bluuebunny/crossref_metadata_2025_split huggingface dataset:
Origin of Structural and Kinematic Properties of the Small Magellanic Cloud
Authors: Bekki Kenji , Chiba Masashi 
Published: April 2009

AbstractWe investigate structural, kinematic and chemical properties of stars and gas in the Small Magellanic Cloud (SMC) interacting with the Large Magellanic Cloud (LMC) and the Galaxy based on a series of self-consistent chemodynamical simulations. We adopt a new ‘dwarf spheroidal model’ in which the SMC initially has both old stars with a spherical spatial distribution and an extended Hi gas disk. We mainly investigate the evolution of the SMC for the last ∼3 Gyr, during which the Magellanic Stream (MS) and the Magellanic Bridge (MB) could have formed as a result of the LMC–SMC–Galaxy interaction. Our principal results, which can be tested against observations, are as follows: The final spatial distribution of the old stars projected onto the sky is spherical, even after strong LMC–SMC–Galaxy interaction, whereas that of the new ones is significantly flattened and appears to form a bar structure. Old stars have a line-of-sight velocity dispersion σ ≃ 30 km s−1 and slow rotation, with a maximum rotational velocity, V < 20 km s−1 and show asymmetry in the radial profiles. New stars have a smaller Σ than old ones and a significant amount of rotation (V/σ > 1). Hi gas shows velocity dispersions of σ = 10–40 km s−1, a high maximum rotational velocity (V ∼ 50 km s−1) and a spatial distribution similar to that of new stars. New stars with ages younger than 3 Gyr show a negative metallicity gradient in the sense that more metal-rich stars are located in the inner regions of the SMC. The MB inevitably contains old stars with surface mass densities of 6−300 × 104 M⊙ deg−2 depending on initial stellar distributions of the modeled SMC. We find that the dwarf spheroidal model can explain more self-consistently the observed kinematic properties of stars and gas, compared with another type of the model (‘the disk model’) in which the SMC initially consists of stellar and gas disks. We suggest that, to better understand its evolution, the SMC needs to be modeled as having a spheroidal component, rather than being a pure disk.
CNVVdb: a database of copy number variations across vertebrate genomes
Authors: Chen Feng-Chi , Chen Yen-Zho , Chuang Trees-Juen 
Published: March 2009

Abstract
Summary: CNVVdb is a web interface for identification of putative copy number variations (CNVs) among 16 vertebrate species using the-same-species self-alignments and cross-species pairwise alignments. By querying genomic coordinates in the target species, all the potential paralogous/orthologous regions that overlap ≥80–100% (adjustable) of the query sequences with user-specified sequence identity (≥60%∼≥90%) are returned. Additional information is also given for the genes that are included in the returned regions, including gene description, alternatively spliced transcripts, gene ontology descriptions and other biologically important information. CNVVdb also provides information of pseudogenes and single nucleotide polymorphisms (SNPs) for the CNV-related genomic regions. Moreover, multiple sequence alignments of shared CNVs across species are also provided. With the combination of CNV, SNP, pseudogene and functional information, CNVVdb can be very useful for comparative and functional studies in vertebrates.
Availability: CNVVdb is freely accessible at http://CNVVdb.genomics.sinica.edu.tw.
Contact: trees@gate.sinica.edu.tw
GetBonNie for building, analyzing and sharing rule-based models
Authors: Hu Bin , Matthew Fricke G. , Faeder James R. , Posner Richard G. , Hlavacek William S. 
Published: March 2009

Abstract
Summary: GetBonNie is a web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for drawing graphs that correspond to BNGL code; (ii) a network-generation engine for translating a set of rules into a chemical reaction network; (iii) simulation engines that implement generate-first, on-the-fly and network-free methods for simulating rule-based models; and (iv) a database for sharing models, parameter values, annotations, simulation tasks and results.
Availability: GetBonNie is free at http://getbonnie.org.
Contact: getbonnie@cs.unm.edu
Mitochondrial function, morphology and metabolic parameters improve after switching from stavudine to a tenofovir-containing regimen
Authors: Gerschenson Mariana , Kim Courtney , Berzins Baiba , Taiwo Babafemi , Libutti Daniel E. , Choi Julia , Chen Diana , Weinstein Jill , Shore Jessica , da Silva Barbara , Belsey Elizabeth , McComsey Grace A. , Murphy Robert L. 
Published: March 2009

AbstractObjectivesHIV-associated lipoatrophy has been associated with mitochondrial dysfunction induced by nucleoside reverse transcriptase inhibitor therapy. We hypothesize that lipid profiles and markers of mitochondrial function will improve in HIV-lipoatrophic patients switched to the nucleotide analogue tenofovir.MethodsTen patients receiving stavudine, lamivudine and lopinavir/ritonavir (Kaletra®) for over 6 years were switched from stavudine to tenofovir for 48 weeks. Subcutaneous fat tissue biopsies, fasting metabolic tests, HIV RNA, CD4 cell count and whole body dual energy X-ray absorptiometry (DEXA) scans were obtained at study entry and week 48. Mitochondrial DNA (mtDNA) copies/cell and mitochondrial morphology were assessed in adipose tissue biopsies, mtDNA 8-oxo-deoxyguanine in peripheral blood mononuclear cells, and glutathione (GSH) and F2-isoprostane in plasma.ResultsThere was no change in limb fat mass by DEXA; however, trunk fat mass increased by 18.9% (P = 0.01). Fasting total cholesterol decreased by 33 mg/dL (P = 0.005) and serum glucose decreased by 4 mg/dL (P = 0.039). mtDNA copies/cell increased from 386 to 1537 (P &lt; 0.001). Transmission electron microscopy showed that mitochondrial cristae were lacking or poorly defined at study entry, whereas mitochondrial inner structures were more well defined and outer membranes were intact at 48 weeks. Oxidative damage decreased in 8/10 patients, GSH increased and F2-isoprostane decreased.ConclusionsThe results from this study demonstrate that systemic and peripheral fat mitochondria improve in patients switched to tenofovir following long-term exposure to stavudine, while continuing protease inhibitor therapy.
Genetic Dissection ofVerticilliumWilt Resistance Mediated by Tomato Ve1
Authors: Fradin Emilie F. , Zhang Zhao , Juarez Ayala Juan C. , Castroverde Christian D.M. , Nazar Ross N. , Robb Jane , Liu Chun-Ming , Thomma Bart P.H.J. 
Published: March 2009

AbstractVascular wilt diseases caused by soil-borne pathogens are among the most devastating plant diseases worldwide. The Verticillium genus includes vascular wilt pathogens with a wide host range. Although V. longisporum infects various hosts belonging to the Cruciferaceae, V. dahliae and V. albo-atrum cause vascular wilt diseases in over 200 dicotyledonous species, including economically important crops. A locus responsible for resistance against race 1 strains of V. dahliae and V. albo-atrum has been cloned from tomato (Solanum lycopersicum) only. This locus, known as Ve, comprises two closely linked inversely oriented genes, Ve1 and Ve2, that encode cell surface receptor proteins of the extracellular leucine-rich repeat receptor-like protein class of disease resistance proteins. Here, we show that Ve1, but not Ve2, provides resistance in tomato against race 1 strains of V. dahliae and V. albo-atrum and not against race 2 strains. Using virus-induced gene silencing in tomato, the signaling cascade downstream of Ve1 is shown to require both EDS1 and NDR1. In addition, NRC1, ACIF, MEK2, and SERK3/BAK1 also act as positive regulators of Ve1 in tomato. In conclusion, Ve1-mediated resistance signaling only partially overlaps with signaling mediated by Cf proteins, type members of the receptor-like protein class of resistance proteins.
Matrix metalloproteinase‐2 expression in stromal tissues is a consistent prognostic factor in stage II colon cancer
Authors: Inafuku Yoshiko , Furuhata Tomohisa , Tayama Makoto , Okita Kenji , Nishidate Toshihiko , Mizuguchi Toru , Kimura Yasutoshi , Hirata Koichi 
Published: March 2009

For patients with stage II colon cancer, the usefulness of adjuvant chemotherapy remains controversial. Therefore, it is important to identify high‐risk indicators. The biological prognostic factors for recurrence might allow further insight into the optimal treatment strategy for patients with node‐negative disease. Matrix metalloproteinase‐2 seems to be one of the essential factors for tumor invasion and lymph node metastasis. In this study, we analyzed the expression of cyclooxygenase‐2 and matrix metalloproteinase‐2 by immunohistochemical staining in 109 patients with stage II colon cancer. A positive correlation was observed between tumor cyclooxygenase‐2 and tumor matrix metalloproteinase‐2 expression (P = 0.0006) and between tumor cyclooxygenase‐2 and stromal matrix metalloproteinase‐2 expression (P < 0.0001). Stromal matrix metalloproteinase‐2 expression was associated with disease‐free survival (P = 0.0095) and was shown to be an independent risk factor for recurrence by multivariate analysis. In addition, we carried out an invasion assay in vitro to investigate whether cyclooxygenase‐2 and matrix metalloproteinase‐2 affected the tumor‐invasive potential of colon cancer cell lines. The invasion assay showed that every cancer cell line acquired invasive potential in coculture with stromal cell lines and the cyclooxygenase‐2 inhibitor suppressed this phenomenon by downregulating the matrix metalloproteinase‐2 expression of stromal cells. In conclusion, these findings suggest that matrix metalloproteinase‐2 expression in stromal cells can be a high‐risk indicator for recurrence in patients with stage II colon cancer. (Cancer Sci 2009; 100: 852–858)
Prognostic implication of SYT–SSX fusion type and clinicopathological parameters for tumor‐related death, recurrence, and metastasis in synovial sarcoma
Authors: Sun Yan , Sun Baocun , Wang Jian , Cai Wenjuan , Zhao Xiulan , Zhang Shiwu , Hao Xishan 
Published: March 2009

The present study aimed to describe the distribution and features of the SYT–SSX fusion gene in Chinese patients with synovial sarcoma (SS), and to analyze the prognostic value of SYT–SSX fusion type and clinicopathological parameters for tumor‐related death, recurrence, and metastasis in SS. SYT–SSX1 and SYT–SSX2 fusion transcripts were tested by reverse transcription–polymerase chain reaction in 141 formalin‐fixed, paraffin‐embedded SS. The prognostic implication of SYT–SSX fusion type and clinicopathological parameters were analyzed by univariate and multivariate survival analyses. SYT–SSX1 and SYT–SSX2 were detected in 50 (34.5%) and 91 (64.5%) tumors, respectively. SYT–SSX1 (risk ratio [RR] = 2.032, P = 0.004), larger tumor size (RR = 1.859, P = 0.008), and aggressive Fédération Nationale des Centers de Lutte Contre le Cancer grade (RR = 2.094, P = 0.001) were adverse predictors for disease‐specific survival. However, SYT–SSX fusion type was not associated with local recurrence‐free survival (P = 0.216). Patients with larger tumors (RR = 2.071, P = 0.005) and those who received marginal excision (RR = 2.556, P = 0.005) had poor local recurrence‐free survival. Besides, SYT–SSX1 (RR = 1.859, P = 0.037), older age (RR = 1.799, P = 0.040), and aggressive International Union Against Cancer stage (RR = 3.690, P < 0.001) proved to be adverse prognostic factors for metastasis‐free survival. In conclusion, compared to SYT–SSX1, SYT–SSX2 was more frequent in Chinese patients with SS. Moreover, SYT–SSX1 was an adverse predictor for disease‐specific survival and metastasis‐free survival, but had no relation to local recurrence‐free survival. In addition, histological grade and tumor size were also important prognostic factors for SS. (Cancer Sci 2009; 100: 1018–1025)
Club Amigas: a promising response to the needs of adolescent Latinas
Authors: Kaplan Carol P. , Turner Sandra G. , Piotrkowski Chaya , Silber Ellen 
Published: April 2009

ABSTRACTThe Latino population in the USA is growing faster than any other group. Latinas are at risk for mental health and substance‐abuse problems and school dropout. Research has shown that the ability to adapt to life in the USA while retaining one's cultural heritage is essential for successful acculturation and may increase the chances for success in school. There is strong evidence that mentoring relationships can enhance teens' social and emotional competence. This paper describes Club Amigas, a mentoring project that paired Latina college students with Latina middle‐school girls. Initial quantitative and qualitative evaluations of programme effectiveness found that, as predicted, mentees' self‐esteem was related to a positive commitment to their Latina identity, and that self‐esteem and positive commitment to Latina identity increased over the programme year.
Linking landscape‐level change to habitat quality: an evaluation of restoration actions on the freshwater habitat of spring‐run Chinook salmon
Authors: JORGENSEN JEFFREY C. , HONEA JON M. , McCLURE MICHELLE M. , COONEY THOMAS D. , ENGIE KIM , HOLZER DAMON M. 
Published: March 2009

Summary1. Conservation planning is often hampered by the lack of causal quantitative links between landscape characteristics, restoration actions and habitat conditions that impact the status of imperilled species. Here we present a first step toward linking actions on the landscape to the population status of endangered stream‐type Chinook salmon (Oncorhynchus tshawytscha).2. We developed relationships between land use, landscape characteristics and freshwater habitat of spring Chinook salmon in the Wenatchee River basin. Available data allowed us to find relationships that described water temperatures at several life stages (prespawning, egg incubation and summer rearing) and substratum characteristics, including fine sediments, cobble and embeddedness. Predictors included altitude, gradient, mean annual precipitation, total and riparian forest cover, road density, impervious surface and alluvium. We used a model averaging approach to account for parameter and model selection uncertainty. Key predictors were total forest cover and impervious surface area for prespawning and summer rearing temperatures; precipitation and stream gradients were important predictors of the percent of fine sediments in stream substrata.3. We estimated habitat conditions using these relationships in three alternative landscape scenarios: historical, no restoration and one that included a set of restoration actions from local conservation planning. We found that prespawning and summer temperatures were estimated to be slightly higher historically relative to current conditions in dry sparsely forested areas, but lower in some important Chinook salmon spawning and rearing areas and lower in those locations under the restoration scenario. Fine sediments were lower in the historical scenario and were reduced as a consequence of restoration actions in two areas currently unoccupied by Chinook salmon that contain reaches with some potential for high quality spawning and rearing. Cobble and embeddedness in general were predicted to be higher historically and changed little as a result of restoration actions relative to current conditions.4. This modelling framework converts suites of restoration actions into changes in habitat condition, thereby enabling restoration planners to evaluate alternative combinations of proposed actions. It also provides inputs to models linking habitat conditions to population status. This approach represents a first step in estimating impacts of restoration strategies, and can provide key information for conservation managers and planners.
A 10‐year decrease in plant species richness on a neotropical inselberg: detrimental effects of global warming?
Authors: FONTY EMILE , SARTHOU CORINNE , LARPIN DENIS , PONGE JEAN‐FRANÇOIS 
Published: March 2009

AbstractThe census of vascular plants across a 10‐year interval (1995–2005) at the fringe of a neotropical rainforest (Nouragues inselberg, French Guiana, South America) revealed that species richness decreased, both at quadrat scale (2 m2) and at the scale of the inselberg (three transects, embracing the whole variation in community composition). Juvenile stages of all tree and shrub species were most severely affected, without any discrimination between life and growth forms, fruit and dispersion types, or seed sizes. Species turnover in time resulted in a net loss of biodiversity, which was inversely related to species occurrence. The most probable cause of the observed species disappearance is global warming, which severely affected northern South America during the last 50 years (+2 °C), with a concomitant increase in the occurrence of aridity.
Linking environmental warming to the fitness of the invasive clam Corbicula fluminea
Authors: WEITERE MARKUS , VOHMANN ANDREAS , SCHULZ NADINE , LINN CATHERINE , DIETRICH DÉSIRÉE , ARNDT HARTMUT 
Published: March 2009

AbstractClimate warming is discussed as a factor that can favour the success of invasive species. In the present study, we analysed potential fitness gains of moderate warming (3 °C above field temperature) on the invasive clam Corbicula fluminea during summer and winter. The experiments were conducted under seminatural conditions in a bypass‐system of a large river (Rhine, Germany). We showed that warming in late summer results in a significant decrease in the clams' growth rates (body mass and shell length increase) and an increase in mortality rate. The addition of planktonic food dampens the negative effect of warming on the growth rates. This suggests that the reason for the negative growth effect of temperature increase in late summer is a negative energetic balance caused by an enhanced metabolic rate at limited food levels. Warming during early summer revealed contrasting effects with respect of body mass (no warming effect) and shell length (increased shell growth with warming). This differential control of both parameters further enhances the loss of the relative (size‐specific) body mass with warming. In contrast, warming in winter had a consistently positive effect on the clams' growth rate as demonstrated in two independent experiments. Furthermore, the reproduction success (as measured by the average number of larvae per clam) during the main breeding period (April) was strongly enhanced by experimental warming during winter, i.e. by eight times during the relatively cold winter 2005/2006 and by 2.6 times during the relatively warm winter 2007/2008. This strong, positive effect of moderate winter warming on the clams' fitness is probably one reason for the recent invasion success of C. fluminea in the northern hemisphere. However, warm summer events might counteract the positive winter warming effect, which could balance out the fitness gains.
T cells as pioneers: antigen‐specific T cells condition inflamed sites for high‐rate antigen‐non‐specific effector cell recruitment
Authors: Ghani Saeed , Feuerer Markus , Doebis Cornelia , Lauer Uta , Loddenkemper Christoph , Huehn Jochen , Hamann Alf , Syrbe Uta 
Published: March 2009

SummaryCellular infiltration is a classic hallmark of inflammation. Whereas the role of T cells in many types of inflammation is well established, the specific impact of antigen recognition on their migration into the site and on the accumulation of other effector cells are still matters of debate. Using a model of an inflammatory effector phase driven by T‐cell receptor (TCR) transgenic T cells, we found (i) that antigen‐specific T cells play a crucial role as ‘pioneer cells’ that condition the tissue for enhanced recruitment of further T effector cells and other leucocytes, and (ii) that the infiltration of T cells is not dependent on antigen specificity. We demonstrate that a small number of antigen‐specific T cells suffice to initiate a cascade of cellular immigration into the antigen‐loaded site. Although antigen drives this process, accumulation of T cells in the first few days of inflammation was not dependent on T‐cell reactivity to the antigen. Both transgenic and wild‐type T effector cells showed enhanced immigration into the site of antigen challenge after the initial arrival and activation of antigen‐specific pioneer cells. This suggests that bystander accumulation of non‐specific effector/memory T cells is a general feature in inflammation. Furthermore, tumour necrosis factor (TNF)‐α and interferon (IFN)‐γ were identified as mediators that contribute to conditioning of the inflammatory site for high‐rate accumulation of T effector cells in this T‐cell‐driven model.
Junctional adhesion molecule (JAM)‐B supports lymphocyte rolling and adhesion through interaction with α4β1 integrin
Authors: Ludwig Ralf J. , Hardt Katja , Hatting Max , Bistrian Roxana , Diehl Sandra , Radeke Heinfried H. , Podda Maurizio , Schön Michael P. , Kaufmann Roland , Henschler Reinhard , Pfeilschifter Josef M. , Santoso Sentot , Boehncke Wolf‐Henning 
Published: March 2009

SummaryJunctional adhesion molecule‐A (JAM‐A), JAM‐B and JAM‐C have been implicated in leucocyte transmigration. As JAM‐B binds to very late activation antigen (VLA)‐4, a leucocyte integrin that contributes to rolling and firm adhesion of lymphocytes to endothelial cells through binding to vascular cell adhesion molecule (VCAM)‐1, we hypothesized that JAM‐B is also involved in leucocyte rolling and firm adhesion. To test this hypothesis, intravital microscopy of murine skin microvasculature was performed. Rolling interactions of murine leucocytes were significantly affected by blockade of JAM‐B [which reduced rolling interactions from 9·1 ± 2·6% to 3·2 ± 1·2% (mean ± standard deviation)]. To identify putative ligands, T lymphocytes were perfused over JAM‐B‐coated slides in a dynamic flow chamber system. JAM‐B‐dependent rolling and sticking interactions were observed at low shear stress [0·3 dyn/cm2: 220 ± 71 (mean ± standard deviation) versus 165 ± 88 rolling (P < 0·001; Mann–Whitney rank sum test) and 2·6 ± 1·3 versus 1·0 ± 0·7 sticking cells/mm2/min (P = 0·026; Mann–Whitney rank sum test) on JAM‐B‐ compared with baseline], but not at higher shear forces (1·0 dyn/cm2). As demonstrated by antibody blocking experiments, JAM‐B‐mediated rolling and sticking of T lymphocytes was dependent on α4 and β1 integrin, but not JAM‐C expression. To investigate whether JAM‐B‐mediated leucocyte–endothelium interactions are involved in a disease‐relevant in vivo model, adoptive transfer experiments in 2,4,‐dinitrofluorobenzene (DNFB)‐induced contact hypersensitivity reactions were performed in mice in the absence or in the presence of a function‐blocking JAM‐B antibody. In this model, JAM‐B blockade during the sensitization phase impaired the generation of the immune response to DNFB, which was assessed as the increase in ear swelling in untreated, DNFB‐challenged mice, by close to 40% [P = 0·037; analysis of variance (anova)]. Overall, JAM‐B appears to contribute to leucocyte extravasation by facilitating not only transmigration but also rolling and adhesion.