitation change in a warmer world. For CKD and CAVIAR respectively, and relative to the no‐continuum case, the solar component of the water vapour feedback is enhanced by about 4 and 9%, the change in clear‐sky downward surface irradiance is 7 and 18% more negative, and the global‐mean precipitation response decreases by 1 and 4%. There is a continued need for improved continuum measurements, especially at atmospheric temperatures and at wavelengths below 2 µm.
Corporate governance and IPO underpricing in a cross‐national sample: A multilevel knowledge‐based view
Authors: Judge William Q. , Witt Michael A. , Zattoni Alessandro , Talaulicar Till , Chen Jean Jinghan , Lewellyn Krista , Hu Helen Wei , Shukla Dhirendra , Bell (Robert) R. Greg , Gabrielsson Jonas , Lopez Felix , Yamak Sibel , Fassin Yves , McCarthy Daniel , Rivas Jose Luis , Fainshmidt Stav , Van Ees Hans
Published: April 2014

Prior studies of IPO underpricing, mostly using agency theory and single‐country samples, have generally fallen short. In this study, we employ the knowledge‐based view (KBV) to explore underpricing across 17 countries. We find that agency indicators are insignificant predictors, board of director knowledge limits underpricing, and external knowledge both substitutes for and complements internal board knowledge. This third finding suggests that future KBV studies should consider how internal and external knowledge states interact with each other. Our study offers new insights into the antecedents of underpricing and extends our understanding of comparative governance and the KBV of the firm. Copyright © 2014 John Wiley & Sons, Ltd.
Elevated mitochondrial biogenesis in skeletal muscle is associated with testosterone‐induced body weight loss in male mice
Authors: Usui Taro , Kajita Kazuo , Kajita Toshiko , Mori Ichiro , Hanamoto Takayuki , Ikeda Takahide , Okada Hideyuki , Taguchi Koichiro , Kitada Yoshihiko , Morita Hiroyuki , Sasaki Tsutomu , Kitamura Tadahiro , Sato Takashi , Kojima Itaru , Ishizuka Tatsuo
Published: April 2014

Androgen reduces fat mass, although the underlying mechanisms are unknown. Here, we examined the effect of testosterone on heat production and mitochondrial biogenesis. Testosterone‐treated mice exhibited elevated heat production. Treatment with testosterone increased the expression level of peroxisome proliferator‐activated receptor‐γ coactivator‐1α (PGC1α), ATP5B and Cox4 in skeletal muscle, but not that in brown adipose tissue and liver. mRNA levels of genes involved in mitochondrial biogenesis were elevated in skeletal muscle isolated from testosterone‐treated male mice, but were down‐regulated in androgen receptor deficient mice. These results demonstrated that the testosterone‐induced increase in energy expenditure is derived from elevated mitochondrial biogenesis in skeletal muscle.
Protein arginine methyltransferase 7 has a novel homodimer‐like structure formed by tandem repeats
Authors: Hasegawa Morio , Toma-Fukai Sachiko , Kim Jun-Dal , Fukamizu Akiyoshi , Shimizu Toshiyuki
Published: April 2014

Protein arginine methyltransferase 7 (PRMT7) is a member of a family of enzymes that catalyze the transfer of methyl groups from S‐adenosyl‐l‐methionine to nitrogen atoms on arginine residues. Here, we describe the crystal structure of Caenorhabditis elegans PRMT7 in complex with its reaction product S‐adenosyl‐l‐homocysteine. The structural data indicated that PRMT7 harbors two tandem repeated PRMT core domains that form a novel homodimer‐like structure. S‐adenosyl‐l‐homocysteine bound to the N‐terminal catalytic site only; the C‐terminal catalytic site is occupied by a loop that inhibits cofactor binding. Mutagenesis demonstrated that only the N‐terminal catalytic site of PRMT7 is responsible for cofactor binding.
Dual-stimuli responsive i-motif/nanoflares for sensing ATP in lysosomes
Authors: Jin Fen , Zheng Jing , Liu Changhui , Yang Sheng , Li Yinhui , Li Jishan , Lian Yan , Yang Ronghua
Published: April 2014

A dual-stimuli responsive i-motif/nanoflare for molecule detection in lysosomes was designed.
Sequential one-pot enzymatic synthesis of oligo-N-acetyllactosamine and its multi-sialylated extensions
Authors: Chien Wei-Ting , Liang Chien-Fu , Yu Ching-Ching , Lin Chien-Hung , Li Si-Peng , Primadona Indah , Chen Yu-Ju , Mong Kwok Kong T. , Lin Chun-Cheng
Published: April 2014

A simple and efficient protocol for the preparative-scale synthesis of various lengths of oligo-N-acetyllactosamine (oligo-LacNAc) and its multi-sialylated extensions.
Efficient photocatalytic hydrogen evolution with end-group-functionalized cobaloxime catalysts in combination with graphite-like C3N4
Authors: Song Xiao-Wei , Wen Hui-Min , Ma Cheng-Bing , Cui Hong-Hua , Chen Hui , Chen Chang-Neng
Published: April 2014

The pyrene-functionalized cobaloxime–g-C3N4 system was active for hydrogen production in CH3CN–H2O mixed solvent with a highest TON of 281.
Chemiluminescence emission in cholesteric liquid crystalline core–shell microcapsules
Authors: Iwai Y. , Kaji H. , Uchida Y. , Nishiyama N.
Published: April 2014

Chemiluminescence behaviour in the core region of water/oil/water double emulsion droplets with cholesteric liquid crystalline middle phase was demonstrated.
Natural variation underlies alterations in Nramp aluminum transporter (
NRAT1
) expression and function that play a key role in rice aluminum tolerance
Authors: Li Jian-Yong , Liu Jiping , Dong Dekun , Jia Xiaomin , McCouch Susan R. , Kochian Leon V.
Published: April 2014

Significance

Acidic soils compose significant land areas in the tropics and subtropics. On acid soils, aluminum (Al) toxicity inhibits root growth, leading to reduced crop yields. Rice is the most Al-tolerant cereal crop. We examined the natural variation in rice Nramp aluminum transporter (
OsNRAT1
), which encodes a transporter mediating Al uptake from the root tip cell wall into the cell, where it is sequestered in the vacuole. We identified tolerant and sensitive
NRAT1
alleles that exhibited lower
NRAT1
expression and reduced Al uptake in the sensitive allele, resulting in a significant reduction in rice Al tolerance. These findings indicate that the NRAT1 transporter plays a major role in rice Al tolerance and open the door for using NRAT1 to improve Al tolerance in other cereal species.
Regular and Novel Metonymy: Can You Curl up with a Good Agatha Christie in Your Second Language?
Authors: Slabakova Roumyana , Cabrelli Amaro Jennifer , Kyun Kang Sang
Published: April 2014

This article presents results of two off-line comprehension tasks investigating the acceptability of unconventional and conventional metonymy by native speakers of Korean and Spanish who speak English as a second language. We are interested in discovering whether learners differentiate between conventional and unconventional metonymy, and whether the acceptability of metonymic expressions in the native language has an effect on learners’ judgments in the second language. The findings of this study constitute further experimental support for the psychological reality of the distinction between conventional and unconventional metonymy, but only in English. Learners of English at intermediate levels of proficiency exhibit transfer from the native language in comprehending metonymic shifts of meanings. Restructuring of the grammar is evident in later stages of development. Finally, complete success in acquiring L2 metonymic patterns is attested in our experimental study. Implications for L2A theories and teaching practices are discussed.
A comprehensive comparison of association estimators for gene network inference algorithms
Authors: Kurt Zeyneb , Aydin Nizamettin , Altay Gökmen
Published: April 2014

Motivation: Gene network inference (GNI) algorithms enable the researchers to explore the interactions among the genes and gene products by revealing these interactions. The principal process of the GNI algorithms is to obtain the association scores among genes. Although there are several association estimators used in different applications, there is no commonly accepted estimator as the best one for the GNI applications. In this study, 27 different interaction estimators were reviewed and 14 most promising ones among them were evaluated by using three popular GNI algorithms with two synthetic and two real biological datasets belonging to Escherichia coli bacteria and Saccharomyces cerevisiae yeast. Influences of the Copula Transform (CT) pre-processing operation on the performance of the interaction estimators are also observed. This study is expected to assist many researchers while studying with GNI applications.

Results: B-spline, Pearson-based Gaussian and Spearman-based Gaussian association score estimators outperform the others for all datasets in terms of the performance and runtime. In addition to this, it is observed that, when the CT operation is used, inference performances of the estimators mostly increase, especially for two synthetic datasets. Detailed evaluations and discussions are given in the experimental results.

Contact:  gokmen.altay@bahcesehir.edu.tr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Lossy compression of quality scores in genomic data
Authors: Cánovas Rodrigo , Moffat Alistair , Turpin Andrew
Published: April 2014

Motivation: Next-generation sequencing technologies are revolutionizing medicine. Data from sequencing technologies are typically represented as a string of bases, an associated sequence of per-base quality scores and other metadata, and in aggregate can require a large amount of space. The quality scores show how accurate the bases are with respect to the sequencing process, that is, how confident the sequencer is of having called them correctly, and are the largest component in datasets in which they are retained. Previous research has examined how to store sequences of bases effectively; here we add to that knowledge by examining methods for compressing quality scores. The quality values originate in a continuous domain, and so if a fidelity criterion is introduced, it is possible to introduce flexibility in the way these values are represented, allowing lossy compression over the quality score data.

Results: We present existing compression options for quality score data, and then introduce two new lossy techniques. Experiments measuring the trade-off between compression ratio and information loss are reported, including quantifying the effect of lossy representations on a downstream application that carries out single nucleotide polymorphism and insert/deletion detection. The new methods are demonstrably superior to other techniques when assessed against the spectrum of possible trade-offs between storage required and fidelity of representation.

Availability and implementation: An implementation of the methods described here is available at https://github.com/rcanovas/libCSAM .

Contact:  rcanovas@student.unimelb.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
A change-point model for identifying 3′UTR switching by next-generation RNA sequencing
Authors: Wang Wei , Wei Zhi , Li Hongzhe
Published: April 2014

Motivation: Next-generation RNA sequencing offers an opportunity to investigate transcriptome in an unprecedented scale. Recent studies have revealed widespread alternative polyadenylation (polyA) in eukaryotes, leading to various mRNA isoforms differing in their 3′ untranslated regions (3′UTR), through which, the stability, localization and translation of mRNA can be regulated. However, very few, if any, methods and tools are available for directly analyzing this special alternative RNA processing event. Conventional methods rely on annotation of polyA sites; yet, such knowledge remains incomplete, and identification of polyA sites is still challenging. The goal of this article is to develop methods for detecting 3′UTR switching without any prior knowledge of polyA annotations.

Results: We propose a change-point model based on a likelihood ratio test for detecting 3′UTR switching. We develop a directional testing procedure for identifying dramatic shortening or lengthening events in 3′UTR, while controlling mixed directional false discovery rate at a nominal level. To our knowledge, this is the first approach to analyze 3′UTR switching directly without relying on any polyA annotations. Simulation studies and applications to two real datasets reveal that our proposed method is powerful, accurate and feasible for the analysis of next-generation RNA sequencing data.

Conclusions: The proposed method will fill a void among alternative RNA processing analysis tools for transcriptome studies. It can help to obtain additional insights from RNA sequencing data by understanding gene regulation mechanisms through the analysis of 3′UTR switching.

Availability and implementation: The software is implemented in Java and can be freely downloaded from http://utr.sourceforge.net/ .

Contact:  zhiwei@njit.edu or hongzhe@mail.med.upenn.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Computational identification of natural peptides based on analysis of molecular evolution
Authors: Toporik Amir , Borukhov Itamar , Apatoff Avihay , Gerber Doron , Kliger Yossef
Published: April 2014

Motivation: Many secretory peptides are synthesized as inactive precursors that must undergo post-translational processing to become biologically active peptides. Attempts to predict natural peptides are limited by the low performance of proteolytic site predictors and by the high combinatorial complexity of pairing such sites. To overcome these limitations, we analyzed the site-wise evolutionary mutation rates of peptide hormone precursors, calculated using the Rate4Site algorithm.

Results: Our analysis revealed that within their precursors, peptide residues are significantly more conserved than the pro-peptide residues. This disparity enables the prediction of peptides with a precision of ∼60% at a recall of 40% [receiver-operating characteristic curve (ROC) AUC 0.79]. Subsequently, combining the Rate4Site score with additional features and training a Random Forest classifier enable the prediction of natural peptides hidden within secreted human proteins at a precision of ∼90% at a recall of 50% (ROC AUC 0.96). The high performance of our method allows it to be applied to full secretomes and to predict naturally occurring active peptides. Our prediction on Homo sapiens revealed several putative peptides in the human secretome that are currently unannotated. Furthermore, the unique expression of some of these peptides implies a potential hormone function, including peptides that are highly expressed in endocrine glands.

Availability and implementation: A pseudocode is available in the Supplementary information.

Contact:  doron.gerber@biu.ac.il or kliger@cgen.com

Supplementary information : Supplementary data are available at Bioinformatics online.
Random survival forests for competing risks
Authors: Ishwaran Hemant , Gerds Thomas A. , Kogalur Udaya B. , Moore Richard D. , Gange Stephen J. , Lau Bryan M.
Published: April 2014

We introduce a new approach to competing risks using random forests. Our method is fully non-parametric and can be used for selecting event-specific variables and for estimating the cumulative incidence function. We show that the method is highly effective for both prediction and variable selection in high-dimensional problems and in settings such as HIV/AIDS that involve many competing risks.
Bimodality of wind-fed accretion in high-mass X-ray binaries
Authors: Karino Shigeyuki
Published: April 2014

We here consider the influence of X-ray photoionization from an accreting neutron star in a high-mass X-ray binary. Our aim is to unveil a new principle governing the X-ray luminosity of X-ray binaries, through a simple analysis of fluid equations simulating line-driven wind flow under the influence of X-ray irradiation. In this study, we solved the equation of motion of the accretion flow while taking into account the line-driven acceleration and X-ray photoionization. Under the influence of X-ray irradiation, we have found that the flow equations have two types of solutions. The first is characterized by a slow wind velocity, which causes a large accretion rate. The second solution is a fast wind flow, which results in a small accretion rate. We find that only the solution with a fast wind and faint X-ray luminosity is a steady solution. On the other hand, a slow wind solution with a large X-ray luminosity is not a realizable solution. In bright X-ray binary systems, the X-ray luminosity would increase until strong X-rays reduce the line-driven acceleration, and cause a stagnation of the wind. This implies an important consequence; that is, the X-ray luminosity of the wind-fed, X-ray emitting binary is settled by the limit of wind stagnation. At the same time, the fast-wind solution with a small X-ray luminosity can also represent a steady state. Bright X-ray sources, such as Vela X-1, would have limiting luminosities of wind stagnation, while faint systems, such as quiescent supergiant fast X-ray transients, could follow the faint solution.
Mucilaginibacter
koreensis sp. nov., isolated from leaf mould
Authors: Park Cheol Su , Han Kyudong , Ahn Tae-Young
Published: April 2014

A Gram-staining-negative, strictly aerobic, rod-shaped, pale-pink pigmented bacterial strain, designated TF8T, was isolated from leaf mould in Cheonan, Republic of Korea. Its taxonomic position was determined through a polyphasic approach. Optimal growth occurred on R2A agar without NaCl supplementation, at 25–28 °C and at pH 6.0–7.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TF8T belongs to the genus

Mucilaginibacter

in the family

Sphingobacteriaceae

. The sequence similarity between 16S rRNA genes of strain TF8T and the type strains of other species of the genus

Mucilaginibacter

ranged from 92.1 to 94.7 %. The closest relatives of strain TF8T were

Mucilaginibacter lutimaris

BR-3T (94.7 %),

M. soli

R9-65T (94.5 %),

M. litoreus

BR-18T (94.5 %),

M. rigui

WPCB133T (94.0 %) and

M. daejeonensis

Jip 10T (93.8 %). The major isoprenoid quinone was MK-7 and the major cellular fatty acids were iso-C15 : 0 (33.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 24.8 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 13.0 %). The major polar lipids of TF8T were phosphatidylethanolamine and three unidentified aminophospholipids. The G+C content of the genomic DNA was 46.2 mol%. On the basis of the data presented here, strain TF8T is considered to represent a novel species of the genus

Mucilaginibacter

, for which the name Mucilaginibacter koreensis sp. nov. is proposed. The type strain is TF8T ( = KACC 17468T = JCM 19323T).
Survey on diversity of marine/saline anaerobic Heterolobosea (Excavata: Discoba) with description of seven new species
Authors: Pánek Tomáš , Ptáčková Eliška , Čepička Ivan
Published: April 2014

Diversity of the anaerobic Heterolobosea (Excavata: Discoba) is only poorly understood, especially in marine environments. We have isolated and cultured 16 strains of anaerobic heteroloboseid amoebae and flagellates from brackish, marine and saline anoxic habitats worldwide. Phylogenetic analyses of SSU rDNA sequences and light-microscopic observations showed that all the strains belong to the family Psalteriomonadidae, the main anaerobic lineage of Heterolobosea, and that they represent eight species from the genera Monopylocystis, Harpagon and Pseudoharpagon. Seven species are newly isolated and described here as Monopylocystis minor n. sp., Monopylocystis robusta n. sp., Monopylocystis elegans n. sp., Monopylocystis disparata n. sp., Harpagon salinus n. sp., Pseudoharpagon longus n. sp. and Pseudoharpagon tertius n. sp. Amoebae, cysts and the ultrastructure of the genus Pseudoharpagon are presented for the first time.
Growth of osteosarcoma cells in a three-dimensional bone-like matrix alters their susceptibility to adeno-associated virus
Authors: Dey Sangeeta , Laredj Leila , Damjanovic Katarina , Muller Manon , Beard Peter
Published: April 2014

Osteosarcoma cells U2OS are partially susceptible to adeno-associated virus (AAV)-2 infection, allowing efficient synthesis of Rep proteins and, in a low percentage of cells, capsid production. It is not clear if this partial susceptibility to infection is due to the bone-cell-like nature of these cells or is a result of their transformed properties. Here, we grew osteosarcoma cells in a biomimetic three-dimensional bone-like matrix composed of calcium phosphate and chitosan, and tested whether this would increase or reduce their permissiveness to virus. The osteosarcoma cells grew in the matrix and began to express the alkaline phosphatase bone cell differentiation marker. This was accompanied by a block to their infection by AAV, as indicated by Rep and capsid production. Infection of cells growing in three-dimensional tissue-like matrices could be, in a wider context, a practical way to mimic in vivo conditions.
A novel approach to propagate flavivirus infectious cDNA clones in bacteria by introducing tandem repeat sequences upstream of virus genome
Authors: Pu Szu-Yuan , Wu Ren-Huang , Tsai Ming-Han , Yang Chi-Chen , Chang Chung-Ming , Yueh Andrew
Published: April 2014

Despite tremendous efforts to improve the methodology for constructing flavivirus infectious cDNAs, the manipulation of flavivirus cDNAs remains a difficult task in bacteria. Here, we successfully propagated DNA-launched type 2 dengue virus (DENV2) and Japanese encephalitis virus (JEV) infectious cDNAs by introducing seven repeats of the tetracycline-response element (7×TRE) and a minimal cytomegalovirus (CMVmin) promoter upstream of the viral genome. Insertion of the 7×TRE-CMVmin sequence upstream of the DENV2 or JEV genome decreased the crypticE. colipromoter (ECP) activity of the viral genome in bacteria, as measured using fusion constructs containing DENV2 or JEV segments and the reporter geneRenillaluciferase in an empty vector. The growth kinetics of recombinant viruses derived from DNA-launched DENV2 and JEV infectious cDNAs were similar to those of parental viruses. Similarly, RNA-launched DENV2 infectious cDNAs were generated by inserting 7×TRE-CMVmin, five repeats of the GAL4 upstream activating sequence, or five repeats ofBamHI linkers upstream of the DENV2 genome. All three tandem repeat sequences decreased the ECP activity of the DENV2 genome in bacteria. Notably, 7×TRE-CMVmin stabilized RNA-launched JEV infectious cDNAs and reduced the ECP activity of the JEV genome in bacteria. The growth kinetics of recombinant viruses derived from RNA-launched DENV2 and JEV infectious cDNAs displayed patterns similar to those of the parental viruses. These results support a novel methodology for constructing flavivirus infectious cDNAs, which will facilitate research in virology, viral pathogenesis and vaccine development of flaviviruses and other RNA viruses.
Mutational analysis of the helicase domain of a replication initiator protein reveals critical roles of Lys 272 of the B′ motif and Lys 289 of the β-hairpin loop in geminivirus replication
Authors: George Biju , Ruhel Rajrani , Mazumder Mohit , Sharma Veerendra Kumar , Jain Swatantra Kumar , Gourinath Samudrala , Chakraborty Supriya
Published: April 2014

Replication initiator protein (Rep) is indispensable for rolling-circle replication of geminiviruses, a group of plant-infecting circular ssDNA viruses. However, the mechanism of DNA unwinding by circular ssDNA virus-encoded helicases is unknown. To understand geminivirus Rep function, we compared the sequence and secondary structure of Rep with those of bovine papillomavirus E1 and employed charged residue-to-alanine scanning mutagenesis to generate a set of single-substitution mutants in Walker A (K227), in Walker B (D261, 262), and within or adjacent to the B′ motif (K272, K286 and K289). All mutants were asymptomatic and viral accumulation could not be detected by Southern blotting in both tomato and N. benthamiana plants. Furthermore, the K272 and K289 mutants were deficient in DNA binding and unwinding. Biochemical studies and modelling data based on comparisons with the known structures of SF3 helicases suggest that the conserved lysine (K289) located in a predicted β-hairpin loop may interact with ssDNA, while lysine 272 in the B′ motif (K272) located on the outer surface of the protein is presumably involved in coupling ATP-induced conformational changes to DNA binding. To the best of our knowledge, this is the first time that the roles of the B′ motif and the adjacent β-hairpin loop in geminivirus replication have been elucidated.
Neural lineage induction reveals multi-scale dynamics of 3D chromatin organization
Authors: Pekowska Aleksandra , Klaus Bernd , Klein Felix Alexander , Anders Simon , Oles Malgorzata , Steinmetz Lars Michael , Bertone Paul , Huber Wolfgang
Published: April 2014

Regulation of gene expression underlies cell identity. Chromatin structure and gene activity are linked at multiple levels, via positioning of genomic loci to transcriptionally permissive or repressive environments and by connecting cis-regulatory elements such as promoters and enhancers. However, the genome-wide dynamics of these processes during cell differentiation has not been characterized. Using tethered chromatin conformation capture (TCC) sequencing we determined global three-dimensional chromatin structures in mouse embryonic stem (ES) and neural stem (NS) cell derivatives. We found that changes in the propensity of genomic regions to form inter-chromosomal contacts are pervasive in neural induction and are associated with the regulation of gene expression. Moreover, we found a pronounced contribution of euchromatic domains to the intra-chromosomal interaction network of pluripotent cells, indicating the existence of an ES cell-specific mode of chromatin organization. Mapping of promoter-enhancer interactions in pluripotent and differentiated cells revealed that spatial proximity without enhancer element activity is a common architectural feature in cells undergoing early developmental changes. Activity-independent formation of higher-order contacts between cis-regulatory elements, predominant at complex loci, may thus provide an additional layer of transcriptional control.
Boom-Bust Turnovers of Megabase-Sized Centromeric DNA inSolanumSpecies: Rapid Evolution of DNA Sequences Associated with Centromeres
Authors: Zhang Haiqin , Koblížková Andrea , Wang Kai , Gong Zhiyun , Oliveira Ludmila , Torres Giovana A. , Wu Yufeng , Zhang Wenli , Novák Petr , Buell C. Robin , Macas Jiří , Jiang Jiming
Published: April 2014

Centromeres are composed of long arrays of satellite repeats in most multicellular eukaryotes investigated to date. The satellite repeat–based centromeres are believed to have evolved from “neocentromeres” that originally contained only single- or low-copy sequences. However, the emergence and evolution of the satellite repeats in centromeres has been elusive. Potato (Solanum tuberosum) provides a model system for studying centromere evolution because each of its 12 centromeres contains distinct DNA sequences, allowing comparative analysis of homoeologous centromeres from related species. We conducted genome-wide analysis of the centromeric sequences in Solanum verrucosum, a wild species closely related to potato. Unambiguous homoeologous centromeric sequences were detected in only a single centromere (Cen9) between the two species. Four centromeres (Cen2, Cen4, Cen7, and Cen10) in S. verrucosum contained distinct satellite repeats that were amplified from retrotransposon-related sequences. Strikingly, the same four centromeres in potato contain either different satellite repeats (Cen2 and Cen7) or exclusively single- and low-copy sequences (Cen4 and Cen10). Our sequence comparison of five homoeologous centromeres in two Solanum species reveals rapid divergence of centromeric sequences among closely related species. We propose that centromeric satellite repeats undergo boom-bust cycles before a favorable repeat is fixed in the population.
Job strain and the risk of severe asthma exacerbations: a meta‐analysis of individual‐participant data from 100 000 European men and women
Authors: Heikkilä K. , Madsen I. E. H. , Nyberg S. T. , Fransson E. I. , Westerlund H. , Westerholm P. J. M. , Virtanen M. , Vahtera J. , Väänänen A. , Theorell T. , Suominen S. B. , Shipley M. J. , Salo P. , Rugulies R. , Pentti J. , Pejtersen J. H. , Oksanen T. , Nordin M. , Nielsen M. L. , Kouvonen A. , Koskinen A. , Koskenvuo M. , Knutsson A. , Ferrie J. E. , Dragano N. , Burr H. , Borritz M. , Bjorner J. B. , Alfredsson L. , Batty G. D. , Singh‐Manoux A. , Kivimäki M. ,   the IPD‐Work Consortium
Published: April 2014

Background

Many patients and healthcare professionals believe that work‐related psychosocial stress, such as job strain, can make asthma worse, but this is not corroborated by empirical evidence. We investigated the associations between job strain and the incidence of severe asthma exacerbations in working‐age European men and women.

Methods

We analysed individual‐level data, collected between 1985 and 2010, from 102 175 working‐age men and women in 11 prospective European studies. Job strain (a combination of high demands and low control at work) was self‐reported at baseline. Incident severe asthma exacerbations were ascertained from national hospitalization and death registries. Associations between job strain and asthma exacerbations were modelled using Cox regression and the study‐specific findings combined using random‐effects meta‐analyses.

Results

During a median follow‐up of 10 years, 1 109 individuals experienced a severe asthma exacerbation (430 with asthma as the primary diagnostic code). In the age‐ and sex‐adjusted analyses, job strain was associated with an increased risk of severe asthma exacerbations defined using the primary diagnostic code (hazard ratio, HR: 1.27, 95% confidence interval, CI: 1.00, 1.61). This association attenuated towards the null after adjustment for potential confounders (HR: 1.22, 95% CI: 0.96, 1.55). No association was observed in the analyses with asthma defined using any diagnostic code (HR: 1.01, 95% CI: 0.86, 1.19).

Conclusions

Our findings suggest that job strain is probably not an important risk factor for severe asthma exacerbations leading to hospitalization or death.
Intrauterine growth restriction – a population‐based study of the association with academic performance and psychiatric health
Authors: Kierulf Strømme Kirsten , Strømme Petter , Bjertness Espen , Lien Lars
Published: April 2014

Aim

To investigate whether intrauterine growth restriction (IUGR), resulting in small for gestational age (SGA) infants, is associated with increased susceptibility to psychiatric problems and academic impairment in late teens.

Methods

A cohort of all 10th‐grade students in Oslo, Norway, followed up between 2001 and 2004 (n = 2131), was linked with foetal growth data. IUGR was considered equal to SGA at the lowest 2.5th, 5th, and 10th percentiles and appropriate for gestational age (AGA) as the highest 90th percentile. Mental health was evaluated using the Hopkins Symptoms Check List and the Strength and Difficulties Questionnaire, and academic achievements and ambitions were self‐reported by the students.

Results

Psychiatric problems were equally prevalent in all groups. However, the SGA girls performed inferiorly compared to their AGA peers in the school subjects English [3.6 vs 3.9 (p = 0.03)], mathematics [4.0 vs 4.3 (p = 0.01)] and social science [4.2 vs 4.4 (p = 0.05)], but not for Norwegian. This association was not observed in boys. There was an association between academic impairment and prematurity, occurring more frequently among immigrants (p < 0.001).

Conclusion

SGA had a small negative impact on academic achievements in adolescent girls, but not boys. There was no association between SGA and psychiatric problems in either gender.
Association of obesity and treated hypertension and diabetes with cognitive ability in bipolar disorder and schizophrenia
Authors: Depp Colin A , Strassnig Martin , Mausbach Brent T , Bowie Christopher R , Wolyniec Paula , Thornquist Mary H , Luke James R , McGrath John A , Pulver Ann E , Patterson Thomas L , Harvey Philip D
Published: April 2014

Objectives

People with bipolar disorder or schizophrenia are at greater risk for obesity and other cardio‐metabolic risk factors, and several prior studies have linked these risk factors to poorer cognitive ability. In a large ethnically homogenous outpatient sample, we examined associations among variables related to obesity, treated hypertension and/or diabetes and cognitive abilities in these two patient populations.

Methods

In a study cohort of outpatients with either bipolar disorder (n = 341) or schizophrenia (n = 417), we investigated the association of self‐reported body mass index and current use of medications for hypertension or diabetes with performance on a comprehensive neurocognitive battery. We examined sociodemographic and clinical factors as potential covariates.

Results

Patients with bipolar disorder were less likely to be overweight or obese than patients with schizophrenia, and also less likely to be prescribed medication for hypertension or diabetes. However, obesity and treated hypertension were associated with worse global cognitive ability in bipolar disorder (as well as with poorer performance on individual tests of processing speed, reasoning/problem‐solving, and sustained attention), with no such relationships observed in schizophrenia. Obesity was not associated with symptom severity in either group.

Conclusions

Although less prevalent in bipolar disorder compared to schizophrenia, obesity was associated with substantially worse cognitive performance in bipolar disorder. This association was independent of symptom severity and not present in schizophrenia. Better understanding of the mechanisms and management of obesity may aid in efforts to preserve cognitive health in bipolar disorder.
Increased temporo‐insular engagement in unmedicated bipolar II disorder: an exploratory resting state study using independent component analysis
Authors: Yip Sarah W , Mackay Clare E , Goodwin Guy M
Published: April 2014

Objectives

Despite numerous structural and functional magnetic resonance imaging studies, the neurobiology of bipolar disorder (BD) is still incompletely understood. Resting‐state functional magnetic resonance imaging (rsFMRI) allows for the study of intrinsic functional connections between brain areas, which may reflect the pathophysiology of BD. Most previous rsFMRI studies conducted in BD have included a majority of medicated patients, making simple interpretation with respect to pathophysiology difficult.

Methods

Participants were 15 antipsychotic agent‐ and mood‐stabilizer‐naïve young adults with bipolar II disorder (BD‐II), and 20 healthy controls group‐matched for gender, age, and cognitive ability. Independent component analysis (ICA) was used to identify eight commonly studied resting‐state networks (RSNs). Between‐group comparisons were conducted using dual regression and corrected for family‐wise error (FWE) across space and the number of components (pFWE < 0.05).

Results

In comparison to controls, participants with BD‐II had increased coherence across several brain regions, including the bilateral insula and putamen, across a temporo‐insular network. No between‐group differences in engagement of the default mode network were found.

Conclusions

This was the first ICA‐based rsFMRI study conducted among unmedicated individuals with BD. Given the young age (mean = 23 years) and antipsychotic agent‐ and mood‐stabilizer‐naïve status of our participants with BD‐II, temporo‐insular functional connectivity is a candidate vulnerability marker for BD. Further work is needed to relate resting‐state differences to detailed understanding of pathophysiology.