bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opportunistic Acoustic Telemetry Platforms: Benefits of Collaboration in the Gulf of Maine
Authors: Goulette Graham S , Hawkes James P , Kocik John F , Manning James P , Music Paul A , Wallinga John P , Zydlewski Gayle Barbin 
Published: October 2014

ABSTRACT
Biologists monitor animal behavior, habitat use, and survival through local telemetry projects. Migratory species cross these lines, connecting projects. Biologists can further these connections by expanding the area monitored, but this step is expensive. We evaluated three opportunistic platforms: (1) oceanographic buoys, (2) commercial fishing gear, and (3) drifters to test the feasibility of expanding coverage while minimizing costs. All Gulf of Maine platforms provided novel data, generating over 15,000 detections from animals released by 18 organizations. Performance was strong for buoys and commercial gear but low recovery hampered drifter utility, although advances in real-time drifter communication should improve future efficacy. Opportunistic platforms proved to be a low-cost method that can benefit researchers across aquatic systems. Animals from other studies connected us with researchers, fostered dialogue, and highlighted information gains from data sharing. Working with fishers and oceanographers also strengthens interdisciplinary and stakeholder communication and can increase overall public understanding and support.
RESUMEN
los biólogos monitorean el comportamiento, uso de hábitat y supervivencia de los animales a través de proyectos locales de telemetría. Las especies migratorias traspasan estos límites y, por consecuencia, representan una oportunidad para conectar los proyectos. Los biólogos pueden llevar aún más allá estos proyectos, expandiendo las áreas monitoreadas, sin embargo dar este paso resulta costoso. En este trabajo, se evalúan tres plataformas de oportunidad: (1) boyas oceanográficas, (2) equipos de pesca comercial y (3) cuerpos de deriva para probar la viabilidad de expandir la cobertura de los proyectos, al mismo tiempo que se minimizan los costos. Todas estas las plataformas en el Golfo de Maine proveen datos nuevos, generando más de 15,000 detecciones de animales liberados por 18 organizaciones. El desempeño fue bueno en el caso de las boyas y del equipo de pesca comercial, pero los cuerpos de deriva redujeron las utilidades debido a su lenta recuperación; no obstante, los avances alcanzados en la comunicación en tiempo real con estos artefactos debieran mejorar su efectividad en el futuro. Las plataformas de oportunidad probaron ser un método de bajo costo que puede beneficiar a los investigadores que trabajan en distintos sistemas acuáticos. Los animales estudiados en otros trabajos, permitieron conectar a los investigadores entre sí, lo que propicia el diálogo y pone en relieve la ganancia de información e intercambio de datos. El trabajo conjunto entre pescadores y oceanógrafos fortalece la interdisciplinariedad y la comunicación con los interesados y, asimismo, puede incrementar el entendimiento y el soporte del público en general.
Phenotypic and Genotypic Heterogeneity among Streptococcus iniae Isolates Recovered from Cultured and Wild Fish in North America, Central America and the Caribbean Islands
Authors: Chou Lucy , Griffin Matt J. , Fraites Trellor , Ware Cynthia , Ferguson Hugh , Keirstead Natalie , Brake John , Wiles Judy , Hawke John P. , Kearney Michael T. , Getchell Rodman G. , Gaunt Patricia , Soto Esteban 
Published: October 2014

Abstract
Streptococcus iniae, the etiological agent of streptococcosis in fish, is an important pathogen of cultured and wild fish worldwide. During the last decade outbreaks of streptococcosis have occurred in a wide range of cultured and wild fish in the Americas and Caribbean islands. To gain a better understanding of the epizootiology of S. iniae in the western hemisphere, over 30 S. iniae isolates recovered from different fish species and geographic locations were characterized phenotypically and genetically. Species identities were determined biochemically and confirmed by amplification and sequencing of the 16S rRNA gene. Repetitive-element palindromic PCR fingerprinting as well as biochemical and antimicrobial susceptibility profiles suggest that a single strain of S. iniae was responsible for two different disease outbreaks among reef fishes in the Caribbean, one in 1999 and another in 2008. Interestingly, a majority of the isolates recovered from cultured fish in the Americas were genetically distinct from the Caribbean isolates and exhibited a trend toward higher minimal inhibitory concentration with respect to several antibiotics as well as greater genetic variability. The biological significance of this genetic variability is unclear, but it could have implications for future vaccine development and treatment.
Received April 20, 2014; accepted July 7, 2014
Relationship between the peak time of hamstring stretch and activation during sprinting
Authors: Higashihara Ayako , Nagano Yasuharu , Ono Takashi , Fukubayashi Toru 
Published: October 2014

AbstractThe purpose of this study was to investigate the time series relationships between the peak musculotendon length and electromyography (EMG) activation during overground sprinting to clarify the risk of muscle strain injury incidence in each hamstring muscle. Full‐body kinematics and EMG of the right biceps femoris long head (BFlh) and semitendinosus (ST) muscles were recorded in 13 male sprinters during overground sprinting at maximum effort. The hamstring musculotendon lengths during sprinting were computed using a three‐dimensional musculoskeletal model. The time of the peak musculotendon length, in terms of the percentage of the running gait cycle, was measured and compared with that of the peak EMG activity. The maximum length of the hamstring muscles was noted during the late swing phase of sprinting. The peak musculotendon length was synchronous with the peak EMG activation in the BFlh muscle, while the time of peak musculotendon length in the ST muscle occurred significantly later than the peak level of EMG activation (p < 0.05). These results suggest that the BFlh muscle is exposed to an instantaneous high tensile force during the late swing phase of sprinting, indicating a higher risk for muscle strain injury.
No Specific Time Window Distinguishes between Community-, Healthcare-, and Hospital-Acquired Bacteremia, but They Are Prognostically Robust
Authors: Gradel Kim Oren , Nielsen Stig Lønberg , Pedersen Court , Knudsen Jenny Dahl , Østergaard Christian , Arpi Magnus , Jensen Thøger Gorm , Kolmos Hans Jørn , Schønheyder Henrik Carl , Søgaard Mette , Lassen Annmarie Touborg ,   for the Danish Collaborative Bacteraemi a Network and the Danish Observational Registry of Infectious Sndromes
Published: October 2014

Objective.We examined whether specific time windows after hospital admission reflected a sharp transition between community and hospital acquisition of bacteremia. We further examined whether different time windows to distinguish between community acquisition, healthcare association (HCA), and hospital acquisition influenced the results of prognostic models.Design.Population-based cohort study.Setting.Hospitals in 3 areas of Denmark (2.3 million inhabitants) during 2000–2011.Methods.We computed graphs depicting proportions of males, absence of comorbidity, microorganisms, and 30-day mortality pertaining to bacteremia 0, 1, 2, …, 30, and 31 days and later after admission. Next, we assessed whether different admission (0–1, 0–2, 0–3, 0–7 days) and HCA (30, 90 days) time windows were associated with changes in odds ratio (OR) and area under the receiver operating characteristic (ROC) curve for 30-day mortality, adjusting for sex, age, comorbidity, and microorganisms.Results.For 56,606 bacteremic episodes, no sharp transitions were detected on a specific day after admission. Among the 8 combined time windows, ORs for 30-day mortality varied from 1.30 (95% confidence interval [CI], 1.23–1.37) to 1.99 (95% CI, 1.48–2.67) for HCA and from 1.36 (95% CI, 1.24–1.50) to 2.53 (95% CI, 2.01–3.20) for hospital acquisition compared with community acquisition. Area under the ROC curve changed marginally from 0.684 (95% CI, 0.679–0.689) to 0.700 (95% CI, 0.695–0.705).Conclusions.No time transitions unanimously distinguished between community and hospital acquisition with regard to sex, comorbidity, or microorganisms, and no difference in 30-day mortality was seen for HCA patients in relation to a 30- or 90-day time window. ORs decreased consistently in the order of hospital acquisition, HCA, and community acquisition, regardless of time window combination, and differences in area under the ROC curve were immaterial.
The Effects of Experience on Preferences: Theory and Empirics for Environmental Public Goods
Authors: Czajkowski Mikołaj , Hanley Nick , LaRiviere Jacob 
Published: October 2014

AbstractThis article develops a choice model for environmental public goods, which allows for consumers to learn about their preferences through consumption experiences. We develop a theoretical model of Bayesian updating, perform comparative statics over the model, and show how the theoretical model can be consistently incorporated into a reduced form econometric model. Our main findings are that in a random utility model (RUM) discrete choice model, a subject's scale should increase and the variability of scale should decrease with experience if subjects are Bayesians. We then estimate the model using field data regarding preferences for one particular public good, water quality. We find strong evidence that additional experience increases scale, thereby making consumer preferences more predictable from the econometrician's perspective. We find supportive but less convincing evidence that experience decreases the variability of scale across subjects.
Measuring the wisdom of the crowds in network-based gene function inference
Authors: Verleyen W. , Ballouz S. , Gillis J. 
Published: October 2014

Abstract
Motivation: Network-based gene function inference methods have proliferated in recent years, but measurable progress remains elusive. We wished to better explore performance trends by controlling data and algorithm implementation, with a particular focus on the performance of aggregate predictions.
Results: Hypothesizing that popular methods would perform well without hand-tuning, we used well-characterized algorithms to produce verifiably ‘untweaked’ results. We find that most state-of-the-art machine learning methods obtain ‘gold standard’ performance as measured in critical assessments in defined tasks. Across a broad range of tests, we see close alignment in algorithm performances after controlling for the underlying data being used. We find that algorithm aggregation provides only modest benefits, with a 17% increase in area under the ROC (AUROC) above the mean AUROC. In contrast, data aggregation gains are enormous with an 88% improvement in mean AUROC. Altogether, we find substantial evidence to support the view that additional algorithm development has little to offer for gene function prediction.
Availability and implementation: The supplementary information contains a description of the algorithms, the network data parsed from different biological data resources and a guide to the source code (available at: http://gillislab.cshl.edu/supplements/).
Contact: jgillis@cshl.edu
deML: robust demultiplexing of Illumina sequences using a likelihood-based approach
Authors: Renaud Gabriel , Stenzel Udo , Maricic Tomislav , Wiebe Victor , Kelso Janet 
Published: October 2014

Abstract
Motivation: Pooling multiple samples increases the efficiency and lowers the cost of DNA sequencing. One approach to multiplexing is to use short DNA indices to uniquely identify each sample. After sequencing, reads must be assigned in silico to the sample of origin, a process referred to as demultiplexing. Demultiplexing software typically identifies the sample of origin using a fixed number of mismatches between the read index and a reference index set. This approach may fail or misassign reads when the sequencing quality of the indices is poor.
Results: We introduce deML, a maximum likelihood algorithm that demultiplexes Illumina sequences. deML computes the likelihood of an observed index sequence being derived from a specified sample. A quality score which reflects the probability of the assignment being correct is generated for each read. Using these quality scores, even very problematic datasets can be demultiplexed and an error threshold can be set.
Availability and implementation: deML is freely available for use under the GPL (http://bioinf.eva.mpg.de/deml/).
Contact: gabriel.reno@gmail.com or kelso@eva.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Fast and accurate site frequency spectrum estimation from low coverage sequence data
Authors: Han Eunjung , Sinsheimer Janet S. , Novembre John 
Published: October 2014

Abstract
Motivation: The distribution of allele frequencies across polymorphic sites, also known as the site frequency spectrum (SFS), is of primary interest in population genetics. It is a complete summary of sequence variation at unlinked sites and more generally, its shape reflects underlying population genetic processes. One practical challenge is that inferring the SFS from low coverage sequencing data in a straightforward manner by using genotype calls can lead to significant bias. To reduce bias, previous studies have used a statistical method that directly estimates the SFS from sequencing data by first computing site allele frequency (SAF) likelihood for each site (i.e. the likelihood a site has each possible allele frequency conditional on observed sequence reads) using a dynamic programming (DP) algorithm. Although this method produces an accurate SFS, computing the SAF likelihood is quadratic in the number of samples sequenced.
Results: To overcome this computational challenge, we propose an algorithm, ‘score-limited DP’ algorithm, which is linear in the number of genomes to compute the SAF likelihood. This algorithm works because in a lower triangular matrix that arises in the DP algorithm, all non-negligible values of the SAF likelihood are concentrated on a few cells around the best-guess allele counts. We show that our score-limited DP algorithm has comparable accuracy but is faster than the original DP algorithm. This speed improvement makes SFS estimation practical when using low coverage NGS data from a large number of individuals.
Availability and implementation: The program will be available via a link from the Novembre lab website (http://jnpopgen.org/).
Contact: ehan416@gmail.com, jnovembre@uchicago.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathways
Authors: Kang Mingon , Zhang Chunling , Chun Hyung-Wook , Ding Chris , Liu Chunyu , Gao Jean 
Published: October 2014

AbstractMotivation: Epistasis is the interactions among multiple genetic variants. It has emerged to explain the ‘missing heritability’ that a marginal genetic effect does not account for by genome-wide association studies, and also to understand the hierarchical relationships between genes in the genetic pathways. The Fisher’s geometric model is common in detecting the epistatic effects. However, despite the substantial successes of many studies with the model, it often fails to discover the functional dependence between genes in an epistasis study, which is an important role in inferring hierarchical relationships of genes in the biological pathway.Results: We justify the imperfectness of Fisher’s model in the simulation study and its application to the biological data. Then, we propose a novel generic epistasis model that provides a flexible solution for various biological putative epistatic models in practice. The proposed method enables one to efficiently characterize the functional dependence between genes. Moreover, we suggest a statistical strategy for determining a recessive or dominant link among epistatic expression quantitative trait locus to enable the ability to infer the hierarchical relationships. The proposed method is assessed by simulation experiments of various settings and is applied to human brain data regarding schizophrenia.Availability and implementation: The MATLAB source codes are publicly available at: http://biomecis.uta.edu/epistasis.Contact: gao@uta.eduSupplementary information: Supplementary data are available at Bioinformatics online.
PSR J1738+0333: the first millisecond pulsar + pulsating white dwarf binary
Authors: Kilic Mukremin , Hermes J. J. , Gianninas A. , Brown Warren R. 
Published: October 2014

Abstract
We report the discovery of the first millisecond pulsar with a pulsating white dwarf (WD) companion. Following the recent discoveries of pulsations in extremely low-mass (ELM, ≤0.3 M⊙) WDs, we targeted ELM WD companions to two millisecond pulsars with high-speed Gemini photometry. We find significant optical variability in PSR J1738+0333 with periods between roughly 1790–3060 s, consistent in time-scale with theoretical and empirical observations of pulsations in ≈0.17 M⊙ He-core ELM WDs. We additionally put stringent limits on a lack of variability in PSR J1909−3744, showing this ELM WD is not variable to &lt;0.1 per cent amplitude. Thanks to the accurate distance and radius estimates from radio timing measurements, PSR J1738+0333 becomes a benchmark for low-mass, pulsating WDs. Future, more extensive time series photometry of this system offers an unprecedented opportunity to constrain the physical parameters (including the cooling age) and interior structure of this ELM WD, and in turn, the mass and spin-down age of its pulsar companion.
Helminth prevalence among adults in rural Kenya: a stool survey for soil-transmitted helminths and schistosomiasis in Nyanza province
Authors: Andereck Jonathan W. , Kipp Aaron M. , Ondiek Michael , Vermund Sten H. 
Published: October 2014

Abstract

Background
Soil-transmitted helminth (STH) prevalence in children is high in rural southwestern Kenya, but adult prevalence data are scarce. A 2010 study of a village in Nyanza province found a pediatric STH prevalence of 44% using a direct stool-smear method. Adult STH prevalence and associated predictors was measured in the same village.

Methods
Adults (≥18 years) presenting at the out-patient department of the small hospital or community outreach events completed a short questionnaire and provided stool samples. Light microscopy for ova and larvae was conducted using a stool concentration technique to improve sensitivity. Multivariable regression models were used to identify predictors of STH prevalence.

Results
Among 344 adults, STH prevalence was 15.7% (54/344). Hookworm was most common (13.1%; 45/344), followed by Ascaris lumbricoides (6.1%; 21/344) and Trichuris trichiura (0.6%; 2/344). Twelve participants (3.5%; 12/344) had multiple STHs and three (0.9%; 3/344) had Schistosoma mansoni. Female sex, older age and lower education level were significant STH predictors.

Conclusions
Adult STH prevalence was lower than previous studies of children from the same village. Adults with the identified risk factors had a prevalence of ≥20%, which may warrant periodic, targeted deworming of adults with these risk factors given the low cost and low toxicity of anthelmintic drugs.
First Report of Tomato mottle mosaic virus Infecting Tomato in the United States
Authors: Webster Craig G. , Rosskopf Erin N. , Lucas Leon , Mellinger H. Charles , Adkins Scott 
Published: October 2014

To the best of our knowledge this is the first report of ToMMV in the United States. Our results provide further characterization of the emerging ToMMV and highlight the continued importance of tobamovirus management in solanaceous crop production. Accepted 9 September 2014. Published 12 October 2014.
First Report of Turnip vein-clearing virus in Garlic Mustard (Alliaria petiolata) in the United States
Authors: Lockhart Ben , Mollov Dimitre , Mason Shauna , Bratsch Sara 
Published: October 2014

The objective of the study was to establish the identity of a tobamo-like virus occurring naturally in garlic mustard in Minnesota, and to determine its role in the etiology of the disease. This is the first report of TVCV infection in garlic mustard. Accepted 18 September 2014. Published 14 October 2014.
Lumbar Retrolisthesis in Aging Spine
Authors: Zhu Feng , Bao Hongda , Liu Zhen , Zhu Zezhang , He Shouyu , Qiu Yong 
Published: October 2014

Study Design:
A retrospective radiographic study.

Objective:
The aim of this study is to demonstrate that lumbar retrolisthesis serves as an important compensatory mechanism and to identify the possible factor related to lumbar retrolisthesis.

Summary of Background Data:
Lumbar instability is one of the common degenerative changes, which presents as 2 radiologic features: anterolisthesis and retrolisthesis. Compared with the extensive studies on anterolisthesis, limit data are available on the characteristics and clinical relevance of lumbar retrolisthesis.

Materials and Methods:
In this study, 105 adult patients with low back pain were prospectively recruited, of which 60 patients had retrolisthesis (group 1) and 45 patients had anterolisthesis (group 2). Another 40 healthy age-matched adults (group 3) were also included to serve as the control group. Sagittal spinopelvic parameters were measured from the standing lateral radiograph, including thoracic kyphosis (TK), thoracolumbar kyphosis (TLK), lumbar lordosis (LL), pelvic incidence (PI), sacrum slope (SS), pelvic tilt (PT), sagittal vertical axis (SVA), spinosacral angle (SSA), and C7 tilt (C7T). In addition, disk degeneration was quantitatively evaluated by Pfirrmann score on T2-weighted magnetic resonance images in patients with retrolisthesis.

Results:
For all the sagittal parameters, SVA, PI, SS, and LL in retrolisthesis group were found to be significantly lower than those in the anterolisthesis group and in the control group, respectively (P<0.05), whereas TLK in retrolisthesis group was significantly larger than other 2 groups (P<0.01). In addition, the average Pfirrmann disk score was 2.11 at levels with retrolisthesis indicating that the disks were not severely degenerated.

Conclusions:
Lumbar retrolisthesis, together with thoracolumbar kyphosis, appears to be associated with mechanisms associated with regulation of sagittal balance. Low PI and disk instability due to degeneration may contribute to the development and progression of retrolisthesis.