bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of Auxiliary Information in Statistical Catch-at-Age (SCA) Analysis of the Saginaw Bay Stock of Walleye in Lake Huron
Authors: Fielder David G. , Bence James R. 
Published: October 2014

Abstract
Estimates of mortality rates and abundance for the Saginaw Bay stock of Walleye Sander vitreus has traditionally been performed with an analysis of tag returns using a Brownie-style analysis. An estimation approach that more fully accounted for sources of exploitation in addition to the recreational fishery in Saginaw Bay and inclusive of the rest of Lake Huron was needed. We developed a statistical catch-at-age model to accomplish this and evaluated four versions including three different treatments of natural mortality (M): a constant value, age-based M values, and time-varying M values. Deviance information criterion model selection procedures indicated that an age-based M model version was optimal. We also evaluated an integrated version that incorporated tag returns as auxiliary information for the recreational component. In this case, model selection was based on conformity between observed and predicted data and model convergence. The integrated version was ruled out due to poor agreement of the observed and predicted values and predictions of abundance that were not reflected by the fisheries. We concluded that the component of the population used for tagging may exhibit dynamics that differ from the rest of the stock. Total annual mortality of Walleyes was greatest for older ages in all fisheries and ranged from 32% for age-2 fish to 39% for fish of ages 10 and older. The recreational fishery accounted for the majority of fishing mortality, but the commercial trap-net fishery in the main basin of Lake Huron and bykill from other trap nets in the bay accounted for proportionally greater fishing mortality of younger ages of fish. Abundance peaked in 2007 at 4 million Walleyes age2 and older, but estimates indicated a previous period of high abundance in the late 1980s, forcing the reconsideration of the past stock as depressed and dependent on stocking.
Received January 8, 2014; accepted June 11, 2014
Low-Cost Restoration Techniques for Rapidly Increasing Wood Cover in Coastal Coho Salmon Streams
Authors: Carah Jennifer K. , Blencowe Christopher C. , Wright David W. , Bolton Lisa A. 
Published: October 2014

Abstract
Like many rivers and streams in forests of the Pacific Northwest, California north coast rivers and streams have been depleted of downed wood through timber harvest and direct wood removal. Due to the important role of wood in creating and maintaining salmonid habitat, wood augmentation has become a common element of stream restoration. Restoration efforts in North America often focus on building anchored, engineered wood structures at the site scale; however, these projects can fail to meet restoration goals at the watershed scale, do not closely mimic natural wood loading processes or dynamics, and can be expensive to implement. For critically imperiled populations of Coho Salmon Oncorhynchus kisutch in California, there is a strong impetus to achieve as much habitat restoration as possible in priority watersheds in the shortest time and with limited resources, so cost-efficient techniques are necessary. In this multi-site project, we investigated unanchored techniques for wood loading to evaluate cost and contribution to salmonid habitat in Mendocino County, California. Over a period of 6 years, 72.4 km of stream were treated with 1,973 pieces of strategically placed wood. We found that unanchored wood loading techniques were much less costly than commonly used anchored techniques, reliably improved habitat, and retained wood at high rates (mean = 92%) in small- to moderate-sized streams, at least over the short term (&lt;6 years). The average cost of design and construction for the unanchored projects was US$259 per log, equivalent to 22% of the cost associated with the anchored wood augmentation methods examined here. Our results suggest that this unanchored wood loading approach has the potential to increase the pace and scale at which wood augmentation projects are implemented in the Pacific Northwest and beyond.
Received January 22, 2014; accepted June 25, 2014
Validation of Annuli Formation in Pectoral Fin Rays from Shovelnose Sturgeon in the Lower Platte River, Nebraska
Authors: Rugg M. L. , Hamel M. J. , Pegg M. A. , Hammen J. J. 
Published: October 2014

Abstract
Fish age is commonly estimated by counting bands on calcified structures. Age estimates are used to calculate information on population dynamics such as growth, mortality, and recruitment. Pectoral fin rays are the most frequently used structure to age sturgeon species, yet little work has been done to validate annuli formation. We collected Shovelnose Sturgeon Scaphirhynchus platorynchus monthly from the lower Platte River, Nebraska, during 2011 and 2012 and removed the leading, left pectoral fin ray from each fish captured. We used marginal increment analysis to assess the validity of annual deposition of growth marks on pectoral fin rays. There were two complete cycles of increasing and decreasing increment values between March and November within each year. Mean marginal increments showed minimal peaks in March, July, and October followed by a decrease in increment length during April, September, and November. However, mean marginal increments were similar between months in both years. These results suggest there is no discernible pattern in growth ring deposition for Shovelnose Sturgeon in the lower Platte River and that their use for age and growth analyses would likely lead to biased estimates. Inaccuracies in age assignment can lead to errors when calculating population dynamic parameters and, ultimately, misguided management decisions. We recommend that alternate methods for estimating the ages of Shovelnose Sturgeon be explored.
Received February 25, 2014; accepted July 4, 2014
RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing
Authors: Gupta Vikas , Estrada April D. , Blakley Ivory , Reid Rob , Patel Ketan , Meyer Mason D. , Andersen Stig Uggerhøj , Brown Allan F. , Lila Mary Ann , Loraine Ann E. 
Published: October 2014

AbstractBackgroundBlueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable breeding berry varieties with enhanced health benefits.ResultsToward this end, we annotated a draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grapeVitis vinifera. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic.Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up and down regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3’ end formation.ConclusionsWe report genome sequence, gene models, functional annotations, and RNA-Seq expression data that provide an important new resource enabling high throughput studies in blueberry. RNA-Seq data are freely available for visualization in Integrated Genome Browser, and analysis code is available from the git repository athttp://bitbucket.org/lorainelab/blueberrygenome.
Analysis of road transport energy consumption and emissions: a case study
Authors: Franco Sainu , Ravibabu Mandla Venkata 
Published: October 2014

Purpose
– The purpose of this study is to examine the growing energy consumption pattern and emissions due to increasing vehicular density in the Vellore district. The transport demand in Indian cities has increased substantially over the past few years. Increasing household incomes and economic development in cities have added to this growing demand.

Design/methodology/approach
– The growth of Vellore town currently is such that in a short period of time, the development is likely to engulf the entire district as one big city, as it happened for Chennai. It is at a transitional stage where it is possible to bring about certain policy changes to prevent the catastrophic effects of urbanization. To test the objectives of the study, statistical and mathematical tools such as mean, coefficient of variation, correlation and regression models are used. Growth of vehicle population in Tamil Nadu in general and Vellore in particular are analyzed by computing the percentage rate of change and trend rate of growth.

Findings
– A study of the past four years shows a tremendous growth in the number of two-wheelers, while the number of buses has declined. The study also shows that public transport fuel consumption is < 20 per cent of the overall fuel consumption. The emission of all greenhouse gases is rising and it shows a linear growth. The increase in emission of CO2 is most alarming.

Research limitations/implications
– The diversity of sources that have been combined together implies a consequent reduction in accuracy. Data from different sources had different geographical boundaries (state, district, region and country). Thus, the data had to be translated to the relevant geographical area by using proportionality ratio. This manipulation does impact on the accuracy of the used data.

Practical implications
– This article provides a framework that can inform decisions makers on consequences in the absence of timely intervention and policy changes.

Originality/value
– Road transport is an inherently complex sector as it deals with a very large number of individual vehicles and factors of influence. The findings have implications for government in general and policy-makers in particular. This article puts together data of a particularly vulnerable region at a time when policy changes could bring about lasting beneficial effects. This region has not been included in any previous research.
Regional cost sharing in expansions of electricity transmission grids
Authors: Nylund Hans 
Published: October 2014

Purpose
– The purpose of this paper is to analyse how the regional effects of expansion can be managed under the constraints of voluntary cooperation. This paper studies international cooperation on electricity transmission expansions in a region of countries that shares a joint electricity infrastructure.

Design/methodology/approach
– Cooperative game theory and the partition-function form were applied in combination with benefit–cost ratios to model and analyse the incentives to cooperate under different cost allocation rules. Empirical background was provided by a case study of a transmission investment agreement made on the Nordic electricity market.

Findings
– Both cost sharing and the composition of expansion plans were identified as ways of reaching regional agreements. It was found that agreements based on proportional division of costs in relation to benefits were the best choice for voluntary cooperation.

Research limitations/implications
– The study did not analyse the effects or relevance of surplus sharing in addition to that implied by cost sharing, nor has it studied the regulatory and legal requirements for implementing side-payments between countries in grid expansions. These issues could benefit from more study.

Practical implications
– The results are relevant for the development of international cooperation on grid expansions and as an input to regulations and policies aimed at promoting regional perspectives, in particular for the case of a single internal energy market in Europe.

Originality/value
– The paper contributes with an analysis of incentives for transmission expansions in a multinational environment subject to voluntary provision and a lack of supranational authorities with decision power.
Analysis of machinery breakdowns in power plants fed by biomass and MSW
Authors: De Antonellis Stefano , De Antonellis Mario 
Published: October 2014

Purpose
– The aim of the study is to identify main failure phenomena and to evaluate reparation costs, reparation time, loss of profit and their relationship with power plant and faulty components age. In this work, several machinery breakdowns occurred in thermal power plants fed by solid biomass, biodiesel, biogas and municipal solid waste, have been investigated. In the period between 2004 and 2012, 23 faults have been analyzed.

Design/methodology/approach
– Each fault has been classified considering: power plant technical specifications, type of damage, reparation cost, reparation time and loss of profit (when data are available). The whole data have been, therefore, compared to find out significant information.

Findings
– It has been pointed out that relevant property damages are mainly caused by old components failure. In addition, the loss of profit is generally much higher than the property damage (six times on average basis).

Originality/value
– The study provides useful information that can be of interest for personnel of energy utilities, banks and insurance companies in managing power plants risks and in planning the availability of energy services.
Spanning information behaviour across the stages of a learning task
Authors: Heinström Jannica , Sormunen Eero , Kaunisto-Laine Sarita 
Published: October 2014

Purpose
– The purpose of this paper is to explore the role of personality (intellectual curiosity, conscientiousness and negative emotionality) and approach to studying (deep, strategic and surface) on students’ learning-related information behaviour in inquiry tasks.

Design/methodology/approach
– Data were collected from 219 senior high school students with the use of three questionnaires.

Findings
– The findings showed that students’ individual traits influenced different aspects of their learning-related information behaviour from information need to information use.

Research limitations/implications
– The results were based on survey data. Reliability issues with the scales are discussed. In future research qualitative data would enrich the understanding of the phenomena.

Practical implications
– The results are informative for teachers and librarians who guide students in inquiry tasks.

Originality/value
– The study spanned learning-related information behaviour across the whole inquiry process: from task construction through task performance to task completion. The findings showed that individual traits were particularly influential at the task completion stage, that is on information use.
The Information School at the University of Sheffield, 1963-2013
Authors: Benson Melanie T. , Willett Peter 
Published: October 2014

Purpose
– The purpose of this paper is to describe the historical development of library and information science (LIS) teaching and research in the University of Sheffield's Information School since its founding in 1963.

Design/methodology/approach
– The history is based on published materials, unpublished school records, and semi-structured interviews with 19 current or ex-members of staff.

Findings
– The School has grown steadily over its first half-century, extending the range of its teaching from conventional programmes in librarianship and information science to include cognate programmes in areas such as health informatics, information systems and multi-lingual information management.

Originality/value
– There are very few published accounts of the history of LIS departments.
Successful treatment of angioma serpiginosum using a novel 532 nm potassium titanyl phosphate (KTP) laser
Authors: Rho Nark Kyoung , Kim Hyree , Kim Hei Sung 
Published: October 2014

AbstractAngioma serpiginosum (AS) is a rare, benign, vascular disorder comprising non‐blanchable punctate red to purple lesions in a gyrate or serpiginous configuration. We report a case of a 38‐year‐old woman with a red colored eruption on her chest which was present since puberty. A novel 532 nm potassium‐titanyl phosphate (KTP) laser (Excel V, Cutera Inc., Brisbane, CA, USA) was applied which resulted in near complete resolution after two sessions of treatment.
Surgical management of umbilical basal cell carcinoma: Published work review and the optimal depth of surgical excision
Authors: Nakamura Yasuhiro , Teramoto Yukiko , Tanaka Ryota , Nakamura Yoshiyuki , Maruyama Hiroshi , Fujisawa Yasuhiro , Sato Sayuri , Fujimoto Manabu , Yamamoto Akifumi 
Published: October 2014

AbstractBasal cell carcinoma (BCC) is a common malignant skin tumor. However, BCC that arise at the umbilicus is rare. We present three cases of umbilical BCC. Each BCC was excised at a different depth level, and all deep surgical margins were negative. All patients had no evidence of local recurrence or metastasis during the follow‐up periods (12, 24, and 52 months). Reviewing the reported cases of umbilical BCC, the BCC cells did not seem to invade into the umbilical scar in most cases, and the deepest invasion levels of tumor cells were up to the middle layer of the subcutaneous tissue. However, the dermatological surgeons have to consider the possibility of surgical excision down to and including the umbilical attachment to the peritoneum, and intraoperative margin assessment should be necessary to avoid the risk of excessive or incomplete excision.
Source–receiver two‐way wave extrapolation for prestack exploding‐reflector modelling and migration
Authors: Alkhalifah Tariq , Fomel Sergey , Wu Zedong 
Published: October 2014

ABSTRACTMost modern seismic imaging methods separate input data into parts (shot gathers). We develop a formulation that is able to incorporate all available data at once while numerically propagating the recorded multidimensional wavefield forward or backward in time. This approach has the potential for generating accurate images free of artiefacts associated with conventional approaches. We derive novel high‐order partial differential equations in the source–receiver time domain. The fourth‐order nature of the extrapolation in time leads to four solutions, two of which correspond to the incoming and outgoing P‐waves and reduce to the zero‐offset exploding‐reflector solutions when the source coincides with the receiver. A challenge for implementing two‐way time extrapolation is an essential singularity for horizontally travelling waves. This singularity can be avoided by limiting the range of wavenumbers treated in a spectral‐based extrapolation. Using spectral methods based on the low‐rank approximation of the propagation symbol, we extrapolate only the desired solutions in an accurate and efficient manner with reduced dispersion artiefacts. Applications to synthetic data demonstrate the accuracy of the new prestack modelling and migration approach.
Management of entomopathogenic fungi in cultures of Tenebrio molitor (Coleoptera: Tenebrionidae)
Authors: Lee Se Jin , Kim Si Hyeon , Nai Yu‐Shin , Je Yeon Ho , Parker Bruce L. , Kim Jae Su 
Published: October 2014

AbstractLarvae of mealworms Tenebrio molitor L. (Coleoptera: Tenebrionidae) have been used as animal feed, but fungal pathogens rapidly downsize the populations, resulting in economic losses. In this work, we established an effective management strategy for fungal pathogens. An entomopathogenic fungus, Beauveria bassiana, was isolated from mealworm cadavers. The bioassay of some isolates of this species at >90% relative humidity revealed that the ERL1575 isolate had the highest virulence. At 20–30% RH, ERL1575 conidia when ingested produced 80% mortality but when sprayed topically produced only <10% mortality. Mealworms that had ingested conidia were exposed to 20, 25, 30 and 35°C and high humidity (>95%) for 5 days. This experiment produced about 90% mortality except at 35°C where mortality was <20%. When 40 fungicides were assayed against ERL1575, fluazinam (1000‐fold) and mancozeb (667‐fold) significantly inhibited conidial germination and/or hyphal growth. When fluazinam and mancozeb were added to the mealworm diet of conidia‐inoculated wheat bran, most were alive 3 days post application. However, 100% mortality resulted 3 days post application in the conidia‐inoculated wheat bran without any fungicides. In conclusion, B. bassiana isolates are pathogenic at <30°C when they are ingested by mealworms but fluazinam and mancozeb can be used for management to control the pathogen in their cultures.
Molecular annotation of ketol‐acid reductoisomerases from Streptomyces reveals a novel amino acid biosynthesis interlock mediated by enzyme promiscuity
Authors: Verdel‐Aranda Karina , López‐Cortina Susana T. , Hodgson David A. , Barona‐Gómez Francisco 
Published: October 2014

SummaryThe 6‐phosphogluconate dehydrogenase superfamily oxidize and reduce a wide range of substrates, making their functional annotation challenging. Ketol‐acid reductoisomerase (KARI), encoded by the ilvC gene in branched‐chain amino acids biosynthesis, is a promiscuous reductase enzyme within this superfamily. Here, we obtain steady‐state enzyme kinetic parameters for 10 IlvC homologues from the genera Streptomyces and Corynebacterium, upon eight selected chemically diverse substrates, including some not normally recognized by enzymes of this superfamily. This biochemical data suggested a Streptomyces biosynthetic interlock between proline and the branched‐chain amino acids, mediated by enzyme substrate promiscuity, which was confirmed via mutagenesis and complementation analyses of the proC, ilvC1 and ilvC2 genes in Streptomyces coelicolor. Moreover, both ilvC orthologues and paralogues were analysed, such that the relationship between gene duplication and functional diversification could be explored. The KARI paralogues present in S. coelicolor and Streptomyces lividans, despite their conserved high sequence identity (97%), were shown to be more promiscuous, suggesting a recent functional diversification. In contrast, the KARI paralogue from Streptomyces viridifaciens showed selectivity towards the synthesis of valine precursors, explaining its recruitment within the biosynthetic gene cluster of valanimycin. These results allowed us to assess substrate promiscuity indices as a tool to annotate new molecular functions with metabolic implications.