bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Habitat Selection of a Top Predator: Considering Growth and Physical Environments in a Spatial Context
Authors: May Cassandra J. , Aday D. Derek , Hale R. Scott , Denlinger Jonathan C. S. , Marschall Elizabeth A. 
Published: February 2012

AbstractMechanisms associated with habitat selection by fishes are often unknown and require both physical habitat and growth environment considerations. We used spatially explicit prey biomass estimates, predator growth rate potential (GRP), bottom slope, predator distance from shore, and substrate data to predict habitat use of the saugeye (walleye Sander vitreus × sauger S. canadensis), a popular sport fish that is stocked throughout the central United States. We used telemetry to determine saugeye locations, acoustics to estimate prey biomass and distributions, and a bioenergetics model to aid in calculation of GRP. Akaike's information criterion was used to determine which habitat variables were most important in explaining saugeye location. Models that included both physical habitat and either GRP or prey density performed better than models that considered only one of these parameter types. The resulting models provided the data to create location suitability maps. In general, saugeyes favored steep slopes over hard substrates in nearshore areas with high biomass of gizzard shad Dorosoma cepedianum or high GRP. This comprehensive analysis suggests that the consideration of both spatial habitat suitability and temporal prey availability may improve fisheries management and conservation through a quantitative appreciation of available resources.
Gencrypt: one-way cryptographic hashes to detect overlapping individuals across samples
Authors: Turchin Michael C. , Hirschhorn Joel N. 
Published: February 2012

Abstract
Summary: Meta-analysis across genome-wide association studies is a common approach for discovering genetic associations. However, in some meta-analysis efforts, individual-level data cannot be broadly shared by study investigators due to privacy and Institutional Review Board concerns. In such cases, researchers cannot confirm that each study represents a unique group of people, leading to potentially inflated test statistics and false positives. To resolve this problem, we created a software tool, Gencrypt, which utilizes a security protocol known as one-way cryptographic hashes to allow overlapping participants to be identified without sharing individual-level data.
Availability: Gencrypt is freely available under the GNU general public license v3 at http://www.broadinstitute.org/software/gencrypt/
Contact: joelh@broadinstitute.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Predicting kinase substrates using conservation of local motif density
Authors: Lai Andy C. W. , Nguyen Ba Alex N. , Moses Alan M. 
Published: February 2012

Abstract
Motivation: Protein kinases represent critical links in cell signaling. A central problem in computational biology is to systematically identify their substrates.
Results: This study introduces a new method to predict kinase substrates by extracting evolutionary information from multiple sequence alignments in a manner that is tolerant to degenerate motif positioning. Given a known consensus, the new method (ConDens) compares the observed density of matches to a null model of evolution and does not require labeled training data. We confirmed that ConDens has improved performance compared with several existing methods in the field. Further, we show that it is generalizable and can predict interesting substrates for several important eukaryotic kinases where training data is not available.
Availability and implementation: ConDens can be found at http://www.moseslab.csb.utoronto.ca/andyl/.
Contact: alan.moses@utoronto.ca
Supplementary Information: Supplementary data are available at Bioinformatics online.
pymzML—Python module for high-throughput bioinformatics on mass spectrometry data
Authors: Bald Till , Barth Johannes , Niehues Anna , Specht Michael , Hippler Michael , Fufezan Christian 
Published: February 2012

Abstract
Summary: pymzML is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data, the standard data format in MS and (iii) a set of functions to compare or handle spectra.
Availability and implementation: pymzML requires Python2.6.5+ and is fully compatible with Python3. The module is freely available on http://pymzml.github.com or pypi, is published under LGPL license and requires no additional modules to be installed.
Contact: christian@fufezan.net
Use of procalcitonin for the diagnosis of pneumonia in patients presenting with a chief complaint of dyspnoea: results from the BACH (Biomarkers in Acute Heart Failure) trial
Authors: Maisel Alan , Neath Sean‐Xavier , Landsberg Judd , Mueller Christian , Nowak Richard M. , Peacock W. Frank , Ponikowski Piotr , Möckel Martin , Hogan Christopher , Wu Alan H.B. , Richards Mark , Clopton Paul , Filippatos Gerasimos S. , Di Somma Salvatore , Anand Inder , Ng Leong L. , Daniels Lori B. , Christenson Robert H. , Potocki Mihael , McCord James , Terracciano Garret , Hartmann Oliver , Bergmann Andreas , Morgenthaler Nils G. , Anker Stefan D. 
Published: February 2012

AimsBiomarkers have proven their ability in the evaluation of cardiopulmonary diseases. We investigated the utility of concentrations of the biomarker procalcitonin (PCT) alone and with clinical variables for the diagnosis of pneumonia in patients presenting to emergency departments (EDs) with a chief complaint of shortness of breath.Methods and resultsThe BACH trial was a prospective, international, study of 1641 patients presenting to EDs with dyspnoea. Blood samples were analysed for PCT and other biomarkers. Relevant clinical data were also captured. Patient outcomes were assessed at 90 days. The diagnosis of pneumonia was made using strictly validated guidelines. A model using PCT was more accurate [area under the curve (AUC) 72.3%] than any other individual clinical variable for the diagnosis of pneumonia in all patients, in those with obstructive lung disease, and in those with acute heart failure (AHF). Combining physician estimates of the probability of pneumonia with PCT values increased the accuracy to >86% for the diagnosis of pneumonia in all patients. Patients with a diagnosis of AHF and an elevated PCT concentration (>0.21 ng/mL) had a worse outcome if not treated with antibiotics (P = 0.046), while patients with low PCT values (<0.05 ng/mL) had a better outcome if they did not receive antibiotic therapy (P = 0.049).ConclusionProcalcitonin may aid in the diagnosis of pneumonia, particularly in cases with high diagnostic uncertainty. Importantly, PCT may aid in the decision to administer antibiotic therapy to patients presenting with AHF in which clinical uncertainty exists regarding a superimposed bacterial infection.Trial registration: NCT00537628
Close link between development and function of gamma−delta T cells
Authors: Shibata Kensuke 
Published: February 2012

ABSTRACTMurine γδ T cells develop as the first T‐cell lineage within the fetal thymus and disproportionately localize in mucosal tissues such as lung, skin, uterus, and intestine of adult mice. These unique developmental features and distribution patterns of γδ T cells enable rapid functioning against various insults from pathogens. γδ T cells are also able to respond to local inflammation and consequently regulate the pathogenesis of autoimmune disorders and development of tumors in mice and humans. Hence, it is clinically important to understand the mechanisms that regulate γδ T cell functions. Recent evidence has shown that generations of effector γδ T cell subsets producing IFN‐γ, IL‐4, and IL‐17 are programmed in the murine thymus before their migration to peripheral tissues. This review outlines our current understanding of the development and function of γδ T cells as they influence both innate and acquired immunity.
Bronchial and alveolar nitric oxide in exercise‐induced bronchoconstriction in asthmatic children
Authors: Chinellato I. , Piazza M. , Peroni D. , Sandri M. , Chiorazzo F. , Boner A. L. , Piacentini G. 
Published: February 2012

SummaryBackgroundEpidemiological studies have shown an association between the severity of exercise‐induced bronchoconstriction (EIB) and fractional exhaled nitric oxide at the flow of 50 mL/s (FeNO50). However, no study has assessed the correlation between alveolar production (Calv) and bronchial flux (JNO) of nitric oxide (NO) and EIB in asthmatic children.ObjectiveTo identify the relationship between severity of EIB and bronchial or alveolar nitric oxide.MethodsOur group included 36 allergic children with intermittent asthma. The EIB was determined by a standard exercise challenge and the severity was expressed as the maximum change in percentage from the baseline value of lung function (ΔFEV1%, ΔFEF25–75%) after exercising. A chemiluminescence analyser at multiple flows was used to calculate FeNO50, JNO and Calv, which reflect large airways, JNO and alveolar concentration of NO respectively.ResultsSixteen (44.4%) children presented a ∆FEV1 ≥ 10%, eight (22.2%) had ∆FEV1 ≥ 15% and nine (25%) children had a ∆FEF25–75 ≥ 26%. A significant correlation was observed between severity of EIB and FeNO50, JNO and Calv. EIB was significantly more severe in children sensitive to indoor allergens compared with outdoor allergens only (P = 0.014); those children showed also higher levels of Calv (P = 0.003) and of JNO (P = 0.044).Conclusions and Clinical RelevanceOur results suggest that inflammation is present in the central and peripheral airways and that it is associated with the severity of EIB.Clinicaltrials.gov NCT00952835.
Altered frequency and phenotype of CD4+ forkhead box protein 3+ T cells and its association with autoantibody production in human immunodeficiency virus-infected paediatric patients
Authors: Argüello R J , Balbaryski J , Barboni G , Candi M , Gaddi E , Laucella S 
Published: February 2012

Summary
The association between immune dysfunction and the development of autoimmune pathology in patients with human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) is not clear. The frequency and phenotype of regulatory T cells, as well as the presence of autoantibodies, were evaluated in a paediatric cohort of HIV-infected patients without clinical evidence of autoimmune disease. Lower absolute counts but higher percentages of total CD4+ forkhead box protein 3 (FoxP3)+ T cells were recorded in children with severe immunosuppression than in those without evidence of immunosuppression. The frequencies of classical CD4+CD25+FoxP3+ regulatory T cells were not altered, whereas CD4+FoxP3+CD25- T cells were found increased significantly in patients with severe immunosuppression. Like classical regulatory T cells, CD4+FoxP3+CD25- T cells display higher cytotoxic T-lymphocyte antigen 4 (CTLA-4) but lower CD127 expression compared with CD4+FoxP3–CD25+ T cells. An improvement in CD4+ T cell counts, along with a decrease in viral load, was associated with a decrease in CD4+FoxP3+CD25- T cells. The majority of the patients with severe immunosuppression were positive for at least one out of seven autoantibodies tested and displayed hypergammaglobulinaemia. Conversely, HIV-infected children without evidence of immunosuppression had lower levels of autoantibodies and total immunoglobulins. A decline in CD4+FoxP3+ T cell numbers or a variation in their phenotype may induce a raise in antigen exposure with polyclonal B cell activation, probably contributing to the generation of autoantibodies in the absence of clinical autoimmune disease.
Effect of nitrogen fertilization on net nitrogen mineralization in a grassland soil, northern China
Authors: Zhang X. , Wang Q. , Gilliam F. S. , Bai W. , Han X. , Li L. 
Published: February 2012

AbstractNitrogen (N) applications can have a significant effect on soil N availability. The effect of 3 years of N fertilization on soil net N mineralization during the growing season (May–September) was studied in 2005 and 2006 in grassland of northern China. The experimental design was a randomized complete block with four replications of five rates of N addition as urea (0, 2, 4, 8 and 16 g N m−2 year−1). Results indicated that net N mineralization rate varied seasonally and between years, ranging from −0.04 to 0.52 μg g−1d−1in 2005 and from −0.09 to 0.39 μg g−1d−1in 2006. Mean N mineralization and nitrification rates were highest in July, in 2005 and 2006, whereas highest ammonification rates occurred in September. Rainfall was significantly correlated with net nitrification. In comparison with the untreated control, N mineralization increased sharply when N fertilization increased from 2 to 8 g N m−2 year−1. Mobile soil NO3−accumulated late in the growing season for the 16 g N m−2 year−1treatment, suggesting the potential for NO3and associated cation leaching. These results suggest that N fertilization of 8 g N m−2 year−1(80 kg N ha−1) is suitable for the management of grassland ecosystems of Inner Mongolia.
Are there trade‐offs between pre‐ and post‐fledging survival in black brent geese?
Authors: Nicolai Christopher A. , Sedinger James S. 
Published: February 2012

Summary1. The growth period is an important determinant of fitness later in life through its effects on first‐year survival and future reproduction. Choices by adult females about where to rear their offspring strongly affect growth rates and offspring fitness in geese.2. Individual female black brent (Branta bernicla nigricans) tend to raise their broods in the same areas each year, and these areas are consistently ranked with respect to growth rates of goslings. Therefore, some females consistently rear their broods on areas resulting in lower post‐fledging fitness.3. We explore the potential that growth rates of offspring (and associated fitness consequences) are traded off against other vital rates influencing fitness of either adult females or goslings. Growth of goslings primarily influences fitness after fledging, so one hypothesis is that survival before fledging, which is influenced by predation, is traded off against growth rates and post‐fledging survival.4. We estimated pre‐fledging and post‐fledging survival for goslings reared on areas used by broods from the Tutakoke River black brent colony. We examined recaptures, recoveries by hunters and resightings of brent marked as goslings with webtags and standard leg rings. These data were analyzed using capture–mark–recapture models in program mark to derive separate estimates of pre‐ and post‐fledging survival for 18 cohorts (1987–2004) of black brent goslings across seven brood rearing areas (BRAs).5. Estimates of pre‐fledging survival probability varied from 0·00 ± 0·00 (mean ± 95% confidence interval) to 0·92 ± 0·1; and estimates of post‐fledging survival probability varied from 0·00 ± 0·00 to 1·00 ± 0·08. Substantial variation existed both among BRAs and years but post‐fledging survival declined substantially during the study.6. Pre‐ and post‐fledging survival were positively correlated, exhibiting a quadratic relationship (ßpost‐fledging survival = 1·00 (±0·47)x−0·83 (±0·480)x2, where x = pre‐fledging survival). Therefore, we did not find a trade‐off between pre‐ and post‐fledging survival in black brent goslings across BRAs, suggesting that factors other than foraging conditions and predation on goslings must influence selection of BRAs.
Global habitat suitability of cold‐water octocorals
Authors: Yesson Chris , Taylor Michelle L. , Tittensor Derek P. , Davies Andrew J. , Guinotte John , Baco Amy , Black Julie , Hall‐Spencer Jason M. , Rogers Alex D. 
Published: February 2012

AbstractAim  Three‐quarters of Octocorallia species are found in deep waters. These cold‐water octocoral colonies can form a major constituent of structurally complex habitats. The global distribution and the habitat requirements of deep‐sea octocorals are poorly understood given the expense and difficulties of sampling at depth. Habitat suitability models are useful tools to extrapolate distributions and provide an understanding of ecological requirements. Here, we present global habitat suitability models and distribution maps for seven suborders of Octocorallia: Alcyoniina, Calcaxonia, Holaxonia, Scleraxonia, Sessiliflorae, Stolonifera and Subselliflorae.Location  Global.Methods  We use maximum entropy modelling to predict octocoral distribution using a database of 12,508 geolocated octocoral specimens and 32 environmental grids resampled to 30 arc‐second (approximately 1 km2) resolution. Additionally, a meta‐analysis determined habitat preferences and niche overlap between the different suborders of octocorals.Results  Suborder Sessiliflorae had the widest potential habitat range, but all records for all suborders implied a habitat preference for continental shelves and margins, particularly the North and West Atlantic and Western Pacific Rim. Temperature, salinity, broad scale slope, productivity, oxygen and calcite saturation state were identified as important factors for determining habitat suitability. Less than 3% of octocoral records were found in waters undersaturated for calcite, but this result is affected by a shallow‐water sampling bias.Main conclusions  The logistical difficulties, expense and vast areas associated with deep‐sea sampling leads to a gap in the knowledge of faunal distributions that is difficult to fill without predictive modelling. Global distribution estimates are presented, highlighting many suitable areas which have yet to be studied. We suggest that approximately 17% of oceans are suitable for at least one suborder but 3.5% may be suitable for all seven. This is the first global habitat suitability modelling study on the distribution of octocorals and forms a useful resource for researchers, managers and conservationists.
A long‐term follow‐up of allergic diseases in Iceland
Authors: Finnbogadóttir Anna Freyja , Árdal Björn , Eiríksson Herbert , Hrafnkelsson Birgir , Valdimarsson Helgi , Lúðvíksson Björn Rúnar , Haraldsson Ásgeir 
Published: February 2012

To cite this article: Finnbogadóttir AF, Árdal B, Eiríksson H, Hrafnkelsson B, Valdimarsson H, Lúðvíksson BRúnar, Haraldsson Á. A long‐term follow‐up of allergic diseases in Iceland. Pediatr Allergy Immunol 2012 Doi: 10.1111/j.1399‐3038.2011.01234.xAbstractIntroduction:  Allergic disorders are an increasing health problem in many countries, in particular among children. We have evaluated the prevalence and manifestations of allergy in a cohort of young Icelanders for more than two decades. Variations in the epidemiology and clinical expression of allergy in different communities may help to identify etiological factors contributing to these disorders.Methods:  A cohort of 179 children has been monitored for allergic manifestations for two decades, at the ages of two, four, eight, and 15 years, and most recently at the age of 21 years involving 120 of the participants.Results:  Cumulative prevalences of 40%, 45%, and 29% have been observed, respectively, for rhinoconjunctivitis, eczema, and asthma during the study period. None had developed rhinoconjunctivitis at the age of about 2 years, but the point prevalence gradually increased to 33% at the age of 21 years. Conversely, the prevalence of eczema was 31% at the age of 2 years, but gradually declined to 8% at the age of 21 years. The prevalence of asthma peaked at 28% at the age of 4 years, but declined thereafter and has remained stable at about 13% from the age of eight to 21 years.Discussion:  The prevalence of allergic diseases is high in Iceland among children and young individuals. Asthma and atopic eczema are very common in childhood, but decreases with age while the prevalence of rhinoconjunctivitis increases markedly. The very high and increasing prevalence of rhinoconjunctivitis among 15‐ to 21‐year‐old individuals is noteworthy.
Targeted oxygen therapy in special care nurseries: Is uniformity a good thing?
Authors: Buckmaster Adam , Arnolda Gaston , Wright Ian , Foster Jann 
Published: February 2012

Aim:  There is wide variation in the commencement of inspired oxygen (FiO2) and the oxygen saturation (SpO2) targets set in special care nurseries (SCNs). Evidence supports minimising unnecessary oxygen exposure. Does the introduction of a protocol advocating the uniform approach of commencing FiO2 at 30% and targeting SpO2 of 94–96% for infants ≥33 weeks gestation with respiratory distress reduce oxygen exposure?Methods:  A ‘Before After’ study was undertaken in three SCNs. Data were recorded for all infants admitted to the SCNs who required oxygen over a 3‐year period. Infants were analysed in gestational age groups: 33–36 weeks (late preterm) and +37 weeks (term/post‐term).Results:  Of the 19 830 infants born, 868 (4%) were treated with oxygen. The introduction of an oxygen‐targeting protocol resulted in a statistically and clinically significant reduction in the proportion of infants who were treated with any oxygen for 1 h or more, 4 h or more and in the proportion who received >30% FiO2 for 1 h or more (all P≤ 0.01). This reduction was significant for infants of both gestational age groups. The median duration of oxygen for term/post‐term infants was reduced from 12 h pre‐protocol to 10 h post‐protocol (P= 0.01); however, no significant difference was found for the preterm group (reduced from 11 to 8 h, P= 0.07).Conclusion:  Introduction of a uniform oxygen protocol in SCNs for infants ≥33 weeks gestation with respiratory distress reduces the number of infants receiving oxygen and, in term infants, the duration of oxygen exposure.
Nurse preparedness for the non‐communicable disease escalation in Thailand: A cross‐sectional survey of nurses
Authors: Kaufman Nicholas D. , Rajataramya Benjaporn , Tanomsingh Saengchom , Ronis David L. , Potempa Kathleen 
Published: February 2012

AbstractChronic diseases are now the largest cause of mortality in Thailand, and form an increasingly large portion of the healthcare landscape. In the Thai health system, many patients with chronic conditions receive care and disease management services from nurses, yet specialized training in chronic diseases is not currently part of standard nursing degree programs. Given the evolving epidemiology of the Thailand population, we questioned whether practicing nurses remain confident in their knowledge and skills in chronic disease management. We conducted a cross‐sectional, self‐efficacy survey of nurses in eight randomly‐selected provinces in Thailand, receiving 468 responses. Nurse self‐efficacy was analyzed in prominent chronic disease types, including cancer, hypertension, diabetes, heart disease, cerebrovascular diseases, and pulmonary diseases. Factors, such as geographic location, education level, continuing education experience, and hospital size, were found to significantly affect nurse self‐efficacy levels; nurses highly prioritized additional training in heart diseases and cerebrovascular diseases, followed by hypertension, cancer, and diabetes.