bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIANA—algorithmic improvements for analysis of data-independent acquisition MS data
Authors: Teleman Johan , Röst Hannes L , Rosenberger George , Schmitt Uwe , Malmström Lars , Malmström Johan , Levander Fredrik 
Published: October 2014

Abstract
Motivation: Data independent acquisition mass spectrometry has emerged as a reproducible and sensitive alternative in quantitative proteomics, where parsing the highly complex tandem mass spectra requires dedicated algorithms. Recently, targeted data extraction was proposed as a novel analysis strategy for this type of data, but it is important to further develop these concepts to provide quality-controlled, interference-adjusted and sensitive peptide quantification.
Results: We here present the algorithm DIANA and the classifier PyProphet, which are based on new probabilistic sub-scores to classify the chromatographic peaks in targeted data-independent acquisition data analysis. The algorithm is capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset. Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide precursors in complex biological samples.
Availability and implementation: DIANA is implemented in scala and python and available as open source (Apache 2.0 license) or pre-compiled binaries from http://quantitativeproteomics.org/diana. PyProphet can be installed from PyPi (https://pypi.python.org/pypi/pyprophet).
Supplementary information: Supplementary data are available at Bioinformatics online.
MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC–MS metabolomic datasets
Authors: Edmands William M. B. , Barupal Dinesh K. , Scalbert Augustin 
Published: October 2014

Abstract
Summary: MetMSLine represents a complete collection of functions in the R programming language as an accessible GUI for biomarker discovery in large-scale liquid-chromatography high-resolution mass spectral datasets from acquisition through to final metabolite identification forming a backend to output from any peak-picking software such as XCMS. MetMSLine automatically creates subdirectories, data tables and relevant figures at the following steps: (i) signal smoothing, normalization, filtration and noise transformation (PreProc.QC.LSC.R); (ii) PCA and automatic outlier removal (Auto.PCA.R); (iii) automatic regression, biomarker selection, hierarchical clustering and cluster ion/artefact identification (Auto.MV.Regress.R); (iv) Biomarker—MS/MS fragmentation spectra matching and fragment/neutral loss annotation (Auto.MS.MS.match.R) and (v) semi-targeted metabolite identification based on a list of theoretical masses obtained from public databases (DBAnnotate.R).
Availability and implementation: All source code and suggested parameters are available in an un-encapsulated layout on http://wmbedmands.github.io/MetMSLine/. Readme files and a synthetic dataset of both X-variables (simulated LC–MS data), Y-variables (simulated continuous variables) and metabolite theoretical masses are also available on our GitHub repository.
Contact: ScalbertA@iarc.fr
PPDMs—a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains
Authors: Kruger Felix A. , Gaulton Anna , Nowotka Michal , Overington John P. 
Published: October 2014

Abstract
Summary: PPDMs is a resource that maps small molecule bioactivities to protein domains from the Pfam-A collection of protein families. Small molecule bioactivities mapped to protein domains add important precision to approaches that use protein sequence searches alignments to assist applications in computational drug discovery and systems and chemical biology. We have previously proposed a mapping heuristic for a subset of bioactivities stored in ChEMBL with the Pfam-A domain most likely to mediate small molecule binding. We have since refined this mapping using a manual procedure. Here, we present a resource that provides up-to-date mappings and the possibility to review assigned mappings as well as to participate in their assignment and curation. We also describe how mappings provided through the PPDMs resource are made accessible through the main schema of the ChEMBL database.
Availability and implementation: The PPDMs resource and curation interface is available at https://www.ebi.ac.uk/chembl/research/ppdms/pfam_maps. The source-code for PPDMs is available under the Apache license at https://github.com/chembl/pfam_maps. Source code is available at https://github.com/chembl/pfam_map_loader to demonstrate the integration process with the main schema of ChEMBL.
Contact: jpo@ebi.ac.uk
Navigating protected genomics data with UCSC Genome Browser in a Box
Authors: Haeussler Maximilian , Raney Brian J. , Hinrichs Angie S. , Clawson Hiram , Zweig Ann S. , Karolchik Donna , Casper Jonathan , Speir Matthew L. , Haussler David , Kent W. James 
Published: October 2014

Abstract
Summary: Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access.
Availability and implementation: Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/).
Contact: genome@soe.ucsc.edu
Disseminated Cutaneous Mycobacterium chelonae Infection in a Patient With Acute Myeloid Leukemia
Authors: Roukens Anna Helena , Mendels Elodie J. , Verbeet Nicolette L. , von dem Borne Peter A. , Nicolae-Cristea Alina R. , Bentvelsen Robbert G. , van Doorn Remco , de Boer Mark G. 
Published: October 2014

Abstract
We report a case of disseminated cutaneous Mycobacterium chelonae infection in a patient who was treated with chemotherapy for acute myeloid leukemia. We discuss the clinical manifestations, diagnosis, and treatment of this unusual infection in neutropenic patients.
Effects of Adjuvant Radiotherapy in Patients With Synovial Sarcoma
Authors: Song Sanghyuk , Park Junghwan , Kim Hak Jae , Kim Il Han , Han Ilkyu , Kim Han-Soo , Kim Suzy 
Published: October 2014

Objectives:To analyze the treatment outcomes and the effects of adjuvant radiotherapy (RT) in patients with synovial sarcoma (SS).Materials and Methods:The medical records of 103 patients treated with definitive surgery for SS, with/without RT, from August 1982 to July 2013 were reviewed retrospectively. The median age of the patients was 33 years (range, 5 to 72 y). The most frequent tumor location was the extremities (79 patients, 77%). Seventy-five patients (73%) received adjuvant RT and 26 (25%) did not. The median dose of adjuvant RT was 61.2 Gy (range, 45 to 66.6 Gy).Results:The median follow-up period was 5.4 years (range, 0.2 to 31.0 y). The 5- and 10-year overall survival rates were 77 % and 65%, respectively. The progression-free survival (PFS) rates at 5 and 10 years were 52% and 43%, respectively. The most common site of initial failure was the lung (24 patients), followed by local recurrence (14 patients). The 5-year local-recurrence-free survival (LRFS) and distant-metastasis-free survival (DMFS) rates were 80% and 63%, respectively. On multivariate analysis, a mitosis count of <10 per 10 high-power fields (HPF) was a significant predictor of better overall survival, PFS, LRFS, and DMFS (P=0.004, <0.001, 0.025, and <0.001, respectively). Adjuvant RT was an additional prognostic factor for better PFS and LRFS (P=0.006 and 0.028, respectively). A positive/uncheckable resection margin was associated with poor prognosis for DMFS (P=0.011). There was no significant difference in LRFS between the higher and lower RT dose groups (<63 Gy group, 89%; ≥63 Gy group, 88%;P=0.772).Conclusions:The lung and primary site were frequent sites of failure in patients treated with definitive surgery for SS. Adjuvant RT improved LRFS and PFS. Frequent mitotic figures (≥10 mitoses per 10 HPF) were the worst prognostic factor for these patients.
Do online communities support research collaboration?
Authors: R. Jamali Hamid , Russell Bill , Nicholas David , Watkinson Anthony 
Published: October 2014

Purpose
– The purpose of this paper is to explore the extent to which academics are engaged with online communities for research purposes, and the research activities, platforms and tools associated with these communities. In addition, the paper aims to discover the benefits, disadvantages and barriers involved in the use of online communities, and especially in regard to the trust and authority issues, so important in scholarly communications.

Design/methodology/approach
– A layered, mixed-methods approach was used for this complex research topic. Interviews were undertaken with social science and humanities researchers, followed up with focus groups in both the USA and UK. This qualitative work was then followed up with an online questionnaire that generated over 1,000 responses.

Findings
– Over half the sample had experience of an online research community and a majority of researchers are making at least occasional use of one or more Web 2.0 services for communicating their research activity; for developing and sustaining networks and collaboration; or for finding out what others are doing. Big differences exist in membership rates according to subject, but not really by age or other demographic factors. The biggest benefit to joining an online community is the ability to seek information in one’s own specialism. Younger researchers are more engaged with online communities.

Research limitations/implications
– The qualitative research was limited to the UK and USA. While use of online communities is now accepted by both established and younger researchers, the main ways of communicating research remain scholarly journals and books.

Practical implications
– The implications for learned societies and publishers are not clear. Journals are confirmed as the primary way of disseminating research. However, it would be easy for these stakeholders to miss how younger researchers expect to connect in digital communities.

Social implications
– With researchers of all ages accepting the existing and importance of online communities and connections, there are few technical or social barriers to using mainstream digital tools to connect professionally.

Originality/value
– There is little published research considering the role of online research communities, so the study is highly original. It is valuable to discover that researchers still prefer to share research findings primarily through journals, rather than through social technologies.
Information needs and information sources of family caregivers of cancer patients
Authors: Chen Shih-chuan 
Published: October 2014

Purpose
– The purpose of this paper is to analyse the information needs of family caregivers of cancer patients. Information sources used by the caregivers were also examined.

Design/methodology/approach
– We interviewed 15 family caregivers (nine females, six males) in Taiwan for this study. The participants were aged from 23 to 67 years, and all except two had attained college or higher degrees. Their relationships with patients included spousal, parental, and that of son or daughter.

Findings
– Family caregivers’ information needs varied along the cancer journey, and they used various information sources to satisfy these needs. Demographic variables affected the information-seeking behaviour of the family caregivers.

Originality/value
– The majority of studies on this topic have been based in western countries. This paper reveals the importance of considering cultural factors. The findings can assist researchers in gaining a greater understanding of the information-seeking behaviour of family caregivers of cancer patients worldwide.
Exploring political discussions by Korean twitter users
Authors: Choi Myunggoon , Sang Yoonmo , Woo Park Han 
Published: October 2014

Purpose– The purpose of this paper is to provide a network analysis of Twitter discussions about Myung-Bak Lee, a former president of South Korea, to gain a better understanding of the dynamics of the public opinion exchange on Twitter.Design/methodology/approach– Opinion leaders in the discussion network were identified by considering the longitudinal distribution of tweets containing the former president’s name, and three types of messages (“followings,” “mentions,” and “retweets”) were analyzed using data collected from November 1, 2011, to April 20, 2012. The sample included 26,150 Twitter users and 892,034 relationships reflecting three types of messages.Findings– The results indicate that the discussion about President Myung-Bak Lee was dominated by liberal Twitter users who already had considerable influence both online and offline. In addition, Twitter users were unlikely to interact with other users with opposing political views.Research limitations/implications– Almost all of the opinion leaders identified in the study held liberal political views, and liberal Twitter users dominated the discussion network. In addition, the Korean Twitter network showed the presence of the homophily phenomenon, implying that opinion leaders’ influence within the Twitter network was limited to other users sharing the same political views. Further, political views of opinion leaders were skewed toward a particular political stance without necessarily representing the opinion of the general public, possibly hindering the democratic process.Originality/value– This study tests the homophily thesis in the context of Twitter users in Korea and contributes to the literature on Twitter-based political discourse by identifying opinion leaders in Korean Twitter networks and examining the phenomenon of homophily within those networks.
Moderating role of religious beliefs on attitudes towards charities and motivation to donate
Authors: Teah Min , Lwin Michael , Cheah Isaac 
Published: October 2014

Purpose
– The purpose of this paper is to examine the relationship between image of charitable organizations, attitudes towards charities and motivation to donate. In addition, the study will investigate the moderating effects of religious beliefs on attitudes towards charities and motivation to donate.

Design/methodology/approach
– Data are collected using a self-administered questionnaire. Trained interviewers employed a mall-intercept method in downtown Kuala Lumpur over both weekdays and weekends. The scales are adapted from established sources.

Findings
– It was found that religious beliefs moderates the relationship between attitudes towards charities and motivation to donate. In addition, image of charitable organizations has a positive influence on attitudes towards charities. It was also found that both image of charitable organizations and attitudes towards charities influence motivation to donate.

Research limitations/implications
– The study is conducted within downtown Kuala Lumpur and is not generalizable across Malaysia and other countries. In addition, this study only looked at general religious beliefs, therefore findings are not specific to a religion. As a result, possible religious differences may be neglected. Lastly, the study only focused on donors and further studies need to be conducted on non-donors to further understand donation behaviour.

Practical implications
– The findings from the study provide valuable insights to charities, government bodies and policy makers as it highlights the linkages between image of charitable organizations, attitudes towards charities and the motivation to donate of past donors. Additionally, religious bodies can also use the findings to formulate communication strategies to benefit charities as well as the broader community.

Originality/value
– The study provides insights into the motivations of donors to donate to charities. More importantly, it also examines the influence of religious beliefs on donation behaviour, thus shedding insights on the opportunities for fundraising by charities.
Where is the profit in a library team?
Authors: Steele Kirstin 
Published: October 2014

Purpose
– The purpose of this article is to resolve my aversion to the concept of teamwork.

Design/methodology/approach
– Opinion.

Findings
– There is a difference in how I perceive different groups referred to as teams, and in how I think each of those would function in a library setting.

Originality/value
– In a literature search about disliking teamwork or the word team, I found little to address my reaction to the concept, either in libraries or in the greater work world. The articles or editorials I did find had more to do with particular teambuilding exercises.
SociaLib: a collaborative digital library model platform using Web 2.0
Authors: Mitropoulos Sarandis , Dimitrios Baltasis George , Rodios Michalis , Douligeris Christos 
Published: October 2014

Purpose
– The purpose of this paper is to present the SociaLib system, which is a collaborative digital library system. The system uses Drupal content management system to implement Web 2.0 functionalities and facilitate collaboration and cooperation between its users. It offers a variety of functions, like wikis, forums and it is also accessible from microbrowsers.

Design/methodology/approach
– The paper starts with a reference to collaboration in Digital Libraries and states related work. Then, it introduces the SociaLib system, including implementation and functionalities. There is also an example of how such a system can be used in a real-world situation. Ideas for future work are also included.

Findings
– The system was evaluated using a usability questionnaire on a subject of 50 people. The results were promising, showing user acceptance and satisfaction.

Originality/value
– This paper offer collaborative solutions to Digital Library users, helping them communicate and cooperate with colleagues on their research. The system uses Web 2.0 functions that enable the user to be more productive and also work mobile if he wishes.
Expectations versus experiences: librarians using open source integrated library systems
Authors: Singh Vandana 
Published: October 2014

Purpose– This paper compares the technical support-related experiences with the expectations of librarians using open source Integrated Library Systems (ILS).Design/methodology/approach– A combination of surveys and triangulating interviews was conducted to obtain the results presented.Findings– The results of this study indicate that there are many channels of technical support available to librarians who use open source ILS. Also, these channels of technical support perform at acceptable levels according to the expectations of librarians using open source software.Research limitations/implications– The results presented in this study are self-reported expectations and experiences of librarians and not observed experiences.Practical implications– The results from this study will provide an insight to librarians contemplating adoption or migration to open source ILS. The results presented here will be useful in decision-making as well as developing a strategy for technical support based on the presented options.Originality/value– The interest in open source ILS has been observed and studied in the last decade, but the technical support of open source systems, which is a critical component of the adoption process, has not received much attention. This paper focuses specifically on the technical support for open source ILS and provides insight into the experiences of librarians.
Investigation of the volitional, non-volitional, emotional, motivational and automatic processes in determining golfers’ intention
Authors: Han Heesup , Hwang Jinsoo 
Published: October 2014

Purpose
– This study was designed with the aim to examine the formation of golfers’ intentions to play golf on traditional golf courses by considering the moderating impact of their outcome beliefs regarding the playing of screen golf. Other goals in this research were to test the mediating impact of desires and to identify the relative importance of study variables in generating intention within the proposed conceptual framework. The Model of Goal-directed Behavior (MGB) was utilized to make a precise prediction of golfers’ intentions.

Design/methodology/approach
– The dataset was developed by distributing surveys in person at screen-golf cafés. A structural equation modeling (SEM) was used to evaluate the fit of the proposed model and assess the hypothesized relationships. Tests for metric invariance were used to examine the moderating impact of outcome beliefs.

Findings
– Results from the SEM revealed that the proposed model predicted golfers’ intentions well, explaining significant amounts of variance. Desire acted as a significant mediator in the proposed conceptual framework. Compared to other study variables, both positive anticipated emotions and subjective norms had superior ability in generating golfers’ intentions to play real golf. Moreover, results from the test for metric invariance indicated that the intensity of golfers’ perceived benefits of playing screen golf affected their decision formation as a moderator, decreasing their intention to play real golf.

Originality/value
– Research considering the impact of screen golf on golfers’ decision-making processes is rare in the golf industry. Filling this gap, the present study successfully demonstrated that golfers’ decision formation is sufficiently explained by the MGB, and their perceived outcomes from playing screen golf represent a possible threat to the traditional golf industry.