bluuebunny/crossref_metadata_2025_split huggingface dataset:
Considering the Use of Walled Gardens for FLOSS Project Communication
Authors: Squire Megan 
Published: April 2017

AbstractAt its core, free, libre, and open source software (FLOSS) is defined by its adherence to a set of licenses that give various freedoms to the users of the software, for example the ability to use the software, to read or modify its source code, and to distribute the software to others. In addition, many FLOSS projects and developers also champion other values related to “freedom” and “openness”, such as transparency, for example in communication and decision-making, or community-orientedness, for example in broadening access, collaboration, and participation. This paper explores how one increasingly common software development practice - communicating inside non-archived, third-party “walled gardens” - puts these FLOSS values into conflict. If communities choose to use non-archived walled gardens for communication, they may be prioritizing one type of openness (broad participation) over another (transparency). We use 18 FLOSS projects as a sample to describe how walled gardens are currently being used for intra-project communication, as well as to determine whether or not these projects provide archives of these communications. Findings will be useful to the FLOSS community as a whole as it seeks to understand the evolution and impact of its communication choices.
Adoption of Academic Tools in Open Source Communities: The Debian Case Study
Authors: Abate Pietro , Di Cosmo Roberto 
Published: April 2017

AbstractComponent repositories play a key role in the open software ecosystem. Managing the evolution of these repositories is a challenging task, and maintainers are confronted with a number of complex issues that need automatic tools to be adressed properly.In this paper, we present an overview of 10 years of research in this field and the process leading to the adoption of our tools in a FOSS community. We focus on the Debian distribution and in particular we look at the issues arising during the distribution lifecycle: ensuring buildability of source packages, detecting packages that cannot be installed and bootstrapping the distribution on a new architecture. We present three tools, distcheck, buildcheck and botch, that we believe of general interest for other open source component repositories.The lesson we have learned during this journey may provide useful guidance for researchers willing to see their tools broadly adopted by the community.
Assessing Code Authorship: The Case of the Linux Kernel
Authors: Avelino Guilherme , Passos Leonardo , Hora Andre , Valente Marco Tulio 
Published: April 2017

AbstractCode authorship is a key information in large-scale open-source systems. Among others, it allows maintainers to assess division of work and identify key collaborators. Interestingly, open-source communities lack guidelines on how to manage authorship. This could be mitigated by setting to build an empirical body of knowledge on how authorship-related measures evolve in successful open-source communities. Towards that direction, we perform a case study on the Linux kernel. Our results show that: (a) only a small portion of developers (26%) makes significant contributions to the code base; (b) the distribution of the number of files per author is highly skewed—a small group of top-authors (3%) is responsible for hundreds of files, while most authors (75%) are responsible for at most 11 files; (c) most authors (62%) have a specialist profile; (d) authors with a high number of co-authorship connections tend to collaborate with others with less connections.
Release Early, Release Often and Release on Time. An Empirical Case Study of Release Management
Authors: Teixeira Jose 
Published: April 2017

AbstractThe dictum of “Release early, release often.” by Eric Raymond as the Linux modus operandi highlights the importance of release management in open source software development. Nevertheless, there are very few empirical studies addressing release management in open source software development. It is already known that most open source software communities adopt either feature-based or time-based release strategies. Each of these has its advantages and disadvantages that are context-specific. Recent research reported that many prominent open source software projects have moved from feature-based to time-based releases. In this longitudinal case study, we narrate how OpenStack shifted towards a liberal six-month release cycle. If prior research discussed why projects should adopt time-based releases and how they can adopt such a strategy, we discuss how OpenStack adapted its software development processes, its organizational design and its tools toward a hybrid release management strategy — a strive for balancing the benefits and drawbacks of feature-based and time-based release strategies.
Technical Lag in Software Compilations: Measuring How Outdated a Software Deployment Is
Authors: Gonzalez-Barahona Jesus M. , Sherwood Paul , Robles Gregorio , Izquierdo Daniel 
Published: April 2017

AbstractLarge software compilations based on free, open source software (FOSS) packages are the basis for many software systems. When they are deployed in production, specific versions of the packages in the compilation are selected for installation. Over time, those versions become outdated with respect to the upstream software from which they are produced, and from the components available in the compilations as well. The fact that deployed components are outdated is not a problem in itself, but there is a price to pay for not being “as much updated as reasonable”. This includes bug fixes and new features that could, at least potentially, be interesting for the deployed system. Therefore, a balance has to be maintained between “being up-to-date” and “keeping the good old working versions”. This paper proposes a theoretical model (the “technical lag”) for measuring how outdated a system is, with the aim of assisting in the decisions about upgrading in production. The paper explores several ways in which technical lag can be implemented, depending on requirements. As an illustration, it presents as well some specific cases in which the evolution of technical lag is computed.
Longitudinal Analysis of the Run-up to a Decision to Break-up (Fork) in a Community
Authors: Azarbakht Amirhosein “Emerson” , Jensen Carlos 
Published: April 2017

AbstractIn this paper, we use a developer-oriented statistical approach to understand what causes people in complex software development networks to decide to fork (break away), and what changes a community goes through in the run-up to a decision to break-up. Developing complex software systems is complex. Software developers interact. They may have the same or different goals, communication styles, or values. Interactions can be healthy or troubled. Troubled interactions cause troubled communities, that face failure. Some of these failures manifest themselves as a community split (known as forking). These failures affects many people; developers and users. Can we save troubled projects? We statistically model the longitudinal socio-grams of software developers and present early indicators and warning signs that can be used to predict an imminent break-up decision.
Designing for Participation: Three Models for Developer Involvement in Hybrid OSS Projects
Authors: Mäenpää Hanna , Kilamo Terhi , Mikkonen Tommi , Männistö Tomi 
Published: April 2017

AbstractThis paper reports governance practices of three profit oriented companies that develop OSS software with the help of their respective open development communities. We explore how the companies allow development contributions from external stakeholders, and what knowledge they let out of their internal software development activities. The results lay ground for further research on how to organize openness of the software development process in hybrid setups where the needs of different stakeholders are partly competing - yet complementary.
Digging into the Eclipse Marketplace
Authors: Krüger Jacob , Corr Niklas , Schröter Ivonne , Leich Thomas 
Published: April 2017

AbstractEclipse is an integrated development environment that can be extended with plug-ins. Thanks to Eclipse’s success, a diverse community has been established with members coming from industry, open-source projects, and others, and a marketplace with more than 1.700 different plug-ins developed. Hence, the question arises how this marketplace is composed: Who contributes plug-ins? Which plug-ins are successful? Are there common characteristics or trends? To answer these questions, extensive investigations are necessary. In this paper, we present (i) an initial approach for corresponding analyses and (ii) preliminary results. Overall, we aim to pave the way for further research addressing, for example, motivations to participate in, or the evolution of, open marketplaces.
Magnetic and Phase Behavior of Magnetic Water‐in‐Oil Microemulsions
Authors: Brown Paul , Mohamed Azmi , Ardyani Tretya , Rogers Sarah E. , Eastoe Julian 
Published: April 2017

AbstractMagnetic water‐in‐oil microemulsions with anisotropic morphology have been generated by mixing single‐chain magnetic surfactants (dodecyltrimethylammonium trichloromonobromoferrate, DTAF) with non‐magnetic di‐chain analogues (didodecyldimethylammonium bromide, DDAB). Full phase diagrams have been mapped as a function of surfactant composition, water content, and temperature. It was shown that for all surfactant concentrations [Surfactanttotal], on replacing 30 wt% DDAB with DTAF optimum (i.e. wt% of the total surfactant) w ratios (w = [water]/[surfactant]) could be achieved; up to w = 120 for [Surfactanttotal] = 0.050 M. Small‐angle neutron scattering (SANS) indicated that microemulsion droplets have a rod‐like morphology with a radius commensurate with the surfactant tail length and an aspect ratio between 6 and 35. In the presence of a large magnetic field (6.7 T) no reorientation of the droplets was observed by SANS.
Shoreline Hardening Affects Nekton Biomass, Size Structure, and Taxonomic Diversity in Nearshore Waters, with Responses Mediated by Functional Species Groups
Authors: Kornis Matthew S. , Bilkovic Donna M. , Davias Lori A. , Giordano Steve , Breitburg Denise L. 
Published: April 2017

Abstract
Coastal shoreline hardening is intensifying due to human population growth and sea level rise. Prior studies have emphasized shoreline-hardening effects on faunal abundance and diversity; few have examined effects on faunal biomass and size structure or described effects specific to different functional groups. We evaluated the biomass and size structure of mobile fish and crustacean assemblages within two nearshore zones (waters extending 3 and 16 m from shore) adjacent to natural (native wetland; beach) and hardened (bulkhead; riprap) shorelines. Within 3 m from shore, the total fish/crustacean biomass was greatest at hardened shorelines, driven by greater water depth that facilitated access to planktivore (e.g., bay anchovy) and benthivore-piscivore (e.g., white perch) species. Small-bodied littoral-demersal species (e.g., Fundulus spp.) had greatest biomass at wetlands. By contrast, total biomass was comparable among shoreline types within 16 m from shore, suggesting the effect of shoreline hardening on fish biomass is largely within extreme nearshore areas immediately at the land/water interface. Shoreline type utilization was mediated by body size across all functional groups: small individuals (≤60 mm) were most abundant at wetlands and beaches, while large individuals (>100 mm) were most abundant at hardened shorelines. Taxonomic diversity analysis indicated natural shoreline types had more diverse assemblages, especially within 3 m from shore, although relationships with shoreline type were weak and sensitive to the inclusion/exclusion of crustaceans. Our study illustrates how shoreline hardening effects on fish/crustacean assemblages are mediated by functional group, body size, and distance from shore, with important applications for management.
Differential regulation of H3S10 phosphorylation, mitosis progression and cell fate by Aurora Kinase B and C in mouse preimplantation embryos
Authors: Li Wenzhi , Wang Peizhe , Zhang Bingjie , Zhang Jing , Ming Jia , Xie Wei , Na Jie 
Published: April 2017

AbstractCoordination of cell division and cell fate is crucial for the successful development of mammalian early embryos. Aurora kinases are evolutionarily conserved serine/threonine kinases and key regulators of mitosis. Aurora kinase B (AurkB) is ubiquitously expressed while Aurora kinase C (AurkC) is specifically expressed in gametes and preimplantation embryos. We found that increasing AurkC level in one blastomere of the 2-cell embryo accelerated cell division and decreasing AurkC level slowed down mitosis. Changing AurkB level had the opposite effect. The kinase domains of AurkB and AurkC were responsible for their different ability to phosphorylate Histone H3 Serine 10 (H3S10P) and regulate metaphase timing. Using an Oct4-photoactivatable GFP fusion protein (Oct4-paGFP) and fluorescence decay after photoactivation assay, we found that AurkB overexpression reduced Oct4 retention in the nucleus. Finally, we show that blastomeres with higher AurkC level elevated pluripotency gene expression, which were inclined to enter the inner cell mass lineage and subsequently contributed to the embryo proper. Collectively, our results are the first demonstration that the activity of mitotic kinases can influence cell fate decisions in mammalian preimplantation embryos and have important implications to assisted reproduction.
Advancing chimeric antigen receptor T cell therapy with CRISPR/Cas9
Authors: Ren Jiangtao , Zhao Yangbing 
Published: April 2017

AbstractThe clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (CRISPR/Cas9) system, an RNA-guided DNA targeting technology, is triggering a revolution in the field of biology. CRISPR/Cas9 has demonstrated great potential for genetic manipulation. In this review, we discuss the current development of CRISPR/Cas9 technologies for therapeutic applications, especially chimeric antigen receptor (CAR) T cell-based adoptive immunotherapy. Different methods used to facilitate efficient CRISPR delivery and gene editing in T cells are compared. The potential of genetic manipulation using CRISPR/Cas9 system to generate universal CAR T cells and potent T cells that are resistant to exhaustion and inhibition is explored. We also address the safety concerns associated with the use of CRISPR/Cas9 gene editing and provide potential solutions and future directions of CRISPR application in the field of CAR T cell immunotherapy. As an integration-free gene insertion method, CRISPR/Cas9 holds great promise as an efficient gene knock-in platform. Given the tremendous progress that has been made in the past few years, we believe that the CRISPR/Cas9 technology holds immense promise for advancing immunotherapy.
Cardiac resynchronization therapy in ischemic and non‐ischemic cardiomyopathy
Authors: Yokoshiki Hisashi , Mitsuyama Hirofumi , Watanabe Masaya , Mitsuhashi Takeshi , Shimizu Akihiko 
Published: April 2017

AbstractCardiac resynchronization therapy (CRT) using a biventricular pacing system has been an effective therapeutic strategy in patients with symptomatic heart failure with a reduced left ventricular ejection fraction (LVEF) of 35% or less and a QRS duration of 130 ms or more. The etiology of heart failure can be classified as either ischemic or non‐ischemic cardiomyopathy. Ischemic etiology of patients receiving CRT is prevalent predominantly in North America, moderately in Europe, and less so in Japan. CRT reduces mortality similarly in both ischemic and non‐ischemic cardiomyopathy, whereas reverse structural left ventricular remodeling occurs more favorably in non‐ischemic cardiomyopathy. Because the substrate for ventricular arrhythmias appears to be more severe in cases of ischemic as compared with non‐ischemic cardiomyopathy, the use of an implantable cardioverter‐defibrillator (ICD) backup method could prolong the long‐term survival, especially of patients with ischemic cardiomyopathy, even in the presence of CRT. The aim of this review article is to summarize the effects of CRT on outcomes and the role of ICD backup in ischemic and non‐ischemic cardiomyopathy.
Building Physician Networks as Part of the Zika Response
Authors: Heard-Garris Nia , Arora Sanjeev , Lurie Nicole 
Published: April 2017

AbstractThe global community needs to easily identify and respond to new and reemerging threats, such as H1N1, Ebola, and most recently Zika. Clinicians are often the first-line providers to recognize these threats, but yet have few opportunities to learn from each other in real time. In this concept article, we describe the ways clinical information is traditionally shared during a public health emergency and then introduce new mechanisms to facilitate physician communication and learning as a part of the response to Zika. (Disaster Med Public Health Preparedness. 2017;11:259–261)
Energy scaling of targeted optimal control of complex networks
Authors: Klickstein Isaac , Shirin Afroza , Sorrentino Francesco 
Published: April 2017

AbstractRecently it has been shown that the control energy required to control a dynamical complex network is prohibitively large when there are only a few control inputs. Most methods to reduce the control energy have focused on where, in the network, to place additional control inputs. Here, in contrast, we show that by controlling the states of a subset of the nodes of a network, rather than the state of every node, while holding the number of control signals constant, the required energy to control a portion of the network can be reduced substantially. The energy requirements exponentially decay with the number of target nodes, suggesting that large networks can be controlled by a relatively small number of inputs as long as the target set is appropriately sized. We validate our conclusions in model and real networks to arrive at an energy scaling law to better design control objectives regardless of system size, energy restrictions, state restrictions, input node choices and target node choices.
Interactions of AMTN, ODAM and SCPPPQ1 proteins of a specialized basal lamina that attaches epithelial cells to tooth mineral
Authors: Fouillen Aurélien , Dos Santos Neves Juliana , Mary Charline , Castonguay Jean-Daniel , Moffatt Pierre , Baron Christian , Nanci Antonio 
Published: April 2017

AbstractA specialized basal lamina (sBL) mediates adhesion of certain epithelial cells to the tooth. It is distinct because it does not contain collagens type IV and VII, is enriched in laminin-332, and includes three novel constituents called amelotin (AMTN), odontogenic ameloblast-associated (ODAM), and secretory calcium-binding phosphoprotein proline-glutamine rich 1 (SCPPPQ1). The objective of this study was to clarify the structural organization of the sBL. Fluorescence and immunogold labeling showed that the three proteins co-localize. Quantitative analysis of the relative position of gold particles on the sBL demonstrates that the distribution of ODAM is skewed towards the cell while that of AMTN and SCPPPQ1 tends towards the tooth surface. Bacterial two-hybrid analysis and co-immunoprecipitation, gel filtration of purified proteins and transmission electron and atomic force microscopies highlight the propensity of AMTN, ODAM, and SCPPPQ1 to interact with and among themselves and form supramolecular aggregates. These data suggest that AMTN, ODAM and SCPPPQ1 participate in structuring an extracellular matrix with the distinctive capacity of attaching epithelial cells to mineralized surfaces. This unique feature is particularly relevant for the adhesion of gingival epithelial cells to the tooth surface, which forms a protective seal that is the first line of defense against bacterial invasion.
Multiplex lexical networks reveal patterns in early word acquisition in children
Authors: Stella Massimo , Beckage Nicole M. , Brede Markus 
Published: April 2017

AbstractNetwork models of language have provided a way of linking cognitive processes to language structure. However, current approaches focus only on one linguistic relationship at a time, missing the complex multi-relational nature of language. In this work, we overcome this limitation by modelling the mental lexicon of English-speaking toddlers as a multiplex lexical network, i.e. a multi-layered network where N = 529 words/nodes are connected according to four relationship: (i) free association, (ii) feature sharing, (iii) co-occurrence, and (iv) phonological similarity. We investigate the topology of the resulting multiplex and then proceed to evaluate single layers and the full multiplex structure on their ability to predict empirically observed age of acquisition data of English speaking toddlers. We find that the multiplex topology is an important proxy of the cognitive processes of acquisition, capable of capturing emergent lexicon structure. In fact, we show that the multiplex structure is fundamentally more powerful than individual layers in predicting the ordering with which words are acquired. Furthermore, multiplex analysis allows for a quantification of distinct phases of lexical acquisition in early learners: while initially all the multiplex layers contribute to word learning, after about month 23 free associations take the lead in driving word acquisition.
Upper semicontinuity of the lamination hull
Authors: Harris Terence L.J. 
Published: April 2017

Let K ⊆ ℝ2×2 be a compact set, let Krc be its rank-one convex hull, and let L (K) be its lamination convex hull. It is shown that the mapping K ↦ L̅(K̅) is not upper semicontinuous on the diagonal matrices in ℝ2×2, which was a problem left by Kolář. This is followed by an example of a 5-point set of 2 × 2 symmetric matrices with non-compact lamination hull. Finally, another 5-point set K is constructed, which has L (K) connected, compact and strictly smaller than Krc.
Draft genome of the lined seahorse, Hippocampus erectus
Authors: Lin Qiang , Qiu Ying , Gu Ruobo , Xu Meng , Li Jia , Bian Chao , Zhang Huixian , Qin Geng , Zhang Yanhong , Luo Wei , Chen Jieming , You Xinxin , Fan Mingjun , Sun Min , Xu Pao , Venkatesh Byrappa , Xu Junming , Fu Hongtuo , Shi Qiong 
Published: April 2017

Abstract
Background: The lined seahorse, Hippocampus erectus, is an Atlantic species and mainly inhabits shallow sea beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly, and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding. Findings: A total of 174.6 Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb, respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo and transcriptome-based prediction methods, we predicted 20 788 protein-coding genes in the generated assembly, which is less than our previously reported gene number (23 458) of the tiger tail seahorse (H. comes). Conclusion: We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior.