bluuebunny/crossref_metadata_2025_split huggingface dataset:
GLANET: genomic loci annotation and enrichment tool
Authors: Otlu Burçak , Firtina Can , Keleş Sündüz , Tastan Oznur 
Published: May 2017

AbstractMotivationGenomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations.ResultsWe present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately. GLANET annotates and performs enrichment analysis on these loci with a rich library. We introduce and perform novel data-driven computational experiments for assessing the power and Type-I error of its enrichment procedure which show that GLANET has attained high statistical power and well-controlled Type-I error rate. As a key feature, users can easily extend its library with new gene sets and genomic intervals. Other key features include assessment of impact of single nucleotide variants (SNPs) on TF binding sites and regulation based pathway enrichment analysis.Availability and implementationGLANET can be run using its GUI or on command line. GLANET’s source code is available at https://github.com/burcakotlu/GLANET. Tutorials are provided at https://glanet.readthedocs.org.Supplementary informationSupplementary data are available at Bioinformatics online.
Flexbar 3.0 – SIMD and multicore parallelization
Authors: Roehr Johannes T , Dieterich Christoph , Reinert Knut 
Published: May 2017

Abstract

Motivation
High-throughput sequencing machines can process many samples in a single run. For Illumina systems, sequencing reads are barcoded with an additional DNA tag that is contained in the respective sequencing adapters. The recognition of barcode and adapter sequences is hence commonly needed for the analysis of next-generation sequencing data. Flexbar performs demultiplexing based on barcodes and adapter trimming for such data. The massive amounts of data generated on modern sequencing machines demand that this preprocessing is done as efficiently as possible.

Results
We present Flexbar 3.0, the successor of the popular program Flexbar. It employs now twofold parallelism: multi-threading and additionally SIMD vectorization. Both types of parallelism are used to speed-up the computation of pair-wise sequence alignments, which are used for the detection of barcodes and adapters. Furthermore, new features were included to cover a wide range of applications. We evaluated the performance of Flexbar based on a simulated sequencing dataset. Our program outcompetes other tools in terms of speed and is among the best tools in the presented quality benchmark.

Availability and implementation
https://github.com/seqan/flexbar
Integrity of immunoglobulin variable regions is supported by GANP during AID-induced somatic hypermutation in germinal center B cells
Authors: Eid Mohammed Mansour Abbas , Shimoda Mayuko , Singh Shailendra Kumar , Almofty Sarah Ameen , Pham Phuong , Goodman Myron F. , Maeda Kazuhiko , Sakaguchi Nobuo 
Published: May 2017

Abstract
Immunoglobulin affinity maturation depends on somatic hypermutation (SHM) in immunoglobulin variable (IgV) regions initiated by activation-induced cytidine deaminase (AID). AID induces transition mutations by C→U deamination on both strands, causing C:G→T:A. Error-prone repairs of U by base excision and mismatch repairs (MMRs) create transversion mutations at C/G and mutations at A/T sites. In Neuberger’s model, it remained to be clarified how transition/transversion repair is regulated. We investigate the role of AID-interacting GANP (germinal center-associated nuclear protein) in the IgV SHM profile. GANP enhances transition mutation of the non-transcribed strand G and reduces mutation at A, restricted to GYW of the AID hotspot motif. It reduces DNA polymerase η hotspot mutations associated with MMRs followed by uracil-DNA glycosylase. Mutation comparison between IgV complementary and framework regions (FWRs) by Bayesian statistical estimation demonstrates that GANP supports the preservation of IgV FWR genomic sequences. GANP works to maintain antibody structure by reducing drastic changes in the IgV FWR in affinity maturation.
Quantifying tidal stream disruption in a simulated Milky Way
Authors: Sandford Emily , Küpper Andreas H. W. , Johnston Kathryn V. , Diemand Jürg 
Published: May 2017

Abstract
Simulations of tidal streams show that close encounters with dark matter subhaloes induce density gaps and distortions in on-sky path along the streams. Accordingly, observing disrupted streams in the Galactic halo would substantiate the hypothesis that dark matter substructure exists there, while in contrast, observing collimated streams with smoothly varying density profiles would place strong upper limits on the number density and mass spectrum of subhaloes. Here, we examine several measures of stellar stream ‘disruption' and their power to distinguish between halo potentials with and without substructure and with different global shapes. We create and evolve a population of 1280 streams on a range of orbits in the Via Lactea II simulation of a Milky Way-like halo, replete with a full mass range of Λcold dark matter subhaloes, and compare it to two control stream populations evolved in smooth spherical and smooth triaxial potentials, respectively. We find that the number of gaps observed in a stellar stream is a poor indicator of the halo potential, but that (i) the thinness of the stream on-sky, (ii) the symmetry of the leading and trailing tails and (iii) the deviation of the tails from a low-order polynomial path on-sky (‘path regularity') distinguish between the three potentials more effectively. We furthermore find that globular cluster streams on low-eccentricity orbits far from the galactic centre (apocentric radius ∼30–80 kpc) are most powerful in distinguishing between the three potentials. If they exist, such streams will shortly be discoverable and mapped in high dimensions with near-future photometric and spectroscopic surveys.
CO excitation in the Seyfert galaxy NGC 7130
Authors: Pozzi F. , Vallini L. , Vignali C. , Talia M. , Gruppioni C. , Mingozzi M. , Massardi M. , Andreani P. 
Published: May 2017

Abstract
We present a coherent multiband modelling of the carbon monoxide (CO) spectral energy distribution of the local Seyfert galaxy NGC 7130 to assess the impact of the active galactic nucleus (AGN) activity on the molecular gas. We take advantage of all the available data from X-ray to the submillimetre, including ALMA data. The high-resolution (∼0.2 arcsec) ALMA CO(6–5) data constrain the spatial extension of the CO emission down to an ∼70 pc scale. From the analysis of the archival Chandra and NuSTAR data, we infer the presence of a buried, Compton-thick AGN of moderate luminosity, L2–10 keV  ∼ 1.6 × 1043 erg s−1. We explore photodissociation and X-ray-dominated-region (PDR and XDR) models to reproduce the CO emission. We find that PDRs can reproduce the CO lines up to J ∼ 6; however, the higher rotational ladder requires the presence of a separate source of excitation. We consider X-ray heating by the AGNs as a source of excitation, and find that it can reproduce the observed CO spectral energy distribution. By adopting a composite PDR+XDR model, we derive molecular cloud properties. Our study clearly indicates the capabilities offered by the current generation of instruments to shed light on the properties of nearby galaxies by adopting state-of-the-art physical modelling.
Intracranial Infectious and Inflammatory Diseases Presenting as Neurosurgical Pathologies
Authors: Rapalino Otto , Mullins Mark E. 
Published: May 2017

Abstract
There are many infectious and inflammatory processes affecting the central nervous system that can simulate other neurosurgical pathologies (e.g. tumor) and may precipitate a brain biopsy for definitive diagnosis if not suspected a priori. The challenge for the healthcare team is to recognize imaging features that support a nonsurgical pathology to avoid unnecessary interventions. This review aims to give a general overview of some common inflammatory and infectious entities that affect the central nervous system, with illustrative examples and highlighting important pearls and pitfalls.
Mark Hepworth: in memoriam
Authors: Jackson Thomas , Willett Peter 
Published: May 2017

Purpose
The purpose of this paper is to honour the contributions of Mark Hepworth to library and information science (LIS).

Design/methodology/approach
The personal views of the two authors, both of whom knew Hepworth for many years.

Findings
The significance of Hepworth’s research in LIS, in particular to studies of information behaviour and information literacy.

Originality/value
Demonstrates the community’s appreciation of Hepworth’s contributions to the discipline.
Assessing information literacy skills among young information age students in Singapore
Authors: Foo Schubert , Majid Shaheen , Chang Yun Ke 
Published: May 2017

Purpose
The purpose of this paper is to assess knowledge of Singapore Grade 5 (11 years old) students’ understanding and proficiency in basic information literacy (IL) skills of defining information tasks, selecting information sources, seeking information from sources and synthesising and using information.

Design/methodology/approach
A 38-item multiple-choice question assessment instrument was used to assess the students’ IL skills based on the i-Competent IL model. The instrument first developed in 2010 was refined and expanded to increase the robustness and accuracy of assessment for the study. It was administered to 17 primary schools in Singapore in November 2015. The maximum possible score of 54 was scaled up to 100 to report the overall mean score for ease of reference and comparison. A total of 2,399 returns were obtained and analysed using Statistical Package for the Social Sciences 22.0 to compute the mean scores, IL stage-level scores. The study also investigated for any significant differences in performance between male and female students, and students with or without access to the internet at home.

Findings
The students achieved an overall mean score of 53.39 which is below a recommended acceptable score of 60 or 70 advocated in a number of past studies. The two worst performing areas of IL skills were synthesising and using information and seeking information from sources with mean scores of 45.89 and 48.81, respectively. A review of the highest number of incorrect answers suggests that students had difficulty in identifying key information from an information task narrative, understanding the use of reference sources and role of librarians, distinguishing between a fact and opinion, and adopting the best strategy for searching. Girls outperformed boys with an overall mean score of 55.38 vs 51.50. Students with internet access at home fared better than those without access to it with a score of 53.67 vs 45.81. The overall poor results of the survey suggest an urgent need to review the IL education landscape in the Singapore school system, revisit polices, priorities and assess the relevance and effectiveness of the IL curriculum, practical hands-on classes, and interventions that are currently employed in schools.

Practical implications
The study helped identify areas of IL skills strengths and weakness among Grade 5 students in Singapore schools. It provides recommendations for follow up actions for education authority and schools to improve the situation.

Originality/value
This study was prompted to provide an assessment after a national IL initiative was launched in 2012 to inculcate IL skills among the school-going children as part of creating a value-driven education system. This is the first reported set of findings for a large-scale survey conducted to measure and ascertain the IL skills level among Grade 5 students.
Is a picture really worth a thousand words?
Authors: Leung Xi , Tanford Sarah , Jiang Lan 
Published: May 2017

Purpose
The purpose of this study was to explore the marketing effectiveness of hotel Facebook messages in terms of promoting favorable attitudes and behavior intentions among potential hotel guests

Design/methodology/approach
An online experiment was conducted with a three (message format) × three (message content), between-subjects factorial design in which three message formats, i.e. word/text, picture and weblink, and three types of message content, i.e. brand, product and interactive, were manipulated.

Findings
The findings indicate that the most effective message format is dependent upon its purpose. Picture messages are most effective for promoting the brand, whereas weblink messages influence intentions to book hotels based on product attributes. Electronic word-of-mouth intention is an important outcome of Facebook marketing, which can be strengthened by word messages and weblink messages about products.

Research limitations/implications
The major limitation of this study is that the study used pseudo Facebook pages and messages created for each experimental condition. Facebook pages can take many forms, so the findings may not generalize to other Facebook pages.

Practical implications
The findings of this study suggest several important practical implications for the hotel industry to leverage Facebook marketing. To foster favorable attitudes and build brand awareness, hotel marketers should include picture messages that prominently feature the brand image. To motivate booking a particular product, word messages describing product features should be provided, along with a weblink that takes the customer directly from product information to a hotel-booking engine.

Originality/value
Although preliminary research has been conducted on Facebook marketing activities, little is known about the effectiveness of Facebook messages. For example, do different types of messages have different effects on marketing effectiveness? What message type is most effective? Thus, the aim of this study is to investigate empirically the effects of different message types on marketing effectiveness. The results of this study will shed light on how hotels can post the most persuasive message content in the most effective message format on their Facebook pages to enhance their fans’ attitudes and increase their purchase intentions.
The influence of social media on the consumers’ hotel decision journey
Authors: Varkaris Eleftherios , Neuhofer Barbara 
Published: May 2017

Purpose
The purpose of this study is to explore “how social media influence the way consumers search, evaluate and select a hotel within the ‘evaluation stage’ of the wider hotel decision-making process”.

Design/methodology/approach
An exploratory qualitative research has been carried out, conducting 12 individual face-to-face, semi-structured, in-depth interviews with social media users, followed by a qualitative thematic analysis.

Findings
Social media transform the consumers’ hotel decision journey by influencing the way consumers search, decide and book hotels. The findings reveal the determinants shaping this process, by shedding light on the perceived value of using social media, consumers’ information search behaviour “then and now”, the advantages and disadvantages of social media use for decision-making, their trustworthiness and the factors that influence the consumers’ hotel decision-journey. The findings are conceptualised in an integrated theoretical model, entitled “hotel consumer decision-journey through social media”.

Research limitations/implications
The study’s scope for qualitative in-depth insights into the “hotel consumer decision-journey through social media” asked for a compromise on a larger sample size and in turn the transferability of the theoretical model beyond service, hospitality and tourism consumer decision-making contexts.

Practical implications
This paper provides strategic implications for hospitality marketing and management for a better understanding of the influence of social media on the hotel customer decision journey. The study shows that a variety of social media with associated content sources and levels add to the complexity of hotel-related information search and decision behaviour. The developed framework not only helps hotel professionals understand consumers’ different levels (e.g. type of content, content source, content level) through which social media might influence decision-making. Various real-life scenarios presented also help practitioners understand the fine nuances of how consumers are influenced by social media and how this causes them to iteratively change their minds and make a final decision towards the rejection or selection of a hotel.

Originality/value
Consumers use social media for a wide spectrum of scenarios in tourism and hospitality, while the influence of social media on the consumers’ hotel decision-making process remains little understood. This study makes a theoretical contribution in that it addresses these existing gaps and bridges consumer behaviour and social media literature in the hotel context to shed light on the “hotel consumer decision journey through social media”. The core contribution is an integrated theoretical model and real-life scenarios that depict the impact of social media on the hotel decision-making.
Private club members’ perceptions of social media
Authors: Kim MiRan , Cichy Ronald 
Published: May 2017

Purpose
Private club members belong to an organization where people with common interests, experiences, backgrounds and professions meet for social and recreational purposes. This study aims to examine the relationships among private club members’ perceptions of social media regarding perceived ease of use, perceived usefulness, perceived enjoyment, attitude toward social media involvement and behavioral intention toward social media usage.

Design/methodology/approach
An online survey was conducted among private club members across the USA (n = 571). The data were analyzed using structural equation modeling.

Findings
The findings of this study center on the perceptions of club members and their beliefs and attitudes associated with their social media usage behavior. This study extends the social media literature by supporting previous studies that suggest a causal flow from perceived ease of use to intrinsic and extrinsic motivations (perceived usefulness, perceived enjoyment) based on a motivational model.

Research limitations/implications
This study is meaningful for revealing the perceptions of private club members and their beliefs and attitudes associated with their social media usage behavior. It is untested whether this study’s model applies to other hospitality businesses. Future research could examine other segments and add other variables such as perceived security and trust.

Practical implications
This study can provide private club managers, and the members of the clubs that they lead, with a better understanding of online social media.

Originality/value
This study is one of a few empirical online social media studies in the area of the private club industry. This study seeks to provide baselines regarding social media perceptions and usage in the hospitality literature by providing a comprehensive model.
Transition from child to adult mental health services: a French retrospective survey
Authors: Schandrin Aurélie , Capdevielle Delphine , Boulenger Jean-Philippe , Batlaj-Lovichi Monique , Russet Frédérick , Purper-Ouakil Diane 
Published: May 2017

PurposeAdolescents and young adults’ mental health problems are an important health issue. However, the current organisation of the care pathway is not robust enough and transition between child and adolescent mental health services (CAMHS) and adult mental health services (AMHS) has been identified as a period of risk. The paper aims to discuss these issues.Design/methodology/approachA retrospective survey was conducted in Montpellier University Hospital concerning transitions organised between CAMHS and AMHS between 2008 and 2009. The aim was to assess if transitions met four criteria identified in literature as warranting an optimal transition.FindingsIn total, 31 transitions were included. Transition was accepted by AMHS in 90 per cent of cases but its organisation was rarely optimal. Relational continuity and transition planning were absent in 80 per cent of cases. The age boundary of 16 often justified the triggering of the transition regardless of patient’s needs. Discontinuity was observed in 48 per cent of transition cases, with an average gap of three months without care. Psychiatrists reported difficulties in working together. Finally, at the moment of the survey (one to three years later), 55 per cent of patients were lost to follow-up.Research limitations/implicationsThis is a retrospective study on a small sample but it reveals important data about transition in France.Practical implicationsTransition process should include collaborative working between CAMHS and AMHS, with cross-agency working and periods of parallel care.Social implicationsTransition-related discontinuity of care is a major socioeconomic and societal challenge for the EU.Originality/valueData related to the collaboration between CAMHS and AMHS services are scarce, especially regarding the transition in France.
Student nurses’ preparation for psychiatric nursing practice: Malawian experiences
Authors: Bvumbwe Thokozani 
Published: May 2017

PurposeThe purpose of this paper is to explore newly graduated nurses’ experiences of their preparation for psychiatric nursing practice in Malawi. Knowledge of how basic or undergraduate nursing training programs prepare nurses for mental health services will inform educators to maximize the teaching and learning processes. Students are a key stakeholder in professional training hence an understanding of their experiences of training programs is critical.Design/methodology/approachA qualitative exploratory study was undertaken. In total, 16 newly graduated nurses with six months work experience at three psychiatric hospitals in Malawi were purposively sampled and recruited into the study. One to one interviews which lasted almost 45 minutes were conducted. Data were analyzed using content analysis.FindingsFindings show that training programs fall short in preparing students for psychiatric nursing practice. Participants reported little attention to the specialty as compared to other specialties by educators. Inadequate academic support during practice sessions was highlighted by the majority of participants.Research limitations/implicationsThe study needed to compare the findings with experiences of students who have been allocated to other nursing specialties.Originality/valuePsychiatric nursing specialty remains the least preferred career choice for many nursing students. However, preservice nursing education programs are expected to socialize, motivate and prepare students for psychiatric practice as well. It is therefore critical to understand gaps that exist in student preparation for psychiatric nursing services in order to improve mental health training.