bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hatchery Steelhead Smolt Release Size Effects on Adult Production and Straying
Authors: Clarke Lance R , Flesher Michael W , Carmichael Richard W 
Published: January 2014

Abstract
Studies have demonstrated higher postrelease survival for larger hatchery steelhead Oncorhynchus mykiss smolts than for smaller ones. However, the ideal release size should also maximize adult returns and minimize interactions of hatchery fish with wild fish. We conducted a study over five release years with paired groups of anadromous hatchery steelhead smolts reared to target sizes of either 90 g (small size) or 113 g (large size). After stream release, we monitored out-migration travel times and survival to a downstream dam using freeze-brand marks in a subsample of each release group. Steelhead smolts that out-migrate quickly may interact less with wild fish. Across all release groups, travel time was about 3 d slower for small-sized smolts than for large ones, but this difference was not statistically significant, and there was no significant difference in the percentage of brands detected at the dam between the two smolt sizes. Coded wire tag recovery was used to compare smolt-to-adult survival (SAS), the number of adults produced per 100 kg of smolts released, and the percentage of adults that strayed. Across all years, large-sized smolts had an average SAS of 1.31% compared with 0.92% for small-sized smolts, a statistically significant difference of 42.0%. The average number of adult steelhead produced per 100 kg of smolts released also was higher for the large-sized group (11.4 adults/100 kg of smolts) over the small-sized group (10.1 adults/100 kg of smolts), though the 12.8% difference was not statistically significant. Adults originating from large-sized smolt releases strayed at a rate of 13.1% compared with a 7.9% rate for the small-sized smolt groups, a difference that was statistically significant. In this study, larger hatchery steelhead smolts had a higher survival after release; however, we found tradeoffs between management objectives associated with maximizing adult production and those aimed at minimizing ecological risks.
Effect of Altering Dietary Protein: Energy Ratios on Juvenile Pallid Sturgeon Growth Performance
Authors: Kittel Elliott C. , Small Brian C. 
Published: January 2014

AbstractPallid SturgeonScaphirhynchus albusare endemic to the large, freshwater, river systems of North America and have long been prized for caviar production. Declining wild populations and fishing prohibitions have created interest in the culture of these fish. Protein and energy are often the first nutrients examined when attempting to identify diets appropriate for a novel culture species. Therefore, the present study evaluated the effects of different dietary protein: energy ratios on Pallid Sturgeon growth and body composition. Twelve semipurified diets composed of four crude protein (CP) levels (32, 39, 46, and 53%) and three gross energy (GE) levels (3,600, 4,200, and 4,800 kcal/kg) were fed to 180 juvenile Pallid Sturgeon for 18 weeks. Diets were offered to triplicate groups of five fish each in separate tanks. Fish were fed 2% body weight daily and sampled every 3 weeks. Mean weight gain and body composition were significantly affected by GE content of the dietary treatment (P≤ 0.05), but not by dietary CP or protein and energy interactions (P> 0.05). The most energetically dense diets yielded significantly larger fish than the least energetically dense diets and the intermediate diets were not significantly different from either extreme. These results suggest that Pallid Sturgeon are able to perform similarly across a wide range of protein: energy ratios (79–147 mg protein/kcal), as long as adequate dietary energy (≥3,800 kcal GE/kg) is provided and essential amino acids are not limiting. This research is the first to evaluate dietary protein: energy ratios forScaphirhynchussturgeon culture.
Development of a Methodology for Intensive Larviculture of Atlantic Croakers
Authors: Lemus Jason T , Sarkisian Brie L , Lee Michael S , Bardon-Albaret Agnes , Saillant Eric A 
Published: January 2014

Abstract
The Atlantic Croaker Micropogonias undulatus (Sciaenidae) is a candidate species for marine baitfish aquaculture in the southeastern United States because of its high value and common use as live bait by recreational fishers. However, an efficient larviculture procedure has not been reported to date; development of such a procedure was the impetus for this study. Embryos were obtained from captive broodstock that were induced to spawn volitionally by using a single injection of a luteinizing hormone releasing hormone agonist. Larvae were cultured at low density (initial density = 6.4 larvae/L) via intensive culture methods, including the use of recirculating filtration systems and of rotifers, brine shrimp Artemia spp., and micropellets as larval foods. The trial was performed in six 1,100-L tanks at a salinity of 14–29‰, with average rearing temperatures of 23.6°C and 24.6°C. At the completion of the study (39 d posthatch), mean SLs were 24.7 mm (SE = 0.738) for larvae cultured at 24.6°C and 23.0 mm (SE = 0.624) for larvae cultured at 23.6°C. Mean survival at 39 d posthatch was 25.9% and did not differ significantly between temperature groups. This work demonstrated a successful methodology for intensive larviculture of Atlantic Croakers and can serve as a platform for the experimentation that will be necessary to develop economically viable procedures for intensive production of this species.
MEMBPLUGIN: studying membrane complexity in VMD
Authors: Guixà-González Ramon , Rodriguez-Espigares Ismael , Ramírez-Anguita Juan Manuel , Carrió-Gaspar Pau , Martinez-Seara Hector , Giorgino Toni , Selent Jana 
Published: January 2014

AbstractSummary: Computer simulations are giving way to more complex and accurate studies of biological membranes by molecular dynamics (MD) simulations. The analysis of MD trajectories comprises the biophysical characterization of membrane properties or the study of protein–lipid interactions and dynamics. However, there is a lack of automated tools to analyse MD simulations of complex membrane or membrane-protein systems. Here we present MEMBPLUGIN, a plugin for the Visual Molecular Dynamics package that provides algorithms to measure a host of essential biophysical properties in simulated membranes. MEMBPLUGIN features are accessible both through a user-friendly graphical interface and as command-line procedures to be invoked in analysis scripts.Availability and implementation: MEMBPLUGIN is a VMD extension written in Tcl. Multi-platform source code, documentation and tutorials are freely available at http://membplugin.sourceforge.net.Contact: toni.giorgino@isib.cnr.it or jana.selent@upf.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape
Authors: Pupov Danil , Kuzin Ivan , Bass Irina , Kulbachinskiy Andrey 
Published: January 2014

Abstract
The σ subunit of bacterial RNA polymerase (RNAP) has been implicated in all steps of transcription initiation, including promoter recognition and opening, priming of RNA synthesis, abortive initiation and promoter escape. The post-promoter-recognition σ functions were proposed to depend on its conserved region σ3.2 that directly contacts promoter DNA immediately upstream of the RNAP active centre and occupies the RNA exit path. Analysis of the transcription effects of substitutions and deletions in this region in Escherichia coli σ70 subunit, performed in this work, suggests that (i) individual residues in the σ3.2 finger collectively contribute to RNA priming by RNAP, likely by the positioning of the template DNA strand in the active centre, but are not critical to promoter escape; (ii) the physical presence of σ3.2 in the RNA exit channel is important for promoter escape; (iii) σ3.2 promotes σ dissociation during initiation and suppresses σ-dependent promoter-proximal pausing; (iv) σ3.2 contributes to allosteric inhibition of the initiating NTP binding by rifamycins. Thus, region σ3.2 performs distinct functions in transcription initiation and its inhibition by antibiotics. The B-reader element of eukaryotic factor TFIIB likely plays similar roles in RNAPII transcription, revealing common principles in transcription initiation in various domains of life.
Transcriptome-wide investigation of genomic imprinting in chicken
Authors: Frésard Laure , Leroux Sophie , Servin Bertrand , Gourichon David , Dehais Patrice , Cristobal Magali San , Marsaud Nathalie , Vignoles Florence , Bed'hom Bertrand , Coville Jean-Luc , Hormozdiari Farhad , Beaumont Catherine , Zerjal Tatiana , Vignal Alain , Morisson Mireille , Lagarrigue Sandrine , Pitel Frédérique 
Published: January 2014

Abstract
Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken.
Adjacent single-stranded regions mediate processing of tRNA precursors by RNase E direct entry
Authors: Kime Louise , Clarke Justin E. , Romero A. David , Grasby Jane A. , McDowall Kenneth J. 
Published: January 2014

Abstract
The RNase E family is renowned for being central to the processing and decay of all types of RNA in many species of bacteria, as well as providing the first examples of endonucleases that can recognize 5′-monophosphorylated ends thereby increasing the efficiency of cleavage. However, there is increasing evidence that some transcripts can be cleaved efficiently by Escherichia coli RNase E via direct entry, i.e. in the absence of the recognition of a 5′-monophosphorylated end. Here, we provide biochemical evidence that direct entry is central to the processing of transfer RNA (tRNA) in E. coli, one of the core functions of RNase E, and show that it is mediated by specific unpaired regions that are adjacent, but not contiguous to segments cleaved by RNase E. In addition, we find that direct entry at a site on the 5′ side of a tRNA precursor triggers a series of 5′-monophosphate-dependent cleavages. Consistent with a major role for direct entry in tRNA processing, we provide additional evidence that a 5′-monophosphate is not required to activate the catalysis step in cleavage. Other examples of tRNA precursors processed via direct entry are also provided. Thus, it appears increasingly that direct entry by RNase E has a major role in bacterial RNA metabolism.
Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry
Authors: Vranken Charlotte , Deen Jochem , Dirix Lieve , Stakenborg Tim , Dehaen Wim , Leen Volker , Hofkens Johan , Neely Robert K. 
Published: January 2014

Abstract
We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).
The impact of market orientation on Chinese retailers' channel relationships
Authors: Chung Jae‐Eun , Huang Ying , Jin Byoungho , Sternquist Brenda 
Published: January 2014

PurposeThis study seeks to examine the influence of market orientation on Chinese buyer‐supplier relations. A model is proposed depicting relationships among retailer market orientation, supplier market intelligence, supplier role performance, and retailer economic and social satisfaction.Design/methodology/approachData were collected from 99 chain store buyers and managers from 25 cities in China. Structural equation modeling was used to analyze the data.FindingsA retailer's market orientation is critical for its own economic and social satisfaction by increasing supplier market intelligence (MI) and supplier role performance.Practical implicationsRetailers' MO increased supplier MI and role performance. This study found that economic performance was more important in channel relationships than social relationships. Therefore, suppliers should focus on improving retailers' economic satisfaction through role performance and market intelligence rather than social satisfaction.Originality/valuePrevious MO literature has focused primarily on the firm's performance and ignored the interactive aspect of business performance among channel members. The current study fills this gap by demonstrating the significant influences of retailer MO on supplier MI and on supplier role performance, as well as on retailer satisfaction – both the economic and social components. To the authors' knowledge, the current study is the first to relate retailer MO, supplier MI, and supplier role performance to two types of retailer satisfaction – i.e. economic and social satisfaction.
A counting history
Authors: Kumarasinghe Sriya 
Published: January 2014

PurposeThe purpose of this paper is to draw attention to the historical evidence of accounting practices in the ancient Asia.Design/methodology/approachThe work is a philosophical poem.FindingsAccounting and auditing had been used in Asia, especially in ancient Ceylon and India before “double‐entry accounting” emerged in the Europe. Archaeological evidence proves that rulers in the ancient era were accountable to the people.Research limitations/implicationsThough Sri Lankan history is more than 2,600 years old, the significance of the archaeological findings in terms of accounting history has not been much investigated. This poem draws researchers' attention to that area of study.Originality/valueThe work raises, in poetic form, the matter of unexplored, ancient accounting practices.
Risk assessment
Authors: Butt Maggie 
Published: January 2014

PurposeThis short poem seeks to encapsulate a cynical view of the value of risk assessment.Design/methodology/approachThe poem was written at the time of the collapse of the banks, despite their elaborate risk assessments. It juxtaposes modern belief in risk assessment with other historical and fallible means of prediction. The poem is a triolet, a medieval French form comprising one eight‐line stanza with a regular rhyming scheme and repetition of lines. It is concise, with nursery rhyme simplicity, and a refrain that sinks into the conscious.FindingsThe images of runes, the tarot, and astrology counterbalance the scientific language and basis of risk assessment and the hard‐nosed, factual business of insurance.Research limitations/implicationsThe poem reminds us that the greatest risk is the one that is impossible to foresee.Originality/valueThe poem is unique in its use of a medieval French form to examine a modern phenomenon.
Understanding multifaceted job satisfaction of retail employees
Authors: Chung Te‐Lin , Rutherford Brian , Park Jungkun 
Published: January 2014

PurposeThis study aims to examine the multi‐faceted job satisfaction of retail employees. In addition, it seeks to investigate the moderating effect of gender on the relations between proposed antecedents and multifaceted job satisfaction. The seven facets of job satisfaction include satisfaction with supervision, overall job satisfaction, company policy and support, promotion, pay, co‐workers, and customers.Design/methodology/approachData for this study constitute a subset of a larger study examining salespeople from both business‐to‐business (B‐T‐B) and retail sales contexts in the USA. A total of 352 usable responses from retail employees were retained. Hypothesized relationships were tested by multiple regression analyses, Chow equality tests, and hierarchical regression analyses.FindingsThe study suggests that perceived organizational support, role ambiguity, and emotional exhaustion are the most influential factors for most facets of retail employees' job satisfaction. Role conflict and work‐family conflict only predict satisfaction with promotion, and family‐work conflict does not predict any facets of job satisfaction. Gender differences only played a part in satisfaction with customers. All other variables, such as perceived organizational support, work‐family conflict, family‐work conflict, and emotional exhaustion affect male and female employees differently.Practical implicationsThe study provides managerial implications, suggesting that there is no one perfect policy to satisfy retail employees in all aspects and retailers should be more careful in assigning tasks to employees.Originality/valueThe literature concerning multifaceted job satisfaction has contributed significantly to understanding sales personnel job satisfaction. However, as many of the job characteristics for B‐T‐B and retail are different, a separate examination of factors influencing retail employees' job satisfaction is necessary. This study extends the current literature examining the job satisfaction of retail employees by borrowing from retail literature concerning global job satisfaction and from sales management literature about multifaceted job satisfaction.
Open source deployment in local government
Authors: Allen Jonathan P. , Geller Dave 
Published: January 2014

PurposeThis paper aims to present a theory of the perceived outcomes of open source software adoption for an organizational IT department.Design/methodology/approachThe paper is an interpretive case study of three open source pilot projects in local government, based on interviews with IT management, IT staff, and users. Data analysis based on constructivist grounded theory is used to generate theory about the perceived organizational outcomes of open source adoption.FindingsOpen source adoption is perceived as an occasion for rapidly developing effective new business applications, even in the context of shrinking IT resources and a poor relationship between IT and the rest of the organization. IT management and staff see the potential to improve their strained relationship with users, and improve their image of themselves as product developers and explorers. Disruptive project strategies, that keep open source adoptions outside of normal resource allocation processes, are consistently associated with open source success.Research limitations/implicationsWhile only exploratory, the case study shows that open source deployments can have a significant impact on the wider organization, up to and including the announcement of the first municipal government policy in the USA requiring that open source be considered for all future software acquisitions.Practical implicationsThe case study offers a pathway for IT departments to achieve better perceived organizational outcomes, using fewer resources, under challenging circumstances.Originality/valueThe paper offers new conjectures on post‐adoption outcomes for open source researchers, and a new mechanism for IT department transformation in the information systems literature.
Estimates of success rates of remote arbitrary code execution attacks
Authors: Sommestad Teodor , Holm Hannes , Ekstedt Mathias 
Published: January 2014

PurposeThe purpose of this paper is to identify the importance of the factors that influence the success rate of remote arbitrary code execution attacks. In other words, attacks which use software vulnerabilities to execute the attacker's own code on targeted machines. Both attacks against servers and attacks against clients are studied.Design/methodology/approachThe success rates of attacks are assessed for 24 scenarios: 16 scenarios for server‐side attacks and eight for client‐side attacks. The assessment is made through domain experts and is synthesized using Cooke's classical method, an established method for weighting experts' judgments. The variables included in the study were selected based on the literature, a pilot study, and interviews with domain experts.FindingsDepending on the scenario in question, the expected success rate varies between 15 and 67 percent for server‐side attacks and between 43 and 67 percent for client‐side attacks. Based on these scenarios, the influence of different protective measures is identified.Practical implicationsThe results of this study offer guidance to decision makers on how to best secure their assets against remote code execution attacks. These results also indicate the overall risk posed by this type of attack.Originality/valueAttacks that use software vulnerabilities to execute code on targeted machines are common and pose a serious risk to most enterprises. However, there are no quantitative data on how difficult such attacks are to execute or on how effective security measures are against them. The paper provides such data using a structured technique to combine expert judgments.