bluuebunny/crossref_metadata_2025_split huggingface dataset:
GeLL: a generalized likelihood library for phylogenetic models
Authors: Money Daniel , Whelan Simon 
Published: March 2015

Abstract
Summary: Phylogenetic models are an important tool in molecular evolution allowing us to study the pattern and rate of sequence change. The recent influx of new sequence data in the biosciences means that to address evolutionary questions, we need a means for rapid and easy model development and implementation. Here we present GeLL, a Java library that lets users use text to quickly and efficiently define novel forms of discrete data and create new substitution models that describe how those data change on a phylogeny. GeLL allows users to define general substitution models and data structures in a way that is not possible in other existing libraries, including mixture models and non-reversible models. Classes are provided for calculating likelihoods, optimizing model parameters and branch lengths, ancestral reconstruction and sequence simulation.
Availability and implementation: http://phylo.bio.ku.edu/GeLL under a GPL v3 license.
Contact: daniel.money@dal.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
L-GRAAL: Lagrangian graphlet-based network aligner
Authors: Malod-Dognin Noël , Pržulj Nataša 
Published: March 2015

Abstract
Motivation: Discovering and understanding patterns in networks of protein–protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge.
Results: We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions.
Availability and implementation: L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/.
Contact: n.malod-dognin@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Mining viral proteins for antimicrobial and cell-penetrating drug delivery peptides
Authors: Freire João Miguel , Almeida Dias Susana , Flores Luís , Veiga Ana Salomé , Castanho Miguel A.R.B. 
Published: March 2015

Abstract
Motivation: The need for more effective and safer pharmaceuticals is a persistent quest. Microbial adaptations create the need to permanently develop new antimicrobials (AMPs), for instance. Similarly, intracellular delivery of drugs is still a challenge and translocation of membranes for drug delivery is an area of intense research. Peptides can be used both as AMP drug leads and drug carrier systems for intracellular delivery. Multifunctional proteins are abundant in viruses but, surprisingly, have never been thoroughly screened for bioactive peptide sequences.
Results: Using the AMPA and CellPPD online tools, we have evaluated the propensity of viral proteins to comprise AMP or cell-penetrating peptides (CPPs). Capsid proteins from both enveloped and non-enveloped viruses, and membrane and envelope proteins from enveloped viruses, in a total of 272 proteins from 133 viruses, were screened to detect the presence of potential AMP and CPP sequences. A pool of 2444 and 426 CPP and AMP sequences, respectively, were discovered. The capsids of flaviviruses are the best sources of these peptides reaching more than 80% of CPP sequence coverage per protein. Selected sequences were tested experimentally and validated the results. Overall, this study reveals that viruses form a natural multivalent biotechnological platform still underexplored in drug discovery and the heterogeneous abundance of CPP/AMP sequences among viral families opens new avenues in viral biology research.
Contacts: aveiga@medicina.ulisboa.pt or macastanho@medicina.ulisboa.pt
Supplementary information: supplementary data are available at Bioinformatics online.
Medical student awareness of and interest in clinical informatics
Authors: Banerjee Rahul , George Paul , Priebe Cedric , Alper Eric 
Published: March 2015

AbstractObjective We aimed to investigate medical students’ attitudes about Clinical Informatics (CI) training and careers.Materials and Methods We distributed a web-based survey to students at four US allopathic medical schools.Results Five hundred and fifty-seven medical students responded. Interest in CI training opportunities (medical school electives, residency electives, or academic fellowships) surpassed respondents’ prior awareness of these opportunities. Thirty percent of student respondents expressed at least some interest in a CI-related career, but they were no more aware of training opportunities than their peers who did not express such an interest.Discussion Almost one third of medical students who responded to our survey expressed an interest in a CI-related career, but they were generally unaware of CI training and mentoring opportunities available to them. Early outreach to such medical students, through elective classes, professional society incentives, or expert partnerships, may positively influence the size and skill set of the future CI workforce.Conclusion We should work as a field to increase the quantity, quality, and publicity of CI learning opportunities for interested medical students.
Technology-mediated interventions for enhancing medication adherence
Authors: Mistry Niraj , Keepanasseril Arun , Wilczynski Nancy L. , Nieuwlaat Robby , Ravall Manthan , Haynes R. Brian ,   the Patient Adherence Review Team
Published: March 2015

Abstract
Background Despite effective therapies for many conditions, patients find it difficult to adhere to prescribed treatments. Technology-mediated interventions (TMIs) are increasingly being used with the hope of improving adherence.
Objective To assess the effects of TMI, intended to enhance patient adherence to prescribed medications, on both medication adherence and clinical outcomes.
Methods A secondary in-depth analysis was conducted of the subset of studies that utilized technology in at least one component of the intervention from an updated Cochrane review on all interventions for enhancing medication adherence. We included studies that clearly described an information and communication technology or medical device as the sole or major component of the adherence intervention.
Results Thirty-eight studies were eligible for in-depth review. Only seven had a low risk of bias for study design features, primary adherence, and clinical outcomes. Eighteen studies used a TMI for education and/or counseling, 11 studies used a TMI for self-monitoring and/or feedback, and nine studies used electronic reminders. Studies used a variety of TMIs, with telephone the most common technology in use. Studies targeted a wide distribution of diseases and used a variety of adherence and clinical outcome measures. A minority targeted children and adolescents. Fourteen studies reported significant effects in both adherence and clinical outcome measures.
Conclusions This review provides evidence for the inconsistent effectiveness of TMI for medication adherence and clinical outcomes. These results must be interpreted with caution due to a lack of high-quality studies.
Development of data representation standards by the human proteome organization proteomics standards initiative
Authors: Deutsch Eric W , Albar Juan Pablo , Binz Pierre-Alain , Eisenacher Martin , Jones Andrew R , Mayer Gerhard , Omenn Gilbert S , Orchard Sandra , Vizcaíno Juan Antonio , Hermjakob Henning 
Published: March 2015

AbstractObjective To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI’s evolution, and future directions and synergies for the group.Materials and Methods The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release.Results We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community.Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and biological phenotypes. The PSI website can be accessed at http://www.psidev.info.
Constraining the distribution of dark matter in dwarf spheroidal galaxies with stellar tidal streams
Authors: Errani Raphaël , Peñarrubia Jorge , Tormen Giuseppe 
Published: March 2015

Abstract
We use high-resolution N-body simulations to follow the formation and evolution of tidal streams associated with dwarf spheroidal galaxies (dSphs). The dSph models are embedded in dark matter (DM) haloes with either a centrally divergent ‘cusp’, or a homogeneous-density ‘core’. In agreement with previous studies, we find that as tides strip the galaxy the evolution of the half-light radius and the averaged velocity dispersion follows well-defined tracks that are mainly controlled by the amount of mass lost. Crucially, the evolutionary tracks behave differently depending on the shape of the DM profile: at a fixed remnant mass, dSphs embedded in cored haloes have larger sizes and higher velocity dispersions than their cuspy counterparts. The divergent evolution is particularly pronounced in galaxies whose stellar component is strongly segregated within their DM halo and becomes more disparate as the remnant mass decreases. Our analysis indicates that the DM profile plays an important role in defining the internal dynamics of tidal streams. We find that stellar streams associated with cored DM models have velocity dispersions that lie systematically above their cuspy counterparts. These results suggest that modelling the dynamics of streams with known dSph progenitors may reveal the distribution of DM on the smallest galactic scales.
Spatially resolved kinematic observations of the planetary nebulae Hen 3-1333 and Hen 2-113
Authors: Danehkar A. , Parker Q. A. 
Published: March 2015

Abstract
We have performed integral field spectroscopy of the planetary nebulae Hen 3-1333 (PNG332.9−09.9) and Hen 2-113 (PNG321.0+03.9), which are unusual in exhibiting dual-dust chemistry and multipolar lobes but also ionized by late-type [WC 10] central stars. The spatially resolved velocity distributions of the Hα emission line were used to determine their primary orientations. The integrated Hα emission profiles indicate that Hen 3-1333 and Hen 2-113 expand with velocities of ∼32 and 23 km s−1, respectively. The Hubble Space Telescope observations suggest that these planetary nebulae have two pairs of tenuous lobes extending upwardly from their bright compact cores. From three-dimensional geometric models, the primary lobes of Hen 3-1333 and Hen 2-113 were found to have inclination angles of about −30° and 40° relative to the line of sight, and position angles of −15° and 65° measured east of north in the equatorial coordinate system, respectively.
(Contrastive) Topic
Authors: Büring Daniel 
Published: March 2015

AbstractThis chapter discusses the semantics and pragmatics of contrastive topics vis-à-vis focus. A semi-formal characterization of its main properties is given, using the techniques of alternative semantics and questions under discussion. This treatment is compared to various analyses proposed in the literature for contrastive topics and arguably related constructions, such as the English rise–fall–rise contour. Finally a brief discussion of non-contrastive topics is provided.
Formation of young massive clusters from turbulent molecular clouds
Authors: Fujii Michiko S. 
Published: March 2015

Abstract
Young massive clusters are as young as open clusters but more massive and compact compared with typical open clusters. The formation process of young massive clusters is still unclear, and it is an open question whether the formation process is the same for typical open clusters or not. We perform a series of N-body simulations starting from initial conditions constructed from the results of hydrodynamical simulations of turbulent molecular clouds. In our simulations, both open clusters and young massive clusters form when we assume a density-dependent star-formation efficiency. We find that a local star-formation efficiency higher than 50% is necessary for the formation of young massive clusters, but open clusters form from less dense regions with a local star formation efficiency of &lt; 50%. We confirm that the young massive clusters formed in our simulations have mass, size, and density profile similar to those of observed young massive clusters such as NGC 3603 and Trumpler 14. We also find that these simulated clusters evolve via hierarchical mergers of sub-clusters within a few mega years, as is suggested by recent simulations and observations. Although we do not assume initial mass segregation, we observe that the simulated massive clusters show a shallower slope of the mass function (Γ ∼ −1) in the cluster center compared to that of the entire cluster (Γ ∼ −1.3). These values are consistent with those of some young massive clusters in the Milky Way such as Westerlund 1 and Arches.
The Aggregate Effect of School Choice: Evidence from a Two-Stage Experiment in India *
Authors: Muralidharan Karthik , Sundararaman Venkatesh 
Published: March 2015

AbstractWe present experimental evidence on the impact of a school choice program in the Indian state of Andhra Pradesh that provided students with a voucher to finance attending a private school of their choice. The study design featured a unique two-stage lottery-based allocation of vouchers that created both student-level and market-level experiments, which allows us to study the individual and the aggregate effects of school choice (including spillovers). After two and four years of the program, we find no difference between test scores of lottery winners and losers on Telugu (native language), math, English, and science/social studies, suggesting that the large cross-sectional differences in test scores across public and private schools mostly reflect omitted variables. However, private schools also teach Hindi, which is not taught by the public schools, and lottery winners have much higher test scores in Hindi. Furthermore, the mean cost per student in the private schools in our sample was less than a third of the cost in public schools. Thus, private schools in this setting deliver slightly better test score gains than their public counterparts (better on Hindi and same in other subjects), and do so at a substantially lower cost per student. Finally, we find no evidence of spillovers on public school students who do not apply for the voucher, or on private school students, suggesting that the positive effects on voucher winners did not come at the expense of other students.
Evaluating conservation and fisheries management strategies by linking spatial prioritization software and ecosystem and fisheries modelling tools
Authors: Metcalfe Kristian , Vaz Sandrine , Engelhard Georg H. , Villanueva Maria Ching , Smith Robert J. , Mackinson Steven 
Published: March 2015

SummaryWell‐designed marine protected area (MPA) networks can deliver a range of ecological, economic and social benefits, and so a great deal of research has focused on developing spatial conservation prioritization tools to help identify important areas.However, whilst these software tools are designed to identifyMPAnetworks that both represent biodiversity and minimize impacts on stakeholders, they do not consider complex ecological processes. Thus, it is difficult to determine the impacts that proposedMPAs could have on marine ecosystem health, fisheries and fisheries sustainability.Using the eastern English Channel as a case study, this paper explores an approach to address these issues by identifying a series ofMPAnetworks using the Marxan and Marxan with Zones conservation planning software and linking them with a spatially explicit ecosystem model developed in Ecopath with Ecosim. We then use these to investigate potential trade‐offs associated with adopting differentMPAmanagement strategies.Limited‐takeMPAs, which restrict the use of some fishing gears, could have positive benefits for conservation and fisheries in the eastern English Channel, even though they generally receive far less attention in research onMPAnetwork design.Our findings, however, also clearly indicate that no‐takeMPAs should form an integral component of proposedMPAnetworks in the eastern English Channel, as they not only result in substantial increases in ecosystem biomass, fisheries catches and the biomass of commercially valuable target species, but are fundamental to maintaining the sustainability of the fisheries.Synthesis and applications. Using the existing software tools Marxan with Zones and Ecopath with Ecosim in combination provides a powerful policy‐screening approach. This could help inform marine spatial planning by identifying potential conflicts and by designing new regulations that better balance conservation objectives and stakeholder interests. In addition, it highlights that appropriate combinations of no‐take and limited‐take marine protected areas might be the most effective when making trade‐offs between long‐term ecological benefits and short‐term political acceptability.
Bikeshare in China as a public service: Comparing government‐run and public‐private partnership operation models
Authors: Lohry Gavin Fynn , Yiu Alice 
Published: March 2015

AbstractChina is now the world leader in public bikeshare systems (PBS) with more bikes and stations in use than the rest of the world combined. The rapid rise of PBS as a viable urban transport option in China has taken place since Hangzhou introduced the first system in 2008 and it has been driven by the desire to address sustainability challenges. Chinese municipal governments have heavily subsidized the development of PBS to encourage non‐motorized transport and offer a flexible, convenient, and low‐cost mobility options to the people. As a subsidized public service, PBS in China has been constructed and operated either under a government‐run (GR) model and public‐private partnership (PPP) model. This paper analyzes the effects of these two operation models on PBS performance and concludes that GR systems have been more effective than PPP systems in achieving higher bike utilization, ridership, and population served. The paper explores the reasons for these differences and finds that the financial incentive structure under the PPP model often leads to results that have conflicts of interest between private companies and the government. GR systems, on the contrary, are much more effective than PBS systems and they are under official transport agencies that are accountable to following the government's desire to make PBS function as a viable transport option instead of a profit‐making business.
Estimating greenhouse gas (GHG) emissions from paratransit in Bandung, Indonesia: Reducing the transaction costs of generating conservative emissions baselines
Authors: Nugroho Sudarmanto Budi , Zusman Eric 
Published: March 2015

AbstractIn developing countries, paratransit often meets essential mobility needs with older, inefficient vehicles that degrade air quality and emit greenhouse gases (GHGs). International climate change finance mechanisms such as the Clean Development Mechanism (CDM) or Green Climate Fund (GCF) could help fund cleaner vehicles. However, these mechanisms require generating a credible business‐as‐usual GHG baseline to compare against actual emissions. For paratransit, irregular scheduling and erratic driving behaviour add to a well‐documented list of factors that make the transaction costs prohibitively expensive for constructing robust transport baselines. This paper compares the relative accuracy and affordability of constructing five baselines for motorcycle taxis or ojeks in Bandung, Indonesia. The baselines that were constructed incorporate data that was gathered from one day and one week studies using revealed preference surveys as well as using real time global positioning systems (GPS) over one week into fuel efficiency and fuel consumption‐based emissions calculation techniques. The calculations show that the week‐long fuel consumption survey data generated the lowest fuel efficiency and highest GHG estimates. Driver survey data may therefore help construct a relatively low cost conservative baseline, especially when triangulated by GPS‐verified distance travelled data. The study concludes with several promising future research areas, including expanding the period of estimation for paratransit; examining the relationship between self‐reported distance and fuel consumption data; optimizing survey administration; and promoting climate finance mechanisms that engage stakeholders to lower the transaction costs of data gathering.