bluuebunny/crossref_metadata_2025_split huggingface dataset:
Text processing through Web services: calling Whatizit
Authors: Rebholz-Schuhmann Dietrich , Arregui Miguel , Gaudan Sylvain , Kirsch Harald , Jimeno Antonio 
Published: November 2007

Abstract
Motivation: Text-mining (TM) solutions are developing into efficient services to researchers in the biomedical research community. Such solutions have to scale with the growing number and size of resources (e.g. available controlled vocabularies), with the amount of literature to be processed (e.g. about 17 million documents in PubMed) and with the demands of the user community (e.g. different methods for fact extraction). These demands motivated the development of a server-based solution for literature analysis.
Whatizit is a suite of modules that analyse text for contained information, e.g. any scientific publication or Medline abstracts. Special modules identify terms and then link them to the corresponding entries in bioinformatics databases such as UniProtKb/Swiss-Prot data entries and gene ontology concepts. Other modules identify a set of selected annotation types like the set produced by the EBIMed analysis pipeline for proteins. In the case of Medline abstracts, Whatizit offers access to EBI's in-house installation via PMID or term query. For large quantities of the user's own text, the server can be operated in a streaming mode (http://www.ebi.ac.uk/webservices/whatizit).
Contact: rebholz@ebi.ac.uk
Sensitization to tomato peel and pulp extracts in the Mediterranean Coast of Spain: prevalence and co‐sensitization with aeroallergens
Authors: Larramendi C. H. , Ferrer A. , Huertas A. J. , García‐Abujeta J. L. , Andreu C. , Tella R. , Cerdà M. T. , Bartra J. , Lavín J. R. , Pagán J. A. , López‐Matas M. A. , Fernández‐Caldas E. , Carnés J. 
Published: November 2007

SummaryBackground
Tomatoes (Lycopersicon esculentum) are consumed world‐wide. The prevalence of sensitization to tomatoes remains unknown.Objective
To determine the prevalence of skin test reactivity to tomato and to describe the characteristics of tomato‐sensitized subjects.Methods
Individuals attending for the first time during the period of the study to six Allergy centres, located along the Mediterranean coast of Spain, reporting respiratory and/or cutaneous symptoms, were included. All patients were skin prick tested with a battery of inhalant allergens and with peel and pulp of Canary tomato extracts.Results
The study included 1734 individuals (757 males, 977 females; 31.9±17.8 years old). The prevalence of sensitization to tomato was 6.52% (113 patients; 65 males, 48 females; 29.5±13 years old). The peel extract was positive in 110 patients and the pulp extract in 47 patients; three patients were positive exclusively to pulp. Only 1.8% of individuals reported symptoms with tomato; 44% of them had skin test negative to both extracts. Among tomato‐sensitized subjects, 16% reported symptoms with tomato, 97% were sensitized to inhalant aeroallergens, including 84% to pollens (mainly Artemisia vulgaris and Platanus hybrida), with differences between Northern and Southern centres.Conclusions
The prevalence found of skin test sensitivity to tomato is high. Peel extracts detected most of the sensitized subjects. Most of the sensitized subjects were asymptomatic and some patients reported symptoms without skin test sensitivity. Positive subjects were very frequently sensitized to pollens, suggesting allergen cross‐reactivity. Regional differences may exist, possibly related to the pattern of sensitization to cross‐reacting pollens.
Probiotics and oral health effects in children
Authors: TWETMAN SVANTE , STECKSÉN‐BLICKS CHRISTINA 
Published: November 2007

Background.  Probiotics are living micro‐organisms added to food which beneficially affect the host by improving its intestinal microbial balance.Objective.  This paper aims to present a general background on probiotics and its health effects in children, and to examine the evidence for oral colonization and the possible impact on oral health in children and young adults.Methods.  For delivery and general health effects, recent systematic reviews, meta‐analyses, and other relevant papers were used. Concerning oral installation and oral effects, a broad search for publications in English was conducted through February 2007 in PubMed. Studies describing an installation or intervention trial in humans with a controlled design and an oral endpoint measure were considered. Fourteen papers with dental focus were identified, of which two were narrative reviews.Results.  Only one study of dental interest was conducted in children. Four papers dealt with oral installation of probiotic bacteria, and although detectable levels were found in saliva shortly after intake, the studies failed to demonstrate a long‐term installation. Seven papers evaluated the effect of lactobacilli‐ or bifidobacteria‐derived probiotics on the salivary levels of caries‐associated bacteria in placebo‐controlled designs. All but one reported a hampering effect on mutans streptococci and/or yeast. The single study carried out in early childhood reported a significant caries reduction in 3‐ to 4‐year‐old children after 7 months of daily consumption of probiotic milk.Conclusion.  Bacteriotheraphy in the form of probiotic bacteria with an inhibitory effect on oral pathogens is a promising concept, especially in childhood, but this may not necessarily lead to improved oral health. Further placebo controlled trials that assess carefully selected and defined probiotic strains using standardized outcomes are needed before any clinical recommendations can be made.
Using habitat distribution models to evaluate large‐scale landscape priorities for spatially dynamic species
Authors: Early Regan , Anderson Barbara , Thomas Chris D. 
Published: November 2007

Summary

Large‐scale conservation planning requires the identification of priority areas in which species have a high likelihood of long‐term persistence. This typically requires high spatial resolution data on species and their habitat. Such data are rarely available at a large geographical scale, so distribution modelling is often required to identify the locations of priority areas. However, distribution modelling may be difficult when a species is either not recorded, or not present, at many of the locations that are actually suitable for it. This is an inherent problem for species that exhibit metapopulation dynamics.
Rather than basing species distribution models on species locations, we investigated the consequences of predicting the distribution of suitable habitat, and thus inferring species presence/absence. We used habitat surveys to define a vegetation category which is suitable for a threatened species that has spatially dynamic populations (the butterfly Euphydryas aurinia), and used this as the response variable in distribution models. Thus, we developed a practical strategy to obtain high resolution (1 ha) large scale conservation solutions for E. aurinia in Wales, UK.
Habitat‐based distribution models had high discriminatory power. They could generalize over a large spatial extent and on average predicted 86% of the current distribution of E. aurinia in Wales. Models based on species locations had lower discriminatory power and were poorer at generalizing throughout Wales.
Surfaces depicting the connectivity of each grid cell were calculated for the predicted distribution of E. aurinia habitat. Connectivity surfaces provided a distance‐weighted measure of the concentration of habitat in the surrounding landscape, and helped identify areas where the persistence of E. aurinia populations is expected to be highest. These identified successfully known areas of high conservation priority for E. aurinia. These connectivity surfaces allow conservation planning to take into account long‐term spatial population dynamics, which would be impossible without being able to predict the species’ distribution over a large spatial extent.
Synthesis and applications. Where species location data are unsuitable for building high resolution predictive habitat distribution models, habitat data of sufficient quality can be easier to collect. We show that they can perform as well as or better than species data as a response variable. When coupled with a technique to translate distribution model predictions into landscape priority (such as connectivity calculations), we believe this approach will be a powerful tool for large‐scale conservation planning.
Biogeography and evolution of European cave salamanders, Hydromantes (Urodela: Plethodontidae), inferred from mtDNA sequences
Authors: Carranza S. , Romano A. , Arnold E. N. , Sotgiu G. 
Published: November 2007

AbstractAim  To infer the phylogenetic relationships and biogeography of Hydromantes, with special emphasis on the European taxa. In particular, we aimed to test: (1) the monophyly of the European species and current views on their interrelationships; and (2) previously proposed timings of the separation of European and American Hydromantes, and of biogeographically important events within Europe.Location  California and the Western Mediterranean Basin, specifically south‐east France, Italy, and the island of Sardinia.Methods  Partial sequences of mitochondrial genes (cytochrome b and 12S rRNA) were obtained from 45 specimens of Hydromantes, including all European extant species and subspecies, and two species from California. In addition, a fragment of the mitochondrial 16S rRNA gene was amplified for 16 specimens. Data sets were aligned using ClustalX, and well‐supported phylogenetic trees were produced using maximum‐likelihood, Bayesian and maximum‐parsimony methods. Estimates of divergence times were obtained with the program r8s, the molecular clock being calibrated using the opening of the Strait of Gibraltar, the final event in the Messinian Salinity Crisis of 5.3 Ma.Results  Separation between the American and European clades occurred approximately 13.5 Ma, most probably before or after westward dispersal across the Bering Land Bridge. In Europe, divergence started in the late Miocene, when Hydromantes (A.) genei separated from other members of the genus 9 Ma and colonized south‐west Sardinia. Movement between the European mainland and Sardinia, by a member of the subgenus Speleomantes, occurred in the Messinian Salinity Crisis, after the Mediterranean Basin desiccated almost completely 5.96 Ma. Subsequent widespread aridification fragmented the geographical ranges of Hydromantes, which live in cool and humid conditions, resulting in the origin of the six species in the subgenus Speleomantes. In contrast, a second period of diversification, in continental Europe 2–1.3 Ma, was probably caused by very cold interludes during the climatic oscillations that characterized the Pleistocene.Main conclusions  The molecular clock used here indicates that the separation of Californian and European Hydromantes occurred more recently than previously believed, and the same is true of some subsequent phylogenetic divergences within Europe. Estimated dates for these divergence events are consistent with known geophysical and climatic events that could have caused or facilitated them.
A topography‐based model of forest cover at the alpine tree line in the tropical Andes
Authors: Bader Maaike Y. , Ruijten Johan J.A. 
Published: November 2007

AbstractAim  To present a method that assesses the influence of environmental variables, including climate, substrate, topography, and anthropogenic disturbances, on the distribution of Andean forest at the tree line, and to compare this forest distribution between areas.Location  Sangay National Park, on the eastern slopes of the Andes in central Ecuador.Methods  A logistic regression model was built using topographical variables and environmental indices, derived from a digital elevation model, to explain forest cover, derived from a Landsat ETM image, in a zone around the average tree line altitude.Results  The model shows that after altitude, which can explain about 80% of forest cover, wetness has the next strongest effect (areas accumulating water, but also cold air, were devoid of forest, resulting in inverted tree lines), followed by eastness (western slopes had forest to higher altitudes). Application of the model in two nearby areas showed that the real tree line was lower than the predicted tree line in both areas, probably owing mainly to macroclimatic differences in one area, and partly also to human land use in the other. The locations with the largest deviations could be the focus of further research concerning human impacts on tree line vegetation.Main conclusions  The tree line is located at lower altitudes on east‐facing slopes, which may be because high levels of radiation are received by east‐facing slopes in the clear mornings, resulting in the photoinhibition of tree seedlings in the páramo. In spite of the limitations of the quality and resolution of the remote sensing data, the presented method provides indications for important ecological factors at the tree line. The method also allows the detection of differences in tree line position between areas, which may reflect climatic differences or the location of anthropogenic disturbances.
A case study exploring the ethical and policy dimensions of allocating acute care resources to a dying patient
Authors: Cooke Mary , Hurley Ciarán 
Published: November 2007

Aims.  We aimed to identify policy, process and ethical issues related to allocation of National Health Service resources when patients with end‐of‐life illness are referred to acute care services.Background.  Sharing healthcare decisions denotes a different partnership between professionals and patients when patients are empowered to define their needs. Implementation of a transition from professional to patient decision‐making appears to be dependent upon its interpretation by personnel delivering care using the local trust policy. The outcome of this is a reformation of responsibility for budget allocation, choice of acute care provider and selecting services, currently in the realm of primary care; be it the general practitioner, community practitioners, or the patient.Design.  We used a ‘lens’ approach to case study analysis in which the lens is constructed of a model of policy analysis and four principles of biomedical ethics. A patient's decision to decline care proposed by an Accident and Emergency department nurse and the nurse's response to that decision expose a policy that restricts the use of ambulance transport and with that, flexibility in responses to patients’ decisions.Findings.  End‐of‐life care partnership decisions require sensitivity and flexibility from all healthcare practitioners. We found that policy‐based systems currently used to deliver care across the primary care – hospital care border are far from seamless and can lead to foreseeable problems.Conclusions.  Health professionals responsible for the care of a patient at the end of life should consider the holistic outcomes of resource allocation decisions for patients.Relevance to clinical practice.  Government and health professional agenda suggest that patients should be given a greater element of control over their healthcare than has historically been the case. When patients take responsibility for their decisions, healthcare personnel should recognize that this signals a shift in the nature of the professional–patient relationship to one of partnership.
RivR and the small RNA RivX: the missing links between the CovR regulatory cascade and the Mga regulon
Authors: Roberts Samantha A. , Scott June R. 
Published: November 2007

SummaryThe CovR/S two‐component system regulates the transcription of many genes that are crucial for the virulence of Streptococcus pyogenes (group A Streptococcus, GAS). Previously, we demonstrated that one gene repressed directly by CovR is rivR, which encodes a member of the RofA‐like family of transcriptional regulators. In this study, we deleted rivR and its downstream gene rivX in a ΔcovR background. Microarray analysis revealed that the products of the rivRX locus exert positive control over the transcription of members of the Mga regulon. Using mutational analysis, we established that rivX encodes a small regulatory RNA. We found that RivR enhances transcriptional activation by Mga in vivo and in vitro. An M1 ΔcovRΔrivRX strain is attenuated for virulence in a murine model of invasive soft tissue infection and this attenuation is complemented by rivRX expressed from a plasmid, demonstrating the importance of the rivRX locus in pathogenesis. This study provides the first link between the CovR and Mga regulatory networks. By integrating the signals received through these two global regulators, GAS is able to select from its repertoire different combinations of specific virulence factors to express in response to a broad spectrum of environmental conditions.
Regulation of hyphal morphogenesis by cdc42 and rac1 homologues in Aspergillus nidulans
Authors: Virag Aleksandra , Lee Maurice P. , Si Haoyu , Harris Steven D. 
Published: November 2007

SummaryThe ability of filamentous fungi to form hyphae requires the establishment and maintenance of a stable polarity axis. Based on studies in yeasts and animals, the GTPases Cdc42 and Rac1 are presumed to play a central role in organizing the morphogenetic machinery to enable axis formation and stabilization. Here, we report that Cdc42 (ModA) and Rac1 (RacA) share an overlapping function required for polarity establishment in Aspergillus nidulans. Nevertheless, Cdc42 appears to have a more important role in hyphal morphogenesis in that it alone is required for the timely formation of lateral branches. In addition, we provide genetic evidence suggesting that the polarisome components SepA and SpaA function downstream of Cdc42 in a pathway that may regulate microfilament formation. Finally, we show that microtubules become essential for the establishment of hyphal polarity when the function of either Cdc42 or SepA is compromised. Our results are consistent with the action of parallel Cdc42 and microtubule‐based pathways in regulating the formation of a stable axis of hyphal polarity in A. nidulans.
CD44 and CD27 delineate B‐precursor stages with different recombination status and with an uneven distribution in nonmalignant and malignant hematopoiesis
Authors: Vaskova M. , Fronkova E. , Starkova J. , Kalina T. , Mejstrikova E. , Hrusak O. 
Published: November 2007

AbstractThe expression of CD27 and CD44 correlate with the genotype of B‐precursor acute lymphoblastic leukemia (ALL). Based on the expression of these antigens, we identified counterparts of TEL/AML1pos and TEL/AML1neg leukemic cells in nonmalignant bone marrow. Although CD27 is known as a marker of mature memory B cells, we recently showed that CD27 is also expressed by malignant and nonmalignant B precursors. Here, we show that CD27 and CD44 delineate stages of B‐precursor development. Well‐established differentiation markers showed that the developmental sequence starts from undetermined progenitors, expressing CD44. Upon B‐lineage commitment, cells gain CD27 and lose CD44. The CD27posCD44neg (CD27 single positive, 27SP) cells are the earliest stage within CD10posCD19pos B precursors and express RAG‐1 and TDT. These cells correspond to TEL/AML1pos ALL (1/4 pediatric B‐precursor ALL). The development follows to CD27/CD44 double‐positive (27/44DP) stage, 44SP stage and CD27/CD44 double‐negative (27/44DN) stage. Before exit to periphery, CD44 is reexpressed. The 27/44DP cells are mostly large and profoundly suppress RAG‐1. Despite their presumably high proliferation potential, 27/44DP cells rarely dominate in leukemia. At 44SP stage, which corresponds to TEL/AML1neg leukemias, RAG‐1 is reexpressed and Ig light chain gene starts to be rearranged.
Topical use of platelet‐rich plasma to influence bone volume in maxillary augmentation: a prospective randomized trial
Authors: Schaaf H. , Streckbein P. , Lendeckel S. , Heidinger K. , Görtz B. , Bein G. , Boedeker R.‐H. , Schlegel K. A. , Howaldt H.‐P. 
Published: November 2007

Background and Objectives  The atrophic posterior maxilla often requires restoration of the alveolar ridge due to a lack of bone quantity and quality before dental implant placement. The aim of this study was to verify the hypothesis that platelet‐rich plasma (PRP) has an influence on bone density in the maxilla after sinus floor elevation in combination with autologous cancellous bone from the iliac crest. Therefore, a randomized, prospective, controlled trial was set up in two centres.Study Design and Methods  Fifty‐three patients who underwent osteoplastic bone grafting for sinus floor elevation were included. The intervention group was treated with defined concentrations of PRP in addition to transplanted bone. Bone biopsy was performed 4 months after augmentation. Bone volume was then measured using the histomorphometric parameter bone volume.Results  The histomorphometric evaluation of the biopsies did not indicate superiority of any of the treatments in terms of bone volume.Conclusion  Topical use of PRP did not improve maxillary bone volume either clinically relevant or statistically significant compared to that in conventionally treated patients. The use of PRP to support bone regeneration cannot be recommended as a standard method for maxillary augmentation.
Inheritance of Blast Resistance and Associated Microsatellite Markers in Rice Cultivar ‘Laxmi’
Authors: Sharma R. C. , Shrestha S. M. , Pandey M. P. 
Published: November 2007

AbstractLeaf blast, caused by Magnaporthe oryzae is a major disease of rice (Oryza sativa L.) in many rice‐growing environments. Rice breeders continuously seek new sources of resistance for improving resistance of commercial cultivars. This study was undertaken to determine the inheritance of blast resistance in the rice cultivar ‘Laxmi’. Both parents, and their F1, F2, backcross, F3 and F4 progeny were studied to determine the inheritance of blast resistance in a cross between resistant (R) ‘Laxmi’ and susceptible (S) ‘Mahsuri’ cultivars. Ten homozygous resistant and 10 homozygous susceptible F5 progeny based on their blast reaction in F3 from the above cross were subjected to microsatellite marker analysis to determine the linkage between resistance and marker. The F1 plants were blast‐resistant. The test cross progeny segregated in a ratio of 1R:1S. The F2 population segregated into 3R:1S ratio. The F3 and F4 progeny showed a segregation ratio of 1R:2Sg (segregating):1S. RM25 and RM310 markers showed association with resistant and susceptible progeny. We conclude that blast resistance in Laxmi is governed by a single dominant gene located on chromosome 8 of rice, which is linked to RM25 and RM310 microsatellite markers. This source of blast resistance could be useful in the Himalayan and other rice‐growing environments. This information could be used in marker‐assisted selection for blast resistance in rice crosses involving Laxmi.