bluuebunny/crossref_metadata_2025_split huggingface dataset:
A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa
Authors: Dupierris Véronique , Masselon Christophe , Court Magali , Kieffer-Jaquinod Sylvie , Bruley Christophe 
Published: May 2009

Abstract
Summary: The IRMa toolbox provides an interactive application to assist in the validation of Mascot® search results. It allows automatic filtering of Mascot® identification results as well as manual confirmation or rejection of individual PSM (a match between a fragmentation mass spectrum and a peptide). Dynamic grouping and coherence of information are maintained by the software in real time. Validated results can be exported under various forms, including an identification database (MSIdb). This allows biologists to compile search results from a whole study in a unique repository in order to provide a summarized view of their project. IRMa also features a fully automated version that can be used in a high-throughput pipeline. Given filter parameters, it can delete hits with no significant PSM, regroup hits identified by the same peptide(s) and export the result to the specified format without user intervention.
Availability: http://biodev.extra.cea.fr/docs/irma (java 1.5 or higher needed)
Contact: christophe.bruley@cea.fr
RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions
Authors: Rueda Oscar M. , Diaz-Uriarte Ramon 
Published: May 2009

Abstract
Summary: Several methods have been proposed to detect copy number changes and recurrent regions of copy number variation from aCGH, but few methods return probabilities of alteration explicitly, which are the direct answer to the question ‘is this probe/region altered?’ RJaCGH fits a Non-Homogeneous Hidden Markov model to the aCGH data using Markov Chain Monte Carlo with Reversible Jump, and returns the probability that each probe is gained or lost. Using these probabilites, recurrent regions (over sets of individuals) of copy number alteration can be found.
Availability: RJaCGH is available as an R package from CRAN repositories (e.g. http://cran.r-project.org/web/packages).
Contact: rueda.om@gmail.com; rueda.om@gmail.com
Dkk‐3 expression in the tumor endothelium: A novel prognostic marker of pancreatic adenocarcinomas
Authors: Fong Dominic , Hermann Martin , Untergasser Gerold , Pirkebner Daniela , Draxl Anna , Heitz Martin , Moser Patrizia , Margreiter Raimund , Hengster Paul , Amberger Albert 
Published: May 2009

Dkk‐3 is proposed to be a new specific marker for tumor endothelial cells. Here we analyzed the clinical relevance of Dkk‐3 expression in pancreas adenocarcinomas and determined its role on endothelial cell growth in vitro. Microvessel density in tumor samples was immunohistochemically determined using Dkk‐3 and CD31 as endothelial cell markers, respectively. Based on the median microvessel density as a cut‐off point, patients were categorized into high and low microvessel density groups and a correlation with survival and clinical parameters was assessed. Moreover, the role of Dkk‐3 expression on chemosensitivity of endothelial cells was analyzed. In contrast to CD31 staining, Dkk‐3‐positive vessels were found only in tumor tissue and Dkk‐3 microvessel density significantly correlated negative with tumor grading. In survival analysis the median survival time was 7 months for patients with Dkk‐3 low, and 15 months for Dkk‐3 high microvessel density (P = 0.0013). Subset analysis of patients receiving gemcitabine therapy showed that overall survival was significantly decreased in Dkk‐3 low tumors than in high tumors (P = 0.009). In Cox regression Dkk‐3 emerged as a significant independent parameter (P = 0.024). Dkk‐3 overexpression in endothelial cells resulted in significantly enhanced growth inhibition after 5‐fluorouracil or gemcitabine treatment compared to control endothelial cells and cancer cell lines. Dkk‐3 low microvessel density was associated with tumor progression and worse clinical outcome. Overexpression of Dkk‐3 enhanced endothelial cell growth inhibition to chemotherapeutic drugs. Therefore, we suggest that Dkk‐3 high microvessel density may help to select patients who may benefit from chemotherapy. (Cancer Sci 2009)
Bone marrow cells from patients with Shwachman‐Diamond syndrome abnormally express genes involved in ribosome biogenesis and RNA processing
Authors: Rujkijyanont Piya , Adams Sally‐Lin , Beyene Joseph , Dror Yigal 
Published: May 2009

SummaryShwachman‐Diamond Syndrome (SDS) is a multi‐system genetic disorder with bone marrow failure. SBDS, the gene associated with SDS, has been postulated to play a role in ribosome biogenesis and RNA processing, but its functions are still unknown. To study whether these pathways are interrupted when Sbds protein is lost, we studied the expression of related genes in patient SBDS−/− cells by an oligonucleotide microarray. We first analysed ribosomal protein (RP) genes, which are normally co‐regulated. In SDS, 27 of the 85 RP genes were downregulated. Among the downregulated RP genes, seven are known to be associated with the inhibition of apoptosis. RPS27L, which mediates p53‐dependent induction of apoptosis, was the only upregulated RP gene. Interestingly, several genes involved in RP mRNA transcription were downregulated without affecting the expression of genes involved in mRNA degradation, suggesting that the downregulation of the RP gene expression might be at the transcriptional level. Importantly we also found dysregulation of multiple genes involved in rRNA transcription and pre‐rRNA processing. We conclude that SDS marrow cells exhibit major dysregulation of RP, RNA processing and RNA transcription genes.
Concurrent occurrence of medullary thyroid carcinoma and papillary thyroid carcinoma in the same thyroid should be considered as coincidental
Authors: Kim Won Gu , Gong Gyungyub , Kim Eui Young , Kim Tae Yong , Hong Suck Joon , Kim Won Bae , Shong Young Kee 
Published: May 2009

SummaryObjectives  The simultaneous occurrence of medullary thyroid carcinoma (MTC) and papillary thyroid carcinoma (PTC) in the same thyroid gland is documented. In this study, we evaluated the prevalence and characteristics of patients with concurrent MTC and PTC.Design  Retrospective analysis of patients with MTC in a single centre and review of the literature.Patients and measurements  Patients with MTC who underwent initial surgical treatment between 1996 and 2006 at Asan Medical Centre, Seoul, Korea were enrolled. We additionally reviewed the medical records of patients who initially underwent surgery for Graves’ disease (GD) or follicular thyroid carcinoma (FTC) during the same period. The concurrent occurrence rate of PTC in MTC patients was compared with that in GD and FTC patients.Results  Ten of 53 (19%) MTC patients displayed the concomitant PTC. In all 10 cases, the MTC and PTC components were separated by normal thyroid tissue, with the maximal diameters of PTC being less than 1·0 cm in the majority of patients. The rates of concurrent PTC in patients with MTC, GD and FTC were 19%, 15% and 19%, respectively, which were not significantly different.Conclusions  Our results suggest that the occurrence of concurrent MTC/PTC is generally a simple reflection of incidental papillary microcarcinoma.
Relationships between structure and function in streams contrasting in temperature
Authors: FRIBERG NIKOLAI , DYBKJÆR JOHN B. , OLAFSSON JON S. , GISLASON GISLI MAR , LARSEN SØREN E. , LAURIDSEN TORBEN L. 
Published: May 2009

Summary1. We studied 10 first‐order Icelandic streams differing in geothermal influence in separate catchments. Summer temperature (August–September) ranged between 6 and 23 °C.2. Macroinvertebrate evenness and species overlap decreased significantly with temperature whereas taxon richness showed no response. In total, 35 macroinvertebrate species were found with Chironomidae the dominant taxonomic group. Macroinvertebrate density increased significantly with temperature. Dominant species in the warm streams wereLymnaea peregraandSimulium vittatum. Algal biomass, macrophyte cover and richness were unrelated to temperature. Densities of trout (Salmo trutta), the only fish species present, reflected habitat conditions and to a lesser degree temperature.3. Density of filter‐feeders increased significantly with temperature whereas scraper density, the other dominant functional feeding group, was unrelated to temperature. Stable isotope analysis revealed a positive relationship between δ15N and temperature across several trophic levels. No pattern was found with regard to δ13C and temperature.4. Leaf litter decomposition in both fine and coarse mesh leaf bags were significantly correlated to temperature. In coarse mesh leaf packs breakdown rates were almost doubled compared with fine mesh, ranging between 0.5 and 1.3 g DW 28 days−1. Nutrient diffusion substrates showed that the streams were primarily nitrogen limited across the temperature gradient while a significant additional effect of phosphorous was found with increasing temperature.5. Structural and functional attributes gave complementary information which all indicated a change with temperature similar to what is found in moderately polluted streams. Our results therefore suggest that lotic ecosystems could be degraded by global warming.
Differences in winter‐hardening between phenotypes of Lolium perenne with contrasting water‐soluble carbohydrate concentrations
Authors: Hanslin H. M. , Höglind M. 
Published: May 2009

AbstractCarbohydrates are essential for the winter‐hardening of temperate grasses, affecting both rate of hardening and level of frost hardiness. The rate and extent of winter‐hardening of contrasting phenotypes of two Lolium perenne cultivars targeted for differences in water‐soluble carbohydrates concentration were quantified under controlled hardening conditions and standardized freeze testing. The phenotype with the lowest water‐soluble carbohydrates concentration had a lower rate of hardening and tolerated less frost than the other phenotypes but the effect of water‐soluble carbohydrate concentrations on the hardening processes levelled off at increasing water‐soluble carbohydrate concentrations, indicating a threshold. Contrasting responses to freezing were found for survival and for potential for tillering and regrowth. Mortality was little affected by the higher test temperatures, while tillering was negatively affected, even at −5°C. Compensatory regrowth of tillers surviving the lower test temperatures partially compensated for the effects of loss of tillers on regrowth. The hardiest phenotypes had a rapid lowering of LT50 during the first 3 d (−1·65°C d−1), acquiring LT50 values at −15°C or below in 10 d. The hypothesis that rate and maximum level of hardening increase with water‐soluble carbohydrates concentrations in stubble is supported by the results.
Influence of herbage species, cultivar and cutting date on fatty acid composition of herbage and lipid metabolism during ensiling
Authors: Van Ranst G. , Fievez V. , Vandewalle M. , De Riek J. , Van Bockstaele E. 
Published: May 2009

AbstractThe fatty acid (FA) concentration of herbage and lipid metabolism in silage, mainly oxidation and lipolysis, of different species (perennial ryegrass, red clover and white clover) and three cultivars of white and red clover at three cutting dates in the growing season (April, July and October) were studied. FA concentration and composition was strongly affected by species and cutting date. Perennial ryegrass had lower concentrations of C16:1, C18:0, C18:1 and C18:2 than red and white clover. Within red and white clover, the effect of cultivar was small. Oxidation of C18:3 during wilting was different between species and cutting date despite similar wilting conditions. Lipolysis in silage was also influenced by cutting date, species and to some extent by cultivar. Furthermore, in some cuts silages of red and white clover displayed a lower lipolysis than silage of perennial ryegrass. On average, over the three cutting dates proportionately 0·903, 0·864 and 0·857 of the membrane lipids in perennial ryegrass, red clover and white clover were hydrolysed during ensiling. In red clover this could be due to the lipid‐protecting properties of polyphenol oxidase (PPO) activity. This was not observed in perennial ryegrass or white clover. Nevertheless, differences in lipolysis in silage between cultivars of red clover were not correlated with PPO activity.
Living on the edge: roads and edge effects on small mammal populations
Authors: Fuentes‐Montemayor Elisa , Cuarón Alfredo D. , Vázquez‐Domínguez Ella , Benítez‐Malvido Julieta , Valenzuela‐Galván David , Andresen Ellen 
Published: May 2009

Abstract

Roads may affect wildlife populations through habitat loss and disturbances, as they create an abrupt linear edge, increasing the proportion of edge exposed to a different habitat. Three types of edge effects have been recognized: abiotic, direct biotic, and indirect biotic.
We explored the direct biotic edge effects of 3‐ to 4‐m wide roads, and also a previously unrecognized type of edge effect: social. We live‐trapped two threatened endemic rodents from Cozumel Island (Oryzomys couesi cozumelae and Reithrodontomys spectabilis) in 16 plots delimited by roads on two sides, to compare edge effects between two adjacent edges (corners), single‐edge and interior forest, on life history and social variables.
No significant edge effects were observed on the life‐history variables, with the exception of differences in body condition between males and females of O. c. cozumelae near edges. Both species showed significant and contrasting effects on their social variables.
O. c. cozumelae was distributed according to its age and sex: the proportion of adults and males was higher in interior than near edges, while juveniles and females were more abundant near edges. More nonreproductive females were present in corners than in single‐edge and interior, while the opposite distribution was observed for nonreproductive males.
The distribution of R. spectabilis was related to its age and reproductive condition, but not to its sex. The proportion of adults was significantly higher in corners, while juveniles were only caught in single‐edge and interior quadrants. The proportion of reproductive individuals was higher in edge than interior quadrants, while reproductive females were only present in edge quadrants.
We found significant differences between the quadrants with the greatest edge exposure in comparison with other quadrants. The social edge effects we identified complement the typology of edge effects recognized in ecological literature. Our study provides insight into the effects that sharp road edges have on biological and social characteristics of small mammal populations, highlighting how such effects vary among species. Our findings have important conservation implications for these threatened species, but are also applicable in a broader context wherever there are abrupt edges caused by linear landscape features.
The effects of thermal biology and refuge availability on the restricted distribution of an alpine lizard
Authors: Monasterio Camila , Salvador Alfredo , Iraeta Pablo , Díaz José A. 
Published: May 2009

AbstractAim  In an effort to disentangle the ecological processes that confine ectotherms to alpine environments, we studied the thermoregulatory and microhabitat selection behaviours of the rock lizard Iberolacerta cyreni, which is endemic to some mountains of central Spain, and of the wall lizard Podarcis muralis, which is a potential competitor of rock lizards.Location  We chose three areas in the Sierra de Guadarrama (central Spain) that differed in their thermal quality [mean deviation of environmental operative temperatures from the lizards’ preferred thermal range (PTR)] and refuge availability: a pine forest (1770 m a.s.l.) in which P. muralis was the only species found, and two mixed shrub and rock sites (1770 and 1900 m a.s.l.) where both species were present.Methods  In the field we collected data on refuge availability, sun exposure, body temperature (Tb) and operative temperature (Te). Thus, we estimated the thermal habitat quality of the areas sampled and the thermoregulation accuracy and effectiveness of both species.Results  The pine forest had the lowest thermal quality and refuge availability. The lower‐elevation shrub site offered the best thermal quality, but refuges were much scarcer than at the higher‐elevation site. Both species thermoregulated accurately, because mean deviations of body temperature (Tb) from PTR were considerably smaller than those of Te. Podarcis muralis had higher Tb values than did I. cyreni, which had similar Tb values at both shrub sites, whereas P. muralis had lower Tb values at higher elevation. Overall, the thermoregulatory effectiveness (extent to which Tb values are closer to the PTR than are Te values) of both species was similar, but whereas I. cyreni thermoregulated more efficiently at higher elevation, the opposite was true for P. muralis. At the lower‐elevation shrub site, I. cyreni remained closer to refuges than did P. muralis.Main conclusions  Our results suggest that the pine forest belt might prevent the expansion of rock lizards towards lower elevations as a result of its low thermal quality and scarcity of refuges, that the thermoregulatory effectiveness of rock lizards in alpine environments depends more on refuge availability than on thermal habitat quality, and that competition with wall lizards is unlikely to explain either the distribution or the thermoregulatory effectiveness of rock lizards.
Cholinergic control of inflammation
Authors: Rosas‐Ballina M. , Tracey K. J. 
Published: May 2009

Abstract.Cytokine production is necessary to protect against pathogens and promote tissue repair, but excessive cytokine release can lead to systemic inflammation, organ failure and death. Inflammatory responses are finely regulated to effectively guard from noxious stimuli. The central nervous system interacts dynamically with the immune system to modulate inflammation through humoral and neural pathways. The effect of glucocorticoids and other humoral mediators on inflammatory responses has been studied extensively in the past decades. In contrast, neural control of inflammation has only been recently described. We summarize autonomic regulation of local and systemic inflammation through the ‘cholinergic anti‐inflammatory pathway’, a mechanism consisting of the vagus nerve and its major neurotransmitter, acetylcholine, a process dependent on the nicotinic acetylcholine receptor α7 subunit. We recapitulate additional sources of acetylcholine and their contribution to the inflammatory response, as well as acetylcholine regulation by acetylcholinesterase as a means to attenuate inflammation. We discuss potential therapeutic applications to treat diseases characterized by acute or chronic inflammation, including autoimmune diseases, and propose future research directions.
Autoimmune associated congenital heart block: integration of clinical and research clues in the management of the maternal / foetal dyad at risk
Authors: Buyon J. P. , Clancy R. M. , Friedman D. M. 
Published: May 2009

Abstract.One of the strongest associations with autoantibodies directed to components of the SSA/Ro‐SSB/La ribonucleoprotein complex is the development of congenital heart block (CHB) in an offspring, an alarming prospect facing 2% of primigravid mothers with these reactivities. This risk is 10‐fold higher in women who have had a previously affected child with CHB. Anti‐Ro/La antibodies are necessary but insufficient to cause disease. In vitro and in vivo experiments suggest that the pathogenesis involves exaggerated apoptosis, macrophage/myfibroblast crosstalk, TGFβ expression and extensive fibrosis in the conducting system and in some cases surrounding myocardium. A disturbing observation is the rapidity of disease progression, with advanced heart block and life‐threatening cardiomyopathy observed <2 weeks from normal sinus rhythm. Once 3rd degree (complete) block is identified, reversal has never been achieved, despite dexamethasone. Current strategies include the evaluation of an early echocardiographic marker of injury, such as a prolonged PR interval and the use of IVIG as a preventative measure for pregnancies of mothers with previously affected children.
Autoantigens in systemic autoimmunity: critical partner in pathogenesis
Authors: Rosen A. , Casciola‐Rosen L. 
Published: May 2009

Abstract.Understanding the mechanisms of human autoimmune rheumatic diseases presents a major challenge, due to marked complexity involving multiple domains, including genetics, environment and kinetics. In spite of this, the immune response in each of these diseases is largely specific, with distinct autoantibodies associated with different disease phenotypes. Defining the basis of such specificity will provide important insights into disease mechanism. Accumulating data suggest an interesting paradigm for antigen selection in autoimmunity, in which target tissue and immune effector pathways form a mutually reinforcing partnership. In this model, distinct autoantibody patterns in autoimmunity may be viewed as the integrated, amplified output of several interacting systems, including: (i) the specific target tissue, (ii) the immune effector pathways that modify antigen structure and cause tissue damage and dysfunction, and (iii) the homeostatic pathways activated in response to damage (e.g. regeneration/differentiation/cytokine effects). As unique antigen expression and structure may occur exclusively under these amplifying circumstances, it is useful to view the molecules targeted as ‘neo‐antigens’, that is, antigens expressed under specific conditions, rather than ubiquitously. This model adds an important new dynamic element to selection of antigen targets in autoimmunity, and suggests that the amplifying loop will only be identified by studying the diseased target tissue in vivo.
Sculpin hybrid zones: natural laboratories for the early stages of speciation
Authors: SWEIGART ANDREA 
Published: May 2009

Firmly rooted as we are in the genomic era, it can seem incredible that as recently as 1974, Lewontin declared, ‘we know virtually nothing about the genetic changes that occur in species formation’. To the contrary, we now know the genetic architecture of phenotypic differences and reproductive isolation between species for many diverse groups of plants, animals, and fungi. In recent years, detailed genetic analyses have produced a small but growing list of genes that cause reproductive isolation, several of which appear to have diverged by natural selection. Yet, a full accounting of the speciation process requires that we understand the reproductive and ecological properties of natural populations as they begin to diverge genetically, as well as the dynamics of newly evolved barriers to gene flow. One promising approach to this problem is the study of natural hybrid zones, where gene exchange between divergent populations can produce recombinant genotypes in situ. In such individuals, genomic variation might be shaped by introgression at universally adaptive or neutral loci, even as regions associated with local adaptation or reproductive isolation remain divergent. In Nolte et al. (2009), the authors take advantage of two independent, recently formed hybrid zones between sculpin species to investigate genome‐wide patterns of reproductive isolation. Using a recently developed genomic clines method, the authors identify marker loci that are associated with isolation, and those that show evidence for adaptive introgression. Remarkably, Nolte et al. (2009) find little similarity between the two hybrid zones in patterns of introgression, a fact that might reflect genetic variation within species or heterogeneous natural selection. In either case, their study system has the potential to provide insight into the early stages of speciation.