bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies
Authors: Lee Young-suk , Krishnan Arjun , Zhu Qian , Troyanskaya Olga G. 
Published: September 2013

Abstract
Motivation: Leveraging gene expression data through large-scale integrative analyses for multicellular organisms is challenging because most samples are not fully annotated to their tissue/cell-type of origin. A computational method to classify samples using their entire gene expression profiles is needed. Such a method must be applicable across thousands of independent studies, hundreds of gene expression technologies and hundreds of diverse human tissues and cell-types.
Results: We present Unveiling RNA Sample Annotation (URSA) that leverages the complex tissue/cell-type relationships and simultaneously estimates the probabilities associated with hundreds of tissues/cell-types for any given gene expression profile. URSA provides accurate and intuitive probability values for expression profiles across independent studies and outperforms other methods, irrespective of data preprocessing techniques. Moreover, without re-training, URSA can be used to classify samples from diverse microarray platforms and even from next-generation sequencing technology. Finally, we provide a molecular interpretation for the tissue and cell-type models as the biological basis for URSA’s classifications.
Availability and implementation: An interactive web interface for using URSA for gene expression analysis is available at: ursa.princeton.edu. The source code is available at https://bitbucket.org/youngl/ursa_backend.
Contact: ogt@cs.princeton.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Discovering combinatorial interactions in survival data
Authors: duVerle David A. , Takeuchi Ichiro , Murakami-Tonami Yuko , Kadomatsu Kenji , Tsuda Koji 
Published: September 2013

AbstractMotivation: Although several methods exist to relate high-dimensional gene expression data to various clinical phenotypes, finding combinations of features in such input remains a challenge, particularly when fitting complex statistical models such as those used for survival studies.Results: Our proposed method builds on existing ‘regularization path-following’ techniques to produce regression models that can extract arbitrarily complex patterns of input features (such as gene combinations) from large-scale data that relate to a known clinical outcome. Through the use of the data’s structure and itemset mining techniques, we are able to avoid combinatorial complexity issues typically encountered with such methods, and our algorithm performs in similar orders of duration as single-variable versions. Applied to data from various clinical studies of cancer patient survival time, our method was able to produce a number of promising gene-interaction candidates whose tumour-related roles appear confirmed by literature.Availability: An R implementation of the algorithm described in this article can be found at https://github.com/david-duverle/regularisation-path-followingContact: dave.duverle@aist.go.jpSupplementary information: Supplementary data are available at Bioinformatics online.
Human skin-derived keratinocytes and fibroblasts co-cultured on 3D poly ε-caprolactone scaffold support in vitro HSC differentiation into T-lineage committed cells
Authors: Palamaro Loredana , Guarino Vincenzo , Scalia Giulia , Antonini Dario , De Falco Luigia , Bianchino Gabriella , Fusco Anna , Romano Rosa , Grieco Vitina , Missero Caterina , Del Vecchio Luigi , Ambrosio Luigi , Pignata Claudio 
Published: September 2013

Abstract
In humans, the thymus is the primary lymphoid organ able to support the development of T cells through its three-dimensional (3D) organization of the thymic stromal cells. Since a remarkable number of similarities are shared between the thymic epithelial cells (TECs) and skin-derived keratinocytes and fibroblasts, in this study we used human keratinocytes seeded with fibroblasts on the 3D poly ε-caprolactone scaffold to evaluate their ability to replace TECs in supporting T-cell differentiation from human haematopoietic stem cells (HSCs). We observed that in the multicellular biocomposite, early thymocytes expressing CD7+CD1a+, peculiar markers of an initial T-cell commitment, were de novo generated. Molecular studies of genes selectively expressed during T-cell development revealed that TAL1 was down-regulated and Spi-B was up-regulated in the cell suspension, consistently with a T-cell lineage commitment. Moreover, PTCRA and RAG2 expression was detected, indicative of a recombinant activity, required for the generation of a T-cell receptor repertoire. Our results indicate that in the multicellular biocomposite, containing skin-derived elements in the absence of thymic stroma, HSCs do start differentiating toward a T-cell lineage commitment. In conclusion, the construct described in this study exerts some properties of a lymphoid organoid, suitable for future clinical applications in cell-based therapies.
Biased usage and preferred pairing of α- and β-chains of TCRs specific for an immunodominant gluten epitope in coeliac disease
Authors: Qiao Shuo-Wang , Christophersen Asbjørn , Lundin Knut E. A. , Sollid Ludvig M. 
Published: September 2013

Abstract
CD4+ T cells that recognize dietary gluten antigens presented by the disease-associated HLA-DQ2 or DQ8 molecules are central players in coeliac disease. Unbiased sequencing of the human TCRα variable (TRAV) and humanTCRβ variable (TRBV) genes of 68 HLA-DQ2.5-glia-α2-specific T cells from coeliac disease patients confirmed previous reports of over-usage of the TRBV7-2 gene segment, a conserved Arg residue in the complementarity-determining region (CDR) 3β loop and prevalent usage of the canonical ASSxRxTDTQY CDR3β loop among T cells with this specificity. In 30 clones that had the canonical TCRβ chain, we found a strict usage of the TRAV26-1 gene segment in the TCRα chain. There was variable usage of the TRAJ genes and diverse CDR3α sequences with no apparent conserved motifs. This study extends previous reports on biased TCR usage in both HLA-DQ2.5- and DQ8-restricted gluten-specific TCRs and provides data for further studies on TRAV and TRBV pairing.
XMM–Newton and Swift spectroscopy of the newly discovered very faint X-ray transient IGR J17494–3030
Authors: Armas Padilla M. , Wijnands R. , Degenaar N. 
Published: September 2013

Abstract
A growing group of low-mass X-ray binaries are found to be accreting at very faint X-ray luminosities of &lt;1036 erg s−1 (2–10 keV). One such system is the new X-ray transient IGR J17494–3030. We present Swift and XMM–Newton observations obtained during its 2012 discovery outburst. The Swift observations trace the peak of the outburst, which reached a luminosity of ∼7 × 1035 (D/8 kpc)2 erg s−1 (2–10 keV). The XMM–Newton data were obtained when the outburst had decayed to an intensity of ∼8 × 1034 (D/8 kpc)2 erg s−1. The spectrum can be described by a power law with an index of Γ ∼ 1.7 and requires an additional soft component with a blackbody temperature of ∼0.37 keV (contributing ∼20 per cent to the total unabsorbed flux in the 0.5–10 keV band). Given the similarities with high-quality spectra of very faint neutron-star low-mass X-ray binaries, we suggest that the compact primary in IGR J17494–3030 is a neutron star. Interestingly, the source intensity decreased rapidly during the ∼12 h XMM–Newton observation, which was accompanied by a decrease in inferred temperature. We interpret the soft spectral component as arising from the neutron-star surface due to low-level accretion, and propose that the observed decline in intensity was the result of a decrease in the mass-accretion rate on to the neutron star.
The REIL1 and REIL2 Proteins ofArabidopsis thalianaAre Required for Leaf Growth in the Cold
Authors: Schmidt Stefanie , Dethloff Frederik , Beine-Golovchuk Olga , Kopka Joachim 
Published: September 2013

AbstractThe evolutionarily conserved proteins REI1-LIKE (REIL1) and REIL2 have four conserved zinc finger domains and are Arabidopsis thaliana homologs of the cytosolic 60S ribosomal maturation factor Rei1p (for Required for isotropic bud growth1 protein) from yeast (Saccharomyces cerevisiae) and its paralog Reh1p (for REI1 homologue1 protein). The yeast and A. thaliana paralogs result from independent gene duplications. The A. thaliana REIL paralogs are required specifically in the cold (10°C) but not for growth at optimal temperature (20°C). A reil1-1 reil2-1 double mutant is arrested at 10°C prior to the emergence of the first rosette leaf. Two allelic reil2 mutants, reil2-1 and reil2-2, form small spoon-shaped leaves at 10°C. This phenomenon reverts after emergence of the inflorescence in the cold or upon shift to 20°C. Except for a slightly delayed germination, a reil1-1 mutant shows no further growth phenotype under the currently investigated conditions. A comparative analysis demonstrates conserved coexpression of orthologous genes from yeast and A. thaliana that are coregulated with yeast rei1 or with A. thaliana REIL2, respectively. The conserved correlations point to a role of A. thaliana REIL proteins in the maturation of the eukaryotic ribosomal 60S subunit. We support this conclusion by heterologous complementation of the cold-induced growth defect of the yeast Ɗrei1 deletion.
Temporal-Spatial Interaction between Reactive Oxygen Species and Abscisic Acid Regulates Rapid Systemic Acclimation in Plants
Authors: Suzuki Nobuhiro , Miller Gad , Salazar Carolina , Mondal Hossain A. , Shulaev Elena , Cortes Diego F. , Shuman Joel L. , Luo Xiaozhong , Shah Jyoti , Schlauch Karen , Shulaev Vladimir , Mittler Ron 
Published: September 2013

Abstract
Being sessile organisms, plants evolved sophisticated acclimation mechanisms to cope with abiotic challenges in their environment. These are activated at the initial site of exposure to stress, as well as in systemic tissues that have not been subjected to stress (termed systemic acquired acclimation [SAA]). Although SAA is thought to play a key role in plant survival during stress, little is known about the signaling mechanisms underlying it. Here, we report that SAA in plants requires at least two different signals: an autopropagating wave of reactive oxygen species (ROS) that rapidly spreads from the initial site of exposure to the entire plant and a stress-specific signal that conveys abiotic stress specificity. We further demonstrate that SAA is stress specific and that a temporal–spatial interaction between ROS and abscisic acid regulates rapid SAA to heat stress in plants. In addition, we demonstrate that the rapid ROS signal is associated with the propagation of electric signals in Arabidopsis thaliana. Our findings unravel some of the basic signaling mechanisms underlying SAA in plants and reveal that signaling events and transcriptome and metabolome reprogramming of systemic tissues in response to abiotic stress occur at a much faster rate than previously envisioned.
TheFragaria vescaHomolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 Represses Flowering and Promotes Vegetative Growth
Authors: Mouhu Katriina , Kurokura Takeshi , Koskela Elli A. , Albert Victor A. , Elomaa Paula , Hytönen Timo 
Published: September 2013

AbstractIn the annual long-day plant Arabidopsis thaliana, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) integrates endogenous and environmental signals to promote flowering. We analyzed the function and regulation of the SOC1 homolog (Fragaria vesca [Fv] SOC1) in the perennial short-day plant woodland strawberry (Fragaria vesca). We found that Fv SOC1 overexpression represses flower initiation under inductive short days, whereas its silencing causes continuous flowering in both short days and noninductive long days, similar to mutants in the floral repressor Fv TERMINAL FLOWER1 (Fv TFL1). Molecular analysis of these transgenic lines revealed that Fv SOC1 activates Fv TFL1 in the shoot apex, leading to the repression of flowering in strawberry. In parallel, Fv SOC1 regulates the differentiation of axillary buds to runners or axillary leaf rosettes, probably through the activation of gibberellin biosynthetic genes. We also demonstrated that Fv SOC1 is regulated by photoperiod and Fv FLOWERING LOCUS T1, suggesting that it plays a central role in the photoperiodic control of both generative and vegetative growth in strawberry. In conclusion, we propose that Fv SOC1 is a signaling hub that regulates yearly cycles of vegetative and generative development through separate genetic pathways.
Intrinsic Disorder in Pathogen Effectors: Protein Flexibility as an Evolutionary Hallmark in a Molecular Arms Race
Authors: Marín Macarena , Uversky Vladimir N. , Ott Thomas 
Published: September 2013

Abstract
Effector proteins represent a refined mechanism of bacterial pathogens to overcome plants’ innate immune systems. These modular proteins often manipulate host physiology by directly interfering with immune signaling of plant cells. Even if host cells have developed efficient strategies to perceive the presence of pathogenic microbes and to recognize intracellular effector activity, it remains an open question why only few effectors are recognized directly by plant resistance proteins. Based on in-silico genome-wide surveys and a reevaluation of published structural data, we estimated that bacterial effectors of phytopathogens are highly enriched in long-disordered regions (&gt;50 residues). These structurally flexible segments have no secondary structure under physiological conditions but can fold in a stimulus-dependent manner (e.g., during protein–protein interactions). The high abundance of intrinsic disorder in effectors strongly suggests positive evolutionary selection of this structural feature and highlights the dynamic nature of these proteins. We postulate that such structural flexibility may be essential for (1) effector translocation, (2) evasion of the innate immune system, and (3) host function mimicry. The study of these dynamical regions will greatly complement current structural approaches to understand the molecular mechanisms of these proteins and may help in the prediction of new effectors.
Policing in partnership: a case study in crime prevention
Authors: Barton Harry , Valero-Silva Nestor 
Published: September 2013

Purpose– This paper aims to outline an exploratory study of how a multi-agency, partnership approach to crime prevention might enable the police more effectively to target their utilisation of resources in order both to reduce local levels of criminality and to improve public confidence. It is set against a backdrop of major police reforms that will require police commanders to demonstrate high levels of accountability in terms of resource and financial utilisation, and to show continuing improvement in levels of public confidence.Design/methodology/approach– A case study approach is adopted; it draws upon both primary and secondary data sources and is framed within a situational approach to crime prevention.Findings– There has been a drop in the levels of burglary in those areas where the home improvement initiative (Decent Homes Programme) has been carried out. The tenants consulted as part of the research reported that they felt safer in their homes as a result. Also, their general level of satisfaction with the police and other agencies has improved.Research limitations/implications– There has been an overall drop in levels of reported crime in terms of burglaries across the UK. It may be asked whether such improvement in Nottingham has been due to a genuine improvement in police performance or is as a consequence of the home improvements. The present paper is a single case study, with no opportunity for a comparative analysis across other police force areas. This limitation could be overcome by other researchers involved in similar Decent Homes Programmes in other cities in the UK.Practical implications– The research illustrates that multi-agency working may indeed help create an improvement in living conditions for residents. It also identifies the fact that, as a result of successful integrated multi-agency approaches to crime prevention, the police are able to save resources in terms of time spent investigating crime.Originality/value– This paper adds tangible evidence to theoretical discourse on the benefits of multi-agency work in the context of social housing
Mediation of strategy on intellectual capital and performance
Authors: Tseng Kuo-An , Lan Yu-Wen , Lu Hao-Chun , Chen Pin-Yu 
Published: September 2013

Purpose
– The purpose of this paper is to explore the mediating effect of business strategy (BS) on intellectual capital (IC) and financial performance (FP). The impact of financial crisis is also a major topic of this research.

Design/methodology/approach
– This study applies BS as mediator to explore the relationships between IC, BS, and FP. Partial least squares is employed to test the reliability and validity of measurements and the significance of path coefficients, and therefore to examine the hypotheses.

Findings
– IC has significant impacts on BS and FP in all samples, as well as in those years before and after the financial crisis. BS has a partial significant mediating effect between IC and FP. BS has significant effects on FP in all samples and pre-financial crisis, but has not in post-financial crisis.

Research limitations/implications
– IC has significant impacts on BS and FP. Moreover, the relationships of IC, BS, and FP are different during pre- and post-financial crisis. The direct effect of IC on FP is confirmed and consistent, and the indirect effect of IC on FP by BS is dependent upon the environment status.

Practical implications
– Enterprises should pay attention to IC, BS, and the related changes in environment status. These help enterprises develop appropriate strategies, maintain competitive advantage, and upgrade FP.

Originality/value
– This study applies BS as mediator, and explores the relationships between IC, BS, and FP. The impact of financial crisis is also discussed. The results may serve as the criteria for strategic performance management.
Extending resource-based theory: considering strategic, ordinary and junk resources
Authors: Warnier Vanessa , Weppe Xavier , Lecocq Xavier 
Published: September 2013

Purpose– The purpose of this paper is to answer the question: how to extend resource-based theory to take into account the contribution of all kinds of resources (including the less regarded ones) to performance? While recognising the importance of strategic resources in building and sustaining a competitive advantage, the authors contend that a symmetric analysis of more available resources can shed new light on the sources and mechanisms of superior performance. Thus, they aim to contribute to an extended theory of resources.Design/methodology/approach– Based on literature review and theorization process, the authors introduce alongside strategic resources, the concepts of “ordinary resources” and “junk resources”, showing how they may contribute to performance with an appropriate business model. Several illustrative cases are discussed to demonstrate that such resources need to be studied by resource-based theory (RBT).Findings– The authors propose shifting the focus of RBT from the study of strategic resources alone in order to consider other types as well: ordinary and junk resources. Such an approach involves significant implications for strategic management theory and management practices.Practical implications– The paper describes the conditions under which ordinary and junk resources (more available to most firms than strategic resources) may generate a competitive advantage. The extended resource-based theory can have implications for society as it may influence managers ' and public attitudes towards underestimated resources and lead to new business models.Originality/value– The approach developed in this article also goes beyond traditional critiques of RBT. Specifically, the authors ' analysis avoids tautological reasoning, distinguishing between: resources; perceptions of their attributes by firms; the services these resources render; the business model implemented to deploy these resources; and the effects in terms of performance. The authors build an extended resource-based theory, allowing the contribution of various kinds of resources to firm performance to be explained.
Does green management matter for donation intentions?
Authors: Walker Matthew 
Published: September 2013

Purpose
– Several factors are known to influence donations to university athletic departments including previous donations and university affiliation. This research aims to build on prior work by examining whether a university's environmental management initiatives can also influence donor behavior.

Design/methodology/approach
– The paper employs a quantitative study on environmental responsibility (ER) and “green management” using donor and non-donor data in the context of a university athletic department to investigate additional (i.e. personal and dispositional) factors that drive donation intentions.

Findings
– Employing tenets of the theory of reasoned action (TRA), the hierarchical regression models confirm prior donor motives and indicate that personal disposition towards the environment and attitude toward environmental initiatives predict donor intentions. These results are set against a backdrop of managerial strategy that seemingly enabled the effects.

Research limitations/implications
– The study should be replicated to advance the decision-making literature. This study focused solely on the attitudinal component of the TRA and only anecdotally accounted for the social norms that might influence the results. Retesting the model where ER is not as well-known or has just been implemented would add credibility to the results. Finally, using a behavioral intention factor limits the explanatory power.

Practical implications
– In a modern giving climate where supply (i.e. donations) is not currently paralleling demand, university athletic departments are continually looking for innovative ways to bolster donor support. The results suggest that ER can be positive for the local community and society at large but also in reciprocal fashion for the organization.

Originality/value
– While results confirming the traditional predictors of donor intentions are not particularly novel, the contribution of this research lies in showing that environmental disposition and importance contribute to the giving dynamic.