bluuebunny/crossref_metadata_2025_split huggingface dataset:
Status and genetic diversity in pigeonpea germplasm from Caribbean and Central American regions at ICRISAT genebank
Authors: Upadhyaya H. D. , Reddy K. N. , Ramachandran Senthil , Kumar Vinod , Singh Sube , Reddy M. Thimma , Irshad Ahmed M. 
Published: November 2014

The genebank at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India holds a collection of 542 accessions from the Caribbean and Central American (CCA) regions, of which 424 were evaluated for eight qualitative and 17 quantitative traits at ICRISAT farm. A hierarchical cluster analysis was performed using the scores of the first nine principal components that resulted in four clusters. The accessions of these four clusters exhibited the following good characteristics: cluster 1 had high pod-bearing length and high seed protein content; those of cluster 2 had high degree of branching, large number of pods per plant and high seed yield per plant; those of cluster 3 had long pods; and those of cluster 4 had larger seeds. In the whole collection of accessions, diversity was found to be maximum (H′ = 0.630+0.026) for plant height and minimum for tertiary branches per plant (H′ = 0.259+0.026). The highest correlation coefficient was observed between racemes per plant and pods per plant (r= 0.914) followed by between pods per plant and seed yield per plant (r= 0.744), and between shelling percentage and the harvest index (r= 0.703). In view of the poor representation of the world collection of pigeonpea (13,771 accessions) from the CCA regions, launching of collection missions in these countries has been suggested to fill gaps and increase the variability. Multi-location evaluation of the collections for agronomic traits at potential locations in the CCA regions and systematic evaluation for nutritional traits and resistance to biotic and abiotic stress could result in the identification of useful genotypes, particularly vegetable types, for use in breeding programmes to develop high-yielding cultivars as well as to release as varieties in these regions.
Assessing Personal Initiative among Vocational Training Students: Development and Validation of a New Measure
Authors: Balluerka Nekane , Gorostiaga Arantxa , Ulacia Imanol 
Published: November 2014

AbstractPersonal initiative characterizes people who are proactive, persistent and self-starting when facing the difficulties that arise in achieving goals. Despite its importance in the educational field there is a scarcity of measures to assess students’ personal initiative. Thus, the aim of the present study was to develop a questionnaire to assess this variable in the academic environment and to validate it for adolescents and young adults. The sample comprised 244 vocational training students. The questionnaire showed a factor structure including three factors (Proactivity-Prosocial behavior, Persistence and Self-Starting) with acceptable indices of internal consistency (ranging between α = .57 and α =.73) and good convergent validity with respect to the Self-Reported Initiative scale. Evidence of external validity was also obtained based on the relationships between personal initiative and variables such as self-efficacy, enterprising attitude, responsibility and control aspirations, conscientiousness, and academic achievement. The results indicate that this new measure is very useful for assessing personal initiative among vocational training students.
Social Identity, Passion and Well-Being in University Students, the Mediating Effect of Passion
Authors: Bernabé Miguel , Lisbona Ana , Palací Francisco José , Martín-Aragón Maite 
Published: November 2014

AbstractResearch on positive emotions associated with the performance of an activity, such as work or study, has increased exponentially in recent years. Passion is understood as an attitude and intense emotion in the performance of an activity, and it has shown both positive and negative consequences for well-being. A link between social identity and positive emotions through social category membership has been described. The aim of this work is to study the relationship between social identity, the dimensions of passion and the positive impact on university responses. A quasi-experimental design was used on a sample of 266 university students from different Spanish universities (Universidad Nacional de Educación a Distancia, Universidad Miguel Hernández and Universidad de Alicante). Descriptive analyzes were performed on the study’s variables using SPSS 18. Structural equation modeling was carried out with AMOS 18 and the mediational analysis with MODMED macro developed by Preacher, Rucker, and Hayes (2007). The results show that the identity of the studies had an indirect effect on positive responses mediated by passion for the studies (RMSEA = .07; CFI = .97; NFI = .96; TLI = .92). It is observed that the harmonious and obsessive dimensions of passion differ in the mediating effect on happiness and satisfaction with studies. Practical and theoretical implications for well-being are discussed.
Biallelic loss-of-function mutation in NIK causes a primary immunodeficiency with multifaceted aberrant lymphoid immunity
Authors: Willmann Katharina L. , Klaver Stefanie , Doğu Figen , Santos-Valente Elisangela , Garncarz Wojciech , Bilic Ivan , Mace Emily , Salzer Elisabeth , Domínguez Conde Cecilia , Sic Heiko , Májek Peter , Banerjee Pinaki P. , Vladimer Gregory I. , Haskoloğlu Şule , Gökalp Bolkent Musa , Küpesiz Alphan , Condino-Neto Antonio , Colinge Jacques , Superti-Furga Giulio , Pickl Winfried F. , van Zelm Menno C. , Eibel Hermann , Orange Jordan S. , Ikincioğulları Aydan , Boztuğ Kaan 
Published: November 2014

AbstractPrimary immunodeficiency disorders enable identification of genes with crucial roles in the human immune system. Here we study patients suffering from recurrent bacterial, viral and Cryptosporidium infections, and identify a biallelic mutation in the MAP3K14 gene encoding NIK (NF-κB-inducing kinase). Loss of kinase activity of mutant NIK, predicted by in silico analysis and confirmed by functional assays, leads to defective activation of both canonical and non-canonical NF-κB signalling. Patients with mutated NIK exhibit B-cell lymphopenia, decreased frequencies of class-switched memory B cells and hypogammaglobulinemia due to impaired B-cell survival, and impaired ICOSL expression. Although overall T-cell numbers are normal, both follicular helper and memory T cells are perturbed. Natural killer (NK) cells are decreased and exhibit defective activation, leading to impaired formation of NK-cell immunological synapses. Collectively, our data illustrate the non-redundant role for NIK in human immune responses, demonstrating that loss-of-function mutations in NIK can cause multiple aberrations of lymphoid immunity.
Assessing trade-offs to inform ecosystem-based fisheries management of forage fish
Authors: Shelton Andrew Olaf , Samhouri Jameal F. , Stier Adrian C. , Levin Philip S. 
Published: November 2014

AbstractTwenty-first century conservation is centered on negotiating trade-offs between the diverse needs of people and the needs of the other species constituting coupled human-natural ecosystems. Marine forage fishes, such as sardines, anchovies and herring, are a nexus for such trade-offs because they are both central nodes in marine food webs and targeted by fisheries. An important example is Pacific herring,Clupea pallisiiin the Northeast Pacific. Herring populations are subject to two distinct fisheries: one that harvests adults and one that harvests spawned eggs. We develop stochastic, age-structured models to assess the interaction between fisheries, herring populations and the persistence of predators reliant on herring populations. We show that egg- and adult-fishing have asymmetric effects on herring population dynamics - herring stocks can withstand higher levels of egg harvest before becoming depleted. Second, ecosystem thresholds proposed to ensure the persistence of herring predators do not necessarily pose more stringent constraints on fisheries than conventional, fishery driven harvest guidelines. Our approach provides a general template to evaluate ecosystem trade-offs between stage-specific harvest practices in relation to environmental variability, the risk of fishery closures and the risk of exceeding ecosystem thresholds intended to ensure conservation goals are met.
Crystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3
Authors: Arimura Yasuhiro , Shirayama Kazuyoshi , Horikoshi Naoki , Fujita Risa , Taguchi Hiroyuki , Kagawa Wataru , Fukagawa Tatsuo , Almouzni Geneviève , Kurumizaka Hitoshi 
Published: November 2014

AbstractThe centromere-specific histone H3 variant, CENP-A, is overexpressed in particular aggressive cancer cells, where it can be mislocalized ectopically in the form of heterotypic nucleosomes containing H3.3. In the present study, we report the crystal structure of the heterotypic CENP-A/H3.3 particle and reveal its “hybrid structure”, in which the physical characteristics of CENP-A and H3.3 are conserved independently within the same particle. The CENP-A/H3.3 nucleosome forms an unexpectedly stable structure as compared to the CENP-A nucleosome and allows the binding of the essential centromeric protein, CENP-C, which is ectopically mislocalized in the chromosomes of CENP-A overexpressing cells.
WemIQ: an accurate and robust isoform quantification method for RNA-seq data
Authors: Zhang Jing , Kuo C.-C. Jay , Chen Liang 
Published: November 2014

Abstract
Motivation: The deconvolution of isoform expression from RNA-seq remains challenging because of non-uniform read sampling and subtle differences among isoforms.
Results: We present a weighted-log-likelihood expectation maximization method on isoform quantification (WemIQ). WemIQ integrates an effective bias removal with a weighted expectation maximization (EM) algorithm to distribute reads among isoforms efficiently. The weight represents the oversampling or undersampling of sequence reads and is estimated through a generalized Poisson model without any presumption on the bias sources and formats. WemIQ significantly improves the quantification of isoform and gene expression as well as the derived exon inclusion rates. It provides robust expression estimates across different laboratories and protocols, which is valuable for the integrative analysis of RNA-seq. For the recent single-cell RNA-seq data, WemIQ also provides the opportunity to distinguish bias heterogeneity from true biological heterogeneity and uncovers smaller cell-to-cell expression variability.
Availability and implementation: WemIQ can be downloaded from http://www-rcf.usc.edu/~liangche/software.html
Contact: liang.chen@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
EPGA: de novo assembly using the distributions of reads and insert size
Authors: Luo Junwei , Wang Jianxin , Zhang Zhen , Wu Fang-Xiang , Li Min , Pan Yi 
Published: November 2014

Abstract
Motivation: In genome assembly, the primary issue is how to determine upstream and downstream sequence regions of sequence seeds for constructing long contigs or scaffolds. When extending one sequence seed, repetitive regions in the genome always cause multiple feasible extension candidates which increase the difficulty of genome assembly. The universally accepted solution is choosing one based on read overlaps and paired-end (mate-pair) reads. However, this solution faces difficulties with regard to some complex repetitive regions. In addition, sequencing errors may produce false repetitive regions and uneven sequencing depth leads some sequence regions to have too few or too many reads. All the aforementioned problems prohibit existing assemblers from getting satisfactory assembly results.
Results: In this article, we develop an algorithm, called extract paths for genome assembly (EPGA), which extracts paths from De Bruijn graph for genome assembly. EPGA uses a new score function to evaluate extension candidates based on the distributions of reads and insert size. The distribution of reads can solve problems caused by sequencing errors and short repetitive regions. Through assessing the variation of the distribution of insert size, EPGA can solve problems introduced by some complex repetitive regions. For solving uneven sequencing depth, EPGA uses relative mapping to evaluate extension candidates. On real datasets, we compare the performance of EPGA and other popular assemblers. The experimental results demonstrate that EPGA can effectively obtain longer and more accurate contigs and scaffolds.
Availability and implementation: EPGA is publicly available for download at https://github.com/bioinfomaticsCSU/EPGA.
Contact: jxwang@csu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
High-Density Lipoprotein-Mediated Cholesterol Efflux Capacity Is Improved by Treatment With Antiretroviral Therapy in Acute Human Immunodeficiency Virus Infection
Authors: Lo Janet , Rosenberg Eric S. , Fitzgerald Michael L. , Bazner Suzane B. , Ihenachor Ezinne J. , Hawxhurst Victoria , Borkowska Alison H. , Wei Jeffrey , Zimmerman Chloe O. , Burdo Tricia H. , Williams Kenneth C. , Freeman Mason W. , Grinspoon Steven K. 
Published: November 2014

Abstract
Background.  Individuals infected with human immunodeficiency virus (HIV) have decreased high-density lipoprotein (HDL)-cholesterol and increased cardiovascular disease (CVD). Reverse cholesterol transport from macrophages may be inhibited by HIV and contribute to increased CVD. Human studies have not investigated longitudinal effects of HIV and antiretroviral therapy (ART) on cholesterol efflux.
Methods.  Subjects with acute HIV infection were randomized to ART or not. Cholesterol efflux capacity was determined ex vivo after exposure of murine macrophages to apolipoprotein B-depleted patient sera obtained at baseline and after 12 weeks.
Results.  After 12 weeks, HIV RNA decreased most in subjects randomized to ART. Available data on cholesterol demonstrated that efflux capacity from Abca1+/+ macrophages was increased most by sera obtained from ART-treated subjects (20.5% ± 5.0% to 24.3 % ± 6.9%, baseline to 12 weeks, P = .007; ART group [n = 6] vs 18.0 % ± 3.9% to 19.1 % ± 2.9%, baseline to 12 weeks, P = .30; untreated group [n = 6] [P = .04 ART vs untreated group]). Change in HIV RNA was negatively associated with change in Abca1+/+ macrophage cholesterol efflux (r = − 0.62, P = .03), and this finding remained significant (P = .03) after controlling for changes in HDL-cholesterol, CD4+ cells, and markers of monocyte or macrophage activation.
Conclusions.  In subjects acutely infected with HIV, ATP-binding cassette transporter A1-mediated cholesterol efflux was stimulated to a greater degree over time by apolipoprotein B-depleted serum from subjects randomized to ART. The improvement in cholesterol efflux capacity is independently related to reduction in viral load.
A coronal hole jet observed with Hinode and the Solar Dynamics Observatory
Authors: Young Peter R. , Muglach Karin 
Published: November 2014

Abstract
A small blowout jet was observed at the boundary of the south polar coronal hole on 2011 February 8 at around 21:00 UT. Images from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO) revealed an expanding loop rising from one footpoint of a compact, bipolar bright point. Magnetograms from the Helioseismic Magnetic Imager (HMI) on board SDO showed that the jet was triggered by the cancelation of a parasitic positive polarity feature near the negative pole of the bright point. The jet emission was present for 25 min and it extended 30 Mm from the bright point. Spectra from the Extreme Ultraviolet Imaging Spectrometer on board Hinode yielded a temperature and density of 1.6 MK and 0.9–1.7 × 108 cm−3 for the ejected plasma. Line-of-sight velocities reached up to 250 km s−1 and were found to increase with height, suggesting plasma acceleration within the body of the jet. Evidence was found for twisting motions within the jet based on variations of the line-of-sight velocities across the jet width. The derived angular speed was in the range (9–12) × 10−3 rad s−1, consistent with previous measurements from jets. The density of the bright point was 7.6 × 108 cm−3, and the peak of the bright point's emission measure occurred at 1.3 MK, with no plasma above 3 MK.
Arabidopsis PIAL1 and 2 Promote SUMO Chain Formation as E4-Type SUMO Ligases and Are Involved in Stress Responses and Sulfur Metabolism
Authors: Tomanov Konstantin , Zeschmann Anja , Hermkes Rebecca , Eifler Karolin , Ziba Ionida , Grieco Michele , Novatchkova Maria , Hofmann Kay , Hesse Holger , Bachmair Andreas 
Published: November 2014

Abstract
The Arabidopsis thaliana genes PROTEIN INHIBITOR OF ACTIVATED STAT LIKE1 (PIAL1) and PIAL2 encode proteins with SP-RING domains, which occur in many ligases of the small ubiquitin-related modifier (SUMO) conjugation pathway. We show that PIAL1 and PIAL2 function as SUMO ligases capable of SUMO chain formation and require the SUMO-modified SUMO-conjugating enzyme SCE1 for optimal activity. Mutant analysis indicates a role for PIAL1 and 2 in salt stress and osmotic stress responses, whereas under standard conditions, the mutants show close to normal growth. Mutations in PIAL1 and 2 also lead to altered sulfur metabolism. We propose that, together with SUMO chain binding ubiquitin ligases, these enzymes establish a pathway for proteolytic removal of sumoylation substrates.
Boosting consumers’ self-efficacy by repositioning the self
Authors: Ben-Ami Michal , Hornik Jacob , Eden Dov , Kaplan Oren 
Published: November 2014

Purpose– This article aims to lend insight into the consumption situation wherein consumers are unmotivated to try new products or behaviors that they perceive as too difficult to adopt as a result of low self-efficacy.Design/methodology/approach– Two experiments were introduced to test hypotheses. In Studies 1 and 2, we demonstrated that enhancing specific self-efficacy (SSE) by repositioning the self, through marketing messages, increased participants’ behavioral intentions toward difficult to adopt (DTA) products.Findings– In this research, an important issue is elucidated in consumer behavior: a phenomenon wherein consumers lack the motivation, as a result of low self-efficacy (i.e. assessing the disparity between their current situation and some desired goals as too wide to bridge over), to try a product that would benefit them. Thus, the marketer’s role in this case is to convince the consumers that they are able to achieve these goals.Research limitations/implications– This study focuses on health and fitness products and on the effectiveness of messages targeted at raising SSE among undergraduate students through verbal persuasion. For better generalizability, it is recommended that future research focus on other product categories (e.g. do-it-yourself products, technological products) aimed at other segments (e.g. elderly consumers) and use other means of boosting consumers’ self-efficacy.Practical implications– The practical importance of the findings is especially relevant in DTA situations in which marketers aim to motivate consumers to engage in effortful consumption tasks.Originality/value– The uniqueness of our approach is, in addition to introducing the theoretical concepts, to demonstrate that marketers can boost individuals’ self-efficacy by means of marketing messages that emphasize their ability to face challenges and, consequently, increase their preferences, behavioral intentions and financial commitments toward a DTA product.
Conceptualising the management of packaging within new product development
Authors: Simms Christopher , Trott Paul 
Published: November 2014

Purpose– The purpose of this study is to: contribute to existing models of new product development (NPD) and provide new understanding of how a new product’s packaging is managed and integrated into the NPD process of fast-moving consumer goods (FMCG) firms and build on prior research, suggesting that firms lack a pipeline of new packaging innovations by uncovering the factors that influence this pipeline issue.Design/methodology/approach– A grounded theory methodology was adopted. Research was conducted through a total of 37 interviews with key informants in the UK FMCG industry, packaging industry and associated firms.Findings– Three distinct levels of packaging development were revealed: skin deep, body modification and format change. The emphasis within many firms is primarily on changes to packaging at the level of the label (skin deep) or aesthetic design (body modification), whilst technological and format changes are overlooked. The factors that contribute to the level at which development is undertaken are identified.Research limitations/implications– Existing literature has largely examined packaging at the level of skin-deep and body modification. The development of new packaging technology has been overlooked. This study’s propositions guide the way forward for further research.Practical implications– For firms, the development of new formats and genuine packaging innovation may be being overlooked. There is a need for them to re-examine their activities to ensure that they are addressing all three levels.Originality/value– This theory-building study has generated a new typology which, alongside the unique framework, reveals the factors influencing the level of emphasis within firms.
The role of convenience in a recreational shopping trip
Authors: Reimers Vaughan , Chao Fred 
Published: November 2014

Purpose
– The purpose of this study is to determine the role of convenience in a recreational shopping trip. In an effort to address the shopping strip’s forfeiture of market share to the mall and the Internet, retail planners have utilised a variety of intervention strategies. One such strategy is to differentiate the strip by emphasising its hedonic attributes. An often overlooked alternative is to compete with both of these formats in a key area of competitive disadvantage – convenience. Whereas these two alternatives have traditionally been regarded as separate strategies, this study examines whether convenience actually serves as a source of satisfaction in a hedonic shopping context.

Design/methodology/approach
– A recreational shopping trip to a shopping strip (also referred to as Main Street or the High Street) in Melbourne, Australia, served as the context for this study. The study used a quantitative survey approach to collect its data and structural equation modelling to analyse it.

Findings
– Surprisingly, the hedonic attributes of a shopping strip do not influence trip satisfaction in the context of a recreational shopping strip. Contrary to a significant body of academic research, it is instead the time-saving and distance-minimising properties of a shopping strip, as well as its overall convenience, which determine satisfaction.

Originality/value
– The results have important implications for Town Centre Management schemes because they suggest that responsibility for providing a hedonic shopping experience rests with its individual retailers. Instead, the role of strip planners is to facilitate the other side of the value-equation by minimising the hassles involved in strip shopping. The results of this study also question the traditional belief that hedonic- and convenience-based rejuvenation strategies should be treated as two distinct strategies. Instead, convenience should be regarded as a prerequisite to a satisfying recreational shopping trip.