bluuebunny/crossref_metadata_2025_split huggingface dataset:
PTEN loss is a context‐dependent outcome determinant in obese and non‐obese endometrioid endometrial cancer patients
Authors: Westin Shannon N. , Ju Zhenlin , Broaddus Russell R. , Krakstad Camilla , Li Jane , Pal Navdeep , Lu Karen H. , Coleman Robert L. , Hennessy Bryan T. , Klempner Samuel J. , Werner Henrica M.J. , Salvesen Helga B. , Cantley Lewis C. , Mills Gordon B. , Myers Andrea P. 
Published: May 2015

Endometrial cancer incidence is increasing, due in part to a strong association with obesity. Mutations in the phosphatidylinositol 3‐kinase (PI3K) pathway, the central relay pathway of insulin signals, occur in the majority of endometrioid adenocarcinomas, the most common form of endometrial cancer. We sought to determine the impact of PI3K pathway alterations on progression free survival in a cohort of endometrioid endometrial cancers. Prognostic utility of PIK3CA, PIK3R1, and PTEN mutations, as well as PTEN protein loss by immunohistochemistry, was explored in the context of patient body mass index. Reverse‐phase protein arrays were utilized to assess protein expression based on PTEN status. Among 187 endometrioid endometrial cancers, there were no statistically significant associations between PFS and PIK3CA, PIK3R1, PTEN mutation or loss. When stratified by body mass index, PTEN loss was associated with improved progression free survival (P < 0.006) in obese (body mass index ≥ 30) patients. PTEN loss resulted in distinct protein changes: Canonical PI3K pathway activation was observed only in the non‐obese population while decreased expression of β‐CATENIN and phosphorylated FOXO3A was observed in obese patients. These data suggest the impact of PTEN loss on tumor biology and clinical outcomes must be interpreted in the context of body mass index, and provide a potential explanation for discrepant reports on the effect of PTEN status and obesity on prognosis in endometrial cancer. This reveals a clinically important interaction between metabolic state and tumor genetics that may unveil the biologic underpinning of obesity‐related cancers and impact ongoing clinical trials with PI3K pathway inhibitors.
Saving a species threatened by trade: a network study of Bali starlingLeucopsar rothschildiconservation
Authors: Jepson Paul R. 
Published: May 2015

AbstractSaving species from extinction is a central tenet of conservation, yet success in this endeavour remains unpredictable and elusive, especially where wildlife trade is involved. Influential conservation policy actors operating internationally advocate strong regulatory and enforcement approaches to governance of wildlife trade. However, a broad body of evidence suggests that in some situations positive incentives for sustainable use may achieve better conservation outcomes. This analysis of efforts over 3 decades to avoid the extinction of the Bali starlingLeucopsar rothschildidraws on network perspectives from environmental governance and geography, and shows how an international project adopting traditional enforcement approaches generated a ‘prestige of ownership’ dynamic among local elites. This placed trade in Bali starlings above the enforcement competencies of the relevant government authority, leading to the demise of the species. Subsequently, two separate Indonesian initiatives created spaces of regulatory flexibility and embraced traits of the starling's phenotype to construct identities for the species suited to the local context. This enrolled a wider range of stakeholders in the conservation of the species, including bird-keeping elites, and led to significant successes in restoring captive and free-flying populations. This case study highlights the potential of conservation networks that involve non-establishment personnel and, while recognizing the appeal of generic enforcement approaches to politicians, funders and the urban public, it adds to an increasing body of evidence that suggests top-down prescriptive conservation frameworks may undermine the ability of situated conservationists to develop interventions appropriate to their political and cultural realities.
Psychotic experiences and PTSD: exploring associations in a population survey
Authors: Alsawy S. , Wood L. , Taylor P. J. , Morrison A. P. 
Published: May 2015

BackgroundExtensive evidence has shown that experiencing a traumatic event and post-traumatic stress disorder (PTSD) are associated with experiences of psychosis. However, less is known about specific PTSD symptoms and their relationship with psychotic experiences. This study aimed to examine the relationship between symptoms of PTSD with paranoia and auditory hallucinations in a large-scale sample.MethodThe Adult Psychiatric Morbidity Survey (APMS) was utilized to examine the prevalence of lifetime trauma, symptoms of PTSD, and experiences of paranoia and auditory hallucinations (n= 7403).ResultsThere were significant bivariate associations between symptoms of PTSD and psychotic experiences. Multiple logistic regression analyses indicated that reliving and arousal symptoms were significant predictors for paranoia while reliving, but not arousal symptoms, also significantly predicted auditory hallucinations. A dose-response relationship was found, the greater the number of PTSD symptoms, the greater the odds were of experiencing both paranoia and hallucinations.ConclusionsThese findings illustrate that symptoms of PTSD are associated with increased odds of experiencing auditory hallucinations and paranoia. Overlaps appear to be present between the symptoms of PTSD and psychotic experiences. Increasing awareness of this association may advance work in clinical practice.
The up-scaling of ecosystem functions in a heterogeneous world
Authors: Lohrer Andrew M. , Thrush Simon F. , Hewitt Judi E. , Kraan Casper 
Published: May 2015

AbstractEarth is in the midst of a biodiversity crisis that is impacting the functioning of ecosystems and the delivery of valued goods and services. However, the implications of large scale species losses are often inferred from small scale ecosystem functioning experiments with little knowledge of how the dominant drivers of functioning shift across scales. Here, by integrating observational and manipulative experimental field data, we reveal scale-dependent influences on primary productivity in shallow marine habitats, thus demonstrating the scalability of complex ecological relationships contributing to coastal marine ecosystem functioning. Positive effects of key consumers (burrowing urchins, Echinocardium cordatum) on seafloor net primary productivity (NPP) elucidated by short-term, single-site experiments persisted across multiple sites and years. Additional experimentation illustrated how these effects amplified over time, resulting in greater primary producer biomass (sediment chlorophyll a content) in the longer term, depending on climatic context and habitat factors affecting the strengths of mutually reinforcing feedbacks. The remarkable coherence of results from small and large scales is evidence of real-world ecosystem function scalability and ecological self-organisation. This discovery provides greater insights into the range of responses to broad-scale anthropogenic stressors in naturally heterogeneous environmental settings.
SpeeDB: fast structural protein searches
Authors: Robillard David E. , Mpangase Phelelani T. , Hazelhurst Scott , Dehne Frank 
Published: May 2015

Abstract
Motivation: Interactions between amino acids are important determinants of the structure, stability and function of proteins. Several tools have been developed for the identification and analysis of such interactions in proteins based on the extensive studies carried out on high-resolution structures from Protein Data Bank (PDB). Although these tools allow users to identify and analyze interactions, analysis can only be performed on one structure at a time. This makes it difficult and time consuming to study the significance of these interactions on a large scale.
Results: SpeeDB is a web-based tool for the identification of protein structures based on structural properties. SpeeDB queries are executed on all structures in the PDB at once, quickly enough for interactive use. SpeeDB includes standard queries based on published criteria for identifying various structures: disulphide bonds, catalytic triads and aromatic–aromatic, sulphur–aromatic, cation–π and ionic interactions. Users can also construct custom queries in the user interface without any programming. Results can be downloaded in a Comma Separated Value (CSV) format for further analysis with other tools. Case studies presented in this article demonstrate how SpeeDB can be used to answer various biological questions. Analysis of human proteases revealed that disulphide bonds are the predominant type of interaction and are located close to the active site, where they promote substrate specificity. When comparing the two homologous G protein-coupled receptors and the two protein kinase paralogs analyzed, the differences in the types of interactions responsible for stability accounts for the differences in specificity and functionality of the structures.
Availability and implementation: SpeeDB is available at http://www.parallelcomputing.ca as a web service.
Contact: d@drobilla.net
Supplementary Information: Supplementary data are available at Bioinformatics online.
Repeat- and error-aware comparison of deletions
Authors: Wittler Roland , Marschall Tobias , Schönhuth Alexander , Mäkinen Veli 
Published: May 2015

Abstract
Motivation: The number of reported genetic variants is rapidly growing, empowered by ever faster accumulation of next-generation sequencing data. A major issue is comparability. Standards that address the combined problem of inaccurately predicted breakpoints and repeat-induced ambiguities are missing. This decisively lowers the quality of ‘consensus’ callsets and hampers the removal of duplicate entries in variant databases, which can have deleterious effects in downstream analyses.
Results: We introduce a sound framework for comparison of deletions that captures both tool-induced inaccuracies and repeat-induced ambiguities. We present a maximum matching algorithm that outputs virtual duplicates among two sets of predictions/annotations. We demonstrate that our approach is clearly superior over ad hoc criteria, like overlap, and that it can reduce the redundancy among callsets substantially. We also identify large amounts of duplicate entries in the Database of Genomic Variants, which points out the immediate relevance of our approach.
Availability and implementation: Implementation is open source and available from https://bitbucket.org/readdi/readdi
Contact: roland.wittler@uni-bielefeld.de or t.marschall@mpi-inf.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Assessing demographic effects of dams on diadromous fish: a case study for Atlantic salmon in the Penobscot River, Maine
Authors: Nieland Julie L. , Sheehan Timothy F. , Saunders Rory 
Published: May 2015

AbstractDams are a major contributor to the historic decline and current low abundance of diadromous fish. We developed a population viability analysis to assess demographic effects of dams on diadromous fish within a river system and demonstrated an application of the model with Atlantic salmon in the Penobscot River, Maine. We used abundance and distribution of wild- and hatchery-origin adult salmon throughout the watershed as performance metrics. Salmon abundance, distribution to upper reaches of the Penobscot watershed, and the number and proportion of wild-origin fish in the upper reaches of the Penobscot watershed increased when dams, particularly mainstem dams, were removed or passage efficiency was increased. Salmon abundance decreased as indirect latent mortality per dam was increased. Salmon abundance increased as marine or freshwater survival rates were increased, but the increase in abundance was larger when marine survival was increased than when freshwater survival was increased. Without hatchery supplementation, salmon abundance equalled zero with low marine and freshwater survival but increased when marine and freshwater survival rates were increased. Models, such as this one, that incorporate biological, environmental, and functional parameters can be used to predict ecological responses of fish populations and can help evaluate and prioritize management and restoration actions for diadromous fish.
Evaluating energy flows through jellyfish and gulf menhaden (Brevoortia patronus) and the effects of fishing on the northern Gulf of Mexico ecosystem
Authors: Robinson Kelly L. , Ruzicka James J. , Hernandez Frank J. , Graham William M. , Decker Mary Beth , Brodeur Richard D. , Sutor Malinda 
Published: May 2015

Abstract
Fishery management production models tend to stress only the elements directly linked to fish (i.e. fish, fish food, and fish predators). Large coastal jellyfish are major consumers of plankton in heavily fished ecosystems; yet, they are frequently not included as model components. We explore the relationship between gulf menhaden (Brevoortia patronus) and the large scyphozoan jellyfish (Aurelia spp. and Chrysaora sp.), and provide an examination of trophic energy transfer pathways to higher trophic levels in the northern Gulf of Mexico. A trophic network model developed within the ECOPATH framework was transformed to an end-to-end model to map foodweb energy flows. Relative changes in functional group productivity to varying gulf menhaden consumption rates, jellyfish consumption rates, and forage fish (i.e. gulf menhaden, anchovies, and herrings) harvest rates were evaluated within a suite of static, alternative energy-demand scenarios using ECOTRAN techniques. Scenario analyses revealed forage fish harvest enhanced jellyfish productivity, which, in turn, depressed menhaden productivity. Modelled increases in forage fish harvest caused pronounced changes in ecosystem structure, affecting jellyfish, marine birds, piscivorous fish, and apex predators. Menhaden were found to be a more efficient and important energy transfer pathway to higher trophic levels compared with jellyfish. A simulated increase in jellyfish abundance caused the relative production of all model groups to decline. These outcomes suggest that jellyfish blooms and forage fish harvest have demonstrable effects on the structure of the northern Gulf of Mexico ecosystem.
Success of Standard Dose Vitamin D Supplementation in Treated Human Immunodeficiency Virus Infection
Authors: Lake Jordan E. , Hoffman Risa M. , Tseng Chi-Hong , Wilhalme Holly M. , Adams John S. , Currier Judith S. 
Published: May 2015

Abstract
Background.  Vitamin D insufficiency is prevalent in human immunodeficiency virus-positive (HIV+) persons. Human immunodeficiency virus and antiretroviral therapy (ART) may create unique risk factors, and the optimal vitamin D repletion and maintenance regimen in HIV+ persons remains unclear.
Methods.  Human immunodeficiency virus-positive adults on suppressive ART underwent routine serum 25-hydroxyvitamin D (25OHD) screening. Persons with vitamin D insufficiency (25OHD &lt;30 ng/mL) received open-label, oral vitamin D3 50 000 international units (IU) twice weekly for 5 weeks, then 2000 IU daily to complete 12 weeks. We predicted 70% (95% confidence interval, 60%–80%) repletion to 25OHD ≥30 ng/mL compared with 85% among historical HIV-negative controls. Eighty participants provided 91% power to detect this difference. Ability to maintain 25OHD ≥30 ng/mL after 24 weeks was also assessed.
Results.  Baseline characteristics were similar between the 82 vitamin D insufficient and 40 sufficient persons enrolled: 95% male, 60% white, 88% nonsmokers, median age 49 years, body mass index 26 kg/m2, and CD4+ T lymphocyte count 520 cells/mm3. After 12 weeks, 81% (66 of 82) of insufficient persons achieved 25OHD ≥30 ng/mL (P = .32 vs historical controls), with only older age (odds ratio [OR] = 1.06; P = .06), higher baseline 25OHD (OR = 1.14; P &lt; .01), white race (OR = 3.39; P = .04), and current smoking (OR = 0.25; P = .06) associated with successful repletion. After 24 weeks, 73% (48 of 66) maintained 25OHD ≥30 ng/mL, with tenofovir (OR = 5.00; P = .01) and abacavir use (OR = 0.23; P = .02) associated with success and failure, respectively, to maintain 25OHD levels.
Conclusions.  The 25OHD repletion rates were comparable between HIV+ adults on suppressive ART and historical HIV-negative controls, indicating that successful oral repletion can be achieved in this population.
A new ray-tracing scheme for 3D diffuse radiation transfer on highly parallel architectures
Authors: Tanaka Satoshi , Yoshikawa Kohji , Okamoto Takashi , Hasegawa Kenji 
Published: May 2015

Abstract
We present a new numerical scheme to solve the transfer of diffuse radiation on three-dimensional mesh grids which is efficient on processors with highly parallel architecture such as recently popular GPUs and CPUs with multi- and many-core architectures. The scheme is based on the ray-tracing method and the computational cost is proportional to $N_{\rm m}^{\,5/3}$, where Nm is the number of mesh grids, and is devised to compute the radiation transfer along each light-ray completely in parallel, with appropriate grouping of the light-rays. We find that the performance of our scheme scales well with the number of adopted CPU cores and GPUs, and also that our scheme is nicely parallelized on a multi-node system by adopting the multiple wave front scheme, and the performance scales well with the amount of computational resources. As numerical tests to validate our scheme and to give a physical criterion for the angular resolution of our ray-tracing scheme, we perform several numerical simulations of the photoionization of neutral hydrogen gas by ionizing radiation sources without the “on-the-spot” approximation, in which the transfer of diffuse radiation by radiative recombination is incorporated in a self-consistent manner.
Trends in Pediatric and Adolescent Anterior Cruciate Ligament Injury and Reconstruction
Authors: Werner Brian C. , Yang Scott , Looney Austin M. , Gwathmey Frank Winston 
Published: May 2015

Background:
With the increasing involvement in organized athletics among children and adolescents, more anterior cruciate ligament (ACL) injuries are being recognized in the skeletally immature population. The goal of the present study is to utilize a national database to characterize the recent epidemiologic trends of ACL injuries, ACL reconstruction, and treatment of associated meniscal and chondral pathology in the pediatric and adolescent populations.

Methods:
A national database was queried for ACL tear (ICD-9 844.2) and arthroscopic reconstruction of an ACL tear (CPT 29888) from 2007 to 2011. Searches were limited by age group to identify pediatric and adolescent cohorts: (1) ages 5 to 9 years old, (2) ages 10 to 14 years old, and (3) ages 15 to 19 years old. A comparative cohort of adult patients from ages 20 to 45 was also created. The database was also queried for concomitant procedures at the same time as ACL reconstruction for each age group, including partial meniscectomy, meniscus repair, microfracture, osteochondral autograft or allograft transfer, and shaving chondroplasty. The χ2 analysis was used to determine statistical significance.

Results:
A total of 44,815 unique pediatric or adolescent patients with a diagnosis of an ACL tear and 19,053 pediatric or adolescent patients who underwent arthroscopic ACL reconstruction were identified. Significant increases in pediatric and adolescent ACL tear diagnosis and reconstruction compared with adult patients were noted. Significant increases in many concomitant meniscus and cartilage procedures in pediatric and adolescent patients compared with adult patients were also noted.

Conclusions:
The present study demonstrates a significant increase in the overall diagnosis of ACL injury and ACL reconstruction in both pediatric and adolescent patients, rising at a rate significantly higher than adults. In addition, pediatric and adolescent patients who undergo ACL reconstruction had significant increases in incidences of concomitant meniscal and cartilage procedures.

Level of Evidence:
Level III—retrospective cohort study.
Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTMsequencing
Authors: Cao Minh Duc , Ganesamoorthy Devika , Elliott Alysha G. , Zhang Huihui , Cooper Matthew A. , Coin Lachlan 
Published: May 2015

AbstractThe recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This opens immense potential to shorten the sample-to-results time and is likely to lead to enormous benefits in rapid diagnosis of bacterial infection and identification of drug resistance. However, there are very few tools available for streaming analysis of real-time sequencing data. Here, we present a framework for streaming analysis of MinION real-time sequence data, together with probabilistic streaming algorithms for species typing, multi-locus strain typing, gene presence strain-typing and antibiotic resistance profile identification. Using three culture isolate samples as well as a mixed-species sample, we demonstrate that bacterial species and strain information can be obtained within 30 minutes of sequencing and using about 500 reads, initial drug-resistance profiles within two hours, and complete resistance profiles within 10 hours. Multi-locus strain typing required more than 15x coverage to generate confident assignments, whereas gene-presence typing could detect the presence of a known strain with 0.5x coverage. We also show that our pipeline can process over 100 times more data than the current throughput of the MinION on a desktop computer.