bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Mixed-Stock Analysis of American Shad in Two Atlantic Coast Fisheries: Delaware Bay, USA, and Inner Bay of Fundy, Canada
Authors: Waldman John , Hasselman Daniel , Bentzen Paul , Dadswell Michael , Maceda Lorraine , Wirgin Isaac 
Published: November 2014

Abstract
American Shad Alosa sapidissima in the Hudson River, New York, and coastwide have shown major long-term declines. A possible contributing factor is commercial fisheries that harvest this population outside of the Hudson River estuary. Using previously published and new reference microsatellite data from 33 baseline populations, our goals were (1) to estimate the proportion of Hudson River American Shad contributing to the two remaining major mixed-stock fisheries along the Atlantic coast in Delaware Bay and the Bay of Fundy and (2) to estimate the proportions of other American Shad stocks contributing to these two fisheries at the highest level of stock specificity. Stock composition estimates for 2009 and 2010 Delaware Bay collections were made using three models that ranged from the most simple question (Hudson River and Delaware Bay populations) to one with all 33 baseline populations included. In all cases, a Hudson River contribution nearly equal to that of the Delaware Bay contribution was observed, indicating a substantial take on the otherwise protected Hudson River population. When all baseline populations were included for the larger 2010 Delaware Bay collection, 19 showed nonzero contributions, largely drawn from mid-Atlantic U.S. rivers. The 2009 Bay of Fundy collection showed contributions from across most of the species’ range but was dominated by northern populations. Mixed-stock analyses of collections from the two sites together indicate that these estuarine fisheries harvested not only proximal populations but those originating from a wide latitudinal range.
Received April 3, 2014; accepted August 5, 2014
Effects of Appendaged Circle Hook Use on Catch Rates and Deep Hooking of Black Sea Bass in a Recreational Fishery
Authors: Bergmann Charles , Driggers William B. , Hoffmayer Eric R. , Campbell Matthew D. , Pellegrin Gilmore 
Published: November 2014

Abstract
Previous studies have demonstrated that circle hooks modified with an appendage can reduce the occurrence of deep hooking in some fishes. To determine whether this modification affects total catch and deep-hooking rate of Black Sea Bass Centropristis striata in a recreational fishery off the coast of Florida, anglers were provided with standardized gear that included one appendaged and one nonappendaged hook. Both hook types were fished equally, and a greater number of Black Sea Bass were caught on appendaged hooks (n = 301) than on nonappendaged hooks (n = 221). There was no significant difference in the mean TL (P = 0.80) of jaw- or deep-hooked fish during the study. Logistic regression was applied to the data using anatomical hooking location as the dependent variable and angler, hook position, and hook type as categorical factors. Hook type was the only significant variable in the final model (P = 0.03) in which fewer fish were deep hooked on appendaged hooks (0.96%) than on nonappendaged hooks (2.11%). Our findings indicate appendaged hooks are capable of reducing deep hooking of Black Sea Bass without reducing catch rates or altering size composition of the catch.
Received February 3, 2014; accepted August 14, 2014
Graphical model for joint segmentation and tracking of multiple dividing cells
Authors: Schiegg Martin , Hanslovsky Philipp , Haubold Carsten , Koethe Ullrich , Hufnagel Lars , Hamprecht Fred A. 
Published: November 2014

Abstract
Motivation: To gain fundamental insight into the development of embryos, biologists seek to understand the fate of each and every embryonic cell. For the generation of cell tracks in embryogenesis, so-called tracking-by-assignment methods are flexible approaches. However, as every two-stage approach, they suffer from irrevocable errors propagated from the first stage to the second stage, here from segmentation to tracking. It is therefore desirable to model segmentation and tracking in a joint holistic assignment framework allowing the two stages to maximally benefit from each other.
Results: We propose a probabilistic graphical model, which both automatically selects the best segments from a time series of oversegmented images/volumes and links them across time. This is realized by introducing intra-frame and inter-frame constraints between conflicting segmentation and tracking hypotheses while at the same time allowing for cell division. We show the efficiency of our algorithm on a challenging 3D+t cell tracking dataset from Drosophila embryogenesis and on a 2D+t dataset of proliferating cells in a dense population with frequent overlaps. On the latter, we achieve results significantly better than state-of-the-art tracking methods.
Availability and implementation: Source code and the 3D+t Drosophila dataset along with our manual annotations will be freely available on http://hci.iwr.uni-heidelberg.de/MIP/Research/tracking/
Contact: fred.hamprecht@iwr.uni-heidelberg.de
Supplementary information: Supplementary material is available at Bioinformatics online.
European lobster stocking requires comprehensive impact assessment to determine fishery benefits
Authors: Ellis Charlie D. , Hodgson David J. , Daniels Carly L. , Boothroyd Dominic P. , Bannister R. Colin A. , Griffiths Amber G. F. 
Published: November 2014

Abstract
Historically, hatcheries in Europe and North America attempted to contribute to the conservation and enhancement of clawed lobster stocks, but lacked monitoring programmes capable of assessing success. In the 1990s, this perspective was changed by the results of restocking and stock enhancement experiments that inserted microwire tags into hatchery-reared juvenile European lobsters (Homarus gammarus) before release. This allowed recapture in sufficient numbers to prove that lobsters had survived and recruited to the mature fishable stock. However, evidence of recruitment still failed to answer key questions about the ultimate ecological and economic benefits. As a result, a growing number of lobster stocking ventures remain hindered by a lack of clear evidence of the effects of their stocking schemes. This review evaluates these experiments and related studies on other fished species, summarizes key findings, and identifies data and knowledge gaps. Although studies of fitness in cultured lobsters provide some of the most encouraging results from the wider field of hatchery-based stocking, the limitations of physical tagging technology have significantly hindered appraisals of stocking impacts. We lack basic knowledge of lobster ecology and population dynamics, especially among prerecruits, and of the impact of stocking on wild lobster population genetics. We advocate the use of genetic methods to further our understanding of population structure, rearing processes, and stocking success. We also recommend that more focused and comprehensive impact assessments are required to provide a robust endorsement or rejection of stocking as a viable tool for the sustainable management of lobster fisheries.
Phenotypic Convergence in Bacterial Adaptive Evolution to Ethanol Stress
Authors: Horinouchi Takaaki , Suzuki Shingo , Hirasawa Takashi , Ono Naoaki , Yomo Tetsuya , Shimizu Hiroshi , Furusawa Chikara 
Published: November 2014

AbstractBacterial cells have a remarkable ability to adapt and evolve to environmental changes, a phenomenon known as adaptive evolution. Adaptive evolution can be explained by phenotypic changes caused by genetic mutations, and by phenotypic plasticity that occur without genetic alteration, although far less is known about the contributions of the latter. In this study, we analyzed phenotypic and genotypic changes inEscherichia colicells during adaptive evolution to ethanol stress. Phenotypic changes were quantified by transcriptome and metabolome analyses and found similar among independently evolved ethanol tolerant strains. The contribution of identified mutations in the tolerant strain was evaluated by using site-directed mutagenesis, which suggested that the fixation of these mutations cannot fully explain the observed ethanol tolerance. The phenotype of ethanol tolerance was stably maintained after an environmental change, suggesting that a mechanism of non-genetic memory contributed to at least part of the adaptation process.
Expansion load: recessive mutations and the role of standing genetic variation
Authors: Peischl Stephan , Excoffier Laurent 
Published: November 2014

AbstractExpanding populations incur a mutation burden – the so-called expansion load. Previous studies of expansion load have focused on co-dominant mutations. An important consequence of this assumption is that expansion load stems exclusively from the accumulation of new mutations occurring in individuals living at the wave front. Using individual-based simulations we study here the dynamics of standing genetic variation at the front of expansions, and its consequences on mean fitness if mutations are recessive. We find that deleterious genetic diversity is quickly lost at the front of the expansion, but the loss of deleterious mutations at some loci is compensated by an increase of their frequencies at other loci. The frequency of deleterious homozygotes therefore increases along the expansion axis whereas the average number of deleterious mutations per individual remains nearly constant across the species range. This reveals two important differences to co-dominant models: (i) mean fitness at the front of the expansion drops much faster if mutations are recessive, and (ii) mutation load can increase during the expansion even if the total number of deleterious mutations per individual remains constant. We use our model to make predictions about the shape of the site frequency spectrum at the front of range expansion, and about correlations between heterozygosity and fitness in different parts of the species range. Importantly, these predictions provide opportunities to empirically validate our theoretical results. We discuss our findings in the light of recent results on the distribution of deleterious genetic variation across human populations, and link them to empirical results on the correlation of heterozygosity and fitness found in many natural range expansions.
Systems-Wide Analysis of Acclimation Responses to Long-Term Heat Stress and Recovery in the Photosynthetic Model OrganismChlamydomonas reinhardtii
Authors: Hemme Dorothea , Veyel Daniel , Mühlhaus Timo , Sommer Frederik , Jüppner Jessica , Unger Ann-Katrin , Sandmann Michael , Fehrle Ines , Schönfelder Stephanie , Steup Martin , Geimer Stefan , Kopka Joachim , Giavalisco Patrick , Schroda Michael 
Published: November 2014

AbstractWe applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42°C for 24 h and back to 25°C for ≥8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions.
The Microtubule Plus-End Tracking Proteins SPR1 and EB1b Interact to Maintain Polar Cell Elongation and Directional Organ Growth in Arabidopsis
Authors: Galva Charitha , Kirik Viktor , Lindeboom Jelmer J. , Kaloriti Despoina , Rancour David M. , Hussey Patrick J. , Bednarek Sebastian Y. , Ehrhardt David W. , Sedbrook John C. 
Published: November 2014

Abstract
The microtubule plus-end tracking proteins (+TIPs) END BINDING1b (EB1b) and SPIRAL1 (SPR1) are required for normal cell expansion and organ growth. EB proteins are viewed as central regulators of +TIPs and cell polarity in animals; SPR1 homologs are specific to plants. To explore if EB1b and SPR1 fundamentally function together, we combined genetic, biochemical, and cell imaging approaches in Arabidopsis thaliana. We found that eb1b-2 spr1-6 double mutant roots exhibit substantially more severe polar expansion defects than either single mutant, undergoing right-looping growth and severe axial twisting instead of waving on tilted hard-agar surfaces. Protein interaction assays revealed that EB1b and SPR1 bind each other and tubulin heterodimers, which is suggestive of a microtubule loading mechanism. EB1b and SPR1 show antagonistic association with microtubules in vitro. Surprisingly, our combined analyses revealed that SPR1 can load onto microtubules and function independently of EB1 proteins, setting SPR1 apart from most studied +TIPs in animals and fungi. Moreover, we found that the severity of defects in microtubule dynamics in spr1 eb1b mutant hypocotyl cells correlated well with the severity of growth defects. These data indicate that SPR1 and EB1b have complex interactions as they load onto microtubule plus ends and direct polar cell expansion and organ growth in response to directional cues.
R&D reporting methods and firm value: evidence from China
Authors: Wang Yanni , Fan Weiguo 
Published: November 2014

Purpose
– The purpose of this paper is to investigate how different research and development (R&D) accounting choice (capitalization and expensing) affects the value of the listed companies under the new Chinese Accounting Standards (CAS) background. According to new CAS, R&D expenditure can either be expensed as incurred as a whole or partly capitalized and partly expensed from 2007.

Design/methodology/approach
– The paper takes the form of an empirical study using a hand-collected sample of 3,664 observations from Chinese listed companies over 2007–2012 timeframe.

Findings
– It is found that different methods of reporting R&D investments do affect the value of listed firms in China. Specifically, the firms that chose to capitalize their R&D investments have higher stock price and return. On the contrary, the companies that select to expense their R&D expenditures have lower stock price and return. It is also found that capitalized R&D investments are positively connected to stock price, while expensed R&D expenditures are negatively related to stock prices.

Research limitations/implications
– This paper researches and finds the value relevance of R&D capitalization and expensing from the accounting report method itself. This explores some interesting research questions. Does choice of accounting method for R&D expenditure affect firm valuation? Do different methods of reporting R&D investments transfer different signal to investors? Does expensed R&D carry a negative signal to investors? So it can expand the existing R&D area of research.

Practical implications
– This paper can provide empirical evidence and decision support for corporate managers, R&D policy makers and investors in a non-mandatory disclosure market of R&D expenditure. Because different R&D accounting choice has different market reactions, managers can choose a favorable method of reporting R&D investments to raise their firm’s stock price. Policy makers should standardize accounting treatment of R&D expenditure, strengthen the disclosure of R&D information and develop a detailed, workable R&D capitalization accounting policies and procedures. Investors can make the right judgment and decision on business innovation capability and future development only by getting more R&D investment information.

Originality/value
– Different from present studies focusing on the value relevance of R&D investment, this paper explores an interesting topic showing how different methods of reporting R&D investment in China affect the value of the firms.
The effect of philanthropic marketing on brand resonance and consumer satisfaction of CSR performance
Authors: Tsui-Hsu Tsai Tracy , Jing Lin Arthur , Y. Li Eldon 
Published: November 2014

Purpose
– This study aims to investigate whether engagement in philanthropic marketing after the 311 Japan earthquake crises had a positive effect on brand resonance and consumer satisfaction of CSR performance for Taiwanese companies. Additionally, the particular phenomenon of media self-regulation was integrated to explore the consolidated impact of philanthropic marketing, media self-regulation and brand resonance on consumer satisfaction of CSR performance.

Design/methodology/approach
– The study used survey method to collect required data. The subjects of the study were 516 adults who were aware of the 311 Japan earthquake crises. Of the 476 survey questionnaires collected, 450 were identified as usable.

Findings
– The results show that the constructs were highly positively correlated, meaning that post-disaster corporate philanthropic marketing can enhance brand resonance and consumer satisfaction of CSR performance. Media self-regulation was found to have a significant influence on philanthropic marketing and brand resonance. However, it did not exert any significant effect on consumer satisfaction of CSR performance.

Research limitations/implications
– Because of the chosen research method and surveyed subjects, the research results may lack generalizability. Therefore, researchers are encouraged to test the proposed research model further with additional subjects and variables.

Practical implications
– A good impression of the brand usually makes consumers generate brand resonance. This study reveals that a higher level of brand resonance may lead to higher consumer satisfaction of CSR performance. This implies that local and international companies should engage in philanthropic marketing programs, as it will not only support charitable organizations but also enhance the firm’s corporate image.

Social implications
– This study points out that the positive coverage of the disaster could give the audience a positive impression, rather than showing provocative, violent or sexual content to push viewership. At the time when disasters become increasingly common, people’s expectations of the media will also elevate. Dramatization, exaggeration and information overload make the audience distrust the media and constantly seek the truth behind the story. Content generated by online bloggers and citizen reporters (ordinary people) is an alternative source for true, fast and in-depth reports.

Originality/value
– This study differs from earlier studies researching disastrous events in that they were taking the perspective of natural sciences, while we adopted the management viewpoint to evaluate the 311 crises and took media self-regulation into account. It is the first to reveal that media’s self-regulated coverage of the disaster seems to have a positive effect on corporate philanthropic marketing and brand resonance.
Knowledge transfer, governance mechanisms in alliance and environmental uncertainty
Authors: Long Yong , Li Peng , You Bo 
Published: November 2014

Purpose– The purpose of this paper is to identify the relationship between knowledge transfer characteristics in alliance and alliance governance mechanisms, the influence of alliance governance mechanisms on knowledge transfer consequences and investigate the role of environmental uncertainty in knowledge transfer of alliance.Design/methodology/approach– Survey data were collected mainly in high-tech industries of China, the firms in which often establish alliance for the purpose of learning and knowledge transfer often takes place in that alliance. Finally, 293 usable samples were included in subsequent analysis. Multiple regression analysis was used to examine the hypotheses.Findings– The extent of relational (/formal) governance mechanism used in alliance has a stronger positive relationship with the extent of tacit (/explicit) knowledge transfer in alliance than with the extent of explicit (/tacit) knowledge transfer in alliance between them; environmental uncertainty impairs relational governance mechanisms and enhances formal governance mechanisms used in alliance; both relational and formal governance mechanisms could facilitate knowledge transfer in alliance; environmental uncertainty hinders knowledge transfer and negatively moderates the relationship between alliance governance mechanisms and knowledge transfer.Originality/value– This paper finds the relationship between knowledge transfer in alliance and alliance governance mechanisms, and the role of environmental uncertainty, providing managers with direct implications about how to manage alliance with different knowledge transfer characteristics for the purpose of facilitating knowledge transfer in alliance; provides managers more details about the dark side of the environmental uncertainty in knowledge transfer, also reminds public policy-makers paying enough attention for the improvement of institutional environment to deal with uncertainty.
Corporate governance, resources, FDI commitment and firm performance
Authors: Tsai Ming-Tien , Tung Wen-Hui 
Published: November 2014

Purpose– This study aims to explore the effects of corporate governance structure and resources on foreign direct investment (FDI) commitment and firm performance.Design/methodology/approach– The data are collected from high-tech firms listed by the Taiwan Stock Exchange. All selected 137 firms have complete FDI and other required data during 2007-2009. The mean values of the variables during the three-year period were used for analysis.Findings– The results indicate that both chief executive officer (CEO) duality and government shareholding affect a firm’s FDI; and the higher the management shareholding ratio, the lower the return on equity. Moreover, a large ownership of substantial shareholders can enhance a firm’s performance; and higher institutional ownership can lead to higher firm performance.Research limitations/implications– This study analyses the limited data from 137 high-tech firms in Taiwan during the three-year period of 2007-2009. Further analyses of other industries, countries and time periods are needed to generalize the conclusions.Practical implications– A firm with CEO duality should increase the ratio of government holding to mitigate the influence of CEO on FDI decisions. When a firm’s performance is poor, the ratio of managerial holdings should be reduced; conversely, the firm could attract more holdings from domestic securities and funds to improve performance.Originality/value– This study provides guidelines for shareholders to analyze governance structure and formulate their investment strategies. Corporate policymakers may use these as the principles for designing a corporate governance structure that could engender optimal firm performance.