bluuebunny/crossref_metadata_2025_split huggingface dataset:
Origin of Atlantic Sturgeon Collected off the Delaware Coast during Spring Months
Authors: Wirgin Isaac , Breece Matthew W. , Fox Dewayne A. , Maceda Lorraine , Wark Kevin W. , King Tim 
Published: January 2015

Abstract
Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus was federally listed under the U.S. Endangered Species Act as five distinct population segments (DPS). Currently, at least 18 estuaries coastwide host spawning populations and the viability of these vary, requiring differing levels of protection. Subadults emigrate from their natal estuaries to marine waters where they are vulnerable to bycatch; one of the major threats to the rebuilding of populations. As a result, identifying the population origin of Atlantic Sturgeon in coastal waters is critical to development of management plans intended to minimize interactions of the most imperiled populations with damaging fisheries. We used mitochondrial DNA control region sequencing and microsatellite DNA analyses to determine the origin of 261 Atlantic Sturgeon collected off the Delaware coast during the spring months. Using individual-based assignment (IBA) testing and mixed stock analysis, we found that specimens originated from all nine of our reference populations and the five DPSs used in the listing determination. Using IBA, we found that the Hudson River population was the largest contributor (38.3%) to our coastal collection. The James (19.9%) and Delaware (13.8%) river populations, at one time thought to be extirpated or nearly so, were the next largest contributors. The three populations combined in the South Atlantic DPS contributed 21% of specimens; the Altamaha River, the largest population in the South Atlantic DPS, only contributed a single specimen to the collection. While the origin of specimens collected on the Delaware coast was most likely within rivers of the New York Bight DPS (52.1%), specimens that originated elsewhere were also well represented. Genetic analyses provide a robust tool to identify the population origin of individual sturgeon outside of their natal estuaries and to determine the quantitative contributions of individual populations to coastal aggregations that are vulnerable to bycatch and other anthropogenic threats.
Received March 17, 2014; accepted September 3, 2014
South Texas Residency Screening, Brief Intervention, and Referral to Treatment (SBIRT) Training: 12-Month Outcomes
Authors: Malone Glenn P. , Vale Arismendez Shruthi , Schneegans Warzinski Suyen , Amodei Nancy , Burge Sandra K. , Wathen Patricia I. , Conde Michelle V. , Palmer Raymond , Williams Janet F. 
Published: January 2015

Background Screening, brief intervention, and referral to treatment (SBIRT) is an efficacious and cost-effective skill set when implemented in primary care settings regarding hazardous alcohol use. This study assesses the impact of medical resident SBIRT training across 3 specialties and identifies predictors of change in trainee behavior, attitudes, and knowledge over 12 months. Methods This program's substance use SBIRT training was developed and tailored to fit diverse curricular objectives and settings across an array of medical residency programs in South Texas. The 329 residents training in pediatrics, family medicine, and internal medicine during 2009–2012 constituted the trainee group reported in this analysis. Surveys assessing SBIRT-related knowledge, current practice, confidence, role responsibility, attitudes, beliefs, and readiness to change were completed by 234 (71%) trainees at 3 time points: pre-training, then 30 days and 12 months post-initial training. Results SBIRT-related knowledge, confidence, and practice increased from pre-training to 12-month follow-up. Residents who reported the least amount of pre-training clinical and/or prior academic exposure to substance use reported the greatest SBIRT practice increases. When controlling for demographic and prior exposure variables, the largest contributor to variance in SBIRT practice was attributed to residents’ confidence in their SBIRT skills. Conclusions SBIRT training that employs diverse educational methodologies as part of customizing the training to residency specialties can similarly enhance SBIRT-related knowledge, confidence, and practice. Trainee report of limited prior clinical or academic exposure to substance use and/or low confidence regarding SBIRT skills and their professional role responsibilities related to substance use predicted trainee success and sustained SBIRT strategy application. When customizing SBIRT training, curriculum developers should consider leveraging and capacity building related to those factors predicting continued use of SBIRT practices.
Use of Penicillin and Streptomycin to Reduce Spread of Bacterial Coldwater Disease II: Efficacy of Using Antibiotics in Diluents and During Water Hardening
Authors: Oplinger Randall W. , Wagner Eric J. , Cavender Wade 
Published: January 2015

Abstract
Bacterial coldwater disease, caused by Flavobacterium psychrophilum, has lead to the loss of significant numbers of hatchery-reared salmonids. The bacteria can be spread from parent to progeny within contaminated sperm and ovarian fluid and can enter the egg during fertilization. The addition of antibiotics to diluents and water-hardening solutions could prevent the spread of the disease. In separate trials, a mixture of 0.197 mg/mL penicillin plus 0.313 mg/mL streptomycin was added to both a 0.5% sodium chloride fertilization diluent and hatchery well water during hardening. Tests showed that the addition of the antibiotics to the diluent and during up to 60 min of water hardening had no effect on the eye-up, hatch and deformity rates of Rainbow Trout Oncorhynchus mykiss eggs compared with the nonantibiotic-treated controls. Also, significant reductions in the prevalence of F. psychrophilum on the surface and inside eggs were observed when compared with controls. These results indicate that the addition of penicillin and streptomycin to diluents and during water hardening can prevent the vertical transmission of bacterial coldwater disease.
Received May 1, 2014; accepted July 10, 2014
Cod pots in a Baltic fishery: are they efficient and what affects their efficiency?
Authors: Königson Sara J. , Fredriksson Ronny E. , Lunneryd Sven-Gunnar , Strömberg Patrick , Bergström Ulf M. 
Published: January 2015

Abstract
With the growing grey seal population in the Baltic Sea, the inshore cod fishery has suffered dramatic increases in both catch losses and damage to fishing gear. To mitigate this situation, cod pots were evaluated as an alternative to traditional gillnets and longlines. During a 3-year study, cod pots were used by commercial fishers in two areas off the coast of Sweden. Using the data from this study, we evaluated catches from pots in relation to other gear types and investigated the effects of environmental and fisheries-related variables such as depth and soak time. The comparison of pots with other gear types showed that, during the first half of the year, the pot fishery generated lower daily catches than the gillnet and longline fisheries at comparable fishing efforts. During the second half of the year, catches in the pot fishery exceeded or were equal to those in the traditional fisheries. Using generalized additive models to evaluate the impact of environmental and fisheries-related variables on pot catches, we showed that, in both areas, the catch per unit effort (cpue) of legal-sized cod was affected by the water depth, the time of year (months), and the soak time. In one of the areas, cpue was also affected by the direction of the water current in relation to the orientation of the string of pots. The cpue of undersized cod was affected by topographic variables such as the slope and the complexity of the bottom, in addition to the water depth, month of the year, and soak time. The results from the study indicate that pots can be a useful alternative gear in the Baltic cod fishery, at least during part of the year. By using our information on how catches are affected by environmental and fisheries-related variables, the pot fishery may be further optimized to increase catches.
Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14
Authors: Ning Yong-Qiang , Ma Ze-Yang , Huang Huan-Wei , Mo Huixian , Zhao Ting-ting , Li Lin , Cai Tao , Chen She , Ma Ligeng , He Xin-Jian 
Published: January 2015

Abstract
The histone demethylase JMJ14 catalyzes histone demethylation at lysine 4 of histone 3 and is involved in transcriptional repression and flowering time control in Arabidopsis. Here, we report that JMJ14 is physically associated with two previously uncharacterized NAC transcription factors, NAC050 and NAC052. The NAC050/052-RNAi plants and the CRISPR-CAS9-mediated nac050/052 double mutant plants show an early flowering phenotype, which is similar to the phenotype of jmj14, suggesting a functional association between JMJ14 and NAC050/052. RNA-seq data indicated that hundreds of common target genes are co-regulated by JMJ14 and NAC50/052. Our ChIP analysis demonstrated that JMJ14 and NAC050 directly bind to co-upregulated genes shared in jmj14 and NAC050/052-RNAi, thereby facilitating H3K4 demethylation and transcriptional repression. The NAC050/052 recognition DNA cis-element was identified by an electrophoretic mobility shift assay at the promoters of its target genes. Together, our study identifies two novel NAC transcription repressors and demonstrates that they are involved in transcriptional repression and flowering time control by associating with the histone demethylase JMJ14.
Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer
Authors: Sebestyén Endre , Zawisza Michał , Eyras Eduardo 
Published: January 2015

Abstract
The determination of the alternative splicing isoforms expressed in cancer is fundamental for the development of tumor-specific molecular targets for prognosis and therapy, but it is hindered by the heterogeneity of tumors and the variability across patients. We developed a new computational method, robust to biological and technical variability, which identifies significant transcript isoform changes across multiple samples. We applied this method to more than 4000 samples from the The Cancer Genome Atlas project to obtain novel splicing signatures that are predictive for nine different cancer types, and find a specific signature for basal-like breast tumors involving the tumor-driver CTNND1. Additionally, our method identifies 244 isoform switches, for which the change occurs in the most abundant transcript. Some of these switches occur in known tumor drivers, including PPARG, CCND3, RALGDS, MITF, PRDM1, ABI1 and MYH11, for which the switch implies a change in the protein product. Moreover, some of the switches cannot be described with simple splicing events. Surprisingly, isoform switches are independent of somatic mutations, except for the tumor-suppressor FBLN2 and the oncogene MYH11. Our method reveals novel signatures of cancer in terms of transcript isoforms specifically expressed in tumors, providing novel potential molecular targets for prognosis and therapy. Data and software are available at: http://dx.doi.org/10.6084/m9.figshare.1061917 and https://bitbucket.org/regulatorygenomicsupf/iso-ktsp.
The ATP-mediated formation of the YgjD–YeaZ–YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli
Authors: Zhang Wenhua , Collinet Bruno , Perrochia Ludovic , Durand Dominique , van Tilbeurgh Herman 
Published: January 2015

Abstract
The essential and universal N6-threonylcarbamoyladenosine (t6A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon–anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (TsaB), YjeE (TsaE) and YrdC (TsaC) proteins are necessary and sufficient for the in vitro biosynthesis of t6A, using tRNA, ATP, L-threonine and bicarbonate as substrates. YrdC synthesizes the short-lived L-threonylcarbamoyladenylate (TCA), and YgjD, YeaZ and YjeE cooperate to transfer the L-threonylcarbamoyl-moiety from TCA onto adenosine at position 37 of substrate tRNA. We determined the crystal structure of the heterodimer YgjD–YeaZ at 2.3 Å, revealing the presence of an unexpected molecule of ADP bound at an atypical site situated at the YgjD–YeaZ interface. We further showed that the ATPase activity of YjeE is strongly activated by the YgjD–YeaZ heterodimer. We established by binding experiments and SAXS data analysis that YgjD–YeaZ and YjeE form a compact ternary complex only in presence of ATP. The formation of the ternary YgjD–YeaZ–YjeE complex is required for the in vitro biosynthesis of t6A but not its ATPase activity.
Using Next-generation RNA Sequencing to Examine Ischemic Changes Induced by Cold Blood Cardioplegia on the Human Left Ventricular Myocardium Transcriptome
Authors: Muehlschlegel Jochen D. , Christodoulou Danos C. , McKean David , Gorham Joshua , Mazaika Erica , Heydarpour Mahyar , Lee Grace , DePalma Steven R. , Perry Tjorvi E. , Fox Amanda A. , Shernan Stanton K. , Seidman Christine E. , Aranki Sary F. , Seidman Jon G. , Body Simon C. 
Published: January 2015

AbstractAbstract
The authors have performed a comprehensive genomic analysis of human heart exposed to cold cardioplegia-induced myocardial ischemia providing novel information regarding gene regulation during ischemia. The results further our understanding of the pathological response of the human heart to stress and identify novel interventional targets for future therapies.
Supplemental Digital Content is available in the text.

Background:
The exact mechanisms that underlie the pathological processes of myocardial ischemia in humans are unclear. Cardiopulmonary bypass with cardioplegic arrest allows the authors to examine the whole transcriptional profile of human left ventricular myocardium at baseline and after exposure to cold cardioplegia-induced ischemia as a human ischemia model.

Methods:
The authors obtained biopsies from 45 patients undergoing aortic valve replacement surgery at baseline and after an average of 79 min of cold cardioplegic arrest. Samples were RNA sequenced and analyzed with the Partek® Genomics Suite (Partek Inc., St. Louis, MO) for differential expression. Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA) and Biobase ExPlain (Biobase GmbH, Wolfenbuettel, Germany) systems were used for functional and pathway analyses.

Results:
Of the 4,098 genes with a mean expression value greater than 5, 90% were down-regulated and 9.1% were up-regulated. Of those, 1,241 were significantly differentially expressed. Gene ontology analysis revealed significant down-regulation in immune inflammatory response and complement activation categories and highly consistent was the down-regulation of intelectin 1, proteoglycan, and secretory leukocyte peptidase inhibitor. Up-regulated genes of interest were FBJ murine osteosarcoma viral oncogene homolog and the hemoglobin genes hemoglobin α1 (HBA1) and hemoglobin β. In addition, analysis of transcription factor–binding sites revealed interesting targets in factors regulating reactive oxygen species production, apoptosis, immunity, cytokine production, and inflammatory response.

Conclusions:
The authors have shown that the human left ventricle exhibits significant changes in gene expression in response to cold cardioplegia-induced ischemia during cardiopulmonary bypass, which provides great insight into the pathophysiology of ventricular ischemia, and thus, may help guide efforts to reduce myocardial damage during surgery.
Individual Differences in Acute Pain-induced Endogenous Analgesia Predict Time to Resolution of Postoperative Pain in the Rat
Authors: Peters Christopher M. , Hayashida Ken-ichiro , Suto Takashi , Houle Timothy T. , Aschenbrenner Carol A. , Martin Thomas J. , Eisenach James C. 
Published: January 2015

AbstractAbstract
In a preclinical model of postoperative nerve injury, weak conditioned pain modulation and spinal noradrenergic depletion predicted persistent pain suggesting possible mechanisms for persistent pain after surgery.

Background:
Chronic postsurgical pain, a significant public health problem, occurs in 10 to 50% of patients undergoing major surgery. Acute pain induces endogenous analgesia termed conditioned pain modulation (CPM), and the strength of CPM preoperatively predicts the likelihood of chronic postsurgical pain. The relation between CPM and recovery from surgery has not been examined in preclinical models.

Methods:
CPM was assessed in individual rats and correlated with each animal’s time course of recovery of hypersensitivity after partial spinal nerve ligation. The role of descending noradrenergic pathways in the spinal cord to mechanisms of CPM and recovery was tested using idazoxan to block noradrenergic receptors or antidopamine β-hydroxylase–conjugated saporin to ablate these pathways. Behavioral hypersensitivity, static weight bearing, and spinal glial activation were measured after partial spinal nerve ligation.

Results:
The strength of CPM varied over two-fold between individuals and was directly correlated with the slope of recovery from hypersensitivity after surgery (P < 0.0001; r = 0.660). CPM induced the release of norepinephrine in the spinal cord and was partially blocked by intrathecal idazoxan or dopamine β-hydroxylase-saporin. Dopamine β-hydroxylase-saporin also slowed recovery and enhanced spinal glial activation after partial spinal nerve ligation surgery. Ongoing activation of these pathways was critical to sustained recovery because intrathecal dopamine β-hydroxylase-saporin given 7 weeks after recovery reinstituted hypersensitivity, while having no effect in animals without previous surgery.

Conclusion:
Collectively, these studies provide a clear back-translation from clinical observations of CPM and chronic postsurgical pain and suggest that the ability to engage ongoing descending endogenous noradrenergic signaling may be critical in determining time course of recovery from hypersensitivity after surgery.
Thai consumers’ purchase decisions and private label brands
Authors: Thanasuta Kandapa 
Published: January 2015

Purpose
– Private label brands have achieved double-digit growth in the Thai market. To expand market share, private label brands need to identify clearly what triggers consumer purchases. The purpose of this paper is to investigate the relationship between consumer decision-making styles and actual purchases of private label products in a Thai market context, using price consciousness, quality consciousness, brand consciousness, value consciousness, and risk perception as factors for investigation.

Design/methodology/approach
– Responses from a total of 240 respondents from four product categories were collected through mall intercepts in five hypermarkets and supermarkets in Bangkok, and a regression-based model was employed to identify the associations.

Findings
– The results indicate a significant relationship between price-conscious and brand-conscious consumers, and private label purchases and show that the relationship between quality-conscious, value-conscious, and risk-adverse consumers and private label purchases is insignificant. It concludes that price-conscious consumers are the ones most likely to purchase private label products in low-differentiation categories. An opposite relationship prevails for consumers who are brand conscious in low-differentiation, high-risk, and low-risk categories.

Research limitations/implications
– The outcomes of this research suggest that private label brands should maintain a low-price strategy while striving for continuous improvement in quality to capture additional quality- and value-conscious consumers. It also suggests that national brands invest in brand-building strategies rather than competing on price.

Originality/value
– This study enhances an understanding of consumer decision-making characteristics for actual private label purchases rather than the intention to purchase and is useful in suggesting an alternative to socio-economic factors as a method of identifying private label purchasers.
Two paths to diversification
Authors: Dhandapani Karthik , Upadhyayula Rajesh S. 
Published: January 2015

Purpose– The purpose of this paper is to examine the impact of related diversification across service offerings and industry domains for professional service firms (PSFs) in emerging economies by integrating the reputational and economies of scope perspectives of diversification. The paper also provides insights into how related diversification impacts small and medium sized firms differently.Design/methodology/approach– Using unique data from the Indian Information Technology industry, the authors examine the impact of related diversification along service offerings and industry domains on export performance of firms.Findings– The results show that related diversification across specializations and industry domains impact performance differently across different firm sizes. While the authors find that related diversification across service offerings has an inverted U shape with performance for the medium sized firms, they do not impact performance for small sized firms. Performance of small firms has a U shaped relationship with relatedness in industry domains. The study shows that reputation transfer across industry domains play a significant role in the performance of small size firms whereas the ability to realize economies of scope by cross selling multiple services across clients do matter for performance of medium sized firms.Practical implications– Managers of small PSFs need to expand along related industry domains whereas managers from medium sized firms can experiment across service offerings to exploit economies of scope.Originality/value– The study contributes to hitherto unexamined research on related diversification in PSFs. The study is one of the few studies to examine relatedness along more than one dimension in an intra-industry context.
The bottom of the pyramid: an integrative approach
Authors: Rabino Samuel 
Published: January 2015

Purpose
– The purpose of this paper is to examine the concept of the bottom of the pyramid (BOP) in the context of the knowledge economy.

Design/methodology/approach
– A conceptual approach integrating the BOP perspective, diffusion of innovations, and the new product development process.

Findings
– This paper structures a framework that might be helpful in advancing the competitiveness and product development capabilities of multinationals.

Practical implications
– The paper provides managers of multinational companies with an organized way of evaluating opportunities in BOP markets in the context of a global knowledge economy.

Originality/value
– The paper incorporates ideas and theories from three business and marketing fields into a framework that could be used as basis for an action plan.