bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes
Authors: Curtis Darren S. , Phillips Aaron R. , Callister Stephen J. , Conlan Sean , McCue Lee Ann 
Published: August 2013

Abstract
Summary: At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid.
Availability and Implementation: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.
Contact: leeann.mccue@pnnl.gov
Imputation of coding variants in African Americans: better performance using data from the exome sequencing project
Authors: Duan Qing , Liu Eric Yi , Auer Paul L. , Zhang Guosheng , Lange Ethan M. , Jun Goo , Bizon Chris , Jiao Shuo , Buyske Steven , Franceschini Nora , Carlson Chris S. , Hsu Li , Reiner Alex P. , Peters Ulrike , Haessler Jeffrey , Curtis Keith , Wassel Christina L. , Robinson Jennifer G. , Martin Lisa W. , Haiman Christopher A. , Le Marchand Loic , Matise Tara C. , Hindorff Lucia A. , Crawford Dana C. , Assimes Themistocles L. , Kang Hyun Min , Heiss Gerardo , Jackson Rebecca D. , Kooperberg Charles , Wilson James G. , Abecasis Gonçalo R. , North Kari E. , Nickerson Deborah A. , Lange Leslie A. , Li Yun 
Published: August 2013

AbstractSummary: Although the 1000 Genomes haplotypes are the most commonly used reference panel for imputation, medical sequencing projects are generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 haplotypes from the Exome Sequencing Project, compared with 2184 haplotypes from 1000 Genomes Project, increased effective sample size by 8.3–11.4% for coding variants with minor allele frequency &lt;1%. No loss of imputation quality was observed using a panel built from phenotypic extremes. We recommend using haplotypes from Exome Sequencing Project alone or concatenation of the two panels over quality score-based post-imputation selection or IMPUTE2’s two-panel combination.Contact: yunli@med.unc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Acoustic surveys for juvenile anchovy in the Bay of Biscay: abundance estimate as an indicator of the next year's recruitment and spatial distribution patterns
Authors: Boyra G. , Martínez U. , Cotano U. , Santos M. , Irigoien X. , Uriarte A. 
Published: August 2013

Abstract
Boyra, G., Martínez, U., Cotano, U., Santos, M., Irigoien, X., and Uriarte, A. 2013. Acoustic surveys for juvenile anchovy in the Bay of Biscay: abundance estimate as an indicator of the next year's recruitment and spatial distribution patterns. – ICES Journal of Marine Science, 70: . A series of acoustic surveys (JUVENA) began in 2003 targeting juvenile anchovy (Engraulis encrasicolus) in the Bay of Biscay. A specific methodology was designed for mapping and estimating juvenile abundance annually, four months after the spawning season. After eight years of the survey, a consistent picture of the spatial pattern of the juvenile anchovy has emerged. Juveniles show a vertical and horizontal distribution pattern that depends on size. The younger individuals are found isolated from other species in waters closer to the surface, mainly off the shelf within the mid-southern region of the bay. The largest juveniles are usually found deeper and closer to the shore in the company of adult anchovy and other pelagic species. In these eight years, the survey has covered a wide range of juvenile abundances, and the estimates show a significant positive relationship between the juvenile biomasses and the one-year-old recruits of the following year. This demonstrates that the JUVENA index provides an early indication of the strength of next year's recruitment to the fishery and can therefore be used to improve the management advice for the fishery of this short-lived species.
Modelling prey consumption and switching by UK grey seals
Authors: Smout Sophie , Rindorf Anna , Hammond Philip S. , Harwood John , Matthiopoulos Jason 
Published: August 2013

AbstractSmout, S., Rindorf, A., Hammond, P. S., Harwood, J., and Matthiopoulos, J. Modelling prey consumption and switching by UK grey seals. – ICES Journal of Marine Science, 71: . Grey seals (Halichoerus grypus) are adaptable generalist predators whose diet includes commercial fish species such as cod. Consumption by the seals may reduce the size of some fish stocks or have an adverse effect on stock recovery programmes, especially because predation may trap sparse prey populations in a “predator pit”. To assess the likely impact of such effects, it is important to know how consumption and consequent predation mortality respond to the changing availability of prey. We present a model of grey seal consumption as a function of the availability of multiple prey types [a Multi-Species Functional Response (MSFR)]. We fit this MSFR to data on seal diet and prey availability (based on the overlap between the distributions of predators and prey). Bayesian methodology was employed to account for uncertainties in both dependent and independent variables, improve estimation convergence by the use of informative priors, and allow the estimation of missing data on prey availability. Both hyperbolic (Type 2) and sigmoidal (Type 3) functional response models were fitted to the data and the Type 3 model was clearly favoured during model selection, supporting the conclusion that seal–prey encounter rates change with prey abundance (sometimes referred to as “switching”). This suggests that some prey species may be vulnerable to predator pit effects. The fitted model reproduced contrasts in diet observed between different regions/years and, importantly, added information to the prior distributions of prey abundance in areas where the availability of some prey species (such as sandeels) was not known. This suggests that the diet of predators such as seals could provide information about the abundance and distribution of prey in areas that are not covered by fisheries and research surveys.
Deep-sea sponge grounds enhance diversity and abundance of epibenthic megafauna in the Northwest Atlantic
Authors: Beazley Lindsay I. , Kenchington Ellen L. , Murillo Francisco Javier , Sacau María del Mar 
Published: August 2013

AbstractBeazley, L. I., Kenchington E. L., Murillo, F. J., and Sacau, M. 2013. Deep-sea sponge grounds enhance diversity and abundance of epibenthic megafauna in the Northwest Atlantic. – ICES Journal of Marine Science, 70: . The influence of structure-forming deep-water sponge grounds on the composition, diversity, and abundance of the local epibenthic megafaunal community of the Flemish Pass area, Northwest Atlantic was statistically assessed. These habitats are considered vulnerable marine ecosystems and, therefore, warrant conservation measures to protect them from bottom fishing activities. The epibenthic megafauna were quantified from four photographic transects, three of which were located on the western slope of the Flemish Cap with an overall depth range of 444–940 m, and the fourth in the southern Flemish Pass between 1328 and 1411 m. We observed a diverse megafaunal community dominated by large numbers of ophiuroids and sponges. On the slope of the Flemish Cap, sponge grounds were dominated by axinellid and polymastid sponges, while the deeper sponge ground in the southern Flemish Pass was formed mainly by geodiids and Asconema sp. The presence of structure-forming sponges was associated with a higher biodiversity and abundance of associated megafauna compared with non-sponge habitat. The composition of megafauna significantly differed between sponge grounds and non-sponge grounds and also between different sponge morphologies. Surface chlorophyll a and near-bottom salinity were important environmental determinants in generalized linear models of megafaunal species richness and abundance.
Effect of region on the food-related benefits to age-0 walleye pollock (Theragra chalcogramma) in association with midwater habitat characteristics in the Gulf of Alaska
Authors: Wilson Matthew T. , Mier Kathryn L. , Jump Christina M. 
Published: August 2013

Abstract
Wilson, M. T., Mier, K. L., and Jump, C. M. 2013. Effect of region on the food-related benefits to age-0 walleye pollock (Theragra chalcogramma) in association with midwater habitat characteristics in the Gulf of Alaska – ICES Journal of Marine Science, 70: . In the western Gulf of Alaska (GOA), we compared age-0 juvenile walleye pollock body weight, food habits, and expected growth rates between two regions during 3 years. The benefit to rearing off Kodiak Island vs. in the Semidi Islands vicinity increased among years with body length because larger fish consumed more euphausiids, and euphausiids were apparently more available in the Kodiak region. This explains previously observed regional variation in body size, condition, and growth rates within the GOA population and points to potential importance of the Kodiak region as a walleye pollock nursery. During September 2005, 2007, and 2009, Kodiak midwater was cooler and saltier than Semidi midwater, presumably due to a relatively narrow continental shelf and greater oceanic influence. Zooplankton composition differed between regions with the greater euphausiid population density off Kodiak being most relevant to walleye pollock food habits. As found historically, age-0 walleye pollock abundance was lower in the Kodiak region than in the Semidi region. However, the Kodiak fish were larger in both length and length-specific weight, and had fuller stomachs than Semidi fish, although differences were not significant in all years. Regional differences were most pronounced during the relatively warm year 2005 when fish were particularly large. Fish dietary mass was dominated by euphausiids, especially for Kodiak fish ≥55 mm standard length. Bioenergetics model output suggests that the greater euphausiid dietary proportion translates into faster growth of the Kodiak fish. The midwater habitat off Kodiak Island might therefore support above-average production of recruits to the GOA adult population due to better condition and likely survival of walleye pollock juveniles, especially when fish are large and thus able to more fully exploit euphausiids, but confirmation of above-average production of recruits depends on our ability to determine spatial structure in juvenile-adult population connectivity.
CYP1A1 and Cnr nitroreductase bioactivated niclosamide in vitro
Authors: Beristain-Castillo Evelyn , Martínez-Vázquez Mariano , Camacho-Carranza Rafael , Espinosa-Aguirre Javier J. 
Published: August 2013

Abstract
Niclosamide produces genotoxic effects, such as point mutations in Salmonella sp., sperm-head abnormalities in mice and clastogenic effects in human lymphocytes in vitro and in vivo. As cytochrome P450 could be involved in the bioactivation of niclosamide, we investigated which subfamily was involved. We used liver microsomal fractions from rats treated with phenobarbital/β-naphthoflavone (PB/β-NF), benzo[a]pyrene (BaP) or cyclohexanol, which are known to induce different cytochrome P450 subfamilies, such as CYP2B, CYP1A1, CYP1A2 and CYP2E1. We also inhibited CYP1A and CYP2E using α-NF and diethyldithiocarbamate to identify the cytochrome P450 involved. Liver-S9 fractions obtained from PB/β-NF- and BaP-treated rats significantly increased the number of revertants induced by niclosamide, while the CYP1A1 inhibitor α-NF decreased the number of revertants. The incubation of niclosamide with CYP1A1 Supersomes™ increased the number of revertants, suggesting that CYP1A1 is responsible for the bioactivation of niclosamide. Nitroreduction is also involved in niclosamide bioactivation, as the nitroreductase-deficient strain YG7132 did not respond to the niclosamide treatment. Our findings indicated that a metabolite, derived from the action of CYP1A1 and a nitroreduction-reaction process, has a key role in the bioactivation of niclosamide.
Increasing the complexity of chromatin: functionally distinct roles for replication-dependent histone H2A isoforms in cell proliferation and carcinogenesis
Authors: Singh Rajbir , Mortazavi Amir , Telu Kelly H. , Nagarajan Prabakaran , Lucas David M. , Thomas-Ahner Jennifer M. , Clinton Steven K. , Byrd John C. , Freitas Michael A. , Parthun Mark R. 
Published: August 2013

Abstract
Replication-dependent histones are encoded by multigene families found in several large clusters in the human genome and are thought to be functionally redundant. However, the abundance of specific replication-dependent isoforms of histone H2A is altered in patients with chronic lymphocytic leukemia. Similar changes in the abundance of H2A isoforms are also associated with the proliferation and tumorigenicity of bladder cancer cells. To determine whether these H2A isoforms can perform distinct functions, expression of several H2A isoforms was reduced by siRNA knockdown. Reduced expression of the HIST1H2AC locus leads to increased rates of cell proliferation and tumorigenicity. We also observe that regulation of replication-dependent histone H2A expression can occur on a gene-specific level. Specific replication-dependent histone H2A genes are either up- or downregulated in chronic lymphocytic leukemia tumor tissue samples. In addition, discreet elements are identified in the 5′ untranslated region of the HIST1H2AC locus that confer translational repression. Taken together, these results indicate that replication-dependent histone isoforms can possess distinct cellular functions and that regulation of these isoforms may play a role in carcinogenesis.
Population Pharmacokinetic Modeling of Hydromorphone in Cardiac Surgery Patients during Postoperative Pain Therapy
Authors: Jeleazcov Christian , Saari Teijo I. , Ihmsen Harald , Mell Jan , Fröhlich Katharina , Krajinovic Ljubica , Fechner Jörg , Schüttler Jürgen 
Published: August 2013

Abstract

Background:
Hydromorphone is a µ-selective opioid agonist used in postoperative pain therapy. This study aimed to evaluate the pharmacokinetics of hydromorphone in cardiac surgery patients during postoperative analgesia with target-controlled infusion and patient-controlled analgesia.

Methods:
In this study, 50 adult patients were enrolled to receive intravenous hydromorphone during postoperative pain therapy. Arterial plasma samples were collected for measurements of drug concentration. Population pharmacokinetic parameters were estimated using nonlinear mixed-effects modeling. Results were validated and simulations were carried out to evaluate results.

Results:
Data from 49 patients (age range, 40–81 yr) were analyzed. The pharmacokinetics of hydromorphone were best described by a three-compartment model. Age was incorporated as a significant covariate for elimination clearance and central volume of distribution. Scaling all parameters with body weight improved the model significantly. The final estimates of the model parameters for the typical adult patient (67 yr old, weighing 70 kg) undergoing cardiac surgery were as follows: CL1 = 1.01 l/min, V1 = 3.35 l, CL2 = 1.47 l/min, V2 = 13.9 l, CL3 = 1.41 l/min, and V3 = 145 l. The elimination clearance decreased by 43% between the age of 40 and 80 yr, and simulations demonstrated that context-sensitive half-time increased from 26 to 84 min in 40- and 80-yr-old subjects, respectively.

Conclusions:
The final pharmacokinetic model gave a robust representation of hydromorphone pharmacokinetics. Inclusion of age and body weight to the model demonstrated a significant influence of these covariates on hydromorphone pharmacokinetics. The application of this patient-derived population model in individualized pain therapy should improve the dosing of hydromorphone in patients undergoing cardiac surgery.
A Genomic-Scale Artificial MicroRNA Library as a Tool to Investigate the Functionally Redundant Gene Space inArabidopsis
Authors: Hauser Felix , Chen Wenxiao , Deinlein Ulrich , Chang Kenneth , Ossowski Stephan , Fitz Joffrey , Hannon Gregory J. , Schroeder Julian I. 
Published: August 2013

AbstractTraditional forward genetic screens are limited in the identification of homologous genes with overlapping functions. Here, we report the analyses and assembly of genome-wide protein family definitions that comprise the largest estimate for the potentially redundant gene space in Arabidopsis thaliana. On this basis, a computational design of genome-wide family-specific artificial microRNAs (amiRNAs) was performed using high-performance computing resources. The amiRNA designs are searchable online (http://phantomdb.ucsd.edu). A computationally derived library of 22,000 amiRNAs was synthesized in 10 sublibraries of 1505 to 4082 amiRNAs, each targeting defined functional protein classes. For example, 2964 amiRNAs target annotated DNA and RNA binding protein families and 1777 target transporter proteins, and another sublibrary targets proteins of unknown function. To evaluate the potential of an amiRNA-based screen, we tested 122 amiRNAs targeting transcription factor, protein kinase, and protein phosphatase families. Several amiRNA lines showed morphological phenotypes, either comparable to known phenotypes of single and double/triple mutants or caused by overexpression of microRNAs. Moreover, novel morphological and abscisic acid–insensitive seed germination mutants were identified for amiRNAs targeting zinc finger homeodomain transcription factors and mitogen-activated protein kinase kinase kinases, respectively. These resources provide an approach for genome-wide genetic screens of the functionally redundant gene space in Arabidopsis.
Measuring the success of library 2.0 technologies in the African context
Authors: Tandi Lwoga Edda 
Published: August 2013

PurposeThis study aims to examine the suitability of information systems (IS) success model in the adoption of library 2.0 technologies among undergraduate students in the African context, and focused at the Muhimbili University of Health and Allied Sciences (MUHAS) of Tanzania.Design/methodology/approachBased on the IS success model, the study re‐specified and validated the IS model to examine adoption of library 2.0 technologies via a structural equation modeling (SEM) approach. The study examined the role of quality (service quality, information quality and system quality) in influencing user perceived net benefits, satisfaction and intention to reuse library 2.0 application. A case study research design was used in this study. Self‐administered questionnaire were distributed to all first year undergraduate students (n=408) at MUHAS, with a rate of return of 71.8%.FindingsThe study findings confirm the validity of using the proposed IS model for library 2.0 adoption assessment. The users’ intention to reuse is quite important, and accurately predicts the usage behaviour of library 2.0 services. The perceived net benefits had the strongest effect on users’ intention to reuse library 2.0 systems than any other determinants within the model. Among the three quality‐related constructs, service quality had the strongest total effect on perceived net benefits and intention to reuse. Compared to system quality, information quality had the largest effect on user satisfaction. It is thus important for librarians to consider all these factors for effective adoption of library 2.0 projects in research and academic institutions.OriginalityThis is the first comprehensive study focusing on the health sciences library patron's usage behaviour of library 2.0 applications in Tanzania, and reveals findings that are useful for planning and implementing library 2.0 initiatives in other institutions with similar conditions.
Student‐driven health promotion activities
Authors: Kostenius Catrine 
Published: August 2013

PurposeThe aim was to examine how students in the arctic region of Sweden experienced creating, leading, and participating in student‐driven health promoting activities in cooperation with their teacher.Design/methodology/approachInspired by the participatory appreciative action research (PAAR) method 19 Swedish students, ages 10‐11 participated in health promotion work in the classroom through creating, leading, participating in and evaluating their own and their peers’ health promoting activities.FindingsStudents developed three themes and related activities which they felt helped them reduce stress and have friendly fun: “the friendly touch” (music and student massage), “the outdoor run for fun” (student physical activity in outdoors), and the sounds of well‐being (music).Practical implicationsThis paper provides a comprehensive understanding of how students experienced creating, leading, and participating in student‐driven health promoting activities in cooperation with their teacher, and reveals that when students were asked to choose health promoting activities, they were not only in line with existing research but were able to reflect on how to develop good practice. Students are competent to lead health promoting activities with the support of their teacher and participating in health promoting activities lead by their peers.Originality/valueThe empowerment‐based group assignment in this study offers an example of implementing health promoting activities in school to increase health literacy useful for health educators and teachers.
Moderating teen drinking: combining social marketing and education
Authors: Rundle‐Thiele Sharyn , Russell‐Bennett Rebekah , Leo Cheryl , Dietrich Timo 
Published: August 2013

PurposeThis paper outlines a pilot study that was undertaken in Australia in 2011 that combined social marketing with education. An intervention targeting 14‐16 year olds to influence attitudes and behavioural intentions towards moderate drinking was developed and tested. Game On:Know alcohol (GO:KA) is a six‐module intervention that is delivered to a year level cohort in an auditorium. GO:KA combines a series of online and offline experiential activities to engage (with) students.Design/methodologyFollowing social marketing benchmark criteria, formative research and competitive analysis were undertaken to create, implement and evaluate an intervention. The intervention was delivered in one all boys’ and one all girls’ school in April and June 2011, respectively. A total of 223 Year 10 students participated in GO:KA with the majority completing both pre‐ and post‐surveys. Paired samples t‐tests and descriptive analysis were used to assess attitudinal and behavioural intention change.FindingsAttitudinal change was observed in both schools while behavioural intentions changed for girls and not boys according to paired samples t‐testing. Post hoc testing indicated gender differences.Research limitationsThe lack of a control group is a key limitation of the current research that can be overcome in the 20 school main study to be conducted in 2013‐2015.Originality/valueThe current study provides evidence to suggest that a combined social marketing and education intervention can change teenage attitudes towards moderate drinking whilst only changing behavioural intentions for female teenagers. Analysis of the intervention provides insight into gender differences and highlights the need for a segmented approach.