bluuebunny/crossref_metadata_2025_split huggingface dataset:
The anisotropic network model web server at 2015 (ANM 2.0)
Authors: Eyal Eran , Lum Gengkon , Bahar Ivet 
Published: January 2015

Abstract
Summary: The anisotropic network model (ANM) is one of the simplest yet powerful tools for exploring protein dynamics. Its main utility is to predict and visualize the collective motions of large complexes and assemblies near their equilibrium structures. The ANM server, introduced by us in 2006 helped making this tool more accessible to non-sophisticated users. We now provide a new version (ANM 2.0), which allows inclusion of nucleic acids and ligands in the network model and thus enables the investigation of the collective motions of protein–DNA/RNA and –ligand systems. The new version offers the flexibility of defining the system nodes and the interaction types and cutoffs. It also includes extensive improvements in hardware, software and graphical interfaces.
Availability and implementation: ANM 2.0 is available at http://anm.csb.pitt.edu
Contact: eran.eyal@sheba.health.gov.il, eyal.eran@gmail.com
Selection of models for the analysis of risk-factor trees: leveraging biological knowledge to mine large sets of risk factors with application to microbiome data
Authors: Zhang Qunyuan , Abel Haley , Wells Alan , Lenzini Petra , Gomez Felicia , Province Michael A. , Templeton Alan A. , Weinstock George M. , Salzman Nita H. , Borecki Ingrid B. 
Published: January 2015

AbstractMotivation: Establishment of a statistical association between microbiome features and clinical outcomes is of growing interest because of the potential for yielding insights into biological mechanisms and pathogenesis. Extracting microbiome features that are relevant for a disease is challenging and existing variable selection methods are limited due to large number of risk factor variables from microbiome sequence data and their complex biological structure.Results: We propose a tree-based scanning method, Selection of Models for the Analysis of Risk factor Trees (referred to as SMART-scan), for identifying taxonomic groups that are associated with a disease or trait. SMART-scan is a model selection technique that uses a predefined taxonomy to organize the large pool of possible predictors into optimized groups, and hierarchically searches and determines variable groups for association test. We investigate the statistical properties of SMART-scan through simulations, in comparison to a regular single-variable analysis and three commonly-used variable selection methods, stepwise regression, least absolute shrinkage and selection operator (LASSO) and classification and regression tree (CART). When there are taxonomic group effects in the data, SMART-scan can significantly increase power by using bacterial taxonomic information to split large numbers of variables into groups. Through an application to microbiome data from a vervet monkey diet experiment, we demonstrate that SMART-scan can identify important phenotype-associated taxonomic features missed by single-variable analysis, stepwise regression, LASSO and CART.Availability and implementation: The SMART-scan approach is implemented in R and is available at https://dsgweb.wustl.edu/qunyuan/software/smartscan/Contact: qunyuan@wustl.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Clonality inference in multiple tumor samples using phylogeny
Authors: Malikic Salem , McPherson Andrew W. , Donmez Nilgun , Sahinalp Cenk S. 
Published: January 2015

Abstract
Motivation: Intra-tumor heterogeneity presents itself through the evolution of subclones during cancer progression. Although recent research suggests that this heterogeneity has clinical implications, in silico determination of the clonal subpopulations remains a challenge.
Results: We address this problem through a novel combinatorial method, named clonality inference in tumors using phylogeny (CITUP), that infers clonal populations and their frequencies while satisfying phylogenetic constraints and is able to exploit data from multiple samples. Using simulated datasets and deep sequencing data from two cancer studies, we show that CITUP predicts clonal frequencies and the underlying phylogeny with high accuracy.
Availability and implementation: CITUP is freely available at: http://sourceforge.net/projects/citup/.
Contact: cenk@sfu.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Top-down vs. bottom-up drivers of recruitment in a key marine invertebrate: investigating early life stages of snow crab
Authors: Émond Kim , Sainte-Marie Bernard , Galbraith Peter S. , Bêty Joël 
Published: January 2015

AbstractMany snow crab fisheries have fluctuated widely over time in a quasi-cyclic way due to highly variable recruitment. The causes of this variability are still debated. Bottom-up processes related to climate variability may strongly affect growth and survival during early life, whereas top-down predator effects may be a major source of juvenile mortality. Moreover, intrinsic density-dependent processes, which have received much less attention, are hypothetically responsible for the cycles in recruitment. This study explored how climate, larval production, intercohort cannibalism and groundfish predation may have affected recruitment of early juvenile snow crab in the northwest Gulf of St Lawrence (eastern Canada) over a period of 23 years. Abundance of early juvenile snow crabs (2.5–22.9 mm in carapace width), representing the first 3 years of benthic life, came from an annual trawl survey and was used to determine cohort strength. Analyses revealed a cyclic pattern in abundance of 0+ crabs that may arise from cohort resonant effects. This pattern consisted of three recruitment pulses but was reduced to two pulses by age 2+, while the interannual variability of cohort strength was dampened. This reconfiguration of the earliest recruitment pattern was dictated primarily by bottom water temperature and cannibalism, which progressively overruled the pre-settlement factors of larval production and surface water temperature that best explained abundance of 0+ crabs. The results strongly suggest that bottom-up and density-dependent processes prevail over top-down control in setting the long-term trends and higher-frequency oscillations of snow crab early recruitment patterns.
Invasive Treatments for Complex Regional Pain Syndrome in Children and Adolescents
Authors: Zernikow Boris , Wager Julia , Brehmer Hannah , Hirschfeld Gerrit , Maier Christoph 
Published: January 2015

AbstractAbstract
This review aimed to synthesize the current evidence on the effectiveness of invasive treatments for complex regional pain syndrome in children and adolescents. Studies on children and adolescents with complex regional pain syndrome that evaluated the effects of invasive treatment were identified in PubMed (search March 2013). Thirty-six studies met the inclusion criteria. Articles reported on a total of 173 children and adolescents with complex regional pain syndrome. Generally, many studies lack methodological quality. The invasive treatments applied most often were singular sympathetic blocks, followed by epidural catheters and continuous sympathetic blocks. Rarely, spinal cord stimulation and pain-directed surgeries were reported. An individual patient frequently received more than one invasive procedure. Concerning outcome, for approximately all patients, an improvement in pain and functional disability was reported. However, these outcomes were seldom assessed with validated tools. In conclusion, the evidence level for invasive therapies in the treatment of complex regional pain syndrome in children and adolescents is weak.
Invasive treatments applied most often in children and adolescents with Complex Regional Pain Syndrome are singular sympathetic blocks, epidural catheters, and continuous sympathetic blocks. However, the current evidence on the effectiveness of this treatment is weak.
Resource allocation and service design in local government: a case study
Authors: Alam Manzurul 
Published: January 2015

Purpose
– Following the introduction of the New Zealand Local Government Amendment Acts (1996, 2002), some significant changes have taken place in resource allocation and service design of local government organizations. The purpose of this paper is to investigate the effect of local government reforms on budgetary processes and service design in a New Zealand local government entity.

Design/methodology/approach
– The paper adopts a qualitative case study research involving semi-structured interviews with the key informants to understand the evolving role of resource allocation the study investigates the budgetary processes in a metropolitan city council.

Findings
– The traditional role of budget has changed to a more active and visible instrument in explaining the effectiveness and efficiency in the use and allocation of resources. Budgets have been given a central role in the management of local government finances. The reform process in New Zealand has enabled local government organizations to organize their activities by using the concepts of public and private goods.

Research limitations/implications
– This is a single local government entity case study. Any generalization of the conclusions from this study should undertaken with care even though there are similarities between New Zealand and other countries even though they operate under different institutional contexts in different countries.

Originality/value
– This paper makes important contribution by highlighting the implications of resource allocation on service design within New Zealand local government entities.
Outcomes of public health reform – service availability in rural areas
Authors: Immonen Mika , Vilko Jyri , Koivuniemi Jouni , Laasonen Kaisu 
Published: January 2015

Purpose– The purpose of this paper is to focus on the availability and demanded locations of health care services in a rural context. The authors analyse subjective experiences because mobility and other individual factors influence the availability of public services.Design/methodology/approach– Results from a mail survey in southeastern Finland are presented. Data collection was conducted using a random sample of 3,000 people from age 60 to 90 years. A total of 1,121 valid responses were received.Findings– The acceptable distance to service sites depends on learned behaviour where differences exist between suburban and rural residents. The authors found that service networks can be sparser in rural areas if the service sites are located in the daily activity space of the residents and travel burdens caused by distance and time are adequately solved. However, continuous downscaling of the provision may lead to the loss of health benefits which is harmful for individuals and expensive for society.Research limitations/implications– Further research should assess a broader variety of residential areas from the perspective of service availability. The results presented do not enable a direct comparison of the service availability between cities and sparsely populated rural areas.Originality/value– The paper contributes to the debate on access barriers to public service in rural regions. The question of availability of public services is topical because increasing overall demand requires urgent productivity improvements in public services. Currently this is solved by centralisation to search economies of scale.
Portfolio management of development projects in Danish municipalities
Authors: Stentoft Arlbjørn Jan , Freytag Per Vagn , Thoms Lisa 
Published: January 2015

Purpose– Danish municipalities are undergoing continuous changes. An important part of these changes are the introduction and implementation of a wide range of development projects. The purpose of this paper is to focus on the challenges of initiation and implementation of development projects in municipalities.Design/methodology/approach– The focus is on development projects, which are defined as projects undertaken to improve the workflow and processes of administrative functions in municipalities. The empirical component is based on two pilot interviews in two municipalities and a quantitative questionnaire distributed to all Danish municipalities.Findings– Extant literature contains limited contributions regarding the overall management of development projects in municipalities. There seems to be an awareness of the importance of developing working procedures to ensure greater efficiency in Danish municipalities, but this development is often not prioritised relative to operational tasks. The absence of prioritisation is an indication of the potential for improving the portfolio management of development projects.Research limitations/implications– The response to the quantitative questionnaire is provided by one employee in a municipality. As such, the research may reveal the views of one individual in particular and not those of the municipality in general.Practical implications– The paper provides empirical evidence of the ambidextrous challenges in the context of public sector management. At a more generic level, the paper highlights the importance of improving portfolio management of development projects.Originality/value– This paper is the first that one to focus on the orchestration of development projects in the public sector (here analysed through Danish municipalities). Management and control of such projects is much more sensitive to political decision processes than are similar tasks in the private sector.
Antecedents to local store loyalty: influence of culture, cosmopolitanism and price
Authors: Pandey Shivendra , Khare Arpita , Bhardwaj Preshth 
Published: January 2015

Purpose
– Cosmopolitanism is on the rise in India and traditionally shoppers have been known to patronize local stores. There is a need therefore to see the effect of cosmopolitanism and culture in context of loyalty towards local stores. Grocery items constitute major portion of purchase from local stores, therefore, pricing was also considered as a variable affecting store loyalty. The paper aims to discuss this issue.

Design/methodology/approach
– The paper used conclusive approach using a structured questionnaire for survey. The sample consisted of 710 respondents. There was almost an equal representation of both genders and also of metropolitan and non-metropolitan consumers.

Findings
– Culture and price affected local store loyalty directly. Cosmopolitanism was not found to have direct effect on loyalty. Within cultural dimensions, masculinity emerged as the most dominating trait. Minor modifications in cultural scale and major modifications in local store loyalty and cosmopolitanism are also suggested.

Research limitations/implications
– The study focuses only on three factors: price, culture, and cosmopolitanism. It does not examine influence of variables like personal values, lifestyle, and personality on local store loyalty behaviour. The research did not examine relationship between nature and type of product purchase decisions and its impact on store choice.

Practical implications
– Local stores need not be unduly worried with the incoming of organized players. The organized players should try to be cheaper and learn some tactics of local stores like customization, etc. There is a case for allowing FDI in multi-brand retail.

Originality/value
– Cosmopolitanism not affecting the local store loyalty directly is the original contribution of the paper. The finding casts doubts on the growth strategy of organized retailers who are opening new stores with the thinking that cosmopolitan consumer will shop from them instead of local retailers.
Impact of organizational justice on job performance in libraries
Authors: Shan Sidra , Ishaq Hafiz Muhammad , Shaheen Maqsood Ahmad 
Published: January 2015

Purpose– The purpose of this paper is to examine the mediating role of leader-member exchange in the relationship between organizational justice and job performance. The study primarily focused on the perception of university libraries personnel regarding organizational justice practices and the quality of their relationship with their supervisors and how such perceptions predict their job performance.Design/methodology/approach– This study tested a sample of 15 university libraries of Islamabad, Pakistan. Data were accumulated through questionnaire and analyzed on SPSS. Descriptive and correlation analysis showed the positive and significant relationship between all variables. Series of separate hierarchical regression analysis were used to test the hypothesis.Findings– The result revealed that all three kinds of organizational justices (distributive justice, procedural justice and interactional justice) predict the job performance but interactional justice along with leader-member exchange impacts more strongly on job performance.Research limitations/implications– The result of this study will assist the library leadership to foster a greater sense of employee worth and teamwork among staff members by implementing organizational justice practices. The study would also enhance the interest of Pakistani Library Information Science professionals and researchers toward behavioral aspects of library administration. Limitation: The results of this study may not be generalized to all universities and other industries of Pakistan as data is collected only from 15 universities of Pakistan. Second, interpretations of results are limited by the cross-sectional design of study and does not allow casual conclusion.Originality/value– According to researcher knowledge very few studies have been conducted on the management side of libraries in Pakistan. This paper is the first study in Pakistan Librarianship that examines the linkage between organizational justice, leader-member exchange and job performance.
A conceptual model of Open Access Institutional Repository in Indonesia academic libraries
Authors: Farida Ida , Tjakraatmadja Jann Hidajat , Firman Aries , Basuki Sulistyo 
Published: January 2015

Purpose
– The purpose of this paper is to attempt to build a conceptual model of Open Access Institutional Repositories (OAIR) in Indonesia academic libraries, viewed from knowledge management (KM) perspective.

Design/methodology/approach
– Literature-based conceptual analysis of previous studies related to open access, institutional repositories viewed from KM perpective.

Findings
– The conceptual model of OAIR emphasizes three variables – people collaboration, process, and technology functions. These variables, with their many elements, are integrated together in order to help the university or Higher Education (HE) institution in capturing its own scholarship produced as a whole. Besides, that integration aims at facilitating knowledge sharing so as to enrich knowledge content and to enhance global access. A process chart of OAIR based on the conceptual model is built to illustrate knowledge content recruitment in Indonesia academic libraries.

Research limitations/implications
– The conceptual model proposed in this paper is not yet formally tested. It needs more research to understand the Indonesian context of OAIR to build a more accurate model, based on the experiences in developing and implementing OAIR in Indonesia HE institutions.

Originality/value
– Many academic libraries in Indonesia develop OAIR to increase the visibility of the scholarship of the parent HE institution. It is significant to view the practice of OAIR in academic library from the KM perspective. KM implementation is almost unheard of in Indonesia universities. However, The OAIR phenomenon in Indonesia academic libraries can be viewed as a KM initiative.
Identifying values of special library professionals of India with reference to the JOCLAI Code of Ethics
Authors: Dutta Nandini 
Published: January 2015

Purpose– The purpose of this paper is to identify a shared set of professional values relevant to the special library professionals of India. This paper deals only with the process of compilation of a master list of relevant values which is a prerequisite for a survey to study preferences of values of the community of library professionals.Design/methodology/approach– Review of literature, both Indian and international, and content analysis were undertaken to develop a set of common professional values relevant to the Indian special library professionals. Findings of empirical studies on core values and statements of core values of library associations provided the basis for identifying the values.Findings– The final shortlisted 16 common core values relevant to the Indian special library professionals include: accountability, collaboration, confidentiality, copyright, cultural diversity, diversity of opinion, equality of access, information literacy, innovation, integrity, intellectual freedom, leadership, literacy, preservation of the record, professional neutrality and service. This master list of values has been derived from the merger of the lists of values derived from JOCLAI Code of Ethics and Koehleret al.’s list along with SLA’s statement of core values. This list can be also used with some modifications for study of preferences of core values of all sections of the Indian library professionals.Originality/value– This paper is about an original initiative undertaken to develop a set of core values relevant to both the special library professionals and the Indian library professionals in general.
Collection development and management within public libraries in Delhi
Authors: Kaur Prabhjeet , Walia Paramjeet Kaur 
Published: January 2015

Purpose
– The purpose of this paper is to find out about the collection development and management in the public libraries governed by the government or its agencies in Delhi and compare them with the international standards for public libraries.

Design/methodology/approach
– In all, Delhi has three chains of public libraries namely Delhi Public Library (DPL), like Hardayal Municipal Public Library (HMPL) and New Delhi Municipal Council (NDMC) public libraries. The librarian/heads of selected branches were approached with a structured questionnaire aimed at collecting information on the collection development and managements in these libraries and selected branches. The data were then analysed and interpreted.

Findings
– It was found that with the advent of ICT and its impact on the society, it is evident that the public libraries are not making the desired effort to reach out to the public and make it more appealing to the users. The main problem with the library remains to be the lack of membership. A few initiatives have been taken, but still there were not many digital services being provided by these public libraries in the present day digital environment.

Research limitations/implications
– The study was limited to the public libraries within the physical region of Delhi only.

Practical implications
– The evaluation sheds light on the existing scenario of public libraries in Delhi and may contribute in their future development.

Social implications
– With the acceptance of the international standards as suggested in the study, the public libraries in Delhi would be better able to provide information resources and services to the masses. The better learned masses make the society more advanced. An information rich society would thus lead to an overall growth and development of the state.

Originality/value
– There have been many studies in the past on DPL but none have intended to cover other public libraries chains like HMPL and NDMC public libraries which are governed by the government or its agencies and are established with aim of imparting information to the population of Delhi. Also, a similar the comparison with international standards was never done earlier.