bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal and Geographic Genetic Divergence: Characterizing Sockeye Salmon Populations in the Chignik Watershed, Alaska, Using Single‐Nucleotide Polymorphisms
Authors: Creelman Elisabeth K. , Hauser Lorenz , Simmons Ryan K. , Templin William D. , Seeb Lisa W. 
Published: June 2011

AbstractThe high fidelity of Pacific salmon Oncorhynchus spp. to their natal spawning habitat often results in genetically divergent populations. Management and conservation of the natural variation within species is critical for maintaining robust populations. The Chignik watershed, Alaska, supports highly productive populations of sockeye salmon Oncorhynchus nerka that vary in return timing and spawning locations among breeding populations, presenting challenges to the management of commercially exploited stocks. We describe the genetic structure of the sockeye salmon populations spawning in the Chignik watershed using 45 single‐nucleotide polymorphisms from 2,013 individuals representing 19 collections of spawning adults. From these data we estimated within‐population statistics and among‐population divergence, detected loci in linkage disequilibrium and loci that are FST outliers, and tested loci for potential use in mixed‐stock assessments. The results indicate significant genetic structure among the sockeye salmon populations in the Chignik watershed at both spatial and temporal scales. This structuring can be largely explained by putative evidence of selection at two markers and the differences in spawn timing between populations. Genetic structure determined at geographic and temporal levels provides a basis for application in the conservation of this resource and the management of commercial and subsistence fisheries.
Does Lower Crab Creek in the Eastern Washington Desert Have a Native Population of Chinook Salmon?
Authors: Small Maureen P. , Burgess Dave , Dean Cheryl , Warheit Kenneth I. 
Published: June 2011

AbstractLower Crab Creek (LCC) in eastern Washington is a groundwater‐fed tributary to the Columbia River at river kilometer 661. The creek traverses agriculturally modified desert habitat, and in several reaches the water quality is poor, summer water temperatures are lethal to fish, and stream habitat is degraded. The creek was thought to be unsuitable for salmonids, yet fall‐run Chinook salmon Oncorhynchus tshawytscha spawn and rear in it. The origin of these fish is uncertain since it is unclear whether LCC was a perennial creek prior to the hydrologic changes in the Columbia River basin stemming from the Columbia Basin Irrigation Project in the 1950s. We used genetic analyses to examine the hypotheses that these fish are (1) random strays, (2) a population founded since the 1950s (by wild or hatchery strays), or (3) an established native population. Chinook salmon juveniles and adults were collected in LCC and genetically characterized with the Chinook salmon microsatellite DNA locus suite in the Genetic Analysis of Pacific Salmonids database. The LCC population of Chinook salmon was found to be significantly different from interior Columbia River basin hatchery and wild populations and to have alleles that are absent from proximal populations. Lower Crab Creek Chinook salmon showed no evidence of recent founding and had genetic diversity, allelic richness, and effective population size similar to those of other Columbia River basin Chinook salmon. The data suggest that a genetically distinct, native population of Chinook salmon inhabits LCC that has adapted to the rigorous environment.
Single‐Nucleotide Polymorphisms (SNPs) under Diversifying Selection Provide Increased Accuracy and Precision in Mixed‐Stock Analyses of Sockeye Salmon from the Copper River, Alaska
Authors: Ackerman Michael W. , Habicht Christopher , Seeb Lisa W. 
Published: June 2011

AbstractGenetic markers are increasingly being used to ascertain the population of origin of individuals or mixtures of individuals in complex aggregations of Pacific salmon Oncorhynchus spp. Multilocus genotype data from single‐nucleotide polymorphisms (SNPs) are especially useful for admixture analyses. Single‐nucleotide polymorphisms can be discovered in nonmodel organisms with relative ease and can be characterized in the coding and regulatory regions of the genome influenced by selection. Those influenced by diversifying selection may show atypically high levels of differentiation among populations and thus be particularly valuable for genetic stock identification in cases where neutral loci show little difference among populations of interest. We identified four SNP loci from a panel of 42 as candidates for diversifying selection (referred to here as nonneutral SNPs) in sockeye salmon O. nerka from the Copper River and adjacent coastal drainages in south‐central Alaska. We evaluated the information content of the four nonneutral loci for use in genetic stock identification and assessed their ability to improve the accuracy and precision of composition estimates. The average measure of informativeness for assignment (In) for neutral loci was 0.019, and the average In for nonneutral loci was 0.064. A simulation‐based approach indicated that the addition of the nonneutral SNP loci to a neutral marker panel provided significantly higher resolution in the assignment of individuals to their populations of origin than would have been accomplished by adding an equal number of neutral loci. Nonneutral SNP loci improved the ability to identify the origin of individual fish and to estimate the composition of Pacific salmon populations in mixed fisheries.
Refining Opportunity Cost Estimates of Not Adopting GM Cotton: An Application in Seven Sub‐Saharan African Countries
Authors: Bouët Antoine , Gruère Guillaume P. 
Published: June 2011

AbstractA computable general equilibrium model is applied to evaluate the opportunity costs of not adopting Bt cotton, a genetically‐modified (GM) insect resistant cotton, in Benin, Burkina‐Faso, Mali, Senegal, Togo, Tanzania, and Uganda when it is adopted in other countries. Our model uniquely employs country‐specific partial adoption rates and factor‐biased productivity shocks in the cotton and oilseed sectors of all adopting regions. Assuming a 50% adoption rate, the opportunity cost of not adopting Bt cotton in the seven surveyed countries amounts to $41 million per year, which is a significant but lower cost than that suggested by the results of previous studies. Trade liberalization only marginally increases this estimate.
Methyl-Analyzer—whole genome DNA methylation profiling
Authors: Xin Yurong , Ge Yongchao , Haghighi Fatemeh G. 
Published: June 2011

Abstract
Summary: Methyl-Analyzer is a python package that analyzes genome-wide DNA methylation data produced by the Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method. Methyl-MAPS is an enzymatic-based method that uses both methylation-sensitive and -dependent enzymes covering &gt;80% of CpG dinucleotides within mammalian genomes. It combines enzymatic-based approaches with high-throughput next-generation sequencing technology to provide whole genome DNA methylation profiles. Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compartments and estimates CpG methylation probabilities at single base resolution.
Availability and implementation: Methyl-Analyzer is available at http://github.com/epigenomics/methylmaps. Sample dataset is available for download at http://epigenomicspub.columbia.edu/methylanalyzer_data.html.
Contact: fgh3@columbia.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Integration of gene normalization stages and co-reference resolution using a Markov logic network
Authors: Dai Hong-Jie , Chang Yen−Ching , Tsai Richard Tzong-Han , Hsu Wen−Lian 
Published: June 2011

Abstract
Motivation: Gene normalization (GN) is the task of normalizing a textual gene mention to a unique gene database ID. Traditional top performing GN systems usually need to consider several constraints to make decisions in the normalization process, including filtering out false positives, or disambiguating an ambiguous gene mention, to improve system performance. However, these constraints are usually executed in several separate stages and cannot use each other's input/output interactively. In this article, we propose a novel approach that employs a Markov logic network (MLN) to model the constraints used in the GN task. Firstly, we show how various constraints can be formulated and combined in an MLN. Secondly, we are the first to apply the two main concepts of co-reference resolution—discourse salience in centering theory and transitivity—to GN models. Furthermore, to make our results more relevant to developers of information extraction applications, we adopt the instance-based precision/recall/F-measure (PRF) in addition to the article-wide PRF to assess system performance.
Results: Experimental results show that our system outperforms baseline and state-of-the-art systems under two evaluation schemes. Through further analysis, we have found several unexplored challenges in the GN task.
Contact: hongjie@iis.sinica.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
Genomic data integration using guided clustering
Authors: Maneck Matthias , Schrader Alexandra , Kube Dieter , Spang Rainer 
Published: June 2011

Abstract
Motivation: In biomedical research transcriptomic, proteomic or metabolomic profiles of patient samples are often combined with genomic profiles from experiments in cell lines or animal models. Integrating experimental data with patient data is still a challenging task due to the lack of tailored statistical tools.
Results: Here we introduce guided clustering, a new data integration strategy that combines experimental and clinical high-throughput data. Guided clustering identifies sets of genes that stand out in experimental data while at the same time display coherent expression in clinical data. We report on two potential applications: The integration of clinical microarray data with (i) genome-wide chromatin immunoprecipitation assays and (ii) with cell perturbation assays. Unlike other analysis strategies, guided clustering does not analyze the two datasets sequentially but instead in a single joint analysis. In a simulation study and in several biological applications, guided clustering performs favorably when compared with sequential analysis approaches.
Availability: Guided clustering is available as a R-package from http://compdiag.uni-regensburg.de/software/guidedClustering.shtml. Documented R code of all our analysis is included in the Supplementary Materials. All newly generated data are available at the GEO database (GSE29700).
Contact: rainer.spang@klinik.uni-regensburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Exploring Potential Noninvasive Biomarkers in Eosinophilic Esophagitis in Children
Authors: Subbarao Girish , Rosenman Marc B. , Ohnuki Lyo , Georgelas Ann , Davis Miriam , Fitzgerald Joseph F. , Molleston Jean P. , Croffie Joseph M. , Pfefferkorn Marian D. , Corkins Mark R. , Lim Joel R. , Steiner Steven J. , Schaefer Elizabeth , Gleich Gerald J. , Gupta Sandeep K. 
Published: June 2011

ABSTRACTBackground and Aims:Eosinophilic esophagitis (EE) continues to present clinical challenges, including a need for noninvasive tools to manage the disease. To identify a marker able to assess disease status in lieu of repeated endoscopies, we examined 3 noninvasive biomarkers, serum interleukin (IL)‐5, serum eosinophil‐derived neurotoxin (EDN), and stool EDN, and examined possible correlations of these with disease phenotype and activity (symptoms and histology) in a longitudinal study of children with EE.Subjects and Methods:Children with EE were studied for up to 24 weeks (12 weeks on 1 of 2 corticosteroid therapies and 12 weeks off therapy). Twenty children with normal esophagogastroduodenoscopies with biopsies were enrolled as controls. Serum IL‐5, serum EDN, and stool EDN were measured at weeks 0, 4, 12, 18, and 24 in children with EE, and at baseline alone for controls. Primary and secondary statistical analyses (excluding and including outlier values of the biomarkers, respectively) were performed.Results:Sixty subjects with EE (46 [75%] boys, mean age 7.5 ± 4.4 years) and 20 normal controls (10 [50%] boys, mean age 6.7 ± 4.1 years) were included. Significant changes in serum EDN (significant decrease from baseline to week 4, and then rebound from week 4 to week 12) occurred. Serum EDN levels were stable after week 12. Serum IL‐5 and stool EDN levels in subjects with EE were not statistically different from those of the control subjects when each time point for the cases was compared with the controls’ 1‐time measurement.Conclusions:Serum EDN levels were significantly higher in subjects with EE than in controls, and the results suggest a possible role, after additional future studies, for serum EDN in establishing EE diagnosis, assessing response to therapy, and/or monitoring for relapse or quiescence.
Acute on Chronic Liver Disease in Children From the Developing World
Authors: Jagadisan Barath , Srivastava Anshu , Yachha Surender Kumar , Poddar Ujjal 
Published: June 2011

ABSTRACTObjectives:A subset of children with chronic liver disease (CLD) decompensate following an acute insult; however, data for children are not readily available. The present study aims to characterize the clinical presentation, etiology, outcome, and determinants of short‐term mortality in children with an acute hepatic insult superimposed over CLD.Patients and Methods:Children of acute on chronic liver disease (ACLD) were grouped as acute on chronic liver failure (ACLF) and non‐ACLF. ACLF was defined as per the definition proposed by Asian Pacific Association for the Study of Liver. The acute insult, etiology of CLD, and clinical and laboratory parameters at admission along with 3‐month outcome were assessed. Receiver operating curve (ROC) was plotted to measure the performance of pediatric end‐stage liver disease (PELD) score in predicting the 3‐month mortality.Results:Of the 36 children with ACLD (median age 9.5; range 3–15 years), 17 fulfilled ACLF criteria and 19 non‐ACLF. CLD was diagnosed for the first time in 86% children during their presentation with a superimposed acute insult. Wilson disease and autoimmune liver disease were the most common underlying etiology. Acute insult was caused by hepatitis E virus (HEV) in 27 (75%) children and hepatitis A virus (HAV) in 10 (28%). The 3‐month mortality of ACLF group was significantly higher than that of non‐ACLF group (59% vs 11%, P = 0.001). PELD score of >25.5 predicted death, with a sensitivity of 100% and specificity of 83.3%.Conclusions:Superinfection with hepatotropic viruses on CLD in children manifests as ACLD: ACLF and non‐ACLF. Hepatitis E virus is the most common superinfection in the population studied. The mortality in ACLF is 5 times higher than that in the non‐ACLF group. PELD score is useful in differentiating likely survivors and nonsurvivors.
Phosphorylation of SOS3-Like Calcium-Binding Proteins by Their Interacting SOS2-Like Protein Kinases Is a Common Regulatory Mechanism in Arabidopsis
Authors: Du Wenming , Lin Huixin , Chen She , Wu Yisheng , Zhang Jun , Fuglsang Anja T. , Palmgren Michael G. , Wu Weihua , Guo Yan 
Published: June 2011

Abstract
The Arabidopsis (Arabidopsis thaliana) genome encodes nine Salt Overly Sensitive3 (SOS3)-like calcium-binding proteins (SCaBPs; also named calcineurin B-like protein [CBL]) and 24 SOS2-like protein kinases (PKSs; also named as CBL-interacting protein kinases [CIPKs]). A general regulatory mechanism between these two families is that SCaBP calcium sensors activate PKS kinases by interacting with their FISL motif. In this study, we demonstrated that phosphorylation of SCaBPs by their functional interacting PKSs is another common regulatory mechanism. The phosphorylation site serine-216 at the C terminus of SCaBP1 by PKS24 was identified by liquid chromatography-quadrupole mass spectrometry analysis. This serine residue is conserved within the PFPF motif at the C terminus of SCaBP proteins. Phosphorylation of this site of SCaBP8 by SOS2 has been determined previously. We further showed that CIPK23/PKS17 phosphorylated CBL1/SCaBP5 and CBL9/SCaBP7 and PKS5 phosphorylated SCaBP1 at the same site in vitro and in vivo. Furthermore, the phosphorylation stabilized the interaction between SCaBP and PKS proteins. This tight interaction neutralized the inhibitory effect of PKS5 on plasma membrane H+-ATPase activity. These data indicate that SCaBP phosphorylation by their interacting PKS kinases is a critical component of the SCaBP-PKS regulatory pathway in Arabidopsis.
Maize opaque5 Encodes Monogalactosyldiacylglycerol Synthase and Specifically Affects Galactolipids Necessary for Amyloplast and Chloroplast Function
Authors: Myers Alan M. , James Martha G. , Lin Qiaohui , Yi Gibum , Stinard Philip S. , Hennen-Bierwagen Tracie A. , Becraft Philip W. 
Published: June 2011

Abstract
The maize (Zea mays) opaque5 (o5) locus was shown to encode the monogalactosyldiacylglycerol synthase MGD1. Null and point mutations of o5 that affect the vitreous nature of mature endosperm engendered an allelic series of lines with stepwise reductions in gene function. C18:3/C18:2 galactolipid abundance in seedling leaves was reduced proportionally, without significant effects on total galactolipid content. This alteration in polar lipid composition disrupted the organization of thylakoid membranes into granal stacks. Total galactolipid abundance in endosperm was strongly reduced in o5- mutants, causing developmental defects and changes in starch production such that the normal simple granules were replaced with compound granules separated by amyloplast membrane. Complete loss of MGD1 function in a null mutant caused kernel lethality owing to failure in both endosperm and embryo development. The data demonstrate that low-abundance galactolipids with five double bonds serve functions in plastid membranes that are not replaced by the predominant species with six double bonds. Furthermore, the data identify a function of amyloplast membranes in the development of starch granules. Finally, the specific changes in lipid composition suggest that MGD1 can distinguish the constituency of acyl groups on its diacylglycerol substrate based upon the degree of desaturation.
Capturing consumer heterogeneity in loyalty evolution patterns
Authors: Yoon Kanghyun , Tran Thanh V. 
Published: June 2011

PurposeThis paper aims to propose a finite‐mixture brand‐choice model, which relaxes the common dichotomous assumption in market segmentation based on consumer loyalty. The model can be used to estimate the optimal number of consumer segments and capture both across‐ and within‐household heterogeneity in consumers' evolutional patterns of loyalty behaviors.Design/methodology/approachThe proposed model is empirically calibrated on a scanner panel data of two product categories, i.e. liquid detergent and toilet tissue obtained from the ERIM scanner panel of AC Nielsen.FindingsEmpirical results suggest that: the dichotomous classification of consumers into loyal and non‐loyal groups is sub‐optimal in capturing the heterogeneity in consumer loyalty. Two evolutional patterns of loyalty behaviors exist, showing that past experience with a particular brand may either increase or decrease the current level of loyalty, and consumers' sensitivity to various marketing variables differs between repeat and switching decisions (i.e. within‐household heterogeneity).Research limitations/implicationsThe proposed model does not capture consumers' inertia/variety‐seeking tendencies. Furthermore, it does not account for the role of scale parameter in capturing consumer heterogeneity.Originality/valueThis study contributes to the stream of research on consumer loyalty and provides important marketing implications for practitioners in designing effective targeting programs as well as attraction/retention strategies.
Mixed methods: a research design for management doctoral dissertations
Authors: Jogulu Uma D. , Pansiri Jaloni 
Published: June 2011

PurposeThis paper seeks to examine two management doctoral research projects to highlight the advantages in mixed methods as the primary research design.Design/methodology/approachThis paper summarises the methods of data collection and analysis which were used by two doctoral students in their management research. The researchers used mixed methods approaches (quantitative and qualitative) to explore different areas of management.FindingsThe paper supports the view that triangulation of research methods strengthens the findings and inferences made for understanding social phenomena in more depth, compared to using a single method.Research limitations/implicationsThe paper relies excessively on two doctoral research projects which utilise sequential mixed methods. Therefore, arguments made in the paper are specific because other doctoral projects that have used different methods from those employed in the two projects were not considered.Practical implicationsEarly researchers, in particular students commencing doctorate studies, should apply mixed methods research because it develops skills in the two most dominant data collection methods used in management research. This paper is a practical guide on how this could be done effectively.Originality/valueThe paper is drawn from two unique doctoral research projects. The paper's originality and value is in providing experiences and practical insights on how mixed methods research is undertaken.
The effects of Belgian outward direct investment in European high‐wage and low‐wage countries on employment in Belgium
Authors: Cuyvers Ludo , Soeng Reth 
Published: June 2011

PurposeThe paper aims at providing evidence on the impact on employment of outward foreign direct investment, particularly from developed countries into low‐wage countries, which is a major concern in many developed countries.Design/methodology/approachThe effects of foreign production undertaken by Belgian foreign‐oriented companies on employment in Belgium are investigated by performing econometric tests for complementarity or substitution between home and affiliate employment. The data are from the Amadeus database and consist of a sample of 254 Belgian parent companies with foreign affiliates in low‐wage and other high‐wage European countries during the 1999‐2007 period.FindingsThe results show that, given the size of parent production in the home country, Belgian multinational enterprises with foreign affiliates in higher‐wage European countries tend to employ more labour at home the more they produce in the host country. This probably reflects the needs of foreign affiliates in higher‐wage European countries for management and supervisory services from parent companies. Another explanation might be that Belgian outward FDI is largely vertical. In contrast, no evidence is found about employment reallocation between parents and affiliates operating in lower‐wage European countries.Originality/valueThe paper provides evidence on overall effects on employment in Belgium of its outward foreign direct investment for the period 1999‐2007, i.e. using the most recent data available. In contrast to many other studies, statistical diagnostic tests were carried out to choose the appropriate model to best fit the data.