bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infections in Children Receiving Extracorporeal Life Support
Authors: Tse-Chang Alena , Midodzi William , Joffe Ari R. , Robinson Joan L. 
Published: January 2011

Objective.To describe risk factors for and the outcome of infections in children receiving extracorporeal life support (ECLS) and to determine the need for removal of foreign bodies with bloodstream infections (BSIs) in children receiving ECLS.Design.Retrospective cohort study.Setting.Tertiary care children's hospital.Patients.Children receiving ECLS from May 1997 through May 2007.Methods.For patients with documented infections, medical records were examined for demographic, clinical, and laboratory details. Patients with and without documented infections were compared with regard to demographic characteristics and ECLS course.Results.One hundred seventeen patients underwent ECLS for a total of 878 days (median, 5.12 days). Thirty-five patients (29.9%) developed 55 infections, including 21 BSIs (38.2%), 20 urinary tract infections (36.4%), 6 ventilator-associated pneumonia episodes (10.9%), 2 viral infections (3.6%), and 6 miscellaneous infections (10.9%). The rates (in cases per 1,000 ECLS-days) were 23.9 for BSI, 22.8 for urinary tract infection, and 6.8 for ventilator-associated pneumonia. There were no significant differences in the demographic characteristics, indications for ECLS, or ECLS course between infected and uninfected patients, except for the median duration of ECLS (10.1 vs 3.8 days; P < .001). One death was attributed to infection. Resolution of BSI occurred without removal of foreign bodies in 18 (85.7%) of 21 children.Conclusions.Longer duration of ECLS was the only identified risk factor for infection. Mortality was not statistically significantly different between infected and uninfected patients. Most BSIs that occurred during ECLS cleared without removal of foreign bodies.
BayesPeak—an R package for analysing ChIP-seq data
Authors: Cairns Jonathan , Spyrou Christiana , Stark Rory , Smith Mike L. , Lynch Andy G. , Tavaré Simon 
Published: January 2011

Abstract
Motivation: Identification of genomic regions of interest in ChIP-seq data, commonly referred to as peak-calling, aims to find the locations of transcription factor binding sites, modified histones or nucleosomes. The BayesPeak algorithm was developed to model the data structure using Bayesian statistical techniques and was shown to be a reliable method, but did not have a full-genome implementation.
Results: In this note we present BayesPeak, an R package for genome-wide peak-calling that provides a flexible implementation of the BayesPeak algorithm and is compatible with downstream BioConductor packages. The BayesPeak package introduces a new method for summarizing posterior probability output, along with methods for handling overfitting and support for parallel processing. We briefly compare the package with other common peak-callers.
Availability: Available as part of BioConductor version 2.6. URL: http://bioconductor.org/packages/release/bioc/html/BayesPeak.html
Contact: jonathan.cairns@cancer.org.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Automated bond order assignment as an optimization problem
Authors: Dehof Anna Katharina , Rurainski Alexander , Bui Quang Bao Anh , Böcker Sebastian , Lenhof Hans-Peter , Hildebrandt Andreas 
Published: January 2011

Abstract
Motivation: Numerous applications in Computational Biology process molecular structures and hence strongly rely not only on correct atomic coordinates but also on correct bond order information. For proteins and nucleic acids, bond orders can be easily deduced but this does not hold for other types of molecules like ligands. For ligands, bond order information is not always provided in molecular databases and thus a variety of approaches tackling this problem have been developed. In this work, we extend an ansatz proposed by Wang et al. that assigns connectivity-based penalty scores and tries to heuristically approximate its optimum. In this work, we present three efficient and exact solvers for the problem replacing the heuristic approximation scheme of the original approach: an A*, an ILP and an fixed-parameter approach (FPT) approach.
Results: We implemented and evaluated the original implementation, our A*, ILP and FPT formulation on the MMFF94 validation suite and the KEGG Drug database. We show the benefit of computing exact solutions of the penalty minimization problem and the additional gain when computing all optimal (or even suboptimal) solutions. We close with a detailed comparison of our methods.
Availability: The A* and ILP solution are integrated into the open-source C++ LGPL library BALL and the molecular visualization and modelling tool BALLView and can be downloaded from our homepage www.ball-project.org. The FPT implementation can be downloaded from http://bio.informatik.uni-jena.de/software/.
Contact: anna.dehof@bioinf.uni-sb.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Isoflurane Activates Intestinal Sphingosine Kinase to Protect against Renal Ischemia–Reperfusion-induced Liver and Intestine Injury
Authors: Kim Minjae , Park Sang Won , Kim Mihwa , D'Agati Vivette D. , Lee H. Thomas 
Published: January 2011

Background
Renal ischemia-reperfusion injury (IRI) is a major cause of acute kidney injury and often leads to multiorgan dysfunction and systemic inflammation. Volatile anesthetics have potent antiinflammatory effects. We aimed to determine whether the representative volatile anesthetic isoflurane protects against acute kidney injury-induced liver and intestinal injury and to determine the mechanisms involved in this protection.

Methods
Mice were anesthetized with pentobarbital and subjected to 30 min of left renal ischemia after right nephrectomy, followed by exposure to 4 h of equianesthetic doses of pentobarbital or isoflurane. Five hours after renal IRI, plasma creatinine and alanine aminotransferase concentrations were measured. Liver and intestine tissues were analyzed for proinflammatory messenger RNA (mRNA) concentrations, histologic features, sphingosine kinase-1 (SK1) immunoblotting, SK1 activity, and sphingosine-1-phosphate concentrations.

Results
Renal IRI with pentobarbital led to severe renal, hepatic, and intestinal injury with focused periportal hepatocyte vacuolization; small-intestinal apoptosis; and proinflammatory mRNA up-regulation. Isoflurane protected against renal IRI and reduced hepatic and intestinal injury via induction of small-intestinal crypt SK1 mRNA, protein and enzyme activity, and increased sphingosine-1-phosphate. We confirmed the importance of SK1 because mice treated with a selective SK inhibitor or mice deficient in the SK1 enzyme were not protected against hepatic and intestinal dysfunction with isoflurane.

Conclusions
Isoflurane protects against multiorgan injury after renal IRI via induction of the SK1/sphingosine-1-phosphate pathway. Our findings may help to unravel the cellular signaling pathways of volatile anesthetic-mediated hepatic and intestinal protection and may lead to new therapeutic applications of volatile anesthetics during the perioperative period.
A spatially explicit approach to trophic interactions and landscape formation: patchiness in small‐scale variability of grazing effects along an intertidal stress gradient
Authors: Díaz Eliecer Rodrigo , McQuaid Christopher David 
Published: January 2011

Summary1. It is well known that grazing contributes to spatial and temporal patterns of algal cover on rocky shores, but this effect has traditionally been studied through grazer exclusion experiments using randomly positioned treatments at particular levels on the shore. Additionally, the effects of grazing on algal composition and biomass are expected to vary across gradients of physical stress and according to grazer size classes.2. We examine two possible sources of spatial variability on rocky shores: (i) across‐shore variability and (ii) size class of grazers. We combined this approach with an across‐shore experiment, with experimental blocks running continuously from low to high shore, to examine the spatial structure of the effect strength of grazing for different size classes of grazers.3. The results indicate that grazing effects vary among zones, habitats and grazer size classes. Micrograzers played a weak role in structuring the algal community and composition. Both macrograzers and mesograzers were important structuring agents on the upper low shore to the mid shore, but only mesograzers were important in tidal pools. Patterns across the shore of grazing effects were dynamic and patchy, acting simultaneously at different scales. The spatial pattern of grazing effects across the shore was also variable in time and was explained by the interactions among physical and biotic factors, often at the longer (10‐m scale) spatial intervals (or lags); mesograzers influenced almost the whole range of lags.4. We conclude, based on cross‐semivariograms, that abiotic factors set variability at large scales, while the effects of biotic factors (in this case grazing) operate simultaneously at scales ranging from small to large.5.Synthesis. Combining zonation and across‐shore experiments indicates that grazing effects do not follow a continuous gradient, but instead have a patchy distribution. This approach provides information about spatial variability that is not available using only the traditional approach, contributing to our understanding of zonation models.
Litter feedbacks, evolutionary change and exotic plant invasion
Authors: Eppinga Maarten B. , Kaproth Matthew A. , Collins Alexandra R. , Molofsky Jane 
Published: January 2011

Summary 1. Understanding the mechanisms driving exotic plant invasions is important for designing successful invader control strategies. Previous studies have highlighted different invasion mechanisms, including alteration of nutrient cycles through plant–soil feedback and evolutionary change toward more competitive genotypes. 2. We explored the possibility of these two mechanisms interactively affecting exotic plant invasion. Using data from recent experiments on the invasion of Phalaris arundinacea (Phalaris) in North American wetlands, we parameterized a classical resource competition model for nutrients and light, and expanded this model by including litter dynamics. We also examined the potential effects of evolutionary changes as observed in another set of recent experiments. 3. Both litter feedbacks and observed evolutionary changes may increase Phalaris’ performance in invasive habitats. These mechanisms may amplify each other and this synergy may accelerate Phalaris invasion in areas where it is already present, leading to a high‐litter state with Phalaris outcompeting other species. In areas with low nutrient supply where Phalaris is not yet present, a combination of litter feedbacks and evolutionary change may induce a critical transition from a low‐litter, native‐species‐dominated state toward a high‐litter, Phalaris‐dominated state. 4. Our model results suggest that the importance of litter feedbacks and evolutionary change could be verified in future empirical studies through non‐additive and nonlinear effects in litter addition experiments, and by increased litter : above‐ground biomass ratios in biogeographical comparisons between plant communities with Phalaris in invasive and native habitats. The latter result may be caused by the accumulation of more recalcitrant litter from invasive genotypes. 5.
Synthesis. Our study illustrates how exotic plant invasions may be exacerbated by the interaction between litter feedbacks and evolutionary change. This interaction may induce a positive feedback in the invasion process, suggesting that even short‐term events, such as a nutrient pulse, may lead to relatively large and rapid ecosystem shifts that could be long‐lasting and difficult to reverse.
The effect of geographic range position on demographic variability in annual plants
Authors: Gerst Katharine L. , Angert Amy L. , Venable D. Lawrence 
Published: January 2011

Summary1. The abundant centre model predicts that species abundance will decline from the centre towards the periphery of the geographic range. Thus, we expect to find decreases from the centre towards the edge in variables related to population dynamics such as population density and reproductive output. However, evidence for this pattern is contradictory, suggesting that geographically peripheral sites may not be ecologically peripheral. Populations may thrive in pockets of suitable habitat at the edge of the range or may be locally adapted to peripheral conditions.2. This study examines how the position of a site within geographic and climatic ranges of 13 species is related to the population dynamics at one common location, The Desert Laboratory at Tumamoc Hill, Tucson, AZ, USA.3. We used data on survival, fecundity, germination fraction and population density from a 25‐year long‐term data set on winter annual plants to determine whether there was a relationship between distance to the centre of the range and population dynamics. Geographic distance was calculated by determining the distance from the Desert Laboratory to the centre of the observed range determined from locality records. Climatic distance was calculated using the niche modelling software,maxent, and subtracting the mean climatic profile for the species range from that of the Desert Laboratory.4. There was no relationship between mean population metrics and distance metrics. We found significant relationships between some geographic distance metrics and variance in fecundity, survival and per‐germinant fecundity, but not germination fraction or population density. We did not find a relationship with any metric of population dynamic variation and climatic distance.5.Synthesis. Our results indicate that geographic distance from the centre of the range of 13 annual plant species more strongly predicts their population dynamics than climatic distance. This study reinforces the importance of examining vital rates and their variation in order to properly capture the effect of position within a range on population dynamics.
Resource synergy in stream periphyton communities
Authors: Hill Walter R. , Roberts Brian J. , Francoeur Steven N. , Fanta Shari E. 
Published: January 2011

Summary 1. Light and nutrients play pivotal roles in determining the growth of autotrophs, yet the potential for synergistic interactions between the two resources in algal communities is poorly understood, especially in stream ecosystems. In this study, light and phosphorus were manipulated in large experimental streams to examine resource colimitation and synergy in stream periphyton. 2. Whole‐stream metabolism was simultaneously limited by light and phosphorus. Increasing the supply of either light or phosphorus resulted in significant increases in primary production and the transformation of the streams from heterotrophy to autotrophy. 3. Resource‐driven changes in periphyton community structure occurred in concert with changes in production. Algal assemblages in highly shaded streams were composed primarily of small diatoms such as Achnanthidium minutissima, whereas larger diatoms such as Melosira varians predominated at higher irradiances. Phosphorus enrichment had relatively little effect on assemblage structure, but it did substantially diminish the abundance of Meridion circulare, a diatom whose mucilaginous colonies were conspicuously abundant in phosphorus‐poor, high‐light streams. Bacterial biomass declined relative to algal biomass with increases in primary productivity, regardless of whether the increases were caused by light or phosphorus. 4. Synergistic effects on primary production appeared to occur because the availability of one resource facilitated the utilization of the other. Light increased the abundance of large diatoms, which are known to convert high concentrations of nutrients into primary production more effectively than smaller taxa. Phosphorus enrichment led to the replacement of Meridion circulare by non‐mucilaginous taxa in phosphorus‐enriched streams, and we hypothesize that this change enabled more efficient use of light in photosynthesis. Higher ratios of chlorophyll a : biomass in phosphorus‐enriched streams may have also led to more efficient photon capture and higher photosynthetic rates. 5.
Synthesis. Our results underscore the potential for resource colimitation, even in habitats where a single resource is as strongly limiting as is light in shaded streams. The capacity of autotrophic communities to respond to more than one limiting resource suggests that prevailing single‐resource models of ecosystem productivity are overly simplistic.
Linking grassland plant diversity to species pools, sorting and plant traits
Authors: Houseman Gregory R. , Gross Katherine L. 
Published: January 2011

Summary1. Variation in species pools can affect plant diversity, but it remains unclear whether the magnitude of the response varies because of resource availability, community invasibility or other environmental factors, and whether colonization along environmental gradients reflects niche‐based species sorting or neutral processes.2. We hypothesized that unimodal diversity–productivity patterns in grasslands are dependent on species pools, with peak richness occurring at intermediate productivity due to species sorting associated with species traits. We used a seed‐addition experiment to test the influence of immigration on plant species richness across multiple grasslands (old fields), each of which encompassed a broad range in productivity. We then tested whether species sorting occurs during colonization, if this varies with site productivity, and whether sorting patterns are associated with species traits 1 and 4 years after seed addition.3. Augmentation of species pools increased species richness across fields with the greatest increase in colonization in all fields at sites with intermediate productivity. The increased diversity following species pool augmentation during colonization (year 1) was associated with seed characteristics, seedling growth rates and allocation, and water use, suggesting that colonization and seedling establishment were the result of species sorting.4. Although there were some changes in trait–environmental relationships between the first and fourth growing season, patterns that were observed in the first year were still apparent in the fourth year, highlighting the persistent importance of species sorting and traits that affect colonization on species distribution and diversity patterns in grasslands.5. Synthesis. Our experimental results suggest that species richness and richness–productivity relationships in successional grasslands are at least partially determined by species sorting and trait–environmental relationships occurring during colonization.
Co‐evolutionary hot and cold spots of selective pressure move in space and time
Authors: Smith D. L. , Ericson L. , Burdon J. J. 
Published: January 2011

Summary1. A long‐term study (19 years) of a host–pathogen metapopulation involving 133–220 separate populations of the wild plantFilipendula ulmariaand its rust pathogenTriphragmium ulmariaeshows marked changes in the occurrence (32–55% demes) and severity of disease and rates of extinction and re‐establishment of individual populations (0.006–0.174 and 0.030–0.195 per annum, respectively) over time.2. Modelling of the spatio‐temporal dynamics of disease demonstrated year‐to‐year changes associated with a range of different environmental features, but also more consistent, longer‐term patterns influenced by a complex suite of factors.3. Both the level of disease and its spatial location varied through time and generated a changing pattern of selective pressure across the metapopulation.4. Synthesis. Our results suggest that co‐evolutionary hot spots and cold spots can be highly dynamic within metapopulations, thereby fuelling the co‐evolutionary process even more than previously suspected.
Spatio‐temporal variations determine plant–microbe competition for inorganic nitrogen in an alpine meadow
Authors: Xu Xingliang , Ouyang Hua , Richter Andreas , Wanek Wolfgang , Cao Guangmin , Kuzyakov Yakov 
Published: January 2011

Summary 1. Plant–microbe competition for available nitrogen (N) has been suggested to be an important mechanism controlling N limitation of plants in a variety of ecosystems. However, spatio‐temporal patterns of competition between plants and microbes for soil N remain unclear. 2. Short‐term 15N tracer experiments were conducted during a growing season (July, August and September) in an alpine meadow on the Tibetan Plateau to unravel spatio‐temporal patterns of plant–microbe competition for NH4+ and NO3−. 3. Alpine plants were poorer competitors than soil microorganisms for inorganic N in July compared with August and September. Occupation of soil volume by roots and root density (high in August and September) played a greater role in plant–microbe competition than air temperature or precipitation (high in July). 4. In topsoils (0–5 cm, highest root density), alpine plants effectively competed with soil microorganisms for N and showed a preference for 15NO3−, while soil microorganisms that preferentially took up 15NH4+ out‐competed plants below 5 cm soil depth (lower root density). Competition between plants and soil microorganisms for inorganic N strongly depended on root density (P < 0.0001, R2 = 0.93, exponential decay model). 5. Synthesis. Plant–microbe competition for inorganic N showed a clear spatio‐temporal pattern in alpine meadows depending on (i) root density and therefore soil depth, (ii) inorganic N form, and (iii) different periods during the growing season. These findings have important implications for our understanding of above‐ground–below‐ground interactions and plant–microbial competition for available N.
Development of Alnus tenuifolia stands on an Alaskan floodplain: patterns of recruitment, disease and succession
Authors: Nossov Dana R. , Hollingsworth Teresa N. , Ruess Roger W. , Kielland Knut 
Published: January 2011

Summary 1. We investigated the population dynamics of the keystone symbiotic N‐fixing species Alnus tenuifolia (thinleaf alder) and the patterns of primary succession on the Tanana River floodplains of interior Alaska, USA. The goals of this study were to characterize (i) the variation in the population structure of thinleaf alder and its influence on ecosystem function; (ii) the role of a fungal disease outbreak in driving the population dynamics of thinleaf alder; (iii) the patterns of landscape‐scale thinleaf alder recruitment; and (iv) the variation in successional pathways across the landscape. 2. Soil N concentrations and pools increased tenfold with thinleaf alder stand age due to the accumulation of N‐rich organic material. Alder stem density varied threefold among early successional stands, and was directly related to soil N. 3. The current outbreak of a fungal disease caused widespread branch dieback and mortality of alder. Young stems were disproportionately susceptible to disease‐induced mortality. Overall disease incidence and mortality of young stems were positively related to alder stem density. 4. Thinleaf alder age structures revealed that landscape‐scale recruitment was pulsed over time. 5. Multiple pathways of primary succession were found using indirect gradient analysis and associated environmental characteristics were described. 6. Synthesis. The population dynamics of thinleaf alder and the inter‐relationship with disease‐driven disturbance can strongly influence soil N accumulation and ecosystem function in primary succession on an active glacial floodplain. The temporal pattern of thinleaf alder recruitment across the landscape appears to reflect the influence of the hydrologic regime on silt bar development and alder dispersal limitation and population dynamics. Differential life history traits explain the predominant successional pathway, but an alternative successional pathway suggests this pattern can be altered by stochastic events, disturbance, environmental variation or other factors.