bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping Quantitative Trait Loci by Controlling Polygenic Background Effects
Authors: Xu Shizhong 
Published: September 2013

AbstractA new mixed-model method was developed for mapping quantitative trait loci (QTL) by incorporating multiple polygenic covariance structures. First, we used genome-wide markers to calculate six different kinship matrices. We then partitioned the total genetic variance into six variance components, one corresponding to each kinship matrix, including the additive, dominance, additive × additive, dominance × dominance, additive × dominance, and dominance × additive variances. The six different kinship matrices along with the six estimated polygenic variances were used to control the genetic background of a QTL mapping model. Simulation studies showed that incorporating epistatic polygenic covariance structure can improve QTL mapping resolution. The method was applied to yield component traits of rice. We analyzed four traits (yield, tiller number, grain number, and grain weight) using 278 immortal F2 crosses (crosses between recombinant inbred lines) and 1619 markers. We found that the relative importance of each type of genetic variance varies across different traits. The total genetic variance of yield is contributed by additive × additive (18%), dominance × dominance (14%), additive × dominance (48%), and dominance × additive (15%) variances. Tiller number is contributed by additive (17%), additive × additive (22%), and dominance × additive (43%) variances. Grain number is mainly contributed by additive (42%), additive × additive (19%), and additive × dominance (31%) variances. Grain weight is almost exclusively contributed by the additive (73%) variance plus a small contribution from the additive × additive (10%) variance. Using the estimated genetic variance components to capture the polygenic covariance structure, we detected 39 effects for yield, 39 effects for tiller number, 24 for grain number, and 15 for grain weight. The new method can be directly applied to polygenic-effect-adjusted genome-wide association studies (GWAS) in human and other species.
Analysis and forecast of the storage needs of soybeans in Brazil
Authors: Patino Marco T. O. , Machado Marina F. , Nascimento Geraldo T. do , Alcantara Milla R. de 
Published: September 2013

The existence of a minimum storage capacity of grains as a condition for the maintenance of regulator physical stocks has been used as a strategic factor in the agribusiness expansion. However, in Brazil the storage infrastructure has not followed the growth of the agricultural sector. This fact is evident in the case of soybeans that currently represent 49% of grain production in the country, whose volume production has been increasing significantly over the years. This study aimed to predict the futureï€ needs of static storage capacity of soybeans from historical data to estimate the investment needed to install storage units in Brazil for the next five years. A statistic analysis of collected data allowed a forecast and identification of the number of storage units that should be installed to meet the storage needs of soybeans in the next five years. It was concluded that by 2015 the soybean storage capacity should be 87 million tons, and to store 49% of soybeans produced, 1,104 storage units should be installed at a cost of R$ 442 million.
La compréhension écrite mal traitée ou maltraitée ?
Authors: Fade Pascale 
Published: September 2013

Le choix d’enseigner la compréhension écrite aux étudiants de 2e année de Deug, spécialistes d’autres disciplines, n’est plus à justifier. Dans la mesure où une grande majorité d’étudiants a étudié la langue de cinq à sept ans dans le secondaire, l’enseignement devrait logiquement prendre appui sur des connaissances existantes et viser la consolidation et l’approfondissement de compétences acquises précédemment. Dans les faits, les performances en compréhension écrite de bon nombre d’étudiants sont médiocres et l’enseignement consiste en la mise en place, et non la consolidation, des compétences spécifiques à la lecture. La question qui vient immédiatement à l’esprit est la suivante : existe-t-il des conditions ou des raisons particulières qui font ou ont fait que les étudiants « ne savent pas lire » ? Pour apporter quelques éléments de réponse à cette question, l’auteur a consulté les textes officiels relatifs à l’enseignement de l’anglais dans les classes de seconde, première et terminale et analysé quatre manuels d’enseignement afin de mesurer la place accordée à la compréhension écrite et la façon dont elle est traitée dans l’enseignement secondaire.
Un centre de ressources au service d’une approche méthodologique de la compréhension de l’anglais oral pour un public de DEUG indifférencié
Authors: Sabiron Jean 
Published: September 2013

Nous relatons dans cet article l’évolution de la nature des prestations d’un Centre de ressources : d’abord, réponse à une demande langagière par la fourniture de documents audiovisuels en vue d’une exposition raisonnée à la langue anglaise authentique, il devient la proposition d’une approche méthodologique multisources intégrée. Celle-ci, de caractère pragmatique, vise à une contextualisation linguistique et extra-linguistique des documents oraux faisant l’objet d’étude, et à la structuration des nouveaux acquis dans une perspective cognitive.
Convergences et divergences : production orale, production écrite
Authors: Perry Evelyn 
Published: September 2013

Dans un premier temps, nous examinons un corpus de 20 000 mots écrits en anglais L2 afin de déterminer une taxinomie d’erreurs lexicales commises par des apprenants d’un niveau moyen-avancé. Ces productions font ensuite l’objet d’une analyse contrastive juxtaposant les six catégories d’erreurs lexicales répertoriées à l’écrit aux erreurs commises à l’oral par d’autres étudiants du même niveau.
Identification of a Tissue-Specific, C/EBPβ-Dependent Pathway of Differentiation for Murine Peritoneal Macrophages
Authors: Cain Derek W. , O’Koren Emily G. , Kan Matthew J. , Womble Mandy , Sempowski Gregory D. , Hopper Kristen , Gunn Michael D. , Kelsoe Garnett 
Published: September 2013

Abstract
Macrophages and dendritic cells (DC) are distributed throughout the body and play important roles in pathogen detection and tissue homeostasis. In tissues, resident macrophages exhibit distinct phenotypes and activities, yet the transcriptional pathways that specify tissue-specific macrophages are largely unknown. We investigated the functions and origins of two peritoneal macrophage populations in mice: small and large peritoneal macrophages (SPM and LPM, respectively). SPM and LPM differ in their ability to phagocytose apoptotic cells, as well as in the production of cytokines in response to LPS. In steady-state conditions, SPM are sustained by circulating precursors, whereas LPM are maintained independently of hematopoiesis; however, both populations are replenished by bone marrow precursors following radiation injury. Transcription factor analysis revealed that SPM and LPM express abundant CCAAT/enhancer binding protein (C/EBP)-β. Cebpb−/− mice exhibit elevated numbers of SPM-like cells but lack functional LPM. Alveolar macrophages are also missing in Cebpb−/− mice, although macrophage populations in the spleen, kidney, skin, mesenteric lymph nodes, and liver are normal. Adoptive transfer of SPM into Cebpb−/− mice results in SPM differentiation into LPM, yet donor SPM do not generate LPM after transfer into C/EBPβ-sufficient mice, suggesting that endogenous LPM inhibit differentiation by SPM. We conclude that C/EBPβ plays an intrinsic, tissue-restricted role in the generation of resident macrophages.
IL-1 Induces Proinflammatory Leukocyte Infiltration and Regulates Fibroblast Phenotype in the Infarcted Myocardium
Authors: Saxena Amit , Chen Wei , Su Ya , Rai Vikrant , Uche Olisambu U. , Li Na , Frangogiannis Nikolaos G. 
Published: September 2013

Abstract
In the infarcted myocardium, activation of the inflammatory cascade clears the wound from dead cells, whereas stimulating matrix degradation and chamber dilation, thus contributing to the development of heart failure. IL-1 is critically involved in the postinfarction inflammatory reaction and mediates adverse dilative remodeling. We hypothesized that IL-1 may regulate postinfarction repair and remodeling through cell-specific actions on leukocytes and fibroblasts. Flow cytometry demonstrated that in mouse infarcts, early recruitment of proinflammatory Ly6Chi cells expressing IL-1R1, the signaling receptor for IL-1, was followed by infiltration with cells expressing the decoy receptor, IL-1R2. Increased expression of IL-1R2 may serve to terminate IL-1–driven inflammation after infarction. Loss of IL-1 signaling in IL-1R1 null mice globally attenuated leukocyte recruitment, reducing the number of infiltrating Ly6Chi and Ly6Clo cells. Nonmyeloid CD11b− cells harvested during the inflammatory phase of cardiac repair exhibited marked upregulation of chemokines and cytokines; their inflammatory activation was IL-1R1 dependent. Moreover, IL-1β attenuated TGF-β–induced contractile activity of fibroblasts populating collagen pads, attenuated α-smooth muscle actin expression, and stimulated matrix metalloproteinase synthesis in an IL-1R1–dependent manner. The effects of IL-1 on TGF-β responses in cardiac fibroblasts were not due to direct effects on Smad activation, but were associated with endoglin suppression and accentuated expression of bone morphogenetic protein and activin membrane-bound inhibitor, a negative regulator of TGF-β signaling. IL-1 may orchestrate fibroblast responses in the infarct; early stimulation of fibroblast IL-1R1 signaling during the inflammatory phase may prevent premature activation of a matrix-synthetic contractile phenotype until the wound is cleared, and the infarct microenvironment can support mesenchymal cell growth.
Cooperation of TLR12 and TLR11 in the IRF8-Dependent IL-12 Response to Toxoplasma gondii Profilin
Authors: Raetz Megan , Kibardin Alexey , Sturge Carolyn R. , Pifer Reed , Li Haiying , Burstein Ezra , Ozato Keiko , Larin Sergey , Yarovinsky Felix 
Published: September 2013

Abstract
TLRs play a central role in the innate recognition of pathogens and the activation of dendritic cells (DCs). In this study, we establish that, in addition to TLR11, TLR12 recognizes the profilin protein of the protozoan parasite Toxoplasma gondii and regulates IL-12 production by DCs in response to the parasite. Similar to TLR11, TLR12 is an endolysosomal innate immune receptor that colocalizes and interacts with UNC93B1. Biochemical experiments revealed that TLR11 and TLR12 directly bind to T. gondii profilin and are capable of forming a heterodimer complex. We also establish that the transcription factor IFN regulatory factor 8, not NF-κB, plays a central role in the regulation of the TLR11- and TLR12-dependent IL-12 response of DCs. These results suggest a central role for IFN regulatory factor 8–expressing CD8+ DCs in governing the TLR11- and TLR12-mediated host defense against T. gondii.
Large Spectrum of HLA-C Recognition by Killer Ig–like Receptor (KIR)2DL2 and KIR2DL3 and Restricted C1 Specificity of KIR2DS2: Dominant Impact of KIR2DL2/KIR2DS2 on KIR2D NK Cell Repertoire Formation
Authors: David Gaëlle , Djaoud Zakia , Willem Catherine , Legrand Nolwenn , Rettman Pauline , Gagne Katia , Cesbron Anne , Retière Christelle 
Published: September 2013

Abstract
The interactions of killer Ig–like receptor 2D (KIR2D) with HLA-C ligands contribute to functional NK cell education and regulate NK cell functions. Although simple alloreactive rules have been established for inhibitory KIR2DL, those governing activating KIR2DS function are still undefined, and those governing the formation of the KIR2D repertoire are still debated. In this study, we investigated the specificity of KIR2DL1/2/3 and KIR2DS1/2, dissected each KIR2D function, and assessed the impact of revisited specificities on the KIR2D NK cell repertoire formation from a large cohort of 159 KIR and HLA genotyped individuals. We report that KIR2DL2+ and KIR2DL3+ NK cells reacted similarly against HLA-C+ target cells, irrespective of C1 or C2 allele expression. In contrast, KIR2DL1+ NK cells specifically reacted against C2 alleles, suggesting a larger spectrum of HLA-C recognition by KIR2DL2 and KIR2DL3 than KIR2DL1. KIR2DS2+ KIR2DL2− NK cell clones were C1-reactive irrespective of their HLA-C environment. However, when KIR2DS2 and KIR2DL2 were coexpressed, NK cell inhibition via KIR2DL2 overrode NK cell activation via KIR2DS2. In contrast, KIR2DL1 and KIR2DS2 had an additive enhancing effect on NK cell responses against C1C1 target cells. KIR2DL2/3/S2 NK cells predominated within the KIR repertoire in KIR2DL2/S2+ individuals. In contrast, the KIR2DL1/S1 NK cell compartment is dominant in C2C2 KIR2DL2/S2− individuals. Moreover, our results suggest that together with KIR2DL2, activating KIR2DS1 and KIR2DS2 expression limits KIR2DL1 acquisition on NK cells. Altogether, our results suggest that the NK cell repertoire is remolded by the activating and inhibitory KIR2D and their cognate ligands.
The MyD88 Pathway in Plasmacytoid and CD4+ Dendritic Cells Primarily Triggers Type I IFN Production against Measles Virus in a Mouse Infection Model
Authors: Takaki Hiromi , Takeda Makoto , Tahara Maino , Shingai Masashi , Oshiumi Hiroyuki , Matsumoto Misako , Seya Tsukasa 
Published: September 2013

Abstract
Infection by measles virus (MV) induces type I IFN via the retinoic acid–inducible gene I/melanoma differentiation–associated gene 5/mitochondrial antiviral signaling protein (MAVS) pathway in human cells. However, the in vivo role of the MAVS pathway in host defense against MV infection remains undetermined. CD150 transgenic (Tg) mice, which express human CD150, an entry receptor for MV, with the disrupting IFNR gene (Ifnar−/−), are susceptible to MV and serve as a model for MV infection. In this study, we generated CD150Tg/Mavs−/− mice and examined MV permissiveness compared with that in CD150Tg/Ifnar−/− mice. MV replicated mostly in the spleen of i.p.-infected CD150Tg/Ifnar−/− mice. Strikingly, CD150Tg/Mavs−/− mice were not permissive to MV in vivo because of substantial type I IFN induction. MV barely replicated in any other organs tested. When T cells, B cells, and dendritic cells (DCs) isolated from CD150Tg/Mavs−/− splenocytes were cultured with MV in vitro, only the DCs produced type I IFN. In vitro infection analysis using CD150Tg/Mavs−/− DC subsets revealed that CD4+ and plasmacytoid DCs, but not CD8α+ and CD8α−CD4− double negative DCs, were exclusively involved in type I IFN production in response to MV infection. Because CD150Tg/Mavs−/− mice turned permissive to MV by anti-IFNAR Ab, type I IFN produced by CD4+ DCs and plasmacytoid DCs plays a critical role in antiviral protection for neighboring cells expressing IFNAR. Induction of type I IFN in these DC subsets was abolished by the MyD88 inhibitory peptide. Thus, production of type I IFN occurs via the MyD88-dependent and MAVS-independent signaling pathway during MV infection.
The Effect of Extension Constraint Knee Bracing on Dynamic Balance, Gait Mechanics, and Joint Alignment
Authors: Butler Robert J. , Queen Robin M. , Wilson Becky , Stephenson John , Barnes C. Lowry 
Published: September 2013

ObjectiveTo examine how an extension constraint knee brace affects active and passive standing knee joint alignment, dynamic balance, and gait mechanics.DesignRepeated‐measures, within‐subjects design.SettingResearch laboratory.ParticipantsPersons (N = 24) with no current diagnosed gait dysfunction or neuromuscular limitations that limit activities of daily living.MethodsAll subjects were tested with use of dynamic balance and gait analysis. Dynamic balance was examined with the Lower Quarter Y Balance Test. Gait analysis was conducted at a freely chosen walking speed for 2 conditions: (1) use of a brace with free range of motion (FROM) and (2) use of a brace with 30‐degree extension constraint (ECON). In a subset of subjects, radiographs were used to examine standing knee alignment for 3 conditions: (1) FROM, (2) use of a knee ECON brace in a relaxed position; and (3) use of a knee ECON brace with maximal volitional quadriceps contraction.Main Outcome MeasuresPeak knee flexion, knee flexion range of motion, peak vertical ground reaction force during weight acceptance and propulsion, and maximum reach distance in the anterior, posteromedial, and posterolateral directions were measured.ResultsDifferences in dynamic balance were observed between ECON and FROM for the anterior reach. Peak knee flexion increased 3.2° and peak knee extension decreased 7.4° in the ECON condition. Vertical GRF values were found to increase bilaterally during ECON at midstance but decreased bilaterally during propulsion. Radiographic images revealed that the ECON elicited a 22.2° flexion contracture with minimal quadriceps activation but only reduced motion by 4.8° with maximal volitional quadriceps activation.ConclusionsExtension constraint knee braces alter joint alignment, dynamic balance, knee mechanics during gait, and vertical loading during gait. However, the changes in motion observed were lower than those induced by the constraining mechanism.
How the approval system affects Chinese scientific journals
Authors: LIN Songqing 
Published: September 2013

ABSTRACTChinese scientific journals are moving in the right direction but developing first‐class academic journals still requires a number of obstacles to be overcome. Before the birth of any journal, a very complex journal approval system (JAS) must be negotiated. The paper will first present the history of the JAS in China and then analyze its effect on the scientific journal system. The JAS poses potential risks to the development of journals, and journal quantity rather than quality is the current priority. This needs to be changed and the JAS should be replaced by a journal registration system. Simultaneously, a system in which entry (start up) and closure, if required, is much easier than at present should be introduced, allowing the market to be the principal arbiter of success or failure.
The new engagement game: the role of gamification in scholarly publishing
Authors: ARMSTRONG David 
Published: September 2013

ABSTRACTGamification – the application of game mechanics to solve problems and engage users – is gathering significant momentum in the wider business world, and there are many ways in which it could benefit librarians, academic publishers, and learned societies. At its core, gamification is a way of tapping into motivational forces to increase individual investment in a system, process, or resource; applied correctly, these mechanics could be used to increase engagement with a publisher's back catalogue, drive society members to explore the value their membership offers, and encourage students to connect with on‐campus learning resources. Gamification can help satisfy both business and audience objectives, but frameworks have to be carefully designed to avoid some of the common pitfalls that such systems face. Although there are few examples of gamification at work in the learned publishing sector, those who are willing to explore, experiment, and iterate on solutions will be better placed to meet the needs of the increasing ‘digital native’ student and academic population.
How to spot Ugly Black Ducklings: the next competitive frontiers in scholarly publishing
Authors: FROEHLICH Peter 
Published: September 2013

ABSTRACTThis paper reviews events of SSP 2013 and AAUP 2013 within the context of Nassim Nicholas Taleb's notions of Black Swans (unexpected game changers) to anticipate the formation of competitive arenas (i.e. new models and revenue streams) for scholarly communications. It examines Tim O'Reilly's keynote address at SSP 2013, the advice of Michael Schrage from the opening Plenary at AAUP 2013, and Tim Sullivan's discussion of Harvard Business Publication's use of a topical blog network as new publishing platform to access global digital communications networks. The essay extrapolates from the case studies presented to overlay the strategies of successful practitioner presses and the advice of sought‐after business consultants on the work of academic houses, to imagine the next competitive frontier(s) in scholarly publishing.
RUBRIQ: tools, services, and software to improve peer review
Authors: STEMMLE Laura , COLLIER Keith 
Published: September 2013

ABSTRACTRubriq is on a mission to put lost time back into research. We estimate that 15 million hours are lost each year to redundant peer review as papers get rejected and flow down the journal prestige pyramid. Rubriq uses an author‐pays model to facilitate fast, independent, and standardized peer review performed by three academic peers who are financially compensated for their efforts. Authors receive the reviews as well as a detailed journal recommendation report in 1–2 weeks. This service is designed to improve journal selection, supplement editorial reviews, and make peer review more portable between journals. The creation of the standardized scorecard is just the first phase of Rubriq's plans to improve the scholarly communication workflow. Through lessons learned over the past year, the Rubriq approach is evolving into a broader set of tools, software, and services designed to speed and improve the scholarly communication process.
Molecular causes of transcriptional response: a Bayesian prior knowledge approach
Authors: Zarringhalam Kourosh , Enayetallah Ahmed , Gutteridge Alex , Sidders Ben , Ziemek Daniel 
Published: September 2013

Abstract
Motivation: The abundance of many transcripts changes significantly in response to a variety of molecular and environmental perturbations. A key question in this setting is as follows: what intermediate molecular perturbations gave rise to the observed transcriptional changes? Regulatory programs are not exclusively governed by transcriptional changes but also by protein abundance and post-translational modifications making direct causal inference from data difficult. However, biomedical research over the last decades has uncovered a plethora of causal signaling cascades that can be used to identify good candidates explaining a specific set of transcriptional changes.
Methods: We take a Bayesian approach to integrate gene expression profiling with a causal graph of molecular interactions constructed from prior biological knowledge. In addition, we define the biological context of a specific interaction by the corresponding Medical Subject Headings terms. The Bayesian network can be queried to suggest upstream regulators that can be causally linked to the altered expression profile.
Results: Our approach will treat candidate regulators in the right biological context preferentially, enables hierarchical exploration of resulting hypotheses and takes the complete network of causal relationships into account to arrive at the best set of upstream regulators. We demonstrate the power of our method on distinct biological datasets, namely response to dexamethasone treatment, stem cell differentiation and a neuropathic pain model. In all cases relevant biological insights could be validated.
Availability and implementation: Source code for the method is available upon request.
Contact: daniel.ziemek@pfizer.com
Supplementary information: Supplementary data are available at Bioinformatics online.