bluuebunny/crossref_metadata_2025_split huggingface dataset:
Xolik: finding cross-linked peptides with maximum paired scores in linear time
Authors: Dai Jiaan , Jiang Wei , Yu Fengchao , Yu Weichuan 
Published: June 2018

Abstract

Motivation
Cross-linking technique coupled with mass spectrometry (MS) is widely used in the analysis of protein structures and protein-protein interactions. In order to identify cross-linked peptides from MS data, we need to consider all pairwise combinations of peptides, which is computationally prohibitive when the sequence database is large. To alleviate this problem, some heuristic screening strategies are used to reduce the number of peptide pairs during the identification. However, heuristic screening strategies may miss some true cross-linked peptides.

Results
We directly tackle the combination challenge without using any screening strategies. With the data structure of double-ended queue, the proposed algorithm reduces the quadratic time complexity of exhaustive searching down to the linear time complexity. We implement the algorithm in a tool named Xolik. The running time of Xolik is validated using databases with different numbers of proteins. Experiments using synthetic and empirical datasets show that Xolik outperforms existing tools in terms of running time and statistical power.

Availability and implementation
Source code and binaries of Xolik are freely available at http://bioinformatics.ust.hk/Xolik.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
GrandPrix: scaling up the Bayesian GPLVM for single-cell data
Authors: Ahmed Sumon , Rattray Magnus , Boukouvalas Alexis 
Published: June 2018

Abstract

Motivation
The Gaussian Process Latent Variable Model (GPLVM) is a popular approach for dimensionality reduction of single-cell data and has been used for pseudotime estimation with capture time information. However, current implementations are computationally intensive and will not scale up to modern droplet-based single-cell datasets which routinely profile many tens of thousands of cells.

Results
We provide an efficient implementation which allows scaling up this approach to modern single-cell datasets. We also generalize the application of pseudotime inference to cases where there are other sources of variation such as branching dynamics. We apply our method on microarray, nCounter, RNA-seq, qPCR and droplet-based datasets from different organisms. The model converges an order of magnitude faster compared to existing methods whilst achieving similar levels of estimation accuracy. Further, we demonstrate the flexibility of our approach by extending the model to higher-dimensional latent spaces that can be used to simultaneously infer pseudotime and other structure such as branching. Thus, the model has the capability of producing meaningful biological insights about cell ordering as well as cell fate regulation.

Availability and implementation
Software available at github.com/ManchesterBioinference/GrandPrix.

Supplementary information
Supplementary data are available at Bioinformatics online.
PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations
Authors: Zhang Peng , Bigio Benedetta , Rapaport Franck , Zhang Shen-Ying , Casanova Jean-Laurent , Abel Laurent , Boisson Bertrand , Itan Yuval 
Published: June 2018

Abstract

Summary
Next-generation sequencing (NGS) generates large amounts of genomic data and reveals about 20 000 genetic coding variants per individual studied. Several mutation damage prediction scores are available to prioritize variants, but there is currently no application to help investigators to determine the relevance of the candidate genes and variants quickly and visually from population genetics data and deleteriousness scores. Here, we present PopViz, a user-friendly, rapid, interactive, mobile-compatible webserver providing a gene-centric visualization of the variants of any human gene, with (i) population-specific minor allele frequencies from the gnomAD population genetic database; (ii) mutation damage prediction scores from CADD, EIGEN and LINSIGHT and (iii) amino-acid positions and protein domains. This application will be particularly useful in investigations of NGS data for new disease-causing genes and variants, by reinforcing or rejecting the plausibility of the candidate genes, and by selecting and prioritizing, the candidate variants for experimental testing.

Availability and implementation
PopViz webserver is freely accessible from http://shiva.rockefeller.edu/PopViz/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Flux tope analysis: studying the coordination of reaction directions in metabolic networks
Authors: Gerstl Matthias P , Müller Stefan , Regensburger Georg , Zanghellini Jürgen 
Published: June 2018

Abstract

Motivation
Elementary flux mode (EFM) analysis allows an unbiased description of metabolic networks in terms of minimal pathways (involving a minimal set of reactions). To date, the enumeration of EFMs is impracticable in genome-scale metabolic models. In a complementary approach, we introduce the concept of a flux tope (FT), involving a maximal set of reactions (with fixed directions), which allows one to study the coordination of reaction directions in metabolic networks and opens a new way for EFM enumeration.

Results
A FT is a (nontrivial) subset of the flux cone specified by fixing the directions of all reversible reactions. In a consistent metabolic network (without unused reactions), every FT contains a ‘maximal pathway’, carrying flux in all reactions. This decomposition of the flux cone into FTs allows the enumeration of EFMs (of individual FTs) without increasing the problem dimension by reaction splitting. To develop a mathematical framework for FT analysis, we build on the concepts of sign vectors and hyperplane arrangements. Thereby, we observe that FT analysis can be applied also to flux optimization problems involving additional (inhomogeneous) linear constraints. For the enumeration of FTs, we adapt the reverse search algorithm and provide an efficient implementation. We demonstrate that (biomass-optimal) FTs can be enumerated in genome-scale metabolic models of B.cuenoti and E.coli, and we use FTs to enumerate EFMs in models of M.genitalium and B.cuenoti.

Availability and implementation
The source code is freely available at https://github.com/mpgerstl/FTA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Exploring drivers of gene expression in the Cancer Genome Atlas
Authors: Rau Andrea , Flister Michael , Rui Hallgeir , Auer Paul L 
Published: June 2018

Abstract

Motivation
The Cancer Genome Atlas (TCGA) has greatly advanced cancer research by generating, curating and publicly releasing deeply measured molecular data from thousands of tumor samples. In particular, gene expression measures, both within and across cancer types, have been used to determine the genes and proteins that are active in tumor cells.

Results
To more thoroughly investigate the behavior of gene expression in TCGA tumor samples, we introduce a statistical framework for partitioning the variation in gene expression due to a variety of molecular variables including somatic mutations, transcription factors (TFs), microRNAs, copy number alternations, methylation and germ-line genetic variation. As proof-of-principle, we identify and validate specific TFs that influence the expression of PTPN14 in breast cancer cells.

Availability and implementation
We provide a freely available, user-friendly, browseable interactive web-based application for exploring the results of our transcriptome-wide analyses across 17 different cancers in TCGA at http://ls-shiny-prod.uwm.edu/edge_in_tcga. All TCGA Open Access tier data are available at the Broad Institute GDAC Firehose and were downloaded using the TCGA2STAT R package. TCGA Controlled Access tier data are available via controlled access through the Genomic Data Commons (GDC). R scripts used to download, format and analyze the data and produce the interactive R/Shiny web app have been made available on GitHub at https://github.com/andreamrau/EDGE-in-TCGA.
Stakeholder expectations, roles and responsibilities in Dutch health promotion for people with intellectual disabilities
Authors: Kuijken N M J , Vlot-van Anrooij K , van Schrojenstein Lantman-de Valk H M J , Leusink G , Naaldenberg J , Nijhuis-van der Sanden M W 
Published: June 2018

Summary
This two-phase, qualitative study aims to obtain an overview of stakeholders in the network of people with intellectual disabilities (ID) and their perceived facilitating and hindering factors, expectations, and perceived roles and responsibilities with regard to health promotion. In phase 1, four workshops were conducted to provide insight into involved stakeholders. In phase 2, 29 semi-structured interviews were conducted with stakeholders regarding their views on health promotion. Data were analysed using stakeholder matrices and a combination of domain and thematic analysis. Daily caregivers were identified as the most important and influential stakeholders. Interviewed stakeholders perceived barriers to a healthy lifestyle as relating mainly to the person with ID and, although they stated that people with ID need support to be able to live healthily, there was ambiguity about roles and responsibilities for providing this support. Daily caregivers are not properly facilitated to support a healthy lifestyle. Stakeholders expressed the need for a culture change towards a greater health promotion ethos in care for people with ID. A facilitating context is needed in which the social network supports autonomy and offers opportunities to adapt to physical, social and emotional challenges. Stakeholders see the importance of, and are willing to support, healthy behaviour. They are hindered by a lack of a shared vision and united system in which all stakeholders know their roles and responsibilities. Promotion of a healthy lifestyle should be part of every service provider employee’s job and propagated throughout the organization as part of its mission and vision.
Routing problems in agricultural cooperatives: a model for optimization of transport vehicle logistics
Authors: Guitián de Frutos Roque M , Casas-Méndez Balbina 
Published: June 2018

AbstractThis study considers the problem of optimizing the routes of vehicles used in an agricultural cooperative that distributes animal feed to its customers. Different peculiarities distinguish our problem from the general Vehicle Routing Problem because there exists a type of time window constraint, truck capacity is limited, trucks are compartmentalized, there are access restrictions for trucks to some farms and our problem has the main objective of maximizing the amount of feed distributed every day and an auxiliary criterion of minimizing the transport costs. We present a mathematical programming formulation of the model that represents the logistics management problem. As solving the exact model is computationally expensive, we opt for a hybrid heuristic approach that first uses an insertion heuristic algorithm to obtain an initial solution and then improvement processes are performed using the so-called simulated annealing metaheuristic. We have built a graphical interface that allows easy use of the system and, in particular, efficient post-optimality analysis. Moreover, this interface can easily interface with other management tools. The utility of our model is shown with real and simulated data sets.
The Kodaira Dimension of Contact 3-Manifolds and Geography of Symplectic Fillings
Authors: Li Tian-Jun , Mak Cheuk Yu 
Published: June 2018

Abstract
We introduce the Kodaira dimension of contact 3-manifolds and establish some basic properties. Contact 3-manifolds with distinct Kodaira dimensions behave differently when it comes to the geography of various kinds of symplectic fillings. On the other hand, we also prove that, given any contact 3-manifold, there is a lower bound of $2\chi +3\sigma $ for all of its minimal symplectic fillings. This is motivated by Stipsicz’s result in [38] for Stein fillings. Finally, we discuss various aspects of exact self-cobordisms of fillable contact 3-manifolds.
Evaluating active learning methods for annotating semantic predications
Authors: Vasilakes Jake , Rizvi Rubina , Melton Genevieve B , Pakhomov Serguei , Zhang Rui 
Published: June 2018

Abstract

Objectives
This study evaluated and compared a variety of active learning strategies, including a novel strategy we proposed, as applied to the task of filtering incorrect semantic predications in SemMedDB.

Materials and methods
We evaluated 8 active learning strategies covering 3 types—uncertainty, representative, and combined—on 2 datasets of 6,000 total semantic predications from SemMedDB covering the domains of substance interactions and clinical medicine, respectively. We also designed a novel combined strategy called dynamic β that does not use hand-tuned hyperparameters. Each strategy was assessed by the Area under the Learning Curve (ALC) and the number of training examples required to achieve a target Area Under the ROC curve. We also visualized and compared the query patterns of the query strategies.

Results
All types of active learning (AL) methods beat the baseline on both datasets. Combined strategies outperformed all other methods in terms of ALC, outperforming the baseline by over 0.05 ALC for both datasets and reducing 58% annotation efforts in the best case. While representative strategies performed well, their performance was matched or outperformed by the combined methods. Our proposed AL method dynamic β shows promising ability to achieve near-optimal performance across 2 datasets.

Discussion
Our visual analysis of query patterns indicates that strategies which efficiently obtain a representative subsample perform better on this task.

Conclusion
Active learning is shown to be effective at reducing annotation costs for filtering incorrect semantic predications from SemMedDB. Our proposed AL method demonstrated promising performance.
Growth and agglomeration in the heterogeneous space: a generalized AK approach
Authors: Boucekkine Raouf , Fabbri Giorgio , Federico Salvatore , Gozzi Fausto 
Published: June 2018

AbstractWe provide an optimal growth spatio-temporal setting with capital accumulation and diffusion across space to study the link between economic growth triggered by capital spatio-temporal dynamics and agglomeration across space. The technology is AK, K being broad capital. The social welfare function is Benthamite. In sharp contrast to the related literature, which considers homogeneous space, we derive optimal location outcomes for any given space distributions for technology and population. Both the transitional spatio-temporal dynamics and the asymptotic spatial distributions are computed in closed form. Concerning the latter, we find, among other results, that: (i) due to inequality aversion, the consumption per capital distribution is much flatter than the distribution of capital per capita; (ii) endogenous spillovers inherent in capital spatio-temporal dynamics occur as capital distribution is much less concentrated than the (pre-specified) technological distribution; (iii) the distance to the center (or to the core) is an essential determinant of the shapes of the asymptotic distributions, that is relative location matters.
Assessment and Treatment of Problem Internet Use
Authors: Young Kimberly 
Published: June 2018

Abstract
Research over the last decade has identified Internet addiction as a new and often unrecognized clinical disorder that impacts a user’s ability to control online use to the extent that it can cause relational, occupational, and social problems. Symptoms of problem Internet use are compared to criteria used to diagnose other addictions. In particular, pathological gambling is compared to problematic Internet use because of overlapping criteria. This chapter describes the diagnostic and treatment implications of the disorder. As technology is used with great frequency, detection and diagnosis of Internet addiction is often difficult. Symptoms may be masked by legitimate use of the Internet, and clinicians may overlook asking questions about technology use because problem Internet use is still a new and often unrecognized condition. This chapter outlines diagnostic conceptualizations of problem Internet use along with assessment and treatment considerations and the newest inclusion in the DSM-5 for Internet Gaming Disorder.
Issues in Arabic Computational Linguistics
Authors: Ditters Everhard 
Published: June 2018

AbstractThis article focuses on the current state of affairs in the field of Arabic computational linguistics. It begins by briefly monitoring relevant trends in phonetics and phonology, morphology, syntax, lexicology, semantics, stylistics, and pragmatics. Then, the chapter describes changes or special accents within formal Arabic syntax. After some evaluative remarks about the approach opted for, it continues with a linguistic description of literary Arabic for analysis purposes as well as an introduction to a formal description, pointing to some early results. The article hints at further perspectives for ongoing research and possible spinoffs such as a formalized description of Arabic syntax in formalized dependency rules as well as a subset thereof for information retrieval purposes.
Political Discussion and Deliberation Online
Authors: Stromer-Galley Jennifer 
Published: June 2018

Abstract
As information and communication technologies have diffused, scholars have turned attention to online informal political discussion and formal deliberation because of the importance of online political talk for constructing society and informing government policy. This chapter examines the research on both formal deliberation and informal discussion online, identifies the importance of this research area, signals its major findings, and examines key unanswered questions. Along the way it argues that more research is needed to understand why women and minorities are less likely to talk politics online; better conceptual clarity is needed about the phenomenon of interest; more experimental work is required to isolate the causes and consequences of channel characteristics and mechanics that produce higher-quality discussion and decisions; and more work is needed that extends across information and communication technologies (ICTs), cross-culturally, and beyond democratically-governed societies.
New Media and Political Campaigns
Authors: Owen Diana 
Published: June 2018

Abstract
New media have been playing an increasingly central role in American elections since they first appeared in 1992. While television remains the main source of election information for a majority of voters, digital communication platforms have become prominent. New media have triggered changes in the campaign strategies of political parties, candidates, and political organizations; reshaped election media coverage; and influenced voter engagement. This chapter examines the stages in the development of new media in elections from the use of rudimentary websites to the rise sophisticated social media. It discusses the ways in which new media differ from traditional media in terms of their form, function, and content; identifies the audiences for new election media; and examines the effects on voter interest, knowledge, engagement, and turnout. Going forward, scholars need to employ creative research methodologies to catalogue and analyze new campaign media as they emerge and develop.
The US Media, Foreign Policy, and Public Support for War
Authors: Aday Sean 
Published: June 2018

Abstract
This chapter focuses on the relationship between news media and US foreign policy, with an emphasis on war—a subset of the latter—given that this has been a growing area of concern in political communication scholarship. Although interest in this topic goes back arguably to the roots of mass communication research, this chapter focuses on the explosion of research on it in the last quarter century. It highlights current theoretical and empirical approaches with an eye toward delineating what former Defense Secretary Donald Rumsfeld memorably called the “known unknowns.” Unanswered questions are also discussed.
Affect and Political Choice
Authors: Crigler Ann N. , Hevron Parker R. 
Published: June 2018

Abstract
Whether political observers and participants applaud or decry the presence of emotions in political decision-making, scholars have begun to view the relationship between affect and reason as a key component of decision-making. This chapter provides an overview of the research on affect and political choice. The authors argue that emotions undergird acts of political choice, not simply as additional variables to explain preferences or actions but also as integral to the processing of information and decision-making. They briefly define affect, emotion and mood and outline some of the methodologies commonly used to measure each of the four emotion functions that are central to political communication and choice. These four functions of emotion – expressive, perceptual/attentional, appraisal, and behavioral – are discussed in relation to political decision-making.
The organization of Danish emergency departments
Authors: Moellekaer Anders , Duvald Iben , Obel Borge , Madsen Bo , Eskildsen Jacob , Kirkegaard Hans 
Published: June 2018

Introduction
Twenty-one new Danish emergency departments (EDs) were established following a 2007 policy reform that included ED autonomy to self-organize. The aim of this study was to describe the organization of the 21 departments and their organizational challenges.

Participants and methods
We used a qualitative design based on COREQ guidelines. All 21 EDs participated, and 123 semi-structured interviews with hospital and ED leaders, physicians, nurses, and secretaries were performed between 2013 and 2015. We used the framework matrix method to investigate the ED goals, setting, structure, staff, task coordination, and incentive structure.

Results
We identified three generic models (virtual, hybrid, and independent). All had goals of high quality of care and high efficiency. The virtual model was staffed by junior physicians and tasks were coordinated by other departments. The hybrid model was staffed by junior physicians and senior physicians according to other departments and the ED. The ED coordinated all activities. The independent model was staffed by junior physicians and senior physicians, and activities were coordinated by the ED. Of the EDs, 19 utilized different organizational models at different times during a 24-h period and on weekdays and weekends. The main challenge of the virtual and hybrid models was high dependency on other departments. The main challenge of the independent model was establishing a high level of quality of emergency medicine.

Discussion and conclusion
We identified three organizational ED models (virtual, hybrid, and independent). Nineteen EDs used more than one organizational model depending on the time of day or day of the week.