bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Drift Video Transects and Maximum Likelihood Geostatistics for Quantifying and Monitoring Exploited Subpopulations of Loxechinus albus at a Mesoscale
Authors: Molinet Carlos , Barahona Nancy , Díaz Manuel , Díaz Patricio A. , Millanao María Olga , Araya Pablo , Subiabre Dagoberto , Niklitschek Edwin J. 
Published: March 2016

Abstract
Population monitoring of benthic species has been complicated by difficulties in defining appropriate spatial units for making observations that are relevant to the management of these fisheries. In many cases, this has led to the application of indirect models of stock evaluation using catch and effort information for estimating global quotas, in spite of the fact that experience suggests that limit reference points should be used. The aim of this study was to research the spatial distribution pattern of the Chilean sea urchin Loxechinus albus at sites identified as fishing beds through direct evaluation. Thus, video transect recordings were used and geostatistical methods were applied to determine the presence of significant spatial units. We found significant spatial structures represented by beds of 1–120 ha with 20,000–2,300,000 sea urchins that revealed fragmentation of the exploited L. albus populations within the study area. Smaller beds were observed close to the landing ports, suggesting that, in the extreme north of the study area, the beds were “in transition” toward becoming unoccupied habitats. This fragmentation is influenced by first-order (habitat availability) and second-order (principally fishing and recruitment) effects. The bed structure observed can be classified as mesoscale, where contraction and expansion dynamics operate. This can lead to persistence, extinction, and reemergence over periods that span more than a generation. Observing the expansion–contraction of these beds can, therefore, be extremely informative when interpreting population and large-scale fishery dynamics. Our hypothesis is that the structure of beds observed is associated with local fishery indicators and therefore can be used to monitor and improve management on a regional scale. This would be particularly useful for such complex regions as the Chilean inland sea, although the methodology requires further adjustment.
Received May 14, 2015; accepted November 12, 2015
Dynamics between the fishbone instability and nonlocal transient transport in HL-2A NBI plasmas
Authors: Chen W. , Xu Y. , Ding X.T. , Shi Z.B. , Jiang M. , Zhong W.L. , Ji X.Q. 
Published: March 2016

Abstract
Understanding of nonlocal electron heat transport is of key importance for current magnetic confinement fusion research. Global nonlocal response presents a fundamental challenge to the standard anomalous transport model based on local microinstabilities and turbulence. Here, we present for the first time a new nonlocal phenomenon triggered by the fishbone instability in HL-2A neutral beam injection plasmas. Rapid core heating leads to a simultaneous decrease in temperature at the plasma edge. The effect reveals fast anomalous transport of core heat pulses to the plasma edge, not compatible with diffusive time scales. More importantly,

variations at different locations are restricted by the intensity of magnetic fluctuations. The

and

form two types of hysteresis loops at two sides of the inversion radius. The ECEIs show that the 2D mode structure of the fishbone is intensive shearing/spiraling during the nonlocal transport. Experimental results suggest that magnetic perturbation, long-range correlation, mesoscale structure and

flow play crucial roles in the nonlocal response. The Hurst exponent and auto-correlation coefficient indicate that the nonlocal transport is potentially linked to the self-organized critical (SOC) dynamics. This work will be beneficial for understanding of the plasma dynamics in future fusion reactors.
MeCorS: Metagenome-enabled error correction of single cell sequencing reads
Authors: Bremges Andreas , Singer Esther , Woyke Tanja , Sczyrba Alexander 
Published: March 2016

Abstract
Summary: We present a new tool, MeCorS, to correct chimeric reads and sequencing errors in Illumina data generated from single amplified genomes (SAGs). It uses sequence information derived from accompanying metagenome sequencing to accurately correct errors in SAG reads, even from ultra-low coverage regions. In evaluations on real data, we show that MeCorS outperforms BayesHammer, the most widely used state-of-the-art approach. MeCorS performs particularly well in correcting chimeric reads, which greatly improves both accuracy and contiguity of de novo SAG assemblies.
Availability and implementation: https://github.com/metagenomics/MeCorS
Contact: abremges@cebitec.uni-bielefeld.de
Supplementary information: Supplementary data are available at Bioinformatics online.
The Barents Sea euphausiids: methodological aspects of monitoring and estimation of abundance and biomass
Authors: Eriksen Elena , Skjoldal Hein Rune , Dolgov Andrey V. , Dalpadado Padmini , Orlova Emma L. , Prozorkevich Dmitry V. 
Published: March 2016

Abstract
Sampling of euphausiids is difficult because of their intermediate size between macrozooplankton and micronekton. The Barents Sea is one of the few marine areas where there have been long-term studies of euphausiids. We have examined three monitoring datasets on euphausiids and consider likely sources of errors associated with the sampling. Results indicated a high degree of patchiness in the distribution of euphausiids, even at the largest scale of sampling with a pelagic trawl. This indicates that euphausiids may occur in large, but infrequent, swarms that have a low probability of being sampled by small nets. The mean biomass of euphausiids sampled with MOCNESS was 2 g wet weight m−2 integrated over the water column, which is an underestimate due to avoidance of large individuals. The mean biomass obtained with pelagic trawl in the upper 60 m of water at night during an autumn survey was 10 g wet weight m−2. The plankton net on bottom trawl collected mean and median density of euphausiids (0.1–0.2 g wet weight m−3) near bottom during a winter survey similar to the values found with pelagic trawl in the upper layer during autumn. The mean density for the autumn survey showed an increase from 2000 to 2011, while the winter survey showed generally a decrease from 2000–2007 to 2011. The increase in the autumn series coincided with a general warming trend presumably with a larger influx of euphausiids with Atlantic water, notably of Meganyctiphanes norvegica. In contrast, the decline during winter may reflect a decrease, particularly of Thysanoessa raschii in the southeastern Barents Sea in the most recent years. Improvements in sampling gears combined with more and better use of acoustical and optical technologies offer great promise for improved monitoring and quantification of the roles of euphausiids in the Barents Sea ecosystem.
Data-driven health management: reasoning about personally generated data in diabetes with information technologies
Authors: Mamykina Lena , Levine Matthew E , Davidson Patricia G , Smaldone Arlene M , Elhadad Noemie , Albers David J 
Published: March 2016

Objective To investigate how individuals with diabetes and diabetes educators reason about data collected through self-monitoring and to draw implications for the design of data-driven self-management technologies.
Materials and Methods Ten individuals with diabetes (six type 1 and four type 2) and 2 experienced diabetes educators were presented with a set of self-monitoring data captured by an individual with type 2 diabetes. The set included digital images of meals and their textual descriptions, and blood glucose (BG) readings captured before and after these meals. The participants were asked to review a set of meals and associated BG readings, explain differences in postprandial BG levels for these meals, and predict postprandial BG levels for the same individual for a different set of meals. Researchers compared conclusions and predictions reached by the participants with those arrived at by quantitative analysis of the collected data.
Results The participants used both macronutrient composition of meals, most notably the inclusion of carbohydrates, and names of dishes and ingredients to reason about changes in postprandial BG levels. Both individuals with diabetes and diabetes educators reported difficulties in generating predictions of postprandial BG; their predictions varied in their correlations with the actual captured readings from r = 0.008 to r = 0.75.
Conclusion Overall, the study showed that identifying trends in the data collected with self-monitoring is a complex process, and that conclusions reached by both individuals with diabetes and diabetes educators are not always reliable. This suggests the need for new ways to facilitate individuals’ reasoning with informatics interventions.
Sociocultural variation in attitudes toward use of genetic information and participation in genetic research by race in the United States: implications for precision medicine
Authors: Dye Timothy , Li Dongmei , Demment Margaret , Groth Susan , Fernandez Diana , Dozier Ann , Chang Jack 
Published: March 2016

AbstractBackground “Precision medicine” (PM) requires researchers to identify actionable genetic risks and for clinicians to interpret genetic testing results to patients. Whether PM will equally benefit all populations or exacerbate existing disparities is uncertain.Methods We ascertained attitudes toward genetic testing and genetic research by race in the United States using the online Amazon mTurk US workforce (n = 403 White; n = 56 African American (AA)). Generalized linear models were used to test differences in beliefs and preferences by race, adjusting for sociodemographics and prior genetic experience.Results AA were less likely than White to believe that genetic tests should be promoted or made available. Further, AA were less likely to want genetic testing results or to participate in genetic research.Conclusions Important dimensions that underlay PM are not universally accepted by all populations. Without clear attention to concerns, AA communities may not equally benefit from the rapidly-emerging trend in PM-centered research and clinical practice.
Two-fraction high-dose-rate brachytherapy within a single day combined with external beam radiotherapy for prostate cancer: single institution experience and outcomes
Authors: Liu Junyang , Kaidu Motoki , Sasamoto Ryuta , Ayukawa Fumio , Yamana Nobuko , Sato Hiraku , Tanaka Kensuke , Kawaguchi Gen , Ohta Atsushi , Maruyama Katsuya , Abe Eisuke , Kasahara Takashi , Nishiyama Tsutomu , Tomita Yoshihiko , Aoyama Hidefumi 
Published: March 2016

Abstract
We investigated the outcomes of treatment for patients with localized prostate cancer (PCa) treated with 3D conformal radiation therapy (3D-CRT) followed by two-fraction high-dose-rate brachytherapy within a single day (2-fr.-HDR-BT/day) at a single institution. A total of 156 consecutive Asian males (median age, 67 years) were enrolled. To compare our findings with those of other studies, we analyzed our results using the D'Amico classification, assigning the patients to low- ( n = 5; 3.2%), intermediate- ( n = 36; 23.1%) and high-risk ( n = 115; 73.7%) groups (Stage T3 PCa patients were classified as high-risk). One patient in the D'Amico low-risk group (20%), 13 intermediate-risk patients (36.1%) and 99 high-risk patients (86.1%) underwent androgen deprivation therapy. We administered a prescription dose of 39 Gy in 13 fractions of 3D-CRT combined with 18 Gy of HDR-BT in two 9-Gy fractions delivered within a single day. We did not distinguish between risk groups in determining the prescription dose. The median follow-up period was 38 months. Of the 156 patients, one died from primary disease and five died from other diseases. The 3-year overall survival (OS) rates were 100%, 100% and 93.7%, and the 3-year ‘biochemical no evidence of disease (bNED)’ rates were 100%, 100% and 96.9% for the D'Amico low-, intermediate- and high-risk groups, respectively. No patient developed ≥ Grade 3 early toxicity. The Grade 3 late genitourinary toxicity rate was 2.6%, and no ≥ Grade 3 late gastrointestinal toxicity occurred. The efficacy and safety of this study were satisfactory, and longer-term follow-up is necessary.
Characteristics of interventional cardiologists and their work practices for the study on radiation-induced lens opacities based on the methodology developed by ELDO—preliminary results
Authors: Domienik Joanna , Gryglak Szymon , Jurewicz Joanna 
Published: March 2016

Abstract
Preliminary results of the Polish epidemiology study on eye lens opacities among interventional cardiologists (ICs), based on the methodology proposed by ELDO (epidemiological studies of radio-induced cataracts in interventional cardiologists and radiologists: methodology implementation), are presented. The aim of the study is to test the hypothesis concerning the excess risk of cataract in the group of ICs. The first results concern the study population characteristics, including the most important confounding factors for cataract, as well as a detailed description of the work practices in interventional cardiology needed in order to reconstruct the cumulative eye lens dose. The data from 69 ICs and 23 controls collected based on the general medical questionnaire and the occupational questionnaire (for ICs only) were analyzed. The mean age of ICs and of the control group was 41 and 44, respectively, while the mean duration of work for exposed physicians was 9 years. The analysis of the data from the occupational questionnaire concerning the procedures performed, the use of various access routes, as well as radiation protection tools (eye lens glasses, ceiling suspended transparent shield, etc.) are also presented. On the basis of this information and additional assumptions about the doses per procedure (as well as reduction factors for various types of radiation measures), the cumulative doses to the eye lens of ICs were evaluated. They ranged up to 1.55 Sv and 0.4 Sv for left and right eye, respectively; however, the dose to only 3% of ICs exceeded the new threshold for development of eye lens opacities (0.5 Gy) proposed by the ICRP.
Effects of stand characteristics on tree species richness in and around a conservation area of northeast Bangladesh
Authors: Pavel Muha Abdullah Al , Mukul Sharif A. , Uddin Mohammad Belal , Harada Kazuhiro , Arfin Khan Mohammed A. S. 
Published: March 2016

AbstractWe investigated the effect of tree cover, forest patch and disturbances on tree species richness in a highly diverse conservation area of northeast Bangladesh. A systematic sampling protocol was adopted and 80 sub-plots from twenty five 1 ha plots were used for the vegetation survey. Linear regression analysis was performed to understand the effect of patch area, disturbances and tree cover on tree species richness. Ordination using Redundancy analysis (RDA) and Non-metric Multi Dimensional Scaling (NMDS) were also performed to explore the tree species compositional similarities along the stand characteristics gradient and locations of the sample plots. Our study revealed that, forest patch size has greater influence on species richness. Areas with medium level of disturbances have shown greater species richness. In constrained ordination the selected explanatory variables regulated the richness of common species. Our findings can be useful for better forest management and restoration of landscapes of conservation needs using ecologically important species.
The Deceptively Simple N170 Reflects Network Information Processing Mechanisms Involving Visual Feature Coding and Transfer Across Hemispheres
Authors: Ince Robin A. A. , Jaworska Kasia , Gross Joachim , Panzeri Stefano , van Rijsbergen Nicola J. , Rousselet Guillaume A. , Schyns Philippe G. 
Published: March 2016

AbstractA key to understanding visual cognition is to determinewhere,whenandhowbrain responses reflect the processing of the specific visual features that modulate categorization behavior—thewhat.The N170 is the earliest Event-Related Potential (ERP) that preferentially responds to faces. Here, we demonstrate that a paradigmatic shift is necessary to interpret the N170 as the product of an information processing network that dynamically codes and transfers face features across hemispheres, rather than as a local stimulus-driven event. Reverse-correlation methods coupled with information-theoretic analyses revealed that visibility of the eyes influences face detection behavior. The N170 initially reflects coding of the behaviorally relevant eye contralateral to the sensor, followed by a causal communication of the other eye from the other hemisphere. These findings demonstrate that the deceptively simple N170 ERP hides a complex network information processing mechanism involving initial coding and subsequent cross-hemispheric transfer of visual features.
Correlation/causation in ecology: towards mechanistic explanations for the Species-Area Relationship
Authors: Prestes Andersonn 
Published: March 2016

AbstractThere is a common intuition in biology that strict laws are very difficult to be found. Still, there are recurrent patterns in nature, suggesting broad generalizations and understanding of phenomena. The problem is that many generalizations in biology, especially in the form of correlations, might be decoupled from causality, weakening their power of explanation. Here, I bring an example on the Species-Area Relationship (SAR). The SAR is a well-known generalization in biology. The recurrent pattern states a positive relationship between area size and species richness. Understanding the mechanisms why there is a correlation between area and diversity remains a major challenge. I suggest an explicitly focus on mechanistic explanations for the SAR. I propose to use the integration, comparison and interpretation of other (associated or secondary) natural patterns in the searching for causal explanations. Areaper semight not account for causality in species diversification or absolute species richness in larger regions. Biotic and abiotic factors of a given area might be studied in order to discover the causal underpinnings of the SAR.
Contour junctions underlie neural representations of scene categories in high-level human visual cortex
Authors: Choo Heeyoung , Walther Dirk. B. 
Published: March 2016

AbstractHumans efficiently grasp complex visual environments, making highly consistent judgments of entry-level category despite their high variability in visual appearance. How does the human brain arrive at the invariant neural representations underlying categorization of real-world environments? We here show that the neural representation of visual environments in scenes-selective human visual cortex relies on statistics of contour junctions, which provide cues for the three-dimensional arrangement of surfaces in a scene. We manipulated line drawings of real-world environments such that statistics of contour orientations or junctions were disrupted. Manipulated and intact line drawings were presented to participants in an fMRI experiment. Scene categories were decoded from neural activity patterns in the parahippocampal place area (PPA), the occipital place area (OPA) and other visual brain regions. Disruption of junctions but not orientations led to a drastic decrease in decoding accuracy in the PPA and OPA, indicating the reliance of these areas on intact junction statistics. Accuracy of decoding from early visual cortex, on the other hand, was unaffected by either image manipulation. We further show that the correlation of error patterns between decoding from the scene-selective brain areas and behavioral experiments is contingent on intact contour junctions. Finally, a searchlight analysis exposes the reliance of visually active brain regions on different sets of contour properties. Statistics of contour length and curvature dominate neural representations of scene categories in early visual areas and contour junctions in high-level scene-selective brain regions.
mixMC: a multivariate statistical framework to gain insight into Microbial Communities
Authors: Lê Cao Kim-Anh , Costello Mary-Ellen , Lakis Vanessa Anne , Bartolo François , Chua Xin-Yi , Brazeilles Rémi , Rondeau Pascale 
Published: March 2016

AbstractCulture independent techniques, such as shotgun metagenomics and 16S rRNA amplicon sequencing have dramatically changed the way we can examine microbial communities. Recently, changes in microbial community structure and dynamics have been associated with a growing list of human diseases. The identification and comparison of bacteria driving those changes requires the development of sound statistical tools, especially if microbial biomarkers are to be used in a clinical setting.We presentmixMC, a novel multivariate data analysis framework for metagenomic biomarker discovery.mixMCaccounts for the compositional nature of 16S data and enables detection of subtle differences when high inter-subject variability is present due to microbial sampling performed repeatedly on the same subjects but in multiple habitats. Through data dimension reduction the multivariate methods provide insightful graphical visualisations to characterise each type of environment in a detailed manner.We appliedmixMCto 16S microbiome studies focusing on multiple body sites in healthy individuals, compared our results with existing statistical tools and illustrated added value of using multivariate methodologies to fully characterise and compare microbial communities.
Silent screams and muffled cries
Authors: Walton Grant W 
Published: March 2016

Purpose– The purpose of this paper is to examine the key causes of and solutions to corruption in Papua New Guinea (PNG) and suggest ways for improving anti-corruption efforts.Design/methodology/approach– This paper comprises a desk-based review of academic literature, policy documents and media.Findings– Fighting corruption in PNG requires an understanding of and response to local political, historic, cultural and economic issues. In particular, anti-corruption actors need to pay attention to: first, the opportunities and threats associated with state politics; second, the structural conditions that cause citizens to support corruption; third, the role of non-state actors in causing corruption; and fourth, ensuring stronger legal responses to corruption that result in prosecutions.Originality/value– This paper highlights key issues which anti-corruption organisations in PNG should address, examines state and non-state causes of corruption, and provides an updated analysis of key drives and solutions to corruption in PNG.