bluuebunny/crossref_metadata_2025_split huggingface dataset:
Populations on the Brink: Low Abundance of Southern Upland Atlantic Salmon in Nova Scotia, Canada
Authors: Gibson A. Jamie F. , Bowlby Heather D. , Hardie David C. , O'Reilly Patrick T. 
Published: December 2011

Abstract
Populations of Atlantic salmon Salmo salar in the Southern Upland region of Nova Scotia, Canada, have declined to very low abundances. Sixty-three rivers in this region—9% of the total number of Canadian rivers that contain Atlantic salmon—are known to have supported populations in the recent past. Annual adult abundance data from four rivers show declines of 83–99% from peak levels in the 1980s; this pattern is consistent with trends in recreational catch within the region. Regionwide comparisons of juvenile density data from more than 50 other rivers indicate significant ongoing declines and provide evidence for river-specific extirpations. Based on surveys conducted in 2000 and again in 2008–2009, total juvenile density decreased substantially at the majority of locations; during the 2008–2009 survey, juveniles were not found at nine sites (four rivers) where they were present in 2000. Although river acidification has significantly contributed to the deterioration or extirpation of Atlantic salmon populations from many Southern Upland rivers during the last century, contemporary declines occurring in nonacidified rivers indicate that other factors are now affecting these populations. Several lines of evidence demonstrate that Southern Upland Atlantic salmon are biologically unique and that their extinction would constitute an irreplaceable loss of Atlantic salmon biodiversity.
Received November 2, 2010; accepted June 2, 2011
Determining Mark Success of 15 Combinations of Enriched Stable Isotopes for the Batch Marking of Larval Otoliths
Authors: Woodcock Skye H. , Gillanders Bronwyn M. , Munro Andrew R. , Crook David A. , Sanger Andrew C. 
Published: December 2011

Abstract
Chemical marking of otoliths via immersion in solutions of enriched stable isotopes provides a means of distinctively marking large batches of hatchery-produced fish. Four enriched stable isotopes (barium: 137Ba and 138Ba; strontium: 88Sr; magnesium: 24Mg) were used individually and in combination to determine mark success and the ability to correctly classify 15 unique batch marks in the otoliths of larval Murray cod Maccullochella peelii. Marking with the enriched stable isotopes 137Ba, 138Ba, and 88Sr (individually or in combination) produced clear and distinctive marks (98% mark success) with 93% of fish correctly classified to their respective isotope mark. Despite exposure of the fish to an altered Mg isotope ratio in the water, a corresponding shift in the otoliths was not observed (8% mark success), and many 24Mg-enriched fish were misclassified. Due to the low cost and minimal effects on hatchery protocols, the use of Sr and Ba isotopes to mark hatchery-reared fish at the larval stage has the potential to be a powerful tool in the production and management of a wide range of fish species.
Received February 25, 2011; accepted May 22, 2011
Ecological Impacts of Non-native Freshwater Fishes
Authors: Cucherousset Julien , Olden Julian D 
Published: December 2011

Abstract
There is a long history of introduction of non-native fishes in fresh waters and the introduction rate has accelerated greatly over time. Although not all introduced fishes have appreciable effects on their new ecosystems, many exert significant ecological, evolutionary, and economic impacts. For researchers, managers, and policy makers interested in conserving freshwater diversity, understanding the magnitude and array of potential impacts of non-native fish species is of utmost importance. The present study provides an illustrative conspectus of the most recent literature reporting ecological impacts of non-native freshwater fishes from a wide range of species and geographic locations and concludes with a prospectus of needed areas of scientific inquiry. Both directly and indirectly, invasive fishes affect a wide range of native organisms from zooplankton to mammals across multiple levels of biological organizations ranging from the genome to the ecosystem. Although a great deal of knowledge has been recently accumulated, this body of knowledge dwarfs in comparison to what we still need to learn. Specifically, we cite the need for additional scientific inquiry to fill knowledge gaps that are principally caused by taxonomically, geographically, disciplinarily, and methodologically unbalanced approaches.
Native Fish Conservation Areas: A Vision for Large-Scale Conservation of Native Fish Communities
Authors: Williams Jack E , Williams Richard N , Thurow Russell F , Elwell Leah , Philipp David P , Harris Fred A , Kershner Jeffrey L , Martinez Patrick J , Miller Dirk , Reeves Gordon H , Frissell Christopher A , Sedell James R 
Published: December 2011

Abstract
The status of freshwater fishes continues to decline despite substantial conservation efforts to reverse this trend and recover threatened and endangered aquatic species. Lack of success is partially due to working at smaller spatial scales and focusing on habitats and species that are already degraded. Protecting entire watersheds and aquatic communities, which we term “native fish conservation areas” (NFCAs), would complement existing conservation efforts by protecting intact aquatic communities while allowing compatible uses. Four critical elements need to be met within a NFCA: (1) maintain processes that create habitat complexity, diversity, and connectivity; (2) nurture all of the life history stages of the fishes being protected; (3) include a long-term enough watershed to provide long-term persistence of native fish populations; and (4) provide management that is sustainable over time. We describe how a network of protected watersheds could be created that would anchor aquatic conservation needs in river basins across the country.
Potential Impact of the Deepwater Horizon Oil Spill on Commercial Fisheries in the Gulf of Mexico
Authors: McCrea-Strub A , Kleisner K , Sumaila U R , Swartz W , Watson R , Zeller D , Pauly D 
Published: December 2011

Abstract
Given the economic and social importance of fisheries in the Gulf of Mexico large marine ecosystem (LME), it is imperative to quantify the potential impacts of the Deepwater Horizon oil spill. To provide a preliminary perspective of the consequences of this disaster, spatial databases of annual reported commercial catch and landed value prior to the spill were investigated relative to the location of the fisheries closures during July 2010. Recent trends illustrated by this study suggest that more than 20% of the average annual U.S. commercial catch in the Gulf has been affected by postspill fisheries closures, indicating a potential minimum loss in annual landed value of US$247 million. Lucrative shrimp, blue crab, menhaden, and oyster fisheries may be at greatest risk of economic losses. Overall, it is evident that the oil spill has impacted a highly productive area of crucial economic significance within the Gulf of Mexico LME. This study draws attention to the need for ongoing and thorough investigations into the economic impacts of the oil spill on Gulf fisheries.
Stream Fragmentation Thresholds for a Reproductive Guild of Great Plains Fishes
Authors: Perkin Joshuah S , Gido Keith B 
Published: December 2011

ABSTRACT:
Impoundments, diversion dams, and stream dewatering have created a mosaic of large river fragments throughout the Great Plains of central North America. Coincident with these habitat changes are massive declines in the distribution and abundance of Great Plains fishes belonging to the “pelagic-spawning” reproductive guild. We analyzed longitudinal fragment lengths (measured in river kilometers, rkm) and literature accounts of population status for eight species from this guild across 60 fragments to derive thresholds in stream length associated with extirpations. Fragment length predicted population status (F2,21 = 30.14, P &lt; 0.01), with lengths averaging 136 ± 21 rkm for extirpated, 226 ± 69 rkm for declining, and 458 ± 137 for stable populations. Fragment length explained 71% of reported extirpations and estimated thresholds in fragment length explained 67% of variation in population persistence. Our findings provide insight into appropriate spatial scales for conducting riverscape conservation approaches that address the hierarchical effects of fragmentation on stream-dwelling fishes.
Iridovirus Infections among Missouri River Sturgeon: Initial Characterization, Transmission, and Evidence for Establishment of a Carrier State
Authors: Kurobe T. , MacConnell E. , Hudson C. , McDowell T. S. , Mardones F. O. , Hedrick R. P. 
Published: December 2011

Abstract
Iridovirus infections of the integument were associated with disease and mortality among hatchery-reared populations of juvenile pallid sturgeon Scaphirhynchus albus and shovelnose sturgeon S. platorynchus from the Missouri River. Virus-infected cells in the integument of fins and body were greatly enlarged, possessed pleomorphic and eccentric nuclei, and exhibited an amphophilic to eosinophilic staining of the cytoplasm in hematoxylin-and-eosin-stained sections. Virus particles found in the host cell cytoplasm were composed of an outer hexagonal capsid measuring 254 nm in diameter and surrounding a dense nucleoid. Despite numerous attempts, the virus could not be propagated on routine cell lines used in fish viral diagnostics or from established cell lines from white sturgeon Acipenser transmontanus, pallid sturgeon, or shovelnose sturgeon. Bath exposures of healthy juvenile pallid sturgeon to a crude extract or a 0.45-μm-filtered extract from the fins of infected fish resulted in transmission of the virus and mortality. At water temperatures of 15°C, the first deaths occurred at approximately 1 month; mortality peaked between 50 and 60 d postexposure, after which surviving fish recovered. Presence of the virus was confirmed among dead and moribund pallid sturgeon by both histology and detection of viral DNA by polymerase chain reaction methods. Feeding of infected tissues and cohabitation with virus-infected shovelnose sturgeon also resulted in successful virus transmission to juvenile pallid sturgeon. Virus infections among experimentally exposed pallid sturgeon that recovered from clinical episodes persisted for at least 8.5 months, and these apparently healthy fish transmitted the virus and disease to juvenile pallid sturgeon by cohabitation. The newly described Missouri River sturgeon iridovirus (MRSIV) as found in pallid sturgeon and shovelnose sturgeon shares many properties with a group of iridoviruses associated with serious skin and gill infections in several species of sturgeon.
Received October 5, 2010; accepted October 26, 2010
Effects of Full-Stream Carbon Filtration on the Development of Head and Lateral Line Erosion Syndrome (HLLES) in Ocean Surgeon
Authors: Stamper M. Andrew , Kittell Michele M. , Patel Erin E. , Corwin Allison L. 
Published: December 2011

Abstract
Head and lateral line erosion syndrome (HLLES) is a common but very poorly understood disease of marine aquarium fish. One suspected etiology is the use of granulated activated carbon (GAC) to filter the water. Seventy-two ocean surgeons Acanthurus bahianus were distributed among three carbon-negative control systems and three GAC-treated systems such that each tank contained approximately the same total body mass. Each replicate system was made up of two 250-L circular tanks with a common filtration system (6 fish per tank, 12 fish per replicate system). The GAC-treated tanks were exposed to full-stream, extruded coconut shell activated carbon, which produced a mean total organic carbon content of 0.4 mg/L. The results of this study indicate that extruded coconut shell activated carbon filtering at full-stream rates can cause HLLES-type lesions in ocean surgeons. The HLLES developed exponentially over 15 d, beginning in the chin region. This was followed by pitting in the cheek region, which expanded until erosions coalesced. Once the carbon was discontinued, the processes reversed in a mean time of 49 d. As the lesions healed, they reverted from the coalesced to the pitted stage and then darkened before returning to normal.
Received September 2, 2010; accepted March 20, 2011
Identifying quantitative trait loci via group-sparse multitask regression and feature selection: an imaging genetics study of the ADNI cohort
Authors: Wang Hua , Nie Feiping , Huang Heng , Kim Sungeun , Nho Kwangsik , Risacher Shannon L. , Saykin Andrew J. , Shen Li ,   For the Alzheimer's Disease Neuroimaging Initiative
Published: December 2011

Abstract
Motivation: Recent advances in high-throughput genotyping and brain imaging techniques enable new approaches to study the influence of genetic variation on brain structures and functions. Traditional association studies typically employ independent and pairwise univariate analysis, which treats single nucleotide polymorphisms (SNPs) and quantitative traits (QTs) as isolated units and ignores important underlying interacting relationships between the units. New methods are proposed here to overcome this limitation.
Results: Taking into account the interlinked structure within and between SNPs and imaging QTs, we propose a novel Group-Sparse Multi-task Regression and Feature Selection (G-SMuRFS) method to identify quantitative trait loci for multiple disease-relevant QTs and apply it to a study in mild cognitive impairment and Alzheimer's disease. Built upon regression analysis, our model uses a new form of regularization, group ℓ2,1-norm (G2,1-norm), to incorporate the biological group structures among SNPs induced from their genetic arrangement. The new G2,1-norm considers the regression coefficients of all the SNPs in each group with respect to all the QTs together and enforces sparsity at the group level. In addition, an ℓ2,1-norm regularization is utilized to couple feature selection across multiple tasks to make use of the shared underlying mechanism among different brain regions. The effectiveness of the proposed method is demonstrated by both clearly improved prediction performance in empirical evaluations and a compact set of selected SNP predictors relevant to the imaging QTs.
Availability: Software is publicly available at: http://ranger.uta.edu/%7eheng/imaging-genetics/
Contact: heng@uta.edu; shenli@iupui.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
GenomeRunner: automating genome exploration
Authors: Dozmorov Mikhail G. , Cara Lukas R. , Giles Cory B. , Wren Jonathan D. 
Published: December 2011

Abstract
Motivation: One of the challenges in interpreting high-throughput genomic studies such as a genome-wide associations, microarray or ChIP-seq is their open-ended nature—once a set of experimentally identified regions is identified as statistically significant, at least two questions arise: (i) besides P-value, do any of these significant regions stand out in terms of biological implications? (ii) Does the set of significant regions, as a whole, have anything in common genome wide? These issues are difficult to address because of the growing number of annotated genomic features (e.g. single nucleotide polymorphisms, transcription factor binding sites, methylation peaks, etc.), and it is difficult to know a priori which features would be most fruitful to analyze. Our goal is to provide partial automation of this process to begin examining associations between experimental features and annotated genomic regions in a hypothesis-free, data-driven manner.
Results: We created GenomeRunner—a tool for automating annotation and enrichment of genomic features of interest (FOI) with annotated genomic features (GFs), in different organisms. Besides simple association of FOIs with known GFs GenomeRunner tests whether the enriched FOIs, as a group, are statistically associated with a large and growing set of genomic features.
Availability: GenomeRunner setup files and source code are freely available at http://sourceforge.net/projects/genomerunner.
Contact: mikhail-dozmorov@omrf.org; Jonathan-Wren@omrf.org; jdwren@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data
Authors: Boeva Valentina , Popova Tatiana , Bleakley Kevin , Chiche Pierre , Cappo Julie , Schleiermacher Gudrun , Janoueix-Lerosey Isabelle , Delattre Olivier , Barillot Emmanuel 
Published: December 2011

Abstract
Summary: More and more cancer studies use next-generation sequencing (NGS) data to detect various types of genomic variation. However, even when researchers have such data at hand, single-nucleotide polymorphism arrays have been considered necessary to assess copy number alterations and especially loss of heterozygosity (LOH). Here, we present the tool Control-FREEC that enables automatic calculation of copy number and allelic content profiles from NGS data, and consequently predicts regions of genomic alteration such as gains, losses and LOH. Taking as input aligned reads, Control-FREEC constructs copy number and B-allele frequency profiles. The profiles are then normalized, segmented and analyzed in order to assign genotype status (copy number and allelic content) to each genomic region. When a matched normal sample is provided, Control-FREEC discriminates somatic from germline events. Control-FREEC is able to analyze overdiploid tumor samples and samples contaminated by normal cells. Low mappability regions can be excluded from the analysis using provided mappability tracks.
Availability: C++ source code is available at: http://bioinfo.curie.fr/projects/freec/
Contact: freec@curie.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Increased Pancreatic Fat Fraction Is Present in Obese Adolescents With Metabolic Syndrome
Authors: Maggio Albane B.R. , Mueller Pascal , Wacker Julie , Viallon Magalie , Belli Dominique C. , Beghetti Maurice , Farpour‐Lambert Nathalie J. , McLin Valérie A. 
Published: December 2011

ABSTRACTObjectives:Little is known about pancreatic fat accumulation and its possible associations with metabolic syndrome (MetS) and glucose metabolism. The aim of the present study was to quantify pancreatic fat fraction (PFF) in lean and obese adolescents and explore its relation to metabolic parameters.Methods:We recruited 25 lean and 24 obese adolescents. PFF and visceral adipose tissue (VAT) were determined using magnetic resonance imaging. We measured blood pressure, fasting glucose, insulin, liver enzymes, leptin, and lipid levels. Obese subjects underwent an oral glucose tolerance test.Results:PFF was significantly higher in obese than in lean subjects (4.8 ± 1.2 vs 3.6 ± 0.9; P < 0.001) and was associated with VAT, γ‐glutamyltransferase, triglycerides, high‐density lipoprotein cholesterol, leptin concentrations, and MetS (P < 0.05 for all). None of the obese subjects had glucose intolerance, but when adjusted for VAT, the following 3 parameters correlated negatively with PFF: fasting and 30‐ minute and 120‐minute insulin levels. We divided subjects into 3 groups: group I, lean without MetS; group II, obese without MetS; and group III, obese with MetS, and observed that PFF increased gradually among groups (I: 3.56% ± 0.88%; II: 4.70% ± 1.06%; III: 5.34% ± 1.49%; P < 0.001).Conclusions:Obese adolescents accumulate fat in the pancreas. PFF correlates with the presence of MetS. Even in the absence of glucose intolerance, pancreatic fat deposition is associated with impaired insulin response to glucose overload. This suggests that β‐cell dysfunction may already be present in nondiabetic obese adolescents, mirroring what has been shown in adults, and that pancreatic fat accumulation may participate in obesity‐associated pancreatic endocrine dysfunction.
Characterization of the genetic diversity, structure and admixture of British chicken breeds
Authors: Wilkinson S. , Wiener P. , Teverson D. , Haley C. S. , Hocking P. M. 
Published: December 2011

SummaryThe characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average FST of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy‐Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average FIS of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual‐based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.
Overexpression of Id3 induces apoptosis of A549 human lung adenocarcinoma cells
Authors: Li X.‐J. , Zhu C.‐D. , Yu W. , Wang P. , Chen F.‐F. , Xia X.‐Y. , Luo B. 
Published: December 2011

AbstractObjectives:  Inhibitor of differentiation 3 (Id3) protein has been implicated in the control of multiple cell death signalling pathways and in aetiology of numerous diseases. The aims of this study were to construct a recombinant eukaryotic expression vector (pEGFP/Id3), containing human Id3 (hId3) fused with enhanced green fluorescent protein (EGFP), and to determine effects of ectopic Id3 overexpression, on human lung adenocarcinoma cell (A549) proliferation.Materials and methods:  Human Id3 cDNA was inserted into pEGFP‐N1 vector to yield the recombinant eukaryotic expression vector pEGFP/Id3. Cells were transfected with pEGFP or pEGFP/Id3, and proliferation of EGFP‐expressing cells was monitored by flow cytometry (FCM) and confocal fluorescence microscopy. RT‐PCR, immunoblotting and immunocytochemistry were used to assess Id3 mRNA transcription and protein expression. Apoptosis was evaluated by Annexin V/7‐AAD staining and FCM, while nuclear morphology of apoptotic cells was examined using Hoechst 33258 staining.Results:  Over 4 days transfection with pEGFP, the proportion of EGFP‐positive A549 cells peaked at approximately 60% by 48 h and remained stable over the next 48 h. In contrast, the proportion of EGFP‐positive cells in cultures transfected with pEGFP/Id3 decreased from a peak of 60% at 48 h to <5% at 96 h, suggesting that Id3 expression inhibited cell proliferation or survival. Annexin V/7‐AAD and Hoechst 33258 staining revealed significantly higher rates of apoptosis in pEGFP/Id3‐transfected cells.Conclusion:  Overexpression of Id3 triggered apoptosis in A549 human lung adenocarcinoma cells, implicating Id3 in negative control of tumour growth. These Id3‐induced pro‐apoptotic signalling pathways require further study, but this preliminary investigation suggests that Id3 regulation could be exploited in anti‐tumour therapies.