bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of a Refuge for Lake Trout in Western Lake Superior II: Simulation of Future Performance
Authors: Akins Andrea L. , Hansen Michael J. , Seider Michael J. 
Published: October 2015

Abstract
Historically, Lake Superior supported one of the largest and most diverse Lake Trout Salvelinus namaycush fisheries in the Laurentian Great Lakes, but Lake Trout stocks collapsed due to excessive fishery exploitation and predation by Sea Lampreys Petromyzon marinus. Lake Trout stocking, Sea Lamprey control, and fishery regulations, including a refuge encompassing Gull Island Shoal (Apostle Islands region), were used to enable recovery of Lake Trout stocks that used this historically important spawning shoal. Our objective was to determine whether future sustainability of Lake Trout stocks will depend on the presence of the Gull Island Shoal Refuge. We constructed a stochastic age-structured simulation model to assess the effect of maintaining the refuge as a harvest management tool versus removing the refuge. In general, median abundances of age-4, age-4 and older (age-4+), and age-8+ fish collapsed at lower instantaneous fishing mortality rates (F) when the refuge was removed than when the refuge was maintained. With the refuge in place, the F that resulted in collapse depended on the rate of movement into and out of the refuge. Too many fish stayed in the refuge when movement was low (0–2%), and too many fish became vulnerable to fishing when movement was high (≥22%); thus, the refuge was more effective at intermediate rates of movement (10–11%). With the refuge in place, extinction did not occur at any simulated level of F, whereas refuge removal led to extinction at all combinations of commercial F and recreational F. Our results indicate that the Lake Trout population would be sustained by the refuge at all simulated F-values, whereas removal of the refuge would risk population collapse at much lower F (0.700–0.744). Therefore, the Gull Island Shoal Refuge is needed to sustain the Lake Trout population in eastern Wisconsin waters of Lake Superior.
Received November 14, 2014; accepted July 7, 2015
Using Redd Attributes, Fry Density, and Otolith Microchemistry to Distinguish the Presence of Steelhead and Rainbow Trout in the Elwha River Dam Removal Project
Authors: McMillan John R. , Pess George R. , Liermann Martin , Morley Sarah A. , McHenry Michael L. , Campbell Lance A. , Quinn Thomas P. 
Published: October 2015

Abstract
The removal of impassable dams can affect stream fish communities in many ways, including allowing previously separated anadromous and resident life history types to intermingle. Recolonization of steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) into areas that were previously occupied solely by resident conspecifics presents a challenge for monitoring because (1) staging or spawning adults may be difficult to directly observe; and (2) the offspring of the two life history forms are indistinguishable during early life. We evaluated the utility of using redd attributes, fry (age-0) size, and fry density to distinguish the presence of steelhead and Rainbow Trout in the Elwha River, Washington. Redd area and substrate size differed between forms: steelhead redds were significantly larger and had a greater median substrate particle size than Rainbow Trout redds. Fry density was significantly higher in steelhead spawning reaches than in Rainbow Trout reaches during both survey years (2010 and 2011). Steelhead fry tended to be slightly larger than Rainbow Trout fry but not significantly so in either year. Additionally, otolith microchemical analyses indicated that all fry collected from newly colonized habitat were of steelhead maternal origin, and these fish were intermediate in size to the steelhead and Rainbow Trout fry collected prior to dam removal. Thus, fry size may not effectively differentiate parental origin despite the tendency of anadromous parents to be larger and to spawn earlier than residents. Redd attributes and fry density may be useful for evaluating the spatial distributions and relative abundances of steelhead and Rainbow Trout after dam removal. Our results have implications for other dam removal projects and other monitored species.
Received April 13, 2015; accepted July 3, 2015
Identification of a characteristic antioxidant, anthrasesamone F, in black sesame seeds and its accumulation at different seed developmental stages
Authors: Furumoto Toshio , Nishimoto Kiyoshi 
Published: October 2015

Abstract
Assay-guided fractionation of the methanol extract from black seeds of sesame (Sesamum indicum L.) led to the isolation of an active compound that had a 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity. This antioxidant was confirmed to be anthrasesamone F, an anthraquinone derivative previously isolated from different black sesame seeds and biogenetically related to other anthrasesamones in sesame roots. The radical scavenging assay showed that anthrasesamone F had more potent activity than Trolox. The content of anthrasesamone F in different parts and at different developmental stages of black sesame seeds was investigated to clarify the accumulation pattern of this antioxidant in the black seeds. Anthrasesamone F was localized in the seed coat of black seeds and accumulated after the seed coat color changed to black. The content of anthrasesamone F increased gradually with seed maturation and drastically on air-drying, the final stage in sesame cultivation.
Induced Spawning and Larval Culture of Golden Trevally
Authors: Broach Jason S , Ohs Cortney L , Palau Andrew , Danson Bryan , Elefante Daniel 
Published: October 2015

Abstract
The Golden Trevally Gnathanodon speciosus is a popular sport, food, and ornamental fish native to the tropical Indo-Pacific region, yet there is little information regarding aquaculture technologies. A group of Golden Trevally broodfish was acquired from a local public aquarium in an effort to attempt captive spawning and larval culture. Broodfish were held in 4,500-L recirculating aquaculture systems and conditioned on a mixed diet of squid, capelin, and krill. Once water temperatures were averaging 26°C, Ovaplant was administered to mature broodfish (six males, two females) in one of the systems. Broodfish spawned on three separate occasions after this hormone administration, releasing probably 35,000 eggs/female during each spawn. Fertile eggs from two of these spawns were used for larval culture attempts. Larvae were stocked into five 104-L tanks at densities up to 173 larvae/L. Throughout larval culture trials, larvae were fed a combination of copepod nauplii, enriched rotifers, Artemia nauplii, and a dry diet, and the tank water was inoculated with live Tahitian strain Isochrysis galbana up to 26 d posthatch (dph). Larvae achieved complete metamorphosis around 30 dph. By 45 dph, nearly 4.3% of the larvae initially stocked survived and reached about 3.7 cm in length. These successful spawning induction and larval culture trials are promising for future development of a commercial-level production industry for Golden Trevally.
JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts
Authors: Lee Donghyung , Williamson Vernell S. , Bigdeli T. Bernard , Riley Brien P. , Webb Bradley T. , Fanous Ayman H. , Kendler Kenneth S. , Vladimirov Vladimir I. , Bacanu Silviu-Alin 
Published: October 2015

Abstract
Motivation: To increase detection power, gene level analysis methods are used to aggregate weak signals. To greatly increase computational efficiency, most methods use as input summary statistics from genome-wide association studies (GWAS). Subsequently, gene statistics are constructed using linkage disequilibrium (LD) patterns from a relevant reference panel. However, all methods, including our own Joint Effect on Phenotype of eQTL/functional single nucleotide polymorphisms (SNPs) associated with a Gene (JEPEG), assume homogeneous panels, e.g. European. However, this renders these tools unsuitable for the analysis of large cosmopolitan cohorts.
Results: We propose a JEPEG extension, JEPEGMIX, which similar to one of our software tools, Direct Imputation of summary STatistics of unmeasured SNPs from MIXed ethnicity cohorts, is capable of estimating accurate LD patterns for cosmopolitan cohorts. JEPEGMIX uses this accurate LD estimates to (i) impute the summary statistics at unmeasured functional variants and (ii) test for the joint effect of all measured and imputed functional variants which are associated with a gene. We illustrate the performance of our tool by analyzing the GWAS meta-analysis summary statistics from the multi-ethnic Psychiatric Genomics Consortium Schizophrenia stage 2 cohort. This practical application supports the immune system being one of the main drivers of the process leading to schizophrenia.
Availability and implementation: Software, annotation database and examples are available at http://dleelab.github.io/jepegmix/.
Contact: donghyung.lee@vcuhealth.org
Supplementary information: Supplementary material is available at Bioinformatics online.
Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology
Authors: Hardcastle Thomas J. 
Published: October 2015

AbstractMotivation: High-throughput data are now commonplace in biological research. Rapidly changing technologies and application mean that novel methods for detecting differential behaviour that account for a ‘large P, small n’ setting are required at an increasing rate. The development of such methods is, in general, being done on an ad hoc basis, requiring further development cycles and a lack of standardization between analyses.Results: We present here a generalized method for identifying differential behaviour within high-throughput biological data through empirical Bayesian methods. This approach is based on our baySeq algorithm for identification of differential expression in RNA-seq data based on a negative binomial distribution, and in paired data based on a beta-binomial distribution. Here we show how the same empirical Bayesian approach can be applied to any parametric distribution, removing the need for lengthy development of novel methods for differently distributed data. Comparisons with existing methods developed to address specific problems in high-throughput biological data show that these generic methods can achieve equivalent or better performance. A number of enhancements to the basic algorithm are also presented to increase flexibility and reduce computational costs.Availability and implementation: The methods are implemented in the R baySeq (v2) package, available on Bioconductor http://www.bioconductor.org/packages/release/bioc/html/baySeq.html.Contact: tjh48@cam.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Cell line name recognition in support of the identification of synthetic lethality in cancer from text
Authors: Kaewphan Suwisa , Van Landeghem Sofie , Ohta Tomoko , Van de Peer Yves , Ginter Filip , Pyysalo Sampo 
Published: October 2015

Abstract
Motivation: The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the literature. While several tools have previously been developed to address cell line recognition, it is unclear whether available systems can perform sufficiently well in realistic and broad-coverage applications such as extracting synthetically lethal genes from the cancer literature. In this study, we revisit the cell line name recognition task, evaluating both available systems and newly introduced methods on various resources to obtain a reliable tagger not tied to any specific subdomain. In support of this task, we introduce two text collections manually annotated for cell line names: the broad-coverage corpus Gellus and CLL, a focused target domain corpus.
Results: We find that the best performance is achieved using NERsuite, a machine learning system based on Conditional Random Fields, trained on the Gellus corpus and supported with a dictionary of cell line names. The system achieves an F-score of 88.46% on the test set of Gellus and 85.98% on the independently annotated CLL corpus. It was further applied at large scale to 24 302 102 unannotated articles, resulting in the identification of 5 181 342 cell line mentions, normalized to 11 755 unique cell line database identifiers.
Availability and implementation: The manually annotated datasets, the cell line dictionary, derived corpora, NERsuite models and the results of the large-scale run on unannotated texts are available under open licenses at http://turkunlp.github.io/Cell-line-recognition/.
Contact: sukaew@utu.fi
Pseudoknots in RNA folding landscapes
Authors: Kucharík Marcel , Hofacker Ivo L. , Stadler Peter F. , Qin Jing 
Published: October 2015

Abstract
Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model and understand these processes, it is necessary to go beyond ground state structures. The study of rugged RNA folding landscapes holds the key to answer these questions. Efficient coarse-graining methods are required to reduce the intractably vast energy landscapes into condensed representations such as barrier trees or basin hopping graphs (BHG) that convey an approximate but comprehensive picture of the folding kinetics. So far, exact and heuristic coarse-graining methods have been mostly restricted to the pseudoknot-free secondary structures. Pseudoknots, which are common motifs and have been repeatedly hypothesized to play an important role in guiding folding trajectories, were usually excluded.
Results: We generalize the BHG framework to include pseudoknotted RNA structures and systematically study the differences in predicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding intermediates or not. We observe that RNAs with pseudoknotted ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseudoknot-free ground state structures. The occurrence and influence of pseudoknotted intermediates on the folding pathway, however, appear to depend very strongly on the individual RNAs so that no general rule can be inferred.
Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and Supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html.
Contact: qin@bioinf.uni-leipzig.de
Supplementary information: Supplementary data are available at Bioinformatics online.
ALP & FALP: C++ libraries for pairwise local alignment E-values
Authors: Sheetlin Sergey , Park Yonil , Frith Martin C. , Spouge John L. 
Published: October 2015

Abstract
Motivation: Pairwise local alignment is an indispensable tool for molecular biologists. In real time (i.e. in about 1 s), ALP (Ascending Ladder Program) calculates the E-values for protein–protein or DNA–DNA local alignments of random sequences, for arbitrary substitution score matrix, gap costs and letter abundances; and FALP (Frameshift Ascending Ladder Program) performs a similar task, although more slowly, for frameshifting DNA-protein alignments.
Availability and implementation: To permit other C++ programmers to implement the computational efficiencies in ALP and FALP directly within their own programs, C++ source codes are available in the public domain at http://go.usa.gov/3GTSW under ‘ALP’ and ‘FALP’, along with the standalone programs ALP and FALP.
Contact: spouge@nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
A method of spherical harmonic analysis in the geosciences via hierarchical Bayesian inference
Authors: Muir J.B. , Tkalčić H. 
Published: October 2015

AbstractThe problem of decomposing irregular data on the sphere into a set of spherical harmonics is common in many fields of geosciences where it is necessary to build a quantitative understanding of a globally varying field. For example, in global seismology, a compressional or shear wave speed that emerges from tomographic images is used to interpret current state and composition of the mantle, and in geomagnetism, secular variation of magnetic field intensity measured at the surface is studied to better understand the changes in the Earth's core. Optimization methods are widely used for spherical harmonic analysis of irregular data, but they typically do not treat the dependence of the uncertainty estimates on the imposed regularization. This can cause significant difficulties in interpretation, especially when the best-fit model requires more variables as a result of underestimating data noise. Here, with the above limitations in mind, the problem of spherical harmonic expansion of irregular data is treated within the hierarchical Bayesian framework. The hierarchical approach significantly simplifies the problem by removing the need for regularization terms and user-supplied noise estimates. The use of the corrected Akaike Information Criterion for picking the optimal maximum degree of spherical harmonic expansion and the resulting spherical harmonic analyses are first illustrated on a noisy synthetic data set. Subsequently, the method is applied to two global data sets sensitive to the Earth's inner core and lowermost mantle, consisting of PKPab-df and PcP-P differential traveltime residuals relative to a spherically symmetric Earth model. The posterior probability distributions for each spherical harmonic coefficient are calculated via Markov Chain Monte Carlo sampling; the uncertainty obtained for the coefficients thus reflects the noise present in the real data and the imperfections in the spherical harmonic expansion.
Repurposing existing agents as adjunct therapies for glioblastoma
Authors: Purow Benjamin 
Published: October 2015

AbstractNumerous non-oncologic medications have been found in the last decade to have anti-cancer properties. While the focus in oncology research should clearly remain on deriving new therapeutic strategies, repurposing these existing medications may offer the potential to rapidly enhance the effectiveness of treatment for resistant cancers. Glioblastoma, the most common and lethal brain cancer, is highly resistant to standard therapies and would benefit from even minor improvements in treatment. Numerous agents already in the clinic for non-cancer applications have been found to also possess potential against cancer or specifically against glioblastoma. These include agents with activities affecting oxidative stress, the immune reponse, epigenetic modifiers, cancer cell metabolism, and angiogenesis and invasiveness. This review serves as a guide for potential ways to repurpose individual drugs alongside standard glioblastoma therapies.
Link for Injured Kids
Authors: Ramirez Marizen , Toussaint Maisha , Woods-Jaeger Briana , Harland Karisa , Wetjen Kristel , Wilgenbusch Tammy , Pitcher Graeme , Jennissen Charles 
Published: October 2015

Objective
Injury, the most common type of pediatric trauma, can lead to a number of adverse psychosocial outcomes, including posttraumatic stress disorder. Currently, few evidence-based parent programs exist to support children hospitalized after a traumatic injury. Using methods in evaluation and intervention research, we completed a formative research study to develop a new program of psychological first aid, Link for Injured Kids, aimed to educate parents in supporting their children after a severe traumatic injury.

Methods
Using qualitative methods, we held focus groups with parents and pediatric trauma providers of children hospitalized at a Level I Children's Hospital because of an injury in 2012. We asked focus group participants to describe reactions to trauma and review drafts of our intervention materials.

Results
Health professionals and caregivers reported a broad spectrum of emotional responses by their children or patients; however, difficulties were experienced during recovery at home and upon returning to school. All parents and health professionals recommended that interventions be offered to parents either in the emergency department or close to discharge among admissions.

Conclusions
Results from this study strongly indicate a need for posttrauma interventions, particularly in rural settings, to support families of children to address the psychosocial outcomes in the aftermath of an injury. Findings presented here describe the process of intervention development that responds to the needs of an affected population.
Neuronal actin dynamics, spine density and neuronal dendritic complexity are regulated by CAP2
Authors: Kumar Atul , Paeger Lars , Kosmas Kosmas , Kloppenburg Peter , Noegel Angelika A. , Peche Vivek 
Published: October 2015

AbstractActin remodeling is indispensable for dendritic spine development, morphology and density which signify learning, memory and motor skills. CAP2 is a regulator of actin dynamics through sequestering G-actin and severing F-actin. In a mouse model, ablation of CAP2 leads to cardiovascular defects and delayed wound healing. This report investigates the role of CAP2 in the brain usingCap2gt/gtmice. Dendritic spine density and neuronal dendritic length were altered inCap2gt/gt. This was accompanied by increased F-actin content and F-actin accumulation in culturedCap2gt/gtneurons. In membrane depolarization assays,Cap2gt/gtsynaptosomes exhibit an impaired F/G actin ratio, indicating altered actin dynamics. We show an interaction between CAP2 and n-cofilin, presumably mediated through the C-terminal domain of CAP2 and is cofilin ser3 phosphorylation dependent. In vivo, the consequences of this interaction were altered phosphorylated cofilin levels and formation of cofilin aggregates in the neurons. Thus, our studies identify a novel role of CAP2 in neuronal development and neuronal actin dynamics.
Detecting and quantifying changing selection intensities from time-sampled polymorphism data
Authors: Shim Hyunjin , Laurent Stefan , Foll Matthieu , Jensen Jeffrey D. 
Published: October 2015

AbstractDuring his well-known debate with Fisher regarding the phenotypic dataset ofPanaxia dominula, Wright (1948) suggested fluctuating selection as a potential explanation for the observed change in frequency. This model has since been invoked in a number of analyses, with the focus of discussion centering mainly on random or oscillatory fluctuations of selection intensities. Here, we present a novel method to consider non-random changes in selection intensities using Wright-Fisher approximate Bayesian (ABC)-based approaches, in order to detect and evaluate a change in selection strength from time-sampled data. This novel method jointly estimates the position of a change point as well as the strength of both corresponding selection coefficients (and dominance for diploid cases) from the allele trajectory. The simulation studies of CP-WFABC reveal the combinations of parameter ranges and input values that optimize performance, thus indicating optimal experimental design strategies. We apply this approach to both the historical dataset ofPanaxia dominulain order to shed light on this historical debate, as well as to whole-genome time-serial data from influenza virus in order to identify sites with changing selection intensities in response to drug treatment