bluuebunny/crossref_metadata_2025_split huggingface dataset:
A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data
Authors: Yang Zi , Michailidis George 
Published: September 2015

Abstract
Motivation: Recent advances in high-throughput omics technologies have enabled biomedical researchers to collect large-scale genomic data. As a consequence, there has been growing interest in developing methods to integrate such data to obtain deeper insights regarding the underlying biological system. A key challenge for integrative studies is the heterogeneity present in the different omics data sources, which makes it difficult to discern the coordinated signal of interest from source-specific noise or extraneous effects.
Results: We introduce a novel method of multi-modal data analysis that is designed for heterogeneous data based on non-negative matrix factorization. We provide an algorithm for jointly decomposing the data matrices involved that also includes a sparsity option for high-dimensional settings. The performance of the proposed method is evaluated on synthetic data and on real DNA methylation, gene expression and miRNA expression data from ovarian cancer samples obtained from The Cancer Genome Atlas. The results show the presence of common modules across patient samples linked to cancer-related pathways, as well as previously established ovarian cancer subtypes.
Availability and implementation: The source code repository is publicly available at https://github.com/yangzi4/iNMF.
Contact: gmichail@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Psychosocial and Functional Outcomes in Youth With Chronic Sickle Cell Pain
Authors: Sil Soumitri , Cohen Lindsey L. , Dampier Carlton 
Published: September 2015

Objective:
To describe chronic pain—pain that is present most days per month over the past 3 months—in youth with sickle cell disease (SCD). This study characterized differences in functional outcomes, psychosocial characteristics, and health care utilization for youth with SCD across 3 groups based on pain frequency: chronic pain, episodic pain, and no SCD pain in the past month.

Materials and Methods:
Children and adolescents (aged 8 to 18 y) with SCD and their parents (n=100) completed measures of functional disability, health-related quality of life, depressive symptoms, pain catastrophizing, pain beliefs, and health care utilization during an outpatient comprehensive sickle cell clinic appointment. On the basis of pain frequency and duration, patients were categorized as follows: (1) chronic (≥3 d of pain per week in the past month lasting ≥3 mo; range, 12 to 31 d/mo), (2) episodic (<3 d of pain per week for the past month; range, 1 to 10 d/mo), and (3) no SCD pain in the past month.

Results:
Consistent with other pediatric chronic pain conditions, youth characterized as having chronic sickle pain (n=40) reported significantly greater functional disability, depressive symptoms, and inpatient admissions for pain relative to patients characterized with having episodic SCD pain (n=40) or no SCD pain (n=20). The chronic and episodic pain groups had comparable levels of pain intensity, pain catastrophizing, and quality of life.

Discussion:
Specific definitions and criteria for chronic sickle pain in youth are needed. Identifying risk and protective factors related to the transition from acute to chronic pain is important to facilitate improved psychosocial functioning.
Characterization of Migraineurs Having Allodynia
Authors: Baykan Betul , Ekizoglu Esme , Karli Necdet , Kocasoy-Orhan Elif , Zarifoglu Mehmet , Saip Sabahattin , Siva Aksel , Ertas Mustafa 
Published: September 2015

Objective:
Allodynia reflects the clinical correlate of central sensitization, but it is usually neglected in clinical headache management. We aimed to report the prevalence and previously unnoticed associations of allodynia in migraineurs by a nationwide face-to-face questionnaire-based study by physicians.

Methods:
A total of 5323 households were examined for headache according to the diagnostic criteria of International Classification of Headache Disorders-II. Detailed headache features, premonitory signs, demographics, socio-economic status, and hormonal status of female individuals were analyzed with regard to the presence of allodynia in patients with definite migraine.

Results:
Allodynia was present in 61.1% of migraineurs in the general population of Turkey. The duration and severity of attacks (P<0.0001), photophobia (P=0.001), phonophobia, and also osmophobia (P<0.0001), as well as premonitory signs (P=0.018), showed significant associations with allodynia. Migraineurs with aura or family history of migraine more often reported allodynia in comparison with those without (P=0.001 and 0.028, respectively). Allodynic migraineurs had a higher rate of physician consults and high levels on the Migraine Disability Assessment questionnaire, reflecting increased burden of headache. Furthermore, migraineurs with allodynia had high probability of attacks close to menses. Migraine improved during pregnancy, but it worsened after menopause or during oral contraceptive use in individuals experiencing allodynia when compared with those without allodynia.

Discussion:
The duration, severity, and disability of migraine attacks, photophobia, phonophobia, and osmophobia, as well as premonitory signs, showed significant associations with allodynia in the general population. Moreover, migraineurs with aura or family history of migraine more often reported allodynia, and allodynic migraneurs were more sensitive to hormonal changes. Allodynia, which seems to indicate higher tendency to central sensitization, should be implemented in daily headache practice to predict the prognosis and high levels of migraineous involvement.
Spiritual Well-being May Reduce the Negative Impacts of Cancer Symptoms on the Quality of Life and the Desire for Hastened Death in Terminally Ill Cancer Patients
Authors: Wang Yin-Chih , Lin Chia-Chin 
Published: September 2015

Background:
Spirituality is a central component of the well-being of terminally ill cancer patients.

Objective:
The aim of this study was to examine the mediating or moderating role of spiritual well-being in reducing the impact of cancer-related symptoms on quality of life and the desire for hastened death in terminally ill cancer patients.

Methods:
Eighty-five terminally ill cancer patients were assessed using the Taiwanese version of the M. D. Anderson Symptom Inventory, the Functional Assessment of Cancer Therapy–General, the Functional Assessment of Chronic Illness Therapy–Spiritual Well-being, the Beck Hopelessness Scale, and the Schedule of Attitudes Toward Hastened Death.

Results:
Spiritual well-being was significantly negatively correlated with symptom severity (r = −0.46, P < .01). Symptom severity negatively correlated with quality of life (r = −0.54) and positively correlated with hopelessness (r = 0.51, P < .01) and the desire for hastened death (r = 0.61, P < .01). Spiritual well-being was a partial mediator and moderator between symptom severity and quality of life. Spiritual well-being was a partial mediator between symptom severity and the desire for hastened death. The meaning subscale of spiritual well-being was a more significant predictor of the desire for hastened death and quality of life than the faith subscale was.

Conclusion:
Spiritual well-being may reduce the negative impacts of cancer on quality of life and the desire for hastened death.

Implications for Practice:
Appropriate spiritual care may reduce the negative impact of severe cancer symptoms on quality of life and the desire for hastened death in terminally ill cancer patients.
Non-null Effects of the Null Range in Biogeographic Models: Exploring Parameter Estimation in the DEC Model
Authors: Massana Kathryn A. , Beaulieu Jeremy M. , Matzke Nicholas J. , O’Meara Brian C. 
Published: September 2015

AbstractHistorical biogeography seeks to understand the distribution of biodiversity in space and time. The dispersal-extinction-cladogenesis (DEC) model, a likelihood-based model of geographic range evolution, is widely used in assessing the biogeography of clades. Robust inference of dispersal and local extinction parameters is crucial for biogeographic inference, and yet a major caveat to its use is that the DEC model severely underestimates local extinction. We suggest that this is mainly due to the way in which the model is constructed to allow observed species to transition into being present in no areas (i.e., null range). By prohibiting transitions into the null range in the transition rate matrix, we were able to better infer local extinction and support this with simulations. This modified model, DEC*, has higher model fit and model adequacy than DEC, suggesting this modification should be considered for DEC and other models of geographic range evolution.
Single-cell phenotyping of human induced pluripotent stem cells by high-throughput imaging
Authors: Christian Volz H. , Heigwer Florian , Wüest Tatjana , Galach Marta , Utikal Jochen , Katus Hugo A. , Boutros Michael 
Published: September 2015

AbstractSingle-cell phenotyping promises to yield insights into biological responses in heterogeneous cell populations. We developed a method based on single-cell analysis to phenotype human induced pluripotent stem cells (hIPSC) by high-throughput imaging. Our method uses markers for morphology and pluripotency as well as social features to characterize perturbations using a meta-phenotype based on mapping single cells to distinct phenotypic classes. Analysis of perturbations on a single cell level enhances the applicability of human induced pluripotent stem cells (hIPSC) for screening experiments taking the inherently increased phenotypic variability of these cells into account. We adapted miniaturized culture conditions to allow for the utilization of hIPSC in RNA interference (RNAi) high-throughput screens and single cell phenotyping by image analysis. We identified key regulators of pluripotency in hIPSC masked in a population-averaged analysis and we confirmed several candidate genes (SMG1,TAF1) and assessed their effect on pluripotency.
Construction of the third generation Zea mays haplotype map
Authors: Bukowski Robert , Guo Xiaosen , Lu Yanli , Zou Cheng , He Bing , Rong Zhengqin , Wang Bo , Xu Dawen , Yang Bicheng , Xie Chuanxiao , Fan Longjiang , Gao Shibin , Xu Xun , Zhang Gengyun , Li Yingrui , Jiao Yinping , Doebley John , Ross-Ibarra Jeffrey , Buffalo Vince , Romay M. Cinta , Buckler Edward S. , Xu Yunbi , Lai Jinsheng , Ware Doreen , Sun Qi 
Published: September 2015

ABSTRACTBackgroundCharacterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole genome sequencing data from 1,218 maize lines, covering pre-domestication and domesticated Zea mays varieties across the world.ResultsA new computational pipeline was set up to process over 12 trillion bp of sequencing data, and a set of population genetics filters were applied to identify over 83 million variant sites.ConclusionsWe identified polymorphisms in regions where collinearity is largely preserved in the maize species. However, the fact that the B73 genome used as the reference only represents a fraction of all haplotypes is still an important limiting factor.
Minding the Gap: eBook package purchasing
Authors: Kerby Erin E. , Trei Kelli 
Published: September 2015

Purpose– This study aims to highlight practical considerations to be made when choosing an eBook package for an institution. Many academic libraries purchase eBooks bundled in packages, either as a time- or cost-saving measure or to build a new subject collection.Design/methodology/approach– The authors searched the Web sites of six major publishers for information on eBook packages, including subject coverage, digital rights management restrictions and usage allowances. The analysis also includes a potential overlap between related subject collections and the ability to purchase titles individually.Findings– Usage allowances, digital rights management restrictions and purchasing options vary considerably from publisher to publisher. There was title overlap between related subject packages found in some publishers. In response to user preferences and needs, many publishers are loosening restrictions on their eBook content, which make purchasing packages a more attractive option for libraries.Originality/value– The landscape of eBook publishing is rapidly changing, which can complicate purchasing decisions. The detailed comparison provided by this study can be used to assist collections developers in making purchasing decisions best suited to their library and avoiding pitfalls such as duplicate purchases.
Build it and they will come: integrating unique collections and undergraduate research
Authors: Cook Matthew 
Published: September 2015

Purpose
– The “build it and they will come approach” is a largely accepted proposition in the library community, particularly in the area of special collections. There is, at times, little critical analysis given to collection development, digitization efforts or information literacy instruction in regard to how these hard-to-serve but research-rich materials might be used in the classroom. Instead, there exists a benevolent know-it-all expert determining which collections warrant preservation, digitization, acquisition and, ultimately, attention. At California State University (CSU) Channel Islands (CI), the user – teachers and students – is the focus of all special collection activities, and we have devised innovative ways to both encourage students and faculty to engage these materials as well as foster their appreciation, awareness and use on campus.

Design/methodology/approach
– This paper explores three ways that librarians at the John Spoor Broome Library encourage and facilitate the use of primary documents housed in unique collections to support undergraduate student research.

Findings
– The use of high-impact teaching practices, like undergraduate research, is an important tool in promoting retention and increasing graduation rates, particularly for underrepresented minorities. At CSU CI and the John Spoor Broome Library, engaging students with primary documents is a focus of unique collections work that benefits both students and the Library alike.

Originality/value
– Digitization is a key component of most special collections work in the library world today, but perhaps efforts focused on promoting use are lacking. At CI, use is the primary focus of all unique collections work and, thus, could be a model for other libraries and archive departments.
Usability evaluation of an academic library website
Authors: Pant Ankur 
Published: September 2015

Purpose
– The paper aims to evaluate the usability of the website of Central Science Library (CSL), University of Delhi. Multi-method approach of evaluation is used with the use of standard checklist and questionnaire survey of representative users. Besides, the information architecture of the website under study is analysed in this paper.

Design/methodology/approach
– Based on the literature review and the author’s experience, a usability assessment tool for library websites was developed by Pant (2013). It comprises standard checklist and questionnaire for users’ survey. In the present study, this framework was used to assess the usability of CSL website. The questionnaire survey of 35 representative users was conducted through random sampling. The results of both methods (standard checklist and questionnaire survey) were analysed for evaluating the website usability.

Findings
– Need for improvement of the website was realised in terms of efficiency, effectiveness and learnability for better usability. Notice board, site search facility, list of services, FAQs and user guides were the most sought after features among others as per the analysis of the questionnaire survey. Besides, the need to enhance the visual appeal of the website was felt. However, information resources provided through the CSL website were found useful for users.

Originality/value
– The paper presents an innovative multi-method approach of website usability assessment while considering six usability attributes: Usefulness, Efficiency, Effectiveness, Learnability, Satisfaction and Accessibility. The approach adopted in this paper is cost effective in comparison to formal usability tests and heuristic evaluation. Therefore, this framework is suitable for libraries having limited budget to ensure the user-centred library website with maximum usability. This paper encourages other libraries to conduct similar website usability evaluation to identify the usability problem areas and users’ perception for their respective website.
Use of e-journals by the scientists of CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi, India
Authors: Qasim Jamal , Khan Abdul Mannan 
Published: September 2015

Purpose
– The purpose of this paper is to analyze the use of electronic journals (e-journals) by the scientists of Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB) – a center of excellence in the field of genomics and integrative biology situated in Delhi, India.

Design/methodology/approach
– The paper is based on the results of a well-structured questionnaire administered to all the scientists of the institute for the purpose of data collection.

Findings
– The main findings are that the scientists are more attracted toward e-journals specially on those provided by CSIR-NISCAIR Consortia, NKRC than those available via direct subscription. From this survey, the investigator has been able to find out that almost all the scientists are consulting e-journals from their campus cabin, not only for research purposes but also to update their own knowledge. The infrastructure to use e-journals are superb and there is no technological problem specially hardware and software support with high bandwidth of Internet speed exists here, as CSIR-IGIB uses largest computing facility (four Tflop/s) in Asia outside Japan (ranked 158th among the World’s Top 500 Super Computers). Respondents also identified that there is dire need for training in using e-resources and retrieving pinpointed information from the databases.

Research limitations/implications
– The present paper consists only of scientists and the geographical area is restricted to CSIR-IGIB, Delhi. The scope of the paper can be extended to additional CSIR libraries. A comparative study can also be made among some biological research libraries of CSIR Institutes.

Originality/value
– There are a number of studies on the use of e-journals by CSIR scientists, but this is the first of its kind which covers scientists of IGIB that has the largest computing facility (four Tflop/s) in Asia outside Japan. As such, it should pave the way for research and lead a model role for other CSIR Institutes as well as elsewhere.
Using a digital library instead of a traditional database
Authors: Trachtengerts Michael , Erkimbaev Adilbek , Zitserman Vladimir , Kobzev Georgii 
Published: September 2015

Purpose
– The purpose of this paper is to reveal main advantages of digital libraries in comparison with technology of common database for data-oriented fields of modern science. As an example, the subject domain “nanomaterials and nanotechnologies” with new features due to evolution of concepts and objects is presented.

Design/methodology/approach
– An analysis of the information system ABCD as a basis for science-oriented digital library was fulfilled. Also, a survey of peculiarities of data in fast developing fields of science was prepared.

Findings
– The results of this paper showed that functional capacities of ABCD satisfy requirements for complex collections and archives of scientific documents. Based on the ABCD tools and this concept, the digital library for storage and systematization of data and documents on nanomaterials and nanotechnologies for the power engineering was constructed. The library combines opportunities of bibliographic, full text and factual information systems.

Originality/value
– This paper gives the foundation for creation of a library that combines services of bibliographic, full text and factual (numerical) information systems. Some analyses of ABCD tools were made before elsewhere, but they did not point on data peculiarities of complexly organized domains: semi-structured data, multitude formats (text, image and tables), interconnection of content with external sources located on other servers or in the Web.
Cross-functional executive involvement and worker involvement in lean manufacturing and sustainability alignment
Authors: Longoni Annachiara , Cagliano Raffaella 
Published: September 2015

Purpose– Lean manufacturing has been demonstrated to increase operations and economic performance, but its alignment with environmental and social sustainability is unclear. The purpose of this paper is to understand how cross-functional executive involvement and worker involvement, in the formulation and implementation of the operations strategy, support the strategic alignment of lean manufacturing and sustainability.Design/methodology/approach– An inductive case study methodology was employed. Such theoretical elaboration is appropriate when extending existing theory (i.e. operations strategy theory and sustainability development theory). Evidence was drawn from ten cross-industry case studies. Within and cross-case analyses were performed.Findings– The results demonstrate that cross-functional executive involvement and worker involvement positively affect the strategic alignment of the lean manufacturing statement and bundles (just-in-time, total quality management, total preventive maintenance, and human resources management) with environmental and social goals and practices. Specifically, the study reveals the impact of cross-functional executive involvement on the formulation of lean manufacturing aligned with environmental and social sustainability. Worker involvement positively affects the actual implementation of lean manufacturing aligned with environmental and social sustainability.Practical implications– This research provides guidance to practitioners regarding how different organizational models lead to different levels of lean manufacturing and sustainability strategic alignment and performance.Originality/value– This research contributes to the operations strategy literature and the sustainability development literature, providing evidence regarding the mechanisms supporting the strategic alignment of lean manufacturing and social and environmental sustainability.