bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dam Removal Increases American Eel Abundance in Distant Headwater Streams
Authors: Hitt Nathaniel P. , Eyler Sheila , Wofford John E. B. 
Published: July 2012

AbstractAmerican eel Anguilla rostrata abundances have undergone significant declines over the last 50 years, and migration barriers have been recognized as a contributing cause. We evaluated eel abundances in headwater streams of Shenandoah National Park, Virginia, to compare sites before and after the removal of a large downstream dam in 2004 (Embrey Dam, Rappahannock River). Eel abundances in headwater streams increased significantly after the removal of Embrey Dam. Observed eel abundances after dam removal exceeded predictions derived from autoregressive models parameterized with data prior to dam removal. Mann–Kendall analyses also revealed consistent increases in eel abundances from 2004 to 2010 but inconsistent temporal trends before dam removal. Increasing eel numbers could not be attributed to changes in local physical habitat (i.e., mean stream depth or substrate size) or regional population dynamics (i.e., abundances in Maryland streams or Virginia estuaries). Dam removal was associated with decreasing minimum eel lengths in headwater streams, suggesting that the dam previously impeded migration of many small‐bodied individuals (<300 mm TL). We hypothesize that restoring connectivity to headwater streams could increase eel population growth rates by increasing female eel numbers and fecundity. This study demonstrated that dams may influence eel abundances in headwater streams up to 150 river kilometers distant, and that dam removal may provide benefits for eel management and conservation at the landscape scale.
Comparison of Radiotelemetry and Microsatellites for Determining the Origin of Yukon River Chinook Salmon
Authors: Flannery Blair G. , Crane Penny A. , Eiler John H. , Beacham Terry D. , Decovich Nick A. , Templin William D. , Schlei Ora L. , Wenburg John K. 
Published: July 2012

Abstract
Chinook salmon Oncorhynchus tshawytscha support important subsistence and commercial fisheries throughout the Yukon River. Low returns and diverse user groups have made management of these fisheries contentious and have necessitated information on the origin of the spawning migration and harvest. Here we compare estimates of individual assignment and stock composition derived from genetic and radiotelemetry data collected from the same Chinook salmon. Radiotelemetry and genetic individual assignments were highly concordant. Agreement between methods for individual assignment was 79% to region and 93% to country when using the most probable genetic criterion, improving to 94% for region and 98% for country when using the ≥95% probability genetic criterion; however, under the more stringent criterion, fewer individuals could be assigned. Further analysis showed that estimates of stock composition based on radiotelemetry and genetic methods were within 6% of each other and were not significantly different. The concordance between estimates of individual assignment and stock composition from the radiotelemetry and genetic methods indicates that both methods are credible tools for fishery assessment of Yukon River Chinook salmon.
Received October 14, 2011; accepted April 17, 2012
Differences in Paddlefish Populations among Impoundments of the Arkansas River, Arkansas
Authors: Leone Frank J. , Stoeckel Joseph N. , Quinn Jeffrey W. 
Published: July 2012

Abstract
Most large rivers within the range of paddlefish Polyodon spathula are fragmented by dams. However, little research has been done to determine if population characteristics (e.g., growth, mortality, density) vary among impoundments within river systems and how this may influence the risk of overfishing. Population characteristics and the potential for commercial overfishing were assessed for paddlefish in three impoundments of the Arkansas River, Arkansas (Pool 13, Ozark Lake, and Lake Dardanelle). Paddlefish (n = 751) were collected with gill nets from November 2003 to March 2005. Paddlefish from the most lentic and most heavily fished pool, Lake Dardanelle, had the lowest catch rate, grew fastest, and had the highest mean condition factor, weight, fecundity, and total annual mortality (67%). In contrast, paddlefish from the most lotic impoundment that was less intensively fished, Pool 13, had the highest catch rate, slowest growth, and the lowest mean condition, weight, fecundity, and total annual mortality (53%). The Lake Dardanelle paddlefish fishery appeared to show signs of commercial overfishing when managed with a 914-mm eye fork length minimum length limit and a 151-d season. Beverton–Holt population simulations modeled by impoundment indicated Lake Dardanelle was more sensitive to overfishing than the other pools. Although there was limited movement among pools, results of this study indicate that population characteristics vary among the three adjacent impoundments on the Arkansas River and that they should be managed as separate management units.
Received November 15, 2011; accepted April 13, 2012
Preliminary Study of Trap Bycatch in the Gulf of Maine's Northern Shrimp Fishery
Authors: Moffett Cinamon , Chen Yong , Hunter Margaret 
Published: July 2012

Abstract
Shrimp are one of the most economically valued and internationally traded fisheries products in the world, but there are persistent concerns over the environmental impact of shrimp fisheries, particularly the bycatch. In the Gulf of Maine (GOM), the northern shrimp Pandalus borealis are fished by two types of gear–trawls and traps. Bycatch rates for the trawl fishery were studied previously, but little has been documented for the trap fishery. In this study, onboard observers quantified bycatch on several trap boats along the central coast of Maine during the 2010 and 2011 fishing seasons (i.e., winter). This study found that the average bycatch level for Maine's northern shrimp trap fishery for the areas covered in the study was 1.21% in 2010 and 1.11% in 2011 by weight of landed catch. Although bycatch level and bycatch species composition varied on both temporal and spatial scales, the level of bycatch involved with the GOM's northern trap shrimp fishery was low compared with the global wild-caught shrimp fisheries. This study adds evidence of the low ecosystem impact of sustainably harvested coldwater trap-caught shrimp. Additional samples are needed for a complete understanding of bycatch levels on both temporal and spatial scales in Maine's northern shrimp trap fishery.
Received June 23, 2011; accepted April 19, 2012
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts
Authors: Ryan Michael C. , Cleland James , Kim RyangGuk , Wong Wing Chung , Weinstein John N. 
Published: July 2012

Abstract
Summary: SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice variation. It displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats.
Availability and implementation: SpliceSeq is freely available at http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview. The application is a Java program that can be launched via a browser or installed locally. Local installation requires MySQL and Bowtie.
Contact: mryan@insilico.us.com
Supplementary Information: Supplementary data are available at Bioinformatics online.
Discriminative local subspaces in gene expression data for effective gene function prediction
Authors: Puelma Tomas , Gutiérrez Rodrigo A. , Soto Alvaro 
Published: July 2012

Abstract
Motivation: Massive amounts of genome-wide gene expression data have become available, motivating the development of computational approaches that leverage this information to predict gene function. Among successful approaches, supervised machine learning methods, such as Support Vector Machines (SVMs), have shown superior prediction accuracy. However, these methods lack the simple biological intuition provided by co-expression networks (CNs), limiting their practical usefulness.
Results: In this work, we present Discriminative Local Subspaces (DLS), a novel method that combines supervised machine learning and co-expression techniques with the goal of systematically predict genes involved in specific biological processes of interest. Unlike traditional CNs, DLS uses the knowledge available in Gene Ontology (GO) to generate informative training sets that guide the discovery of expression signatures: expression patterns that are discriminative for genes involved in the biological process of interest. By linking genes co-expressed with these signatures, DLS is able to construct a discriminative CN that links both, known and previously uncharacterized genes, for the selected biological process. This article focuses on the algorithm behind DLS and shows its predictive power using an Arabidopsis thaliana dataset and a representative set of 101 GO terms from the Biological Process Ontology. Our results show that DLS has a superior average accuracy than both SVMs and CNs. Thus, DLS is able to provide the prediction accuracy of supervised learning methods while maintaining the intuitive understanding of CNs.
Availability: A MATLAB® implementation of DLS is available at http://virtualplant.bio.puc.cl/cgi-bin/Lab/tools.cgi
Contact: tfpuelma@uc.cl
Supplementary Information: Supplementary data are available at http://bioinformatics.mpimp-golm.mpg.de/.
Dysnatraemia in heart failure
Authors: Deubner Nikolas , Berliner Dominik , Frey Anna , Güder Gülmisal , Brenner Susanne , Fenske Wiebke , Allolio Bruno , Ertl Georg , Angermann Christiane E. , Störk Stefan 
Published: July 2012

AimsTo investigate in detail the correlates of dysnatremia, and to estimate its differential prognostic relevance in patients with heart failure with reduced or preserved LVEF.BackgroundHyponatraemia has been shown to carry important prognostic information in patients with heart failure with reduced left ventricular ejection fraction (LVEF). However, exact serum sodium cut‐off levels are not defined and the implications for heart failure with preserved ejection fraction (HF‐pEF) are unclear. The prognostic value of hypernatraemia has not been investigated systematically. Therefore, the aim of this study was to investigate in detail the correlates of dysnatraemia, and to estimate its differential prognostic relevance in patients with heart failure with reduced or preserved LVEF.Methods and resultsOne thousand consecutive patients with heart failure of any cause and severity from the Würzburg Interdisciplinary Network for Heart Failure registry were included. Non‐linear models for the association between serum sodium and mortality risk were calculated using restricted cubic splines and Cox proportional hazard regression. Median follow‐up time for survivors was 5.1 years.ResultsIndependent correlates of dysnatraemia included guideline‐recommended medication for chronic heart failure, indicators of renal function, and reverse associations with established cardiac risk factors. Overall mortality was 56%. Both hyponatraemia (n = 72) and hypernatraemia (n = 98) were associated with a significantly increased mortality risk: hazard ratio (HR) 2.10, 95% confidence interval (CI) 1.60–2.77; and HR 1.91, 95% CI 1.49–2.45, respectively. A U‐shaped association of serum sodium with mortality risk was found. Prognosis was best for patients with high normal sodium levels, i.e. 140–145 mmol/L.ConclusionsBoth hypo‐ and hypernatraemia indicate a markedly compromised prognosis in heart failure regardless of LVEF. Sodium levels within the reference range carry differential information on survival, with serum levels of 135–139 mmol/L indicating an increased mortality risk.
Phospholamban R14del mutation in patients diagnosed with dilated cardiomyopathy or arrhythmogenic right ventricular cardiomyopathy: evidence supporting the concept of arrhythmogenic cardiomyopathy
Authors: van der Zwaag Paul A. , van Rijsingen Ingrid A.W. , Asimaki Angeliki , Jongbloed Jan D.H. , van Veldhuisen Dirk J. , Wiesfeld Ans C.P. , Cox Moniek G.P.J. , van Lochem Laura T. , de Boer Rudolf A. , Hofstra Robert M.W. , Christiaans Imke , van Spaendonck‐Zwarts Karin Y. , Lekanne dit Deprez Ronald H. , Judge Daniel P. , Calkins Hugh , Suurmeijer Albert J.H. , Hauer Richard N.W. , Saffitz Jeffrey E. , Wilde Arthur A.M. , van den Berg Maarten P. , van Tintelen J. Peter 
Published: July 2012

AimsTo investigate whether phospholamban gene (PLN) mutations underlie patients diagnosed with either arrhythmogenic right ventricular cardiomyopathy (ARVC) or idiopathic dilated cardiomyopathy (DCM).Methods and resultsWe screened a cohort of 97 ARVC and 257 DCM unrelated index patients for PLN mutations and evaluated their clinical characteristics. PLN mutation R14del was identified in 12 (12 %) ARVC patients and in 39 (15 %) DCM patients. Haplotype analysis revealed a common founder, estimated to be between 575 and 825 years old. A low voltage electrocardiogram was present in 46 % of R14del carriers. Compared with R14del– DCM patients, R14del+ DCM patients more often demonstrated appropriate implantable cardioverter defibrillator discharge (47 % vs. 10 %, P < 0.001), cardiac transplantation (18 % vs. 2 %, P < 0.001), and a family history for sudden cardiac death (SCD) at < 50 years (36 % vs. 16 %, P = 0.007). We observed a similar pattern in the ARVC patients although this was not statistically significant. The average age of 26 family members who died of SCD was 37.7 years. Immunohistochemistry in available myocardial samples revealed absent/depressed plakoglobin levels at intercalated disks in five of seven (71 %) R14del+ ARVC samples, but in only one of nine (11 %) R14del+ DCM samples (P = 0.03).ConclusionsThe PLN R14del founder mutation is present in a substantial number of patients clinically diagnosed with DCM or ARVC. R14del+ patients diagnosed with DCM showed an arrhythmogenic phenotype, and SCD at young age can be the presenting symptom. These findings support the concept of ‘arrhythmogenic cardiomyopathy’.
A Ubiquitin Ligase of Symbiosis Receptor Kinase Involved in Nodule Organogenesis
Authors: Yuan Songli , Zhu Hui , Gou Honglan , Fu Weiwei , Liu Lijing , Chen Tao , Ke Danxia , Kang Heng , Xie Qi , Hong Zonglie , Zhang Zhongming 
Published: July 2012

Abstract
The symbiosis receptor kinase (SymRK) is required for morphological changes of legume root hairs triggered by rhizobial infection. How protein turnover of SymRK is regulated and how the nodulation factor signals are transduced downstream of SymRK are not known. In this report, a SymRK-interacting E3 ubiquitin ligase (SIE3) was shown to bind and ubiquitinate SymRK. The SIE3-SymRK interaction and the ubiquitination of SymRK were shown to occur in vitro and in planta. SIE3 represents a new class of plant-specific E3 ligases that contain a unique pattern of the conserved CTLH (for C-terminal to LisH), CRA (for CT11-RanBPM), and RING (for Really Interesting New Gene) domains. Expression of SIE3 was detected in all tested tissues of Lotus japonicus plants, and its transcript level in roots was enhanced by rhizobial infection. The SIE3 protein was localized to multiple subcellular locations including the nuclei and plasma membrane, where the SIE3-SymRK interaction took place. Overexpression of SIE3 promoted nodulation in transgenic hairy roots, whereas downregulation of SIE3 transcripts by RNA interference inhibited infection thread development and nodule organogenesis. These results suggest that SIE3 represents a new class of E3 ubiquitin ligase, acts as a regulator of SymRK, and is involved in rhizobial infection and nodulation in L. japonicus.
Multiple entity farms: a growing and challenging phenomenon
Authors: Featherstone Allen M. , Wood Mark A. , Herbel Kevin L. , Langemeier Michael R. 
Published: July 2012

PurposeUnderstanding complex farming organizations is important in the USA given the rapid consolidation of the agricultural production sector. Multiple entity farms arise from a desire to enhance the ability to transfer the farm from one generation to the next, a desire to affect tax liability, and a desire to affect legal liability. To determine the extent of the multiple entity phenomena and the complications that multiple entities can cause in data collection, the purpose of this article is to address the importance of multiple entities in Kansas.Design/methodology/approachAn overview of reasons leading to additional organizational complexity are discussed. Two case farms are presented to understand the depth of the complexity and how that complexity has implications for data collection.FindingsThe number of multiple entity farms is expected to continue to increase. Obtaining data through the Agricultural Resource Management Survey (ARMS) will become more difficult as production agriculture increases the use of multiple entities. ARMS must reconsider how multiple entity organizations are handled. Possible solutions include an alternative system for data collection of multiple entity farms. Documenting the prevalence of multiple entity organizations in the production sector and tracing through how those organizations are currently handled is critical to understanding potential impacts on the current data collected.Originality/valueThe National Research Council completed a review of ARMS that addressed challenges in keeping the survey relevant into the future. However, research that examines the construction of financial statements and other information had not been conducted since the early 1990s. This study fills part of that gap.
Keeping ARMS relevant: increasing its usability
Authors: Blank Steven C. , Klinefelter Danny 
Published: July 2012

PurposeThe Agricultural Resource Management Survey (ARMS) conducted annually by the USDA's Economic Research Service collects data on US agriculture, ranging from production practices to the financial condition of farm and ranch enterprises and the farm household. The purpose of this article is to consider what could make ARMS useful from a farmer's point of view.Design/methodology/approachA Delphi method is used to gather input from a panel of experts.FindingsResults show that increasing the usability of the ARMS to agricultural producers involves expanding the content and relevance of the data collected. Specific types of data needed are identified. Also, recommendations are made concerning how the usefulness and relevance of the data could be increased by refining the sample frame. Finally, it is argued here that after making some adjustments to the ARMS sample frame to create nationally representative data, the ARMS project could serve as a hugely important basis for reporting economic performance levels for American agriculture.Originality/valueThis study offers insights from agricultural finance experts on how the ARMS could be improved to expand the quality and usefulness of its output for both professionals and agricultural producers.
Keeping ARMS relevant: extracting additional information from ARMS
Authors: Featherstone Allen M. , Park Timothy A. , Weber Jeremy G. 
Published: July 2012

PurposeThe purpose of this paper is to discuss opportunities to obtain more information from the Agricultural Resource Management Survey (ARMS). Specifically, the paper will explore the issue of survey nonresponse, the development of pseudo panels, and more frequent updating of cost of production data on an enterprise basis.\Design/methodology/approachResearchers from the Land Grant University System and the Economic Research Service have relied on ARMS to evaluate the effect of agricultural, macroeconomic, and other factors on the US farm sector, farm businesses, and the households that manage them. This paper will identify gaps in understanding and proposes approaches to extract additional information from ARMS.FindingsThe relevance of ARMS in the future will depend on the ability to continue to understand potential pitfalls and areas of additional research that can develop new procedures to extract additional information. Three issues which are in need of further study include continuing to examine the issue of non‐response, refining methods to develop pseudo panel data, and examining methods to develop commodity specific financial information between the commodity specific surveys.Originality/valueThe National Research Council completed a review of ARMS to address challenges in keeping the survey relevant into the future. However, research that examines the construction of financial statements and other information had not been conducted since the early 1990s. This study fills part of that gap.
Reporting and usability of ARMS income and balance sheet data
Authors: Wilson Christine A. , Moss Charles B. , Brown D. Scott 
Published: July 2012

PurposeThe purpose of this research is to examine the usability and communication methods of the Agricultural Resource Management Survey (ARMS) data. Recommendations for improving access and usability are proposed to Economic Research Service (ERS).Design/methodology/approachThe current methods for accessing the ARMS data are described. Several accounting issues related to the usability of the data are presented. Cost of production issues related to the data are also discussed.FindingsRecommendations to ERS include: increase efforts to disseminate the ARMS results more widely, make the ARMS web tool easier to access, develop partnerships with universities, increase the value of the web tool by providing more information on the data that are already available, consider the accounting items of extraordinary income, inventory valuations, and nonmonetary income and consider issues related to cost of production items.Originality/valueBy identifying the factors limiting the current use of the ARMS data, changes can be made that may result in wider dissemination and use of the data.
Easy to chew, but hard to swallow – consumer perception of neutrally marinated meat
Authors: Konstantin Nissen Nina , Sandøe Peter , Holm Lotte 
Published: July 2012

PurposeMeat which has been injected or tumbled with water, salt, sugar and other ingredients, has been available on the Danish market for some decades and is now becoming increasingly common. However, it is not known whether this so‐called neutrally marinated meat will be appropriated by consumers in the long term, or will be destined to be a marginal second rate product. The purpose of this paper is to explore the views of consumers on neutrally marinated meat, including acceptance and potential problems for appropriation.Design/methodology/approachFour focus group interviews were conducted involving 27 Danish consumers with various socio‐demographic backgrounds.FindingsThe interviewed consumers had very little prior knowledge of neutrally marinated meat, and expressed ambivalent attitudes when introduced to it. They had favourable reactions to its taste, texture and robustness and saw the potentially low price as a positive feature. But they also viewed neutrally marinated meat as unnatural, unauthentic and potentially risky to health. Furthermore, concern was expressed due to the lack of information available to consumers and due to suspicion of unfair prices. The focus group interviews also showed that categorisation of neutrally marinated meat in different social contexts is not settled, underlining a sense of ambivalence among consumers. So, even though neutrally marinated meat is being consumed it is unclear if and when conceptual appropriation will take place.Originality/valueThis study provides a broader perspective on consumer perception of new products than found in conventional sensorial tests, including views on the processing, health aspects, ethical aspects and convenience aspects.