bluuebunny/crossref_metadata_2025_split huggingface dataset:
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae
Authors: Mandel Jennifer R. , Dikow Rebecca B. , Funk Vicki A. , Masalia Rishi R. , Staton S. Evan , Kozik Alex , Michelmore Richard W. , Rieseberg Loren H. , Burke John M. 
Published: February 2014

• Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta‐tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses.• Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family.• Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.
Introduction
Authors: Wang Xiaoming 
Published: February 2014

Comment s’articulent la participation de la Chine à l’expansion du capitalisme mondial et son appartenance à un modèle de développement non occidental, a priori contradictoire ? Quand le Parti communiste chinois veut raccorder la Chine avec le monde, il s’agit de la raccorder à l’expansion du capitalisme, raccord que défendent culturellement les Chinois enrichis. Mais le choix n’est peut-être pas le même sur le court ou le long terme. C’est ce dont débattent, à partir de positions différentes, les six auteurs chinois réunis ici.
La révolution industrieuse et la prospérité commune
Authors: Luo Gang , Wang Shuliu , Le Gall Pierre-Yves 
Published: February 2014

La révolution industrieuse des pays asiatiques s’est appuyée sur la force des bras et a donc eu une grande capacité redistributive. C’est l’augmentation du revenu et du bien-être des populations qui est le moteur. C’est ce qui donne aux régions défavorisées leur capacité de résistance à la crise. Il faut déplacer vers elle le centre de gravité du pays et les inclure dans le nouveau modèle de développement. Mais on devra affronter le problème ethnique des non Han plus présents dans ces régions, et les différences de modèles culturels : les régions côtières sont plus occidentalisées.
La protection sociale en Chine
Authors: Wang Shaoguang 
Published: February 2014

Depuis le début du xxi e siècle, la Chine essaie de construire un marché social qui pallie les effets de l’économie de marché. L’État a organisé des transferts sociaux pour lutter contre les inégalités régionales et la pauvreté des ruraux. 59 millions de pauvres urbains bénéficient d’un revenu minimum d’existence garanti. 800 millions de Chinois bénéficient d’un système d’assurance santé, en voie d’extension dans les zones rurales. Les trois régimes de retraite couvrent 80 % de la population adulte de plus de 16 ans. Des aides au logement ont été mises en place. En douze ans le budget consacré à la protection sociale a été multiplié par 10 et fait maintenant 10,5 % du PIB.
Le face-à-face citadins/nature
Authors: Blanc Nathalie 
Published: February 2014

La protection de l’environnement peut-elle être justifiée par des considérations esthétiques, telles que la beauté des animaux, ou des paysages ? Ou bien doit-elle obéir à une éthique environnementale scientifique ? Ou bien dans l’éthique du care se préoccuper de prendre soin ? Il faut reconnaître la co-appartenance des êtres vivants dans un même cadre matériel, l’entretien de leur solidarité à travers les âges, la nécessité de former des valeurs communes à partir de pratiques différentes. Ces questions sont examinées dans plusieurs cas : le rapport à l’animal de compagnie, l’expérience botanique d’un artiste refusée par un musée comme ne relevant pas de l’art, l’invention de formes écologiques refusées par le public comme technocratiques.
De l'exploitation à l'exploit
Authors: Amilec Alicia , Citton Yves 
Published: February 2014

Dans leur livre The Exploit. A Theory of Networks , Alexander Galloway et Eugene Thacker montrent en quoi les protocoles consistent un nouveau paradigme de contrôle et d’exploitation à l’âge de la biopolitique. Pour contrer les effets d’homogénéisation et de soumission induits par cette nouvelle forme de pouvoir, ils invitent à développer des interventions relevant de « l’exploit » : exploiter les failles des protocoles pour y insérer des virus ou pour y cultiver des formes de non-existence déjouant les dispositifs qui permettent aux réseaux de nous exploiter. Alicia Amilec présente leur cadre de pensée, en explicite les enjeux et en tire des raisons de préférer les perspectives de liberté aux lamentations sur les déconvenues d’Internet.
Le bonheur comme rétribution du travail artistique
Authors: Sinigaglia Jérémy 
Published: February 2014

Les professions artistiques bénéficient d’une représentation flatteuse qui en fait l’antithèse du travail aliéné : le bonheur au travail des travailleurs du spectacle compenserait aisément la précarité de l’emploi, l’irrégularité des revenus, l’instabilité de la protection sociale qui caractérisent le secteur artistique. L’article propose de déconstruire ces représentations avec trois arguments principaux. Premièrement, les conditions de l’épanouissement personnel des professionnels du spectacle dépendent très directement de leurs inégales capacités à ajuster leurs aspirations aux chances objectives de les voir se réaliser. Deuxièmement, le plaisir pris au travail ne permettant pas toujours de compenser les effets de la précarité de l’emploi et les désagréments de la course aux cachets et aux subventions, les travailleurs sont conduits à chercher leur bonheur en marge voire en dehors des formes d’emploi consacrées. Troisièmement, si les artistes se disent globalement heureux malgré la difficulté de leurs conditions d’emploi, c’est d’une part parce que l’expression de leur éventuelle souffrance est illégitime (car comparée à celle jugée plus grande des salariés des autres secteurs économiques) et d’autre part qu’elle les conduirait à remettre en cause une partie de l’ illusio (la croyance dans le don en particulier) qui fonde leur engagement dans la carrière.
CD24-Triggered Caspase-Dependent Apoptosis via Mitochondrial Membrane Depolarization and Reactive Oxygen Species Production of Human Neutrophils Is Impaired in Sepsis
Authors: Parlato Marianna , Souza-Fonseca-Guimaraes Fernando , Philippart François , Misset Benoît ,   Captain Study Group, Jacqmin Sébastien , Journois Didier , Lagrange Alix , Pinot de Villechenon Gabrielle , Aissaoui Nadia , Diehl Jean-Luc , Guerot Emmanuel , Venot Marion , Hamzaoui Olfa , Prat Dominique , Sztrymf Benjamin , Annane Djillali , Maxime Virginie , Polito Andrea , Lecomte Laurence , Bournaud Elsa , Audureau Etienne , Quinquis Laurent , Rouquette Alexandra , Bruel Cédric , Fournier Julien , Garrouste-Orgeas Maïté , Gregoire Charles , Lau Nicolas , Max Adeline , Bouhemad Belaïd , Ethuin Frédéric , Bedos Jean-Pierre , Crosnier Pierrick , Laurent Virginie , Merceron Sybille , Pachot Alexandre , Moucadel Virginie , Fitting Catherine , Puchois Virginie , Adib-Conquy Minou , Cavaillon Jean-Marc 
Published: February 2014

Abstract
Apoptosis is the most common pathway of neutrophil death under both physiological and inflammatory conditions. In this study, we describe an apoptotic pathway in human neutrophils that is triggered via the surface molecule CD24. In normal neutrophils, CD24 ligation induces death through depolarization of the mitochondrial membrane in a manner dependent on caspase-3 and caspase-9 and reactive oxygen species. Proinflammatory cytokines such as TNF-α, IFN-γ, and GM-CSF upregulated the expression of CD24 in vitro, favoring the emergence of a new CD16high/CD24high subset of cultured neutrophils. We observed that CD24 expression (at both mRNA and protein levels) was significantly downregulated in neutrophils from sepsis patients but not from patients with systemic inflammatory response syndrome. This downregulation was reproduced by incubation of neutrophils from healthy controls with corticosteroids or with plasma collected from sepsis patients, but not with IL-10 or TGF-β. Decreased CD24 expression observed on sepsis neutrophils was associated with lack of functionality of the molecule, because cross-ligation of CD24 failed to trigger apoptosis in neutrophils from sepsis patients. Our results suggest a novel aspect of CD24-mediated immunoregulation and represent, to our knowledge, the first report showing the role of CD24 in the delayed/defective cell death in sepsis.
All-Trans Retinoic Acid–Triggered Antimicrobial Activity against Mycobacterium tuberculosis Is Dependent on NPC2
Authors: Wheelwright Matthew , Kim Elliot W. , Inkeles Megan S. , De Leon Avelino , Pellegrini Matteo , Krutzik Stephan R. , Liu Philip T. 
Published: February 2014

Abstract
A role for vitamin A in host defense against Mycobacterium tuberculosis has been suggested through epidemiological and in vitro studies; however, the mechanism is unclear. In this study, we demonstrate that vitamin A–triggered antimicrobial activity against M. tuberculosis requires expression of NPC2. Comparison of monocytes stimulated with all-trans retinoic acid (ATRA) or 1,25-dihydroxyvitamin D3 (1,25D3), the biologically active forms of vitamin A and vitamin D, respectively, indicates that ATRA and 1,25D3 induce mechanistically distinct antimicrobial activities. Stimulation of primary human monocytes with ATRA did not result in expression of the antimicrobial peptide cathelicidin, which is required for 1,25D3 antimicrobial activity. In contrast, ATRA triggered a reduction in the total cellular cholesterol concentration, whereas 1,25D3 did not. Blocking ATRA-induced cellular cholesterol reduction inhibits antimicrobial activity as well. Bioinformatic analysis of ATRA- and 1,25D3-induced gene profiles suggests that NPC2 is a key gene in ATRA-induced cholesterol regulation. Knockdown experiments demonstrate that ATRA-mediated decrease in total cellular cholesterol content and increase in lysosomal acidification are both dependent upon expression of NPC2. Expression of NPC2 was lower in caseous tuberculosis granulomas and M. tuberculosis–infected monocytes compared with normal lung and uninfected cells, respectively. Loss of NPC2 expression ablated ATRA-induced antimicrobial activity. Taken together, these results suggest that the vitamin A–mediated antimicrobial mechanism against M. tuberculosis requires NPC2-dependent expression and function, indicating a key role for cellular cholesterol regulation in the innate immune response.
Aging and Cytomegalovirus Infection Differentially and Jointly Affect Distinct Circulating T Cell Subsets in Humans
Authors: Wertheimer Anne M. , Bennett Michael S. , Park Byung , Uhrlaub Jennifer L. , Martinez Carmine , Pulko Vesna , Currier Noreen L. , Nikolich-Žugich Dragana , Kaye Jeffrey , Nikolich-Žugich Janko 
Published: February 2014

Abstract
The impact of intrinsic aging upon human peripheral blood T cell subsets remains incompletely quantified and understood. This impact must be distinguished from the influence of latent persistent microorganisms, particularly CMV, which has been associated with age-related changes in the T cell pool. In a cross-sectional cohort of 152 CMV-negative individuals, aged 21–101 y, we found that aging correlated strictly to an absolute loss of naive CD8, but not CD4, T cells but, contrary to many reports, did not lead to an increase in memory T cell numbers. The loss of naive CD8 T cells was not altered by CMV in 239 subjects (range 21–96 y), but the decline in CD4+ naive cells showed significance in CMV+ individuals. These individuals also exhibited an absolute increase in the effector/effector memory CD4+ and CD8+ cells with age. That increase was seen mainly, if not exclusively, in older subjects with elevated anti-CMV Ab titers, suggesting that efficacy of viral control over time may determine the magnitude of CMV impact upon T cell memory, and perhaps upon immune defense. These findings provide important new insights into the age-related changes in the peripheral blood pool of older adults, demonstrating that aging and CMV exert both distinct and joint influence upon blood T cell homeostasis in humans.
Decidual Neutrophil Infiltration Is Not Required for Preterm Birth in a Mouse Model of Infection-Induced Preterm Labor
Authors: Rinaldi Sara F. , Catalano Rob D. , Wade Jean , Rossi Adriano G. , Norman Jane E. 
Published: February 2014

Abstract
Parturition is associated with a leukocyte influx into the intrauterine tissues; however, the exact role these leukocytes play in the onset of labor remains unclear. Neutrophil infiltration of the uteroplacental tissues has been particularly associated with infection-associated preterm labor (PTL) in both women and mouse models. In this study, we investigated the role of neutrophils in a mouse model of infection-induced PTL. Intrauterine administration of LPS on day 17 of gestation resulted in a 7-fold increase in the number of decidual neutrophils compared with control mice receiving PBS (p &lt; 0.01; n = 8–11). We hypothesized that neutrophil influx is necessary for PTL and that neutrophil depletion would abolish preterm birth. To test this hypothesis, mice were depleted of neutrophils by treatment with anti–Gr-1, anti–Ly-6G, or the appropriate IgG control Ab on day 16 of gestation prior to LPS on day 17 (n = 6–7). Successful neutrophil depletion was confirmed by flow cytometry and immunohistochemistry. Neutrophil depletion with Gr-1 resulted in reduced uterine and placental Il-1β expression (p &lt; 0.05). Neutrophil depletion with Ly-6G reduced uterine Il-1β and Tnf-α expression (p &lt; 0.05). However, neutrophil depletion with either Ab did not delay LPS-induced preterm birth. Collectively, these data show that decidual neutrophil infiltration is not essential for the induction of infection-induced PTL in the mouse, but that neutrophils contribute to the LPS-induced inflammatory response of the uteroplacental tissues.
Hyperspace Dynamics of Generic Maps of the Cantor Space
Authors: Bernardes Nilson C. , Vermersch Rômulo M. 
Published: February 2014

AbstractWe study the hyperspace dynamics induced fromgeneric continuous maps and fromgeneric
homeomorphisms of the Cantor space, with emphasis on the notions of Li– Yorke chaos, distributional
chaos, topological entropy, chain continuity, shadowing, and recurrence.
Nitrogen cycling in deeply oxygenated sediments: Results in Lake Superior and implications for marine sediments
Authors: Li Jiying , Katsev Sergei 
Published: February 2014

To understand the nitrogen (N) cycle in sediments with deep oxygen penetration, we measured pore‐water profiles to calculate N fluxes and rates at 13 locations in Lake Superior in water depths ranging from 26 to 318 m. Sediments with high oxygen demand, such as in nearshore or high‐sedimentation areas, contribute disproportionally to benthic N removal, despite covering only a small portion of the lake floor. These sediments are nitrate sinks (average 0.16 mmol m−2 d−1) and have denitrification rates (average 0.76 mmol m−2 d−1) that are comparable to those in coastal marine sediments. The deeply oxygenated (4 to > 12 cm) offshore sediments are nitrate sources (average 0.26 mmol m−2 d−1) and generate N2 at lower rates (average 0.10 mmol m−2 d−1). Ammonium is nitrified with high efficiency (90%), and nitrification supports > 50% of denitrification nearshore and µ 100% offshore. Oxygen consumption by nitrification accounts for 12% of the total sediment oxygen uptake. About 2% of nitrate reduction is coupled to oxidation of iron, a rarely detected pathway. Our Lake Superior N budget indicates significant contributions from sediment—water exchanges and N2 production and is closer to balance than previous budgets. Our results reveal that sediment N cycling in large freshwater lakes is similar to that in marine systems. They further suggest that denitrification rates in slowly accumulating, well‐oxygenated sediments cannot be described by the same relationship with total oxygen uptake as in high‐sedimentation areas; hence, global models should treat abyssal ocean sediments differently than coastal and shelf sediments.
Effect of the Association between Citric Acid and EDTA on Root Surface Etching
Authors: Leite Fabio Renato Manzolli , Nascimento Gustavo Giacomelli , Leite Elza Regina Manzolli , Leite Amauri Antiquera , Sampaio José Eduardo Cezar 
Published: February 2014

ABSTRACT

Objective
This study aims to compare the clot stabilization on root surfaces conditioned with citric acid and ethylenediaminetetraacetic acid (EDTA).

Materials and methods
Scaled root samples (n = 100) were set in five groups: group I–control group (saline solution); group II (24% EDTA); group III (25% citric acid); group IV (EDTA + citric acid); group V (citric acid + EDTA). Fifty samples were assessed using the root surface modification index (RSMI). The other 50 received a blood drop after conditioning. Clot formation was assessed using blood elements adhesion index (BEAI). A blind examiner evaluated photomicrographs. Statistical analysis considered p < 0.05.

Results
Groups-III and G-V attained the best results for RSMI and BEAI in comparison to control. The worst results for clot stabilization were seen in group-II. EDTA employment before citric acid (group-IV) reduced clot formation in comparison to citric acid use alone (group-III).

Conclusion
Root conditioning with citric acid alone and before EDTA had the best results for smear layer removal and clot stabilization. EDTA inhibited clot stabilization on root surface and must have a residual activity once it has diminished clot adhesion to root even after citric acid conditioning. Thus, EDTA can be used to neutralize citric acid effects on periodontal cells without affecting clot stabilization.

Clinical significance
To demonstrate that citric acid use on root surfaces previously affected by periodontal disease may favor clot stabilization and may have a beneficial effect on surgical outcomes. Also, EDTA can be used to neutralize citric acid effects on periodontal cells.

How to cite this article
Leite FRM, Nascimento GG, Leite ERM, Leite AA, Sampaio JEC. Effect of the Association between Citric Acid and EDTA on Root Surface Etching. J Contemp Dent Pract 2013;14(5):796-800.
Estimation of Serum Copper and Zinc Levels in Oral Submucous Fibrosis: An Atomic Absorption Spectroscopic Study
Authors: Neethi H 
Published: February 2014

ABSTRACTBackground and objectivesBiochemical derangements of microelements although reported in oral cancer is poorly understood in oral submucous fibrosis (OSMF). Hence, the present study was carried out to estimate and compare the serum copper and zinc levels among different histopathological stages of OSMF with that of healthy controls.Materials and methodsThirty histopathologically diagnosed cases of OSMF and 30 healthy controls reporting to MS Ramaiah Dental College and Hospital (MSRDCH), Bengaluru, were included in the study. The histopathological staging of OSMF was done as per criteria given by Pindborg and Sirsat (1966). Blood samples were collected and the serum copper and zinc levels were estimated using atomic absorption spectroscopy. The results were statistically analyzed using independent t-test and Kruskal-Wallis test.ResultsThe mean serum copper levels were increased (p < 0.0005) and zinc levels were decreased (p < 0.01) in OSMF patients when compared to that of controls. The mean serum copper levels showed an increasing trend from stage I to IV (p = 0.004) while zinc levels showed a decreasing trend from stage I to IV (p = 0.04) in OSMF patients.ConclusionThe serum copper and zinc levels in OSMF showed a significant difference in comparison to that of controls and between the histopathological stages. These findings indicate that serum copper and zinc may have a contributory role in the etiopathogenesis of OSMF.Clinical relevanceAlthough the role of the trace elements as etiological factors is minor, derangements noted in the serum copper and zinc levels could be correlated with diseased progression and possibly explain the transformation of OSMF into malignancy. Thus, they can be used as prognostic markers and can be of value for proactive intervention.How to cite this articleNeethi H, Patil S, Rao RS. Estimation of Serum Copper and Zinc Levels in Oral Submucous Fibrosis: An Atomic Absorption Spectroscopic Study. J Contemp Dent Pract 2013;14(5):801-805.
An in vitro Study to Compare the Effectiveness of F-file with Ultrasonically Activated K-file to Remove Smear Layer by using a Scanning Electron Microscope
Authors: Kumar B Shiva , Shenvi Suresh 
Published: February 2014

ABSTRACTAimThe aim of this study was to compare the effectiveness of the F-file with an ultrasonically activated #15 K-file in removing the smear layer after biomechanical instrumentation along with irrigation of Saline, NaOCl and with or without a flush of EDTA.Materials and methodsSixty decoronated human premolar teeth with a single canal were instrumented with ProTaper using S1, S2 and F1 series to produce the smear layer and randomly divided into two groups. Group A used Ultrasonics and group B used F-file for activation of irrigants respectively. Each group was further divided in to three subgroups consisting of 10 teeth in each as I, II, III consisting of saline, NaOCl, NaOCl and EDTA as irrigants respectively. SEM micrographs were taken and amount of smear layer removal was analyzed by using Chi-square statistics tests.ResultsMost effective smear layer removal was seen only when EDTA was used. There was no statistically significant difference between the groups A and B in removal of smear layer.ConclusionThere was no increase in smear layer between use of F-file when compared with the Ultrasonically activated K-file.Clinical significanceThe F-file although does not have a superior efficacy than the ultrasonics in removal of smear layer from root canals but when used along with EDTA, can be an effective alternative for the dentists who are unable to bear the initial setup cost of ultrasonics.How to cite this articleShenvi S, Kumar BS. Anin vitroStudy to Compare the Effectiveness of F-file with Ultrasonically Activated K-file to Remove Smear Layer by using a Scanning Electron Microscope. J Contemp Dent Pract 2013;14(5):825-829.