bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Importance of Supporting Adolescents’ Autonomy in Promoting Physical-Sport Exercise
Authors: Moreno-Murcia Juan Antonio , Hernández Elisa Huéscar 
Published: April 2014

AbstractThis study was conducted toward the objective of analyzing certain factors that influence physical activity in Spanish adolescent students using self-determination theory (Deci & Ryan, 1985; 2000) as a framework. Participants included 698 physical education students whose perception of the autonomy support provided by their teachers was assessed in and out of the class context. Also assessed were social goals of responsibility and relationship with others, basic psychological needs, and intrinsic motivation, which is part of self-determination theory (SDT). Finally, the “intention” factor posited by the theory of planned behavior (TPB) and students’ rate of exercise in the last twelve months were considered. The results of structural equations modeling suggest autonomy education, autonomy support, and social goals positively predicted certain psychological mediators, which in turn positively predicted students’ intrinsic motivation, which was a positive predictor of intention, and that of rate of exercise. The results also highlight the benefit of promoting autonomy to enhance students’ physical exercise practice.
Catalan and Hungarian Validation of the Zuckerman-Kuhlman-Aluja
Personality Questionnaire (ZKA-PQ)
Authors: Surányi Zsuzsanna , Aluja Anton 
Published: April 2014

AbstractThe goal of this study was to examine the cross-cultural validity and reliability
of the Zuckerman-Kuhlman-Aluja Personality Questionnaire (ZKA-PQ) – a
recently published instrument for assessing the Zuckerman’s
Alternative Five Factor Personality Model – in Catalan and Hungarian
speaking populations. The samples consisted of 1,564 subjects from Catalonia and
1,647 from Hungary. Results showed a clear five-factor structure and acceptable
alpha reliabilities of the ZKA-PQ in both countries. Facets alpha average was
80.35 and 74.10 for Catalans and Hungarians respectively. The factorial
congruency coefficients indicated that both structures were equivalent, with a
global value of .97. However, the robust structure obtained with EFA yielded
poor fit indices in the subsequent CFA. Altogether, the psychometric findings
were similar to those obtained in the original validation study carried out in
Spanish and English populations. Main country differences were found only in
Neuroticism factor, with Hungarians scoring significantly lower that Catalans.
Nevertheless, country, sex and age explained only 18.6 % of Neuroticism variance
(adjusted R squared = .186). Country differences had only medium
effect size [F(1, 3188) = 292, p
< .001, η2 = .0841].
Knee extension fatigue attenuates repeated force production of the elbow flexors
Authors: Halperin Israel , Aboodarda Saied J. , Behm David G. 
Published: April 2014

AbstractNon‐local muscle fatigue has been demonstrated with unilateral activities, where fatiguing one limb alters opposite limb forces. Fewer studies have examined if non‐local fatigue occurs with unrelated muscles. The purpose of this study was to investigate if knee extensors fatigue alters elbow flexors force and electromyography (EMG) activity. Eighteen males completed a control and fatiguing session (randomised). Blood lactate was initially sampled followed by three maximal voluntary contractions (MVC) with the elbow flexors and two with the knee extensors. Thereafter, subjects either sat (control) or performed five sets of bilateral dynamic knee extensions to exhaustion using a load equal to the dominant limb MVC (1‐min rest between sets). Immediately afterwards, subjects were assessed for blood lactate and unilateral knee extensors MVC, and after 1 min performed a single unilateral elbow flexor MVC. Two minutes later, subjects performed 12 unilateral elbow flexor MVCs (5 s contraction/10 s rest) followed by a third blood lactate test. Compared to control, knee extensor force dropped by 35% (p < 0.001; ES = 1.6) and blood lactate increased by 18% (p < 0.001; ES = 2.8). Elbow flexor forces were lower after the fatiguing protocol only during the last five MVCs (p < 0.05; ES = ∼0.58; ∼5%). No changes occurred between conditions in EMG. Elbow flexor forces significantly decreased after knee extensors fatigue. The effect was revealed during the later stages of the repeated MVCs protocol, demonstrating that non‐local fatigue may have a stronger effect on repeated rather than on single attempts of maximal force production.
GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms
Authors: Wang Jia-Hong , Zhao Ling-Feng , Lin Pei , Su Xiao-Rong , Chen Shi-Jun , Huang Li-Qiang , Wang Hua-Feng , Zhang Hai , Hu Zhen-Fu , Yao Kai-Tai , Huang Zhong-Xi 
Published: April 2014

Summary: Identifying biological functions and molecular networks in a gene list and how the genes may relate to various topics is of considerable value to biomedical researchers. Here, we present a web-based text-mining server, GenCLiP 2.0, which can analyze human genes with enriched keywords and molecular interactions. Compared with other similar tools, GenCLiP 2.0 offers two unique features: (i) analysis of gene functions with free terms (i.e. any terms in the literature) generated by literature mining or provided by the user and (ii) accurate identification and integration of comprehensive molecular interactions from Medline abstracts, to construct molecular networks and subnetworks related to the free terms.
Availability and implementation: http://ci.smu.edu.cn.
Contact: zxhuang@smu.edu.cn
Supplementary information: Supplementary Data are available at Bioinformatics online.
Standard error estimation using the EM algorithm for the joint modeling of survival and longitudinal data
Authors: Xu Cong , Baines Paul D. , Wang Jane-Ling 
Published: April 2014

AbstractJoint modeling of survival and longitudinal data has been studied extensively in the recent literature. The likelihood approach is one of the most popular estimation methods employed within the joint modeling framework. Typically, the parameters are estimated using maximum likelihood, with computation performed by the expectation maximization (EM) algorithm. However, one drawback of this approach is that standard error (SE) estimates are not automatically produced when using the EM algorithm. Many different procedures have been proposed to obtain the asymptotic covariance matrix for the parameters when the number of parameters is typically small. In the joint modeling context, however, there may be an infinite-dimensional parameter, the baseline hazard function, which greatly complicates the problem, so that the existing methods cannot be readily applied. The profile likelihood and the bootstrap methods overcome the difficulty to some extent; however, they can be computationally intensive. In this paper, we propose two new methods for SE estimation using the EM algorithm that allow for more efficient computation of the SE of a subset of parametric components in a semiparametric or high-dimensional parametric model. The precision and computation time are evaluated through a thorough simulation study. We conclude with an application of our SE estimation method to analyze an HIV clinical trial dataset.
Cohort resonance: a significant component of fluctuations in recruitment, egg production, and catch of fished populations
Authors: Botsford Louis W. , Holland Matthew D. , Field John C. , Hastings Alan 
Published: April 2014

Abstract
Hjort (1914. Fluctuations in the great fisheries of northern Europe. Rapport et Procès-Verbaux des Réunions du Conseil Permanent International pour l'exploration de la Mer, XX: 1–228) identified two important aspects of the early life of fish as being important determinants of fluctuations in year-class strength: changes in nutrition and transport. He dismissed a third possible influence, changes in the abundance of the reproductive stock. Here, we describe how a recently discovered characteristic behaviour of age-structured populations termed cohort resonance, which does involve changes in adult abundance, can have a substantial effect on fluctuations in fished populations. Cohort resonance involves selectively greater sensitivity of age-structured populations to generational frequencies and to very low frequencies in the environmental signal influencing a population. This frequency-dependent selectivity has been shown to increase with fishing, as do the total amounts of variability in recruitment, egg production, and catch. Cohort resonance differs from other recent model mechanisms proposed to explain the observed increase in variability with fishing in that it does not require over-compensatory density-dependence. It stems from the compensatory ascending limb of the egg–recruit relationship, and is a characteristic of a stable population driven by a random environment. We demonstrate the differences in frequency selectivity and increases in variability with fishing among three different Pacific coast species with different longevity: coho salmon (Oncorhynchus kisutch; ∼3 years), Pacific hake (Merluccius productus; ∼25 years), and Pacific Ocean perch (Sebastes alutus; ∼90 years). The shortest lived, coho salmon is the most sensitive to environmental variability, but variability in egg production and catch both increase more rapidly with fishing in the longer-lived species. Understanding cohort resonance will aid in anticipation of predicted potential changes in the frequency content of the physical environment with changing climate (e.g. more frequent El Niños), and it provides a warning regarding the possible confounding of increasing sensitivity to slow change due to fishing with actual slow change of population parameters due to climate change. Our understanding of the role of cohort resonance in population variability will be enhanced by further identification of empirical examples. We describe some of the challenges in this effort.
First Report of Peanut mottle virus Infecting Soybean in South Korea
Authors: Lim S. , Lee Y.-H. , Igori D. , Zhao F. , Yoo R. H. , Lee S.-H. , Baek I. Y. , Moon J. S. 
Published: April 2014

In July 2013, soybean (Glycine max) plants at the research field in Daegu, South Korea, showed virus-like symptoms, such as mosaic, mottle, yellowing, and stunting. Overall, there were approximately 1% of soybean plants that showed these symptoms. Sixteen soybean samples were collected based on visual symptoms and subjected to laboratory characterization. Total RNA was extracted from each sample with the Tri Reagent (Molecular Research Center, Cincinnati, OH) and cDNA was synthesized using random N25 primer with RevertAid Reverse Transcriptase (Thermo Scientific, Waltham, MA), according to the manufacturers' instructions. All samples were tested by PCR with Prime Taq Premix (2X) (GeNet Bio, Daejeon, Korea) and primer sets specific to Soybean mosaic virus (SMV; 5′-CATATCAGTTTGTTGGGCA-3′ and 5′-TGCCTATACCCTCAACAT-3′), Peanut stunt virus (PSV; 5′-TGACCGCGTGCCAGTAGGAT-3′ and 5′-AGGTDGCTTTCTWTTGRATTTA-3′), Soybean yellow mottle mosaic virus (SYMMV; 5′-CAACCCTCAGCCACATTCAACTAT-3′ and 5′-TCTAACCACCCCACCCGAAGGATT-3′), and Soybean yellow common mosaic virus (SYCMV; 5′-TTGGCTGAGAGGAGTGGCTT-3′ and 5′-TGCGGTCGTGTAGTCAGTG-3′). Among 16 samples tested, five were positive for SMV and two for SYMMV. Three samples were found infected by both SMV and SYMMV and four by both SMV and PSV. Since two of the symptomatic samples were not infected by viruses described above, a pair of primers specific to Peanut mottle virus (PeMoV; 5′-GCTGTGAATTGTTGTTGAGAA-3′ and 5′-ACAATGATGAAGTTCGTTAC-3′) was tested (1). All 16 samples were subjected to RT-PCR with primers specific to PeMoV. Four were found positive for PeMoV. Two of them were already found infected with SYMMV. In order to identify the complete nucleotide sequences of PeMoV coat protein (CP), another primer set (5′-TGAGCAGGAAAGAATTGTTTC-3′ and 5′-GGAAGCGATATACACACCAAC-3′) was used. RT-PCR product was cloned into RBC TA Cloning Vector (RBC Bioscience, Taipei, Taiwan) and the nucleotide sequence of the insert was determined by Macrogen (Seoul, Korea). CP gene of the PeMoV (GenBank Accession No. KJ664838) showed the highest nucleotide sequence identity with PeMoV isolate Habin (KF977830; 99% identity), and the highest amino acid identity with GenBank Accession No. ABI97347 (100% identity). In order to fulfill Koch's postulates, several G. max cv. Williams 82 were inoculated with the extracts of PeMoV-infected leaf tissue. At 14 days post-inoculation, plants showed systemic mottle symptoms. These symptomatic plants were subjected to RT-PCR, and the nucleotide sequences of the PCR product were found identical to that of the virus in the inoculum. To our knowledge, this is the first report of soybean-infecting PeMoV, a member of the genus Potyvirus in the family Potyviridae, in South Korea. Reference: (1) R. G. Dietzgen et al. Plant Dis. 85:989, 2001.
First Report of Clover yellow vein virus on Glycine max in Korea
Authors: Shin J.-C. , Kim M.-K. , Kwak H.-R. , Choi H.-S. , Kim J.-S. , Park C.-Y. , Cha B. J. 
Published: April 2014

Glycine max (Soybean) is the most important edible crop in Korea. In Korea, eight viruses have been reported to infect soybean, including Alfalfa mosaic virus (AMV), Cowpea mosaic virus (CPMV), Cucumber mosaic virus (CMV), Soybean dwarf virus (SbDV), Soybean mosaic virus (SMV), Soybean yellow common mosaic virus (SYCMV), Soybean yellow mottle virus (SYMMV), and Peanut stunt virus (PSV) (1). In 2012, Glycine max were observed in Daegu, South Korea, with mosaic and mottling symptoms on leaves. Samples with virus-like symptoms (n = 151) were collected from Daegu including legume genetic resource field. Virus particles were filamentous rod shaped, average length 760 nm, and were analyzed by RT-PCR using specific primers for several Potyviruses and previously reported viruses infecting soybean. Only two samples showing mosaic and mottling symptoms were identified as Clover yellow vein virus (ClYVV) based on RT-PCR using primers specific for ClYVV (5′-GTTGGCTTGGTTGACACTGA-3′ and 5′-CTTCGATCATGGATGCACA-3′). The sequences of amplified fragments were 97 to 98% similar with ClYVV. ClYVV is a distinct species in the genus Potyvirus and family Potyviridae. ClYVV is transmitted by several species of aphids and by mechanical inoculation (2). ClYVV was first reported on Gentiana scabra, and the disease has never been reported in soybean fields in Korea. The biological properties and full genome sequence of the selected ClYVV isolate of apparent virus symptoms between two samples were analyzed. The ClYVV isolate was inoculated to local lesion plants, re-isolated from local lesions three times, and propagated in Nicotiana benthamiana, and then named ClYVV-Gm. The ClYVV-Gm induced local lesions on inoculated leaves of N. tabacum cv. Xanthi-nc, Tetragonia expansa, and systemic symptoms on upper leaves of Chenopodium amaranticolor, C. quinoa, and N. clevelandii. The ClYVV-Gm caused mosaic and mottling symptoms on Glycine max cv. Kwangan and Phaseolus vulgaris. The genome of ClYVV-Gm was determined to be 9,584 nucleotides in length (GenBank Accession No. KF975894), and it shared 83% to 97% nucleotide identity with the sequences of 27 previously reported ClYVV isolates including Vicia fava and Pisum sativum. Despite low occurrence of ClYVV in Glycine max, ClYVV has a broad host range including tobacco, weed species, and soybean, which can lead to spreading of the virus. Our results indicate that emergence of ClYVV could become a problem to Leguminosae in Korea. To our knowledge, this is the first biological and molecular report of ClYVV infecting Glycine max in Korea. References: (1) Y. H. Lee et al. Korea Soybean Digest 29:7, 2012. (2) T. Sasaya et al. Phytopathology 87:1014, 1997.
Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions
Authors: Laurent Sacha , Robinson-Rechavi Marc , Salamin Nicolas 
Published: April 2014

ABSTRACTRecent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing frameworks to model this diversity either focus on changes between lineages, neglecting global effects such as mass extinctions, or focus on changes over time which would affect all lineages. Yet it seems probable that both lineages differences and mass extinctions affect the same groups. Here we used simulations to test the performance of two widely used methods, under complex scenarios. We report good performances, although with a tendency to over-predict events when increasing the complexity of the scenario. Overall, we find that lineage shifts are better detected than mass extinctions. This work has significance for assessing the methods currently used for estimating changes in diversification using phylogenies and developing new tests.
Photobody Localization of Phytochrome B Is Tightly Correlated with Prolonged and Light-Dependent Inhibition of Hypocotyl Elongation in the Dark
Authors: Van Buskirk Elise K. , Reddy Amit K. , Nagatani Akira , Chen Meng 
Published: April 2014

AbstractPhotobody localization of Arabidopsis (Arabidopsis thaliana) phytochrome B (phyB) fused to green fluorescent protein (PBG) correlates closely with the photoinhibition of hypocotyl elongation. However, the amino-terminal half of phyB fused to green fluorescent protein (NGB) is hypersensitive to light despite its inability to localize to photobodies. Therefore, the significance of photobodies in regulating hypocotyl growth remains debatable. Accumulating evidence indicates that under diurnal conditions, photoactivated phyB persists into darkness to inhibit hypocotyl elongation. Here, we examine whether photobodies are involved in inhibiting hypocotyl growth in darkness by comparing the PBG and NGB lines after the red light-to-dark transition. Surprisingly, after the transition from 10 μmol m−2 s−1 red light to darkness, PBG inhibits hypocotyl elongation three times longer than NGB. The disassembly of photobodies in PBG hypocotyl nuclei correlates tightly with the accumulation of the growth-promoting transcription factor PHYTOCHROME-INTERACTING FACTOR3 (PIF3). Destabilizing photobodies by either decreasing the light intensity or adding monochromatic far-red light treatment before the light-to-dark transition leads to faster PIF3 accumulation and a dramatic reduction in the capacity for hypocotyl growth inhibition in PBG. In contrast, NGB is defective in PIF3 degradation, and its hypocotyl growth in the dark is nearly unresponsive to changes in light conditions. Together, our results support the model that photobodies are required for the prolonged, light-dependent inhibition of hypocotyl elongation in the dark by repressing PIF3 accumulation and by stabilizing the far-red light-absorbing form of phyB. Our study suggests that photobody localization patterns of phyB could serve as instructive cues that control light-dependent photomorphogenetic responses in the dark.
Chronic exposure to low‐dose radiation atChernobyl favours adaptation to oxidative stress in birds
Authors: Galván Ismael , Bonisoli‐Alquati Andrea , Jenkinson Shanna , Ghanem Ghanem , Wakamatsu Kazumasa , Mousseau Timothy A. , Møller Anders P. 
Published: April 2014

SummaryIonizing radiation produces oxidative stress, but organisms can adapt to their exposure with physiological adaptive responses. However, the role of radioadaptive responses in wild populations remains poorly known.At Chernobyl, studies of birds and other taxa including humans show that chronic exposure to radiation depletes antioxidants and increases oxidative damage. Here, we present analyses of levels of the most important intracellular antioxidant (i.e. glutathione,GSH), its redox status,DNAdamage and body condition in 16 species of birds exposed to radiation at Chernobyl. We use an approach that allows considering the individual bird as the sampling unit while controlling for phylogenetic effects, thus increasing the statistical power by avoiding the use of species means as done for most previous comparative studies.As a consequence, we found a pattern radically different from previous studies in wild populations, showing thatGSHlevels and body condition increased, and oxidative stress andDNAdamage decreased, with increasing background radiation. Thus, when several species are considered, the overall pattern indicates that birds are not negatively affected by chronic exposure to radiation and may even obtain beneficial hormetic effects following an adaptive response. Analysis of the phylogenetic signal supports the existence of adaptation in the studied traits, particularly inGSHlevels andDNAdamage.We also show that, under equal levels of radiation, the birds that produce larger amounts of the pigment pheomelanin and lower amounts of eumelanin pay a cost in terms of decreasedGSHlevels, increased oxidative stress andDNAdamage, and poorer body condition. Radiation, however, diminished another potential cost of pheomelanin, namely its tendency to produce free radicals when exposed to radiation, because it induced a change towards the production of less pro‐oxidant forms of pheomelanin with higher benzothiazole‐to‐benzothiazine ratios, which may have facilitated the acclimation of birds to radiation exposure.Our findings represent the first evidence of adaptation to ionizing radiation in wild animals, and confirm that pheomelanin synthesis represents an evolutionary constraint under stressful environmental conditions because it requiresGSHconsumption.
Bile‐induced peptidoglycan remodelling in Salmonella enterica
Authors: Hernández Sara B. , Cava Felipe , Pucciarelli M. Graciela , García‐del Portillo Francisco , de Pedro Miguel A. , Casadesús Josep 
Published: April 2014

SummaryChanges in the peptidoglycan (PG) structure of Salmonella enterica are detected in the presence of a sublethal concentration of sodium deoxycholate (DOC): (i) lower proportions of Braun lipoprotein (Lpp)‐bound muropeptides; (ii) reduced levels of muropeptides cross‐linked by L(meso)‐diaminopimelyl‐D(meso)‐diaminopimelic acid (L‐D) peptide bridges (3‐3 cross‐links). Similar structural changes are found in S. enterica cultures adapted to grow in the presence of a lethal concentration of DOC, suggesting that reduced anchoring of Braun protein to PG and low occurrence of 3‐3 cross‐links may increase S. enterica resistance to bile. This view is further supported by additional observations: (i) A triple mutant lacking L,D‐transpeptidases YbiS, ErfK, and YcfS, which does not contain Lpp anchored to PG, is hyper‐resistant to bile; (ii) enhanced 3‐3 cross‐linking upon overexpression of YnhG transpeptidase causes a decrease in bile resistance. These observations suggest that remodelling of the cell wall may be added to the list of adaptive responses that permit survival of S. enterica in the presence of bile.