bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trajectoires « révolutionnaires » en Tunisie
Authors: Allal Amin 
Published: December 2012

Résumé Derrière un unanimisme de façade, le moment révolutionnaire est vécu différemment et diverses dynamiques de radicalisation sont à l’œuvre. Si une majorité d’individus s’engagent sans être des opposants encartés, il faut éviter le piège de « l’immaculée contestation ». Pour cela, nous analysons d’une part, l’épreuve que constituent les protestations qui se multiplient depuis 2008 dans la Tunisie de « l’intérieur », et d’autre part, les contre-conduites qui se muent sous certaines conditions en contestation du régime. L’étude diachronique, basée sur des entretiens répétés depuis 2006, identifie les ressorts de ces mobilisations : situations socioprofessionnelles, sociabilités de quartiers et familiales, (en)jeux générationnels, mémoires des luttes passées et expériences de répression. Simultanément l’approche ethnographique révèle la part de contingence de ces implications dans un soulèvement populaire aussi intense que rapide.
Sur les sentiers de la révolution
Authors: El Chazli Youssef 
Published: December 2012

Résumé Les événements ayant secoué l’Égypte au début de l’année 2011, et ayant pris depuis le nom de « Révolution du 25 janvier », soulèvent de nombreuses questions. Parmi celles-ci, l’interrogation sur la participation massive d’une population considérée comme apathique ou dépolitisée est centrale. En effet, on peut penser qu’il n’y a rien de particulièrement « révolutionnaire » à voir des militants aguerris protester collectivement une énième fois. En revanche, élucider le passage à l’action de ces dizaines de milliers de personnes qui n’avaient jamais participé politiquement pose problème. Cet article tente de contribuer à la compréhension de ce phénomène à partir de l’étude localisée de la mobilisation de jeunes Cairotes fin janvier/début février 2011.
La structuration de la révolution yéménite
Authors: Bonnefoy Laurent , Poirier Marine 
Published: December 2012

Résumé En s’intéressant aux mobilisations nées du processus révolutionnaire yéménite engagé en janvier 2011, cet article, né d’une longue expérience de terrain partagée, étudie les interactions entre des pratiques émergentes et les « propriétés structurelles des systèmes sociaux ». Il fait l’hypothèse d’une dualité du processus révolutionnaire qui apparaît comme produit par les acteurs qui le portent mais aussi comme contraint par une structure historique, sociale et politique. Il interroge ainsi la capacité de l’événement révolutionnaire à générer de l’innovation militante mais également à poindre lui-même du croisement entre les pratiques émergentes et la reprise en main du processus par des réseaux de mobilisation existants et des acteurs politiques déjà institutionnalisés.
Isolation of Human CD4/CD8 Double-Positive, Graft-Versus-Host Disease–Protective, Minor Histocompatibility Antigen–Specific Regulatory T Cells and of a Novel HLA-DR7–Restricted HY-Specific CD4 Clone
Authors: Eljaafari Assia , Yuruker Ozel , Ferrand Christophe , Farre Annie , Addey Caroline , Tartelin Marie-Laure , Thomas Xavier , Tiberghien Pierre , Simpson Elizabeth , Rigal Dominique , Scott Diane 
Published: December 2012

Abstract
Minor histocompatibility (H) Ags are classically described as self-peptides derived from intracellular proteins that are expressed at the cell surface by MHC class I and class II molecules and that induce T cell alloresponses. We have isolated three different T cell populations from a skin biopsy of a patient suffering from acute graft-versus-host disease following sex-mismatched HLA-identical bone marrow transplantation. The first population was: 1) CD4+/CD8+ double-positive; 2) specific for an HLA class I–restricted autosomal Ag; 3) expressed a Tr1 profile with high levels of IL-10, but low IL-2 and IFN-γ; and 4) exerted regulatory function in the presence of recipient APCs. The second was CD8 positive, specific for an HLA class I–restricted autosomally encoded minor H Ag, but was only weakly cytotoxic. The third was CD4 single positive, specific for an HLA-DR7–restricted HY epitope and exerted both proliferative and cytotoxic functions. Identification of the peptide recognized by these latter cells revealed a new human HY epitope, TGKIINFIKFDTGNL, encoded by RPS4Y and restricted by HLA-DR7. In this paper, we show human CD4/CD8 double-positive, acute graft-versus-host disease–protective, minor H Ag–specific regulatory T cells and identify a novel HLA-DR7/ HY T cell epitope, encoded by RPS4Y, a potential new therapeutic target.
Cutting Edge: Ly9 (CD229), a SLAM Family Receptor, Negatively Regulates the Development of Thymic Innate Memory-like CD8+ T and Invariant NKT Cells
Authors: Sintes Jordi , Cuenca Marta , Romero Xavier , Bastos Ricardo , Terhorst Cox , Angulo Ana , Engel Pablo 
Published: December 2012

Abstract
Signaling lymphocytic activation molecule family receptors and the specific adapter signaling lymphocytic activation molecule–associated protein modulate the development of innate-like lymphocytes. In this study, we show that the thymus of Ly9-deficient mice contains an expanded population of CD8 single-positive cells with the characteristic phenotype of innate memory-like CD8+ T cells. Moreover, the proportion of these innate CD8+ T cells increased dramatically postinfection with mouse CMV. Gene expression profiling of Ly9-deficient mice thymi showed a significant upregulation of IL-4 and promyelocytic leukemia zinc finger. Analyses of Ly9−/−IL4ra−/− double-deficient mice revealed that IL-4 was needed to generate the thymic innate CD8+ T cell subset. Furthermore, increased numbers of invariant NKT cells were detected in Ly9-deficient thymi. In wild-type mice, IL-4 levels induced by α-galactosylceramide injection could be inhibited by a mAb against Ly9. Thus, Ly9 plays a unique role as an inhibitory cell surface receptor regulating the size of the thymic innate CD8+ T cell pool and the development of invariant NKT cells.
Perceptions of prenatal and obstetric care in Sub‐Saharan Africa
Authors: Brighton Aimee , D'Arcy Rhiannon , Kirtley Shona , Kennedy Stephen 
Published: December 2012

AbstractBackgroundThe maternal mortality ratio in Sub‐Saharan Africa remains high, despite progress in reducing maternal mortality in other parts of the world.ObjectiveTo explore the perceptions of women and communities to identify barriers to the uptake of obstetric services.Search strategyA systematic review of qualitative studies exploring perceptions of pregnancy and obstetric services, with thematic synthesis of the included studies.Selection criteriaQualitative studies reporting findings from focus group discussions and in‐depth interviews between 1996 and 2009 were included.Data collection and analysisThematic synthesis involved collating and reviewing quotations taken directly from included studies. Themes were generated and clustered for analysis.Main resultsTwenty‐seven studies were included and 6 major themes identified: perceptions of healthcare workers; perceptions of the hospital environment; cultural perceptions of women; cultural perceptions of pregnancy; perceptions of traditional birth attendants and traditional healers; and role of the community in pregnancy and birth.ConclusionCommunity attitudes regarding cultural beliefs and interactions with healthcare providers were identified as barriers to the utilization of healthcare services during pregnancy in Sub‐Saharan Africa. These prevent engagement with prenatal care and timely use of medical services. Addressing the barriers will be seminal to the success of any healthcare intervention.
Motivations and preferences of rural Nigerian women undergoing cervical cancer screening via visual inspection with acetic acid
Authors: Chigbu Chibuike O. , Onyebuchi Azubuike K. , Ajah Leonard O. , Onwudiwe Elijah N. 
Published: December 2012

AbstractObjectiveTo determine the motivations and preferences of women participating in visual inspection with acetic acid (VIA) mass cervical cancer screening programs in southeastern Nigeria.MethodsBy means of interviewer‐based questionnaires, data were collected from women participating in mass cervical cancer screenings with VIA in 3 randomly selected communities in each of 2 southeastern Nigerian states between March 1, 2011, and March 31, 2012.ResultsA total of 2312 women were interviewed. Support from husband and community opinion leaders were the most frequently reported factors that motivated the women to participate in the screening. Most participants expected an immediate result for the screening test and immediate treatment for any abnormalities detected.ConclusionCommunity‐based advocacy for cervical cancer screening is a very effective method of creating awareness for cervical cancer screening. Support from spouses and community leaders are important factors in a woman's decision to utilize cervical cancer screening services in southeastern Nigeria. Immediate results and treatments would make the most impact. Family and community participation should be integrated into cervical cancer prevention programs. This, together with a “see and treat” approach, may be central to overcoming the poor utilization of cervical cancer screening services in Nigeria and similar rural settings.
Brain size and the compensation of Alzheimer's disease symptoms: A longitudinal cohort study
Authors: Guo Liang‐Hao , Alexopoulos Panagiotis , Wagenpfeil Stefan , Kurz Alexander , Perneczky Robert ,   Alzheimer's Disease Neuroimaging Initiative
Published: December 2012

AbstractBackgroundGreater intracranial volume (ICV) has been associated with less severe Alzheimer's disease (AD) symptoms at a given level of cerebral pathology. In this study we examine whether ICV modulates the association between clinical disease progression on the one hand and brain atrophy or the apolipoprotein E genotype on the other.MethodsSix hundred seventy‐four subjects were studied from the AD Neuroimaging Initiative (ADNI). Subjects included 204 controls, 144 patients with AD dementia, and 326 with amnestic mild cognitive impairment (aMCI). Longitudinal analyses were conducted applying generalized estimating equations to examine the influence of ICV on clinical deterioration and atrophy progression. Follow‐up data were available for up to 60 months after the baseline visit (mean 31.42 months, SD 13.12 months).ResultsICV was not directly associated with clinical worsening or atrophy progression. However, ICV attenuated the impact of atrophy and the apolipoprotein E ε4 allele on clinical disease progression in aMCI.ConclusionGreater ICV, that is, premorbid brain size, seems to protect against clinical deterioration in the face of AD‐related brain atrophy in aMCI. The results support the theory of a compensatory role of brain reserve in contrast to a neuroprotective role. The protective effects of morphologic reserve seem to be limited to early clinical AD; once a certain threshold of neurodegenerative burden is passed, a larger premorbid brain no longer offers an advantage in this context.
Influences of Cyclic, High Temperatures on Juvenile Channel Catfish Growth and Feeding
Authors: Arnold Michael B , Torrans Eugene L , Allen Peter J 
Published: December 2012

Abstract
Effects of high summer temperatures on Channel Catfish Ictalurus punctatus are poorly understood, particularly for thermal regimes that mimic pond aquaculture conditions. Therefore, this study examined the effects of three cycling upper-range temperature regimes (23–27°C, 27–31°C, and 31–35°C) characteristic of aquaculture environments in the Mississippi Delta. Feed conversion ratio, feed consumption, specific growth rate, activity levels, survival, and overall growth in terms of wet weight and TL were measured in fingerling channel catfish over an 8-week period in a flow-through, multiple-tank system. Specific growth rate, feed consumption, TL, and wet weight of fish increased significantly in the 27–31°C treatment in contrast to the 23–27°C and 31–35°C treatments. Feed conversion ratio was lowest in the 27–31°C treatment, whereas activity levels were highest in the 31–35°C treatment. Survival significantly decreased for catfish in the warmest treatment compared with catfish in the coolest treatment. These results indicate that high temperatures decrease growth in Channel Catfish, largely due to reduced food consumption and feed conversion and increased levels of activity. Therefore, increases in temperatures, such as from climate change, present challenges to the culture and management of Channel Catfish.
ChromoZoom: a flexible, fluid, web-based genome browser
Authors: Pak Theodore R. , Roth Frederick P. 
Published: December 2012

Abstract
Summary: Current web-based genome browsers require repetitious user input to scroll over long distances, alter the drawing density of elements or zoom through multiple orders of magnitude. Generally, either the server or the client is responsible for the majority of data processing, resulting in either servers having to receive and handle data relevant only to one user, or clients redundantly processing widely viewed data. ChromoZoom pre-renders and caches general-use tracks into tiled images on the server and serves them in an interactive web interface with inertial scrolling and precise, fluent zooming via the mouse wheel or trackpad. Custom tracks in several formats can be rendered by client-side code alongside the pre-rendered tracks, minimizing server load because of user-specific rendering and eliminating the need to transmit private data. ChromoZoom thereby enables rapid and simultaneous exploration of curated, experimental and personal genomic datasets.
Availability: Human and yeast genome researchers may browse recent assemblies within ChromoZoom at http://chromozoom.org/. Source code is available at http://github.com/rothlab/chromozoom/.
Contact: fritz.roth@utoronto.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
nestly—a framework for running software with nested parameter choices and aggregating results
Authors: McCoy Connor O. , Gallagher Aaron , Hoffman Noah G. , Matsen Frederick A. 
Published: December 2012

Abstract
Summary: The execution of a software application or pipeline using various combinations of parameters and inputs is a common task in bioinformatics. In the absence of a specialized tool to organize, streamline and formalize this process, scientists must write frequently complex scripts to perform these tasks. We present nestly, a Python package to facilitate running tools with nested combinations of parameters and inputs. nestly provides three components. First, a module to build nested directory structures corresponding to choices of parameters. Second, the nestrun script to run a given command using each set of parameter choices. Third, the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. We also include a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds.
Availability: Source, documentation and tutorial examples are available at http://github.com/fhcrc/nestly. nestly can be installed from the Python Package Index via pip; it is open source (MIT license).
Contact: cmccoy@fhcrc.org or matsen@fhcrc.org
A knowledge-based orientation potential for transcription factor-DNA docking
Authors: Takeda Takako , Corona Rosario I. , Guo Jun-tao 
Published: December 2012

Abstract
Motivation: Computational modeling of protein–DNA complexes remains a challenging problem in structural bioinformatics. One of the key factors for a successful protein–DNA docking is a potential function that can accurately discriminate the near-native structures from decoy complexes and at the same time make conformational sampling more efficient. Here, we developed a novel orientation-dependent, knowledge-based, residue-level potential for improving transcription factor (TF)-DNA docking.
Results: We demonstrated the performance of this new potential in TF–DNA binding affinity prediction, discrimination of native protein–DNA complex from decoy structures, and most importantly in rigid TF–DNA docking. The rigid TF–DNA docking with the new orientation potential, on a benchmark of 38 complexes, successfully predicts 42% of the cases with root mean square deviations lower than 1 Å and 55% of the cases with root mean square deviations lower than 3 Å. The results suggest that docking with this new orientation-dependent, coarse-grained statistical potential can achieve high-docking accuracy and can serve as a crucial first step in multi-stage flexible protein–DNA docking.
Availability and implementation: The new potential is available at http://bioinfozen.uncc.edu/Protein_DNA_orientation_potential.tar.
Contact: jguo4@uncc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine
Authors: Matsuta Yoshihiko , Ito Masahiro , Tohsato Yukako 
Published: December 2012

Abstract
Motivation: The enzyme nomenclature system, commonly known as the enzyme commission (EC) number, plays a key role in classifying and predicting enzymatic reactions. However, numerous reactions have been described in various pathways that do not have an official EC number, and the reactions are not expected to have an EC number assigned because of a lack of articles published on enzyme assays. To predict the EC number of a non-classified enzymatic reaction, we focus on the structural similarity of its substrate and product to the substrate and product of reactions that have been classified.
Results: We propose a new method to assign EC numbers using a maximum common substructure algorithm, mutual information and a support vector machine, termed the Enzyme COmmission numbers Handler (ECOH). A jack-knife test shows that the sensitivity, precision and accuracy of the method in predicting the first three digits of the official EC number (i.e. the EC sub-subclass) are 86.1%, 87.4% and 99.8%, respectively. We furthermore demonstrate that, by examining the ranking in the candidate lists of EC sub-subclasses generated by the algorithm, the method can successfully predict the classification of 85 enzymatic reactions that fall into multiple EC sub-subclasses. The better performance of the ECOH as compared with existing methods and its flexibility in predicting EC numbers make it useful for predicting enzyme function.
Availability: ECOH is freely available via the Internet at http://www.bioinfo.sk.ritsumei.ac.jp/apps/ecoh/. This program only works on 32-bit Windows.
Contact: yukako@sk.ritsumei.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Fas deficiency in mice with the Balb/c background induces blepharitis with allergic inflammation and hyper-IgE production in conjunction with severe autoimmune disease
Authors: Takahashi Suzuka , Futatsugi-Yumikura Shizue , Fukuoka Ayumi , Yoshimoto Tomohiro , Nakanishi Kenji , Yonehara Shin 
Published: December 2012

AbstractFas (CD95) is a cell surface death receptor belonging to the tumor necrosis factor receptor superfamily, which mediates apoptosis-inducing signaling when activated by Fas ligand or its agonistic antibody. lpr mice with a loss of apoptosis-inducing function mutation in the Fas gene develop systemic autoimmune disease and lymphadenopathy but not allergic inflammation. In the case of Fas mutations including lpr and knockout (KO), background genes determine the incidence and severity of lymphadenopathy and histopathological manifestation of systemic autoimmunity: MRL-lpr/lpr mice and C57BL/6-lpr/lpr or C57BL/6 Fas KO mice develop severe and minimum disease, respectively. We generated Fas KO mice with the Balb/c background that show severer autoimmune phenotypes than MRL-lpr/lpr mice, such as critical infiltration of mononuclear cells into lung, liver and spleen, elevated serum levels of auto-antibodies and a decreased life span. To our astonishment, Balb/c Fas KO mice spontaneously develop blepharitis with not only autoimmune inflammation with deposition of auto-antibody but also allergic inflammation with infiltration by eosinophils and mast cells and show the capacity to strongly increase serum level of IgE and IgG1 along with their aging. Thus, Fas expression regulates development of not only autoimmune disease but also allergic inflammation.
Early Cone Setting in Picea abies acrocona Is Associated with Increased Transcriptional Activity of a MADS Box Transcription Factor
Authors: Uddenberg Daniel , Reimegård Johan , Clapham David , Almqvist Curt , von Arnold Sara , Emanuelsson Olof , Sundström Jens F. 
Published: December 2012

Abstract
Conifers normally go through a long juvenile period, for Norway spruce (Picea abies) around 20 to 25 years, before developing male and female cones. We have grown plants from inbred crosses of a naturally occurring spruce mutant (acrocona). One-fourth of the segregating acrocona plants initiate cones already in their second growth cycle, suggesting control by a single locus. The early cone-setting properties of the acrocona mutant were utilized to identify candidate genes involved in vegetative-to-reproductive phase change in Norway spruce. Poly(A+) RNA samples from apical and basal shoots of cone-setting and non-cone-setting plants were subjected to high-throughput sequencing (RNA-seq). We assembled and investigated 33,383 expressed putative protein-coding acrocona transcripts. Eight transcripts were differentially expressed between selected sample pairs. One of these (Acr42124_1) was significantly up-regulated in apical shoot samples from cone-setting acrocona plants, and the encoded protein belongs to the MADS box gene family of transcription factors. Using quantitative real-time polymerase chain reaction with independently derived plant material, we confirmed that the MADS box gene is up-regulated in both needles and buds of cone-inducing shoots when reproductive identity is determined. Our results constitute important steps for the development of a rapid cycling model system that can be used to study gene function in conifers. In addition, our data suggest the involvement of a MADS box transcription factor in the vegetative-to-reproductive phase change in Norway spruce.
Pipecolic Acid, an Endogenous Mediator of Defense Amplification and Priming, Is a Critical Regulator of Inducible Plant Immunity
Authors: Návarová Hana , Bernsdorff Friederike , Döring Anne-Christin , Zeier Jürgen 
Published: December 2012

Abstract
Metabolic signals orchestrate plant defenses against microbial pathogen invasion. Here, we report the identification of the non-protein amino acid pipecolic acid (Pip), a common Lys catabolite in plants and animals, as a critical regulator of inducible plant immunity. Following pathogen recognition, Pip accumulates in inoculated Arabidopsis thaliana leaves, in leaves distal from the site of inoculation, and, most specifically, in petiole exudates from inoculated leaves. Defects of mutants in AGD2-LIKE DEFENSE RESPONSE PROTEIN1 (ALD1) in systemic acquired resistance (SAR) and in basal, specific, and β-aminobutyric acid–induced resistance to bacterial infection are associated with a lack of Pip production. Exogenous Pip complements these resistance defects and increases pathogen resistance of wild-type plants. We conclude that Pip accumulation is critical for SAR and local resistance to bacterial pathogens. Our data indicate that biologically induced SAR conditions plants to more effectively synthesize the phytoalexin camalexin, Pip, and salicylic acid and primes plants for early defense gene expression. Biological priming is absent in the pipecolate-deficient ald1 mutants. Exogenous pipecolate induces SAR-related defense priming and partly restores priming responses in ald1. We conclude that Pip orchestrates defense amplification, positive regulation of salicylic acid biosynthesis, and priming to guarantee effective local resistance induction and the establishment of SAR.