bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary alteration of ALOX15 specificity optimizes the biosynthesis of antiinflammatory and proresolving lipoxins
Authors: Adel Susan , Karst Felix , González-Lafont Àngels , Pekárová Mária , Saura Patricia , Masgrau Laura , Lluch José M. , Stehling Sabine , Horn Thomas , Kuhn Hartmut , Heydeck Dagmar 
Published: July 2016

Significance
Lipoxygenases are lipid-peroxidizing enzymes that have been classified according to their reaction specificity. ALOX15 (12/15-lipoxygenase) has been implicated in inflammatory resolution via biosynthesis of antiinflammatory and proresolving lipoxins. We found that lower mammals including lower primates express arachidonic acid 12-lipoxygenating ALOX15 orthologs, whereas higher primates express 15-lipoxygenating enzymes. Gibbons constitute the missing link interconnecting 12- and 15-lipoxygenating ALOX15 orthologs. To explore the evolutionary driving force for this specificity alteration, we quantified the lipoxin synthase activity of 12- and 15-lipoxygenating ALOX15 orthologs and observed that the lipoxin synthase activities of 15-lipoxygenating enzymes were significantly higher. These results suggest an evolution of ALOX15 specificity, which optimizes the biosynthetic capacity for antiinflammatory and proresolving lipoxins.
Alaska's Sablefish Fishery after Individual Fishing Quota (IFQ) Program Implementation: an International Economic Market Model
Authors: Warpinski Stephanie , Herrmann Mark , Greenberg Joshua A. , Criddle Keith R. 
Published: July 2016

Abstract
Alaska is the world's principal supplier of Sablefish Anoplopoma fimbria, a buttery-flavored whitefish greatly prized in Japan. Sablefish are distributed from Baja California to western Japan, but the majority of commercial catches are from the Gulf of Alaska and the Aleutian Islands off Alaska. The volume and value of landings of this long-lived demersal fish are comparable to those of the well-known Pacific Halibut Hippoglossus stenolepis. As with Pacific Halibut, Alaska region catches of Sablefish are managed under an individual fishing quota (IFQ) program implemented in 1995. We present a simultaneous-equation market model for Sablefish and use it to examine the linkages between landings volume and exvessel prices and revenues, including the sensitivity of Alaska exvessel prices and revenues to changes in landings, the implementation of IFQs, and changes in the Japanese economy. The model simulations indicate that markets could absorb substantially more Sablefish than can be sustainably harvested from the current stock of Sablefish in the Alaska region. However, sluggishness in the Japanese economy has resulted in overall downward pressure on Alaska region Sablefish exvessel prices. The model simulations indicate that the implementation of IFQs in this fishery significantly increased exvessel revenues as a consequence of the longer seasons that resulted from the end to the “race for the fish.” In addition, we find that implementation has helped buffer the fishery against revenue losses associated with reduced catch limits triggered by the decline of Sablefish biomass in the Alaska region.
Received May 18, 2015; accepted March 1, 2016 Published online July 14, 2016
The effect of badminton‐specific exercise on badminton short‐serve performance in competition and practice climates
Authors: Duncan Michael J. , Chan Cheryl K.Y. , Clarke Neil D. , Cox Martin , Smith Mike 
Published: July 2016

AbstractThis study examined the effects of changes in physiological and psychological arousal on badminton short‐serve performance in competitive and practice climates. Twenty competitive badminton players (10 males and 10 females) volunteered to participate in the study following ethics approval. After familiarisation, badminton short‐serve performance was measured at rest, mid‐way through and at the end of a badminton‐specific exercise protocol in two conditions; competition vs. practice. Ratings of cognitive and somatic anxiety were assessed at three time points prior to badminton short‐serve performance using the Mental Readiness Form 3. Heart rate and rating of perceived exertion (RPE) were assessed during the exercise protocol. Results indicated that better short‐serve performance was evident in practice compared to competition (P = .034). RPE values were significantly higher in the competition condition compared to practice (P = .007). Cognitive anxiety intensity was significantly lower post‐exercise in the practice condition compared to competition (P = .001). Cognitive anxiety direction showed greater debilitation post‐exercise in the competition condition compared to practice (P = .01). Somatic anxiety intensity increased from pre‐, to mid‐ to post‐exercise (P = .001) irrespective of condition. This study suggests that badminton serve performance is negatively affected when physiological arousal, via badminton‐specific exercise, and cognitive anxiety, via perceived competition, are high.
MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ
Authors: Legland David , Arganda-Carreras Ignacio , Andrey Philippe 
Published: July 2016

Motivation: Mathematical morphology (MM) provides many powerful operators for processing 2D and 3D images. However, most MM plugins currently implemented for the popular ImageJ/Fiji platform are limited to the processing of 2D images.
Results: The MorphoLibJ library proposes a large collection of generic tools based on MM to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins. We illustrate how MorphoLibJ can facilitate the exploitation of 3D images of plant tissues.
Availability and Implementation: MorphoLibJ is freely available at http://imagej.net/MorphoLibJ
Contact: david.legland@nantes.inra.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena
Authors: Tohsato Yukako , Ho Kenneth H. L. , Kyoda Koji , Onami Shuichi 
Published: July 2016

Motivation: Rapid advances in live-cell imaging analysis and mathematical modeling have produced a large amount of quantitative data on spatiotemporal dynamics of biological objects ranging from molecules to organisms. There is now a crucial need to bring these large amounts of quantitative biological dynamics data together centrally in a coherent and systematic manner. This will facilitate the reuse of this data for further analysis.
Results: We have developed the Systems Science of Biological Dynamics database (SSBD) to store and share quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei and whole organisms in a wide variety of model organisms from Escherichia coli to Mus musculus. The data are provided in Biological Dynamics Markup Language format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis.
Availability and Implementation: SSBD is accessible at http://ssbd.qbic.riken.jp.
Contact: sonami@riken.jp
LAMPLINK: detection of statistically significant SNP combinations from GWAS data
Authors: Terada Aika , Yamada Ryo , Tsuda Koji , Sese Jun 
Published: July 2016

Summary: One of the major issues in genome-wide association studies is to solve the missing heritability problem. While considering epistatic interactions among multiple SNPs may contribute to solving this problem, existing software cannot detect statistically significant high-order interactions. We propose software named LAMPLINK, which employs a cutting-edge method to enumerate statistically significant SNP combinations from genome-wide case–control data. LAMPLINK is implemented as a set of additional functions to PLINK, and hence existing procedures with PLINK can be applicable. Applied to the 1000 Genomes Project data, LAMPLINK detected a combination of five SNPs that are statistically significantly accumulated in the Japanese population.
Availability and Implementation: LAMPLINK is available at http://a-terada.github.io/lamplink/.
Contact: terada@cbms.k.u-tokyo.ac.jp or sese.jun@aist.go.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets
Authors: Hourdel Véronique , Volant Stevenn , O’Brien Darragh P. , Chenal Alexandre , Chamot-Rooke Julia , Dillies Marie-Agnès , Brier Sébastien 
Published: July 2016

Motivation: With the continued improvement of requisite mass spectrometers and UHPLC systems, Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) workflows are rapidly evolving towards the investigation of more challenging biological systems, including large protein complexes and membrane proteins. The analysis of such extensive systems results in very large HDX-MS datasets for which specific analysis tools are required to speed up data validation and interpretation.Results: We introduce a web application and a new R-package named ‘MEMHDX’ to help users analyze, validate and visualize large HDX-MS datasets. MEMHDX is composed of two elements. A statistical tool aids in the validation of the results by applying a mixed-effects model for each peptide, in each experimental condition, and at each time point, taking into account the time dependency of the HDX reaction and number of independent replicates. Two adjusted P-values are generated per peptide, one for the ‘Change in dynamics’ and one for the ‘Magnitude of ΔD’, and are used to classify the data by means of a ‘Logit’ representation. A user-friendly interface developed with Shiny by RStudio facilitates the use of the package. This interactive tool allows the user to easily and rapidly validate, visualize and compare the relative deuterium incorporation on the amino acid sequence and 3D structure, providing both spatial and temporal information.Availability and Implementation: MEMHDX is freely available as a web tool at the project home page http://memhdx.c3bi.pasteur.frContact: marie-agnes.dillies@pasteur.fr or sebastien.brier@pasteur.frSupplementary information: Supplementary data is available at Bioinformatics online.
LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads
Authors: El-Metwally Sara , Zakaria Magdi , Hamza Taher 
Published: July 2016

Abstract
Motivation: The deluge of current sequenced data has exceeded Moore’s Law, more than doubling every 2 years since the next-generation sequencing (NGS) technologies were invented. Accordingly, we will able to generate more and more data with high speed at fixed cost, but lack the computational resources to store, process and analyze it. With error prone high throughput NGS reads and genomic repeats, the assembly graph contains massive amount of redundant nodes and branching edges. Most assembly pipelines require this large graph to reside in memory to start their workflows, which is intractable for mammalian genomes. Resource-efficient genome assemblers combine both the power of advanced computing techniques and innovative data structures to encode the assembly graph efficiently in a computer memory.
Results: LightAssembler is a lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of g -spaced sequenced k -mers and the other holding k -mers classified as likely correct, using a simple statistical test. LightAssembler contains a light implementation of the graph traversal and simplification modules that achieves comparable assembly accuracy and contiguity to other competing tools. Our method reduces the memory usage by 50% compared to the resource-efficient assemblers using benchmark datasets from GAGE and Assemblathon projects. While LightAssembler can be considered as a gap-based sequence assembler, different gap sizes result in an almost constant assembly size and genome coverage.
Availability and implementation: https://github.com/SaraEl-Metwally/LightAssembler
Contact: sarah_almetwally4@mans.edu.eg
Supplementary information: Supplementary data are available at Bioinformatics online.
Identifying the best fishing-suitable areas under the new European discard ban
Authors: Paradinas Iosu , Marín Marcial , Grazia Pennino Maria , López-Quílez Antonio , Conesa David , Barreda David , Gonzalez Maria , María Bellido José ,   Handling editor: Ernesto Jardim
Published: July 2016

Abstract
The spatial management of fisheries has been repeatedly proposed as a discard mitigation measure. A number of studies have assessed the fishing suitability of an area based on units of by-catch or discard per unit effort. However, correct identification of fishing-suitable areas should assess biomass loss with respect to the benefits. This study therefore, proposes the analysis of by-catch ratios, which do represent benefit vs. loss and are standardized to a wide range of effort characteristics. Furthermore, our study proposes the use of two ratios: the proportion of total unwanted biomass out of the total catch as an indicator of the overall ecological impact, and the proportion of unwanted but regulated species biomass as a proxy for the economic impact on fishers resulting from the new European discard ban that prohibits the discard of regulated species. These discard ratios are modelled by means of a Bayesian hierarchical model, specifically, a spatio-temporal beta regression model, which has several advantages over the traditional arcsine transformation. Results confirm the standardizing capacity of by-catch ratios across vessels and identify at least two economically fishing-suitable areas where discards ratios are minimized by reducing unwanted catch.
Social contacts and den sharing among suburban striped skunks during summer, autumn, and winter
Authors: Theimer Tad C. , Maestas Jesse M. , Bergman David L. 
Published: July 2016

Abstract
Determining social contacts among solitary carnivores is difficult given their often nocturnal and secretive nature. We used proximity-sensing radiocollars to quantify social contacts and den sharing among striped skunks (Mephitis mephitis) in suburban Flagstaff, Arizona, United States, in summer, autumn, and winter 2012–2013. During June and July, we followed 6 males and 5 females and, in spite of overlapping home ranges, they had few social contacts (range = 0–7), and all were brief, nocturnal encounters. From October through February, we followed 8 males and 9 females and found that patterns of contacts were similar for males and females except for significantly higher diurnal contacts (co-denning) among females in winter. Females varied in denning behavior; 1 female denned continuously in the same location from early November to late January, while at the other extreme 1 female moved among 10 different dens across the same time period. Several females moved to new communal dens in late January, resulting in new combinations of females co-denning. Males visited multiple female dens throughout winter. Overall, our data were consistent with previous studies in documenting overlapping home ranges of both sexes with few social contacts in summer, male intolerance but lack of male territoriality, and divergent social behavior in winter, with females co-denning while males generally denned alone. Our study differed from others in documenting more social interaction and movement during winter, often through nocturnal visits by males to female dens, and a shift in denning associations among females near the end of January.
The Exclusive Economic Zone
Authors: Andreone Gemma 
Published: July 2016

Abstract
The role of the Economic Exclusive Zone (EEZ) in the international law of the sea remains a controversial issue two decades after the 1982 United Nations Convention on the Law of the Sea (LOSC) came into force. This chapter examines the evolution of the concept and its juridical nature, and the legal regime applicable to the EEZ. It considers the future development of the EEZ legal regime, exploring the principal controversial features that may influence its course.
The Deep Seabed
Authors: Lodge Michael 
Published: July 2016

Abstract
The deep seabed is the part of the seabed that is beyond national jurisdiction and is referred to as ‘the Area’ in the UN Convention on the Law of the Sea (LOSC). This chapter discusses the legal regime of the deep seabed. It covers the legal status of the Area and its resources; the International Seabed Authority; the regulation of ‘activities in the Area’; commercial exploitation; reserved areas; sponsorship by states parties; dispute settlement; and responsibility of the International Seabed Authority under Article 82 (4) of the LOSC.
Can Non-State Actors Mount an Armed Attack?
Authors: Trapp Kimberley N. 
Published: July 2016

Abstract
Article 2(4) of the UN Charter prohibits the use of force between States. In so doing, it addresses itself to a strictly interstate context and does not speak to the phenomenon of uses of force by non-state actors (NSAs). The question examined in this chapter is whether the exception to that prohibition—the right to use force in self-defence—is nevertheless responsive to the war-making capacity of NSAs. Otherwise put, is the definition of ‘armed attack’ in Article 51 of the UN Charter (and related customary international law) conditioned on the attacker being a state? In exploring this question, the chapter considers whether attribution is a necessary condition (in ratione personae terms) for the applicability of Article 51 by assessing the language of the Charter (including its travaux préparatoires), jurisprudence of the International Court of Justice, and state practice.
The Problem of Imminence in an Uncertain World
Authors: Lubell Noam 
Published: July 2016

Abstract
This chapter deals with the concept of imminence within the context of anticipatory self-defence under international law. It examines the meaning of imminence, its interpretation, what it might justify and/or exclude, and whether it can be upheld as a criterion to face modern challenges. It outlines the requirement of imminence in relation to the debatable right to anticipatory self-defence, paying particular attention to the development of state practice and the opinions of commentators. It considers the specific context of terrorism and weapons of mass destruction, and examines the reasons that these are sometimes seen as necessitating a new conception of imminence. The chapter provides an analysis of what new approaches might mean, and whether they can be contained within an understanding of imminence. In so doing, the chapter analyses the notion of certainty, the need for evidence, and the effect of the scale of threat on the decision-making process.
Necessity
Authors: Corten Olivier 
Published: July 2016

Abstract
This chapter examines the doctrine of necessity as an element of the prohibition of the use of force and as a subsidiary condition of the legality of self-defence. It begins by discussing the thesis of necessity as a general justification of the use of force within the context of the international law of responsibility. It then analyses necessity as a condition enshrined in self-defence and in the United Nations collective security system. The chapter also considers the methodological problems that arise from any interpretation of the concept of necessity, especially with respect to the use of force. It highlights the fact that the International Law Commission, the International Court of Justice, and state practice have never recognized necessity as a general justification to use force.
Muscovite Political Culture
Authors: Kollmann Nancy 
Published: July 2016

Abstract
This chapter reveals the deep structures of Muscovite politics by explaining first its theoretical foundations (in which written texts and symbolic representations combined to present a consistent worldview) and then its practical operations (heavily dependent on kinship, marriage and patronage networks). Though it focuses on the period from Ivan III (r. 1462–1505) to the end of the seventeenth century, the chapter ends by considering the impact of Peter I (r. 1682–1725). Change trumped continuity with regard to political culture. Yet, even as they constructed a political rhetoric and elite culture on Western models, Peter and his successors echoed traditional Muscovy in their evocations of Orthodoxy, their patronage and largesse, and their patrimonial claims to power. And they achieved time-honoured Muscovite goals by maintaining stability among factional groups, enriching their elites, expanding the Empire and presiding over dynamic economic growth.
What Do We Think We Know?
Authors: Benedict Cathy 
Published: July 2016

Abstract
This chapter argues for a pedagogy of recognition and against a simplistic, didactic educative stance of “preparing students for social justice.” The question this chapter pursues is not how to best prepare or produce a student to be socially just, but rather how educators can facilitate moments of freedom, or “acting out with others” (Arendt, 1958, p. 198). Pedagogical engagements that disconnect individuals from acts of humanity and grace and the development of self-fueled ideological aims ensure competition, domination, and superiority. This suggests an interrogation of those engagements that have been, as Arendt (1998) suggests, “uncritically and slavishly accepted” (p. 179). The chapter examines concepts and constructs that are taken for granted—furthering individual pride, creating and posting class rules, and building upon “what is known”—revealing that social justice or socially just actions are neither the reproduction of an existing discourse nor preparation for future goal-oriented behaviors.
Multiculturalism and Social Justice
Authors: Campbell Patricia Shehan , Roberts J. Christopher 
Published: July 2016

Abstract
Social justice, with its emphasis on identifying and rectifying inequalities that exist in society, is a concept that in many ways parallels multiculturalism. This chapter argues that multiculturalizing the curriculum is an essential means by which to move toward more socially just educational experiences. It turns to the work of pioneering educationist James Banks, applying his Levels of Curriculum Reform to learning experiences in music education. These tiered levels—contributions, additive, transformative, and social action—provide a sequential pathway by which educators unversed in working with multicultural content can create curricula that lead to a more multicultural and socially just educational enterprise.
The Ethics of Policy
Authors: Schmidt Patrick 
Published: July 2016

Abstract
This chapter delineates the need for policy thought as a key element of the education and professional life of any teacher, and in particular of those charged to educate in and through music. This argument is built upon the ethical imperative of bringing music educators and policy together, the positive implications such approximation may have, and how it can impact social justice work in music education. The policy realm is commonly seen as “above our pay grade,” beyond our duties and responsibilities, and outside the reach of our capacities. But nothing could be further from the truth. This chapter offers a framework and rationale that show how social justice and policy are entwined, while arguing that both areas are integral parts of the political lives of teachers.