bluuebunny/crossref_metadata_2025_split huggingface dataset:
AFNI and Clustering: False Positive Rates Redux
Authors: Cox Robert W , Reynolds Richard C , Taylor Paul A 
Published: July 2016

AbstractIn response to reports of inflated false positive rate (FPR) in FMRI group analysis tools, a series of replications, investigations, and software modifications were made to address this issue. While these investigations continue, significant progress has been made to adapt AFNI to fix such problems. Two separate lines of changes have been made. First, a long-tailed model for the spatial correlation of the FMRI noise characterized by autocorrelation function (ACF) was developed and implemented into the 3dClustSim tool for determining the cluster-size threshold to use for a given voxel-wise threshold. Second, the 3dttest++ program was modified to do randomization of the voxel-wise t-tests and then to feed those randomizedt-statistic maps into 3dClustSim directly for cluster-size threshold determination-without any spatial model for the ACF. These approaches were tested with the Beijing subset of the FCON-1000 data collection. The first approach shows markedly improved (reduced) FPR, but in many cases is still above the nominal 5%. The second approach shows FPRs clustered tightly about 5% across all per-voxelp-value thresholds ≤ 0.01. Ift-tests from a univariate GLM are adequate for the group analysis in question, the second approach is what the AFNI group currently recommends for thresholding. If more complex per-voxel statistical analyses are required (where permutation/randomization is impracticable), then our current recommendation is to use the new ACF modeling approach coupled with a per-voxelp-threshold of 0.001 or below. Simulations were also repeated with the now infamously “buggy” version of 3dClustSim: the effect of the bug on FPRs was minimal (of order a few percent).
Massively parallel digital transcriptional profiling of single cells
Authors: Zheng Grace X.Y. , Terry Jessica M. , Belgrader Phillip , Ryvkin Paul , Bent Zachary W. , Wilson Ryan , Ziraldo Solongo B. , Wheeler Tobias D. , McDermott Geoff P. , Zhu Junjie , Gregory Mark T. , Shuga Joe , Montesclaros Luz , Masquelier Donald A. , Nishimura Stefanie Y. , Schnall-Levin Michael , Wyatt Paul W , Hindson Christopher M. , Bharadwaj Rajiv , Wong Alexander , Ness Kevin D. , Beppu Lan W. , Deeg H. Joachim , McFarland Christopher , Loeb Keith R. , Valente William J. , Ericson Nolan G. , Stevens Emily A. , Radich Jerald P. , Mikkelsen Tarjei S. , Hindson Benjamin J. , Bielas Jason H. 
Published: July 2016

ABSTRACTCharacterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of up to tens of thousands of single cells per sample. Cell encapsulation in droplets takes place in ∼6 minutes, with ∼50% cell capture efficiency, up to 8 samples at a time. The speed and efficiency allow the processing of precious samples while minimizing stress to cells. To demonstrate the system′s technical performance and its applications, we collected transcriptome data from ∼¼ million single cells across 29 samples. First, we validate the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. Then, we profile 68k peripheral blood mononuclear cells (PBMCs) to demonstrate the system′s ability to characterize large immune populations. Finally, we use sequence variation in the transcriptome data to determine host and donor chimerism at single cell resolution in bone marrow mononuclear cells (BMMCs) of transplant patients. This analysis enables characterization of the complex interplay between donor and host cells and monitoring of treatment response. This high-throughput system is robust and enables characterization of diverse biological systems with single cell mRNA analysis.
A Novel Family of Genomics Islands Across Multiple Species ofStreptococcus
Authors: Wang Jing , Wang Changjun , Feng Weizhong , Feng Youjun , Zhi Liming , Li Wenjuan , Yao Yi , Jiang Shibo , Tang Jiaqi 
Published: July 2016

AbstractThe genusStreptococcusis one of the most genomically diverse and important human and agricultural pathogens. The acquisition of genomic islands (GIs) plays a central role in adaptation to new hosts in the genus pathogens. The research presented here employs a comparative genomics approach to define a novel family of GIs in the genusStreptococcuswhich also appears across strains of the same species. Specifically, we identified 9Streptococcusgenomes out of 67 sequenced genomes analyzed, and we termed these as 15bpStreptococcusgenomic islands, or 15SGIs, including i) insertion adjacent to the 3’ end of ribosomel7/l12gene, ii) large inserts of horizontally acquired DNA, and iii) the presence of mobility genes (integrase) and replication initiators. We have identified a novel family of 15SGIs and seems to be important in species differentiation and adaptation to new hosts. It plays an important role during strain evolution in the genusStreptococcus.
The role of brain oscillations in predicting the sensory consequences of your actions
Authors: Cao Liyu , Thut Gregor , Gross Joachim 
Published: July 2016

AbstractBeing able to predict self-generated sensory consequences is an important feature of normal brain functioning. In the auditory domain, self-generated sounds lead to smaller brain responses compared to externally generated sounds. Here we investigated the role of brain oscillations underlying this effect. With magnetoencephalography, we show that self-generated sounds are associated with increased pre-stimulus alpha power and decreased post-stimulus gamma power and alpha/beta phase locking in auditory cortex. All these oscillatory changes are correlated with changes in evoked responses. Furthermore, they correlate with each other across participants, supporting the idea that they constitute a neural information processing sequence for self-generated sounds, with pre-stimulus alpha power representing prediction and post-stimulus gamma power representing prediction error, which is further processed with post-stimulus alpha/beta phase resetting. Additional cross-trial analysis provides further support for the proposed sequence that might reflect a general mechanism for the prediction of self-generated sensory input.
Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells
Authors: Wirbel Jakob , Cutillas Pedro , Saez-Rodriguez Julio 
Published: July 2016

AbstractCellular signaling, predominantly mediated by phosphorylation through protein kinases, is found to be deregulated in most cancers. Accordingly, protein kinases have been subject to intense investigations in cancer research, to understand their role in oncogenesis and to discover new therapeutic targets. Despite great advances, an understanding of kinase dysfunctioning in cancer is far from complete.A powerful tool to investigate phosphorylation is mass-spectrometry (MS)-based phosphoproteomics, which enables the identification of thousands of phosphorylated peptides in a single experiment. Since every phosphorylation event results from the activity of a protein kinase, high-coverage phosphoproteomics data should indirectly contain comprehensive information about the activity of protein kinases.In this chapter, we discuss the use of computational methods to predict kinase activity scores from MS-based phosphoproteomics data. We start with a short explanation of the fundamental features of the phosphoproteomics data acquisition process from the perspective of the computational analysis. Next, we briefly review the existing databases with experimentally verified kinase-substrate relationships and present a set of bioinformatic tools to discover novel kinase targets. We then introduce different methods to infer kinase activities from phosphoproteomics data and these kinase-substrate relationships. We illustrate their application with a detailed protocol of one of the methods, KSEA (Kinase Substrate Enrichment Analysis). This method is implemented in Python within the framework of the open-source Kinase Activity Toolbox (kinact), which is freely available athttp://github.com/saezlab/kinact/.
Meta-analysis reveals taxon- and life stage-dependent effects of ocean acidification on marine calcifier feeding performance
Authors: Clements Jeff C. 
Published: July 2016

AbstractWhile ocean acidification is considered among the greatest threats to marine ecosystems, its effects on the feeding performance of marine calcifiers remain uncertain. I conducted a meta-analysis of effect sizes (LnRR) assessing the impacts of acidification on the feeding ability of three groups of marine calcifiers - molluscs, arthropods, and echinoderms. Results suggested taxon-dependent effects of acidification on calcifier feeding performance, with depressed feeding observed for molluscs, echinoderms, and when all taxa were considered. However, ocean acidification had no effect on feeding performance in marine arthropods and larval feeding performance appeared more vulnerable than that of juveniles and adults. Feeding performance was not related to acclimation time norpCO2level. This study suggests that the feeding performance of molluscs and early life-stage echinoderms may be depressed in a more acidic ocean, but that arthropod feeding performance is unlikely to suffer. Such changes in feeding performance could contribute to slower growth and development in the early life stages of these organisms and could potentially contribute to changes in community and ecosystem structure where these organisms coexist. Finally, feeding performance could, at least in part, moderate the degree to which molluscs and echinoderms can use food to overcome acidification effects early in life.
Crystal structure of the antigen-binding fragment of a monoclonal antibody specific for the multidrug-resistance-linked ABC transporter human P-glycoprotein
Authors: Esser Lothar , Shukla Suneet , Zhou Fei , Ambudkar Suresh V. , Xia Di 
Published: July 2016

P-glycoprotein (P-gp) is a polyspecific ATP-dependent transporter linked to multidrug resistance in cancers that plays important roles in the pharmacokinetics of a large number of drugs. The drug-resistance phenotype of P-gp can be modulated by the monoclonal antibody UIC2, which specifically recognizes human P-gp in a conformation-dependent manner. Here, the purification, sequence determination and high-resolution structure of the Fab fragment of UIC2 (UIC2/Fab) are reported. Purified UIC2/Fab binds human P-gp with a 1:1 stoichiometry. Crystals of UIC2/Fab are triclinic (space groupP1), with unit-cell parametersa= 40.67,b= 44.91,c= 58.09 Å, α = 97.62, β = 99.10, γ = 94.09°, and diffracted X-rays to 1.6 Å resolution. The structure was determined by molecular replacement and refined to 1.65 Å resolution. The asymmetric unit contains one molecule of UIC2/Fab, which exhibits a positively charged antigen-binding surface, suggesting that it might recognize an oppositely charged extracellular epitope of P-gp.
Investigating current paradigms in supply chain risk management – a bibliometric study
Authors: Kilubi Irene 
Published: July 2016

Purpose– The purpose of this paper is to analyse the intellectual structure and research fronts of discipline of supply chain risk management (SCRM), in order to identify the knowledge groups in the research area to date, as well as to reveal any relationships between these subfields and the central influential trends.Design/methodology/approach– By means of a bibliometric study, the 32 most co-cited articles on SCRM published in 16 top business-related academic journals are analysed using multivariate statistical techniques, i.e. multi-dimensional scaling, cluster analysis and correspondence factor analysis.Findings– The results demonstrate a clearly identifiable structure as a result of the performed co-citation analysis. The conducted cluster analysis and factor bring forward that the research field is arranged in five different areas of interest: explaining supply chain (SC) risk phenomena, concepts, frameworks and insights of SCRM; modelling risks for SCs; inventory risks affecting supply efficiency; SC and product design methods; and SC risk mitigating strategies.Originality/value– Overall, the intellectual structure of SCRM is first examined through a bibliometric approach using quantitative techniques – for improved understanding of its origins, and to identify the state of the science – and to offer suggestions for future studies that could cover current gaps. This study represents the potential to advance the SCRM literature landscape.
A method for evaluating business models implementation process
Authors: Batocchio Antonio , Ghezzi Antonio , Rangone Andrea 
Published: July 2016

Purpose
– The purpose of this paper is to identify and discuss the reasons why business models fail, while also identifying the features necessary to develop a method that enables the evaluation of the implementation process of the business model, and is able to help in its development.

Design/methodology/approach
– The proposed method (roadmap for implementation of business models – RIBM) is composed of nine steps, and seven initials conditions (limitations). Such conditions reduce its complexity (e.g. performance management system is defined in the company).

Findings
– Some reasons why business models fail (alignment between value proposition and customer segment (value proposition); business model financial viability (costs and revenue); environmental constraints not fully integrated with the design of the business model (environment); business model execution (management), etc.) and made some considerations about the implementation of business models.

Research limitations/implications
– This work was developed in a small business (with a small team and the external member). The business complexity level and number of processes involved are much smaller when compared with a mid-size or large company. Another factor that contributed to mitigating the problem is that the enterprise had a well-structured report once the owners had made annual analysis and discussed how to improve and expand the business.

Practical implications
– In this application, RIBM showed a potential tool to minimize flaws in implementation processes of business models.

Originality/value
– The business model concept is relatively new in the literature. And because of its strategic importance has been the target of all major schools in the area. This work, in particular, deals with the question-related failures that occur in the process of implementing business models.
The value space: how firms facilitate value creation
Authors: Lindman Martti , Pennanen Kyösti , Rothenstein Jens , Scozzi Barbara , Vincze Zsuzsanna 
Published: July 2016

Purpose
– The purpose of this paper is to investigate the firm’s role in the value creation process. In particular, after categorizing the activities that firms carry out to facilitate the creation of value, the “value space,” an actionable framework within which different dimensions of value creation are integrated, is developed and discussed.

Design/methodology/approach
– The framework is built up on process theory, an in-depth review of the literature and a multiple case study carried out on 65 European firms in the furniture industry.

Findings
– The value space is both a practical and theoretically based framework which contributes to the development of a more holistic and “actionable” view on the role of firm in the value creation process; also it provides managers with a tool to support the analysis, management and innovation of the value creation process.

Originality/value
– The systematic categorization of firms’ activities and their subsequent integration into a value creation framework are a missing piece in terms of understanding the value creation process carried out by firms. Also, by facilitating the analysis and innovation of the value creation process, the framework can be used to support both exploitative and explorative business process management.
Achieving efficiency without sacrificing effectiveness: a pragmatic approach to integrating learning into the work flow
Authors: Hoyle Robin 
Published: July 2016

Purpose
The purpose of this paper is to outline practical approaches to the integration of learning into the workflow based on a pragmatic analysis of different organizational experiences and to look at the difference in efficiency and effectiveness when designing such approaches.

Design/methodology/approach
This is a viewpoint article based on interviews with practitioners.

Findings
Integrating learning into the workflow requires a well-resourced and focused approach which may seem counter-intuitive in twenty-first-century hyper connected organizations.

Originality/value
This viewpoint article brings together new information from practical application of established theories in workplace learning and development. It will be of use for all learning and development (L&D) practitioners seeking to preserve effectiveness while harnessing work-based approaches.
Enhancing team performance through transactive memory
Authors: Chatterjee Srabasti 
Published: July 2016

Purpose
The major focus in the current scenario in organizational settings has shifted from individual performance to team performance. The current study investigates team performance and its antecedents from both social and cognitive dimensions and hence provides a qualitative and synopsis of the same. There is one such antecedent transactive memory which collectively looks into both the facets. For more than a decade after the very emergence of this concept, a plethora of work has been done to relate team performance and transactive memory. In an attempt to understand both these multi-dimensional constructs, and to comprehend the interrelationships in a better way, this paper aims to analyze the impact of transactive memory on team performance and how to improve it in organizations.

Design/methodology/approach
The paper is purely conceptual. So it uses other earlier studies to make necessary propositions.

Findings
The present study tries to qualitatively analyze the impact of transactive memory on team performance with respect to the various dimensions of team performance both task process and relational performance. The results of the study show a positive relationship between the three dimensions of transactive memory – credibility, consensus and specilaization and team performance. The study also provides recommendations to improvise transactive memory in organizations.

Research limitations/implications
The paper is not empirical, so further empirical analysis could enrich the results.

Originality/value
The paper is original in terms of giving solutions to increase transactive memory in organizational set up.
Tourism disaster resilience scorecard for destinations (TDRSD): the case of Manta, Ecuador
Authors: Basurto-Cedeño Estefania Mercedes , Pennington-Gray Lori 
Published: July 2016

Purpose– The purpose of this paper is to develop nine criteria for tourism disaster resilience scorecard for destinations (TDRSD) by using the “disaster resilience scorecard for cities, based on UNISDR’s ten essentials”. As a surrogate for the city, the Convention and Visitors Bureau (CVB) is used at the destination level to manage and oversee disasters within the perspective of a visitor. The initial section of the paper revises the scorecard to adapt to the destination, while the second part of the paper applies the scorecard to a specific city destination. The TDRSD scorecard for CVBs was used to evaluate the destination of Manta, Ecuador.Design/methodology/approach– The approach included four stages. The first stage was to use a Delphi technique to evaluate and adapt the UNIDSRR scorecard to a destination (tourism) context. The second stage included conducting interviews with members of the Manta CVB and Mesa 5 (Emergency Management Department of Manta). Consequently, each answer was paired with support for the item and criteria score. Finally, the weak and strong scores were identified for each essential and match them up with recommendations and trends available in literature.Findings– This study set out to do three things: suggest that a similar scorecard is necessary for destinations; adapt the UNIDSR scorecard to a destination focus; and apply the TDRSD to Manta, Ecuador. Overall, these goals were met. But most interestingly, findings suggest some troubling outcomes.Originality/value– The study allowed to undercover gaps in the current risk management plan of the destination, while providing an evaluation of the engineering resilience of the tourism sector of Manta in case of a disaster.
Mobile tourist guide supporting a smart city initiative: a Brazilian case study
Authors: Cacho Andréa , Mendes-Filho Luiz , Estaregue Daniela , Moura Brunna , Cacho Nélio , Lopes Frederico , Alves Cristiano 
Published: July 2016

Purpose
– The purpose of this paper is to describe a smart city initiative presenting a mobile tourist guide developed for Natal, Brazil.

Design/methodology/approach
– This study has employed an exploratory case study approach to gain more knowledge about a smart city initiative and a mobile tourist guide in Brazil. The city of Natal was selected for this case study since it was one of the host cities during the FIFA World Cup 2014. The collected data for this research came from government (e.g. Natal Smart City plan), academic sources (e.g. Metropole Digital Institute (IMD)), and tourists’ information from the mobile tourist guide application.

Findings
– The smart city initiative of Natal, and the mobile tourist guide (named Find Natal) responsible for collecting, processing, sharing, storing and analysing the tourist behaviour were detailed in the paper. The Smart City Consortium in Natal is developing an interoperable and distributed infrastructure that is advancing the state-of-the-art in information and communication technologies (ICT) for planning and managing smart cities. The IMD implemented an application, which aims to enhance the traveller’s experience through software programs designed to leverage the infrastructure mechanisms behind the city. The data gathered by the application was analysed to show how it was used during the 2014 FIFA World Cup.

Originality/value
– The results show a developed ICT initiative in a Latin American country. This study offers a starting point for destinations willing to implement and deploy a smart city initiative.
Six principles for shared management: a framework for the integrated economy
Authors: Lichtenthaler Ulrich 
Published: July 2016

Purpose
This paper aims to suggest the framework of shared management, which comprises six major principles. These principles indicate that essential strategy guidelines of firms have been transformed.

Design/methodology/approach
This is a conceptual paper, which draws on recent management innovations and transformations of management practices. Thus, the paper builds on prior academic and practitioner contributions.

Findings
Management recently has become more SHARED, i.e. sustainable, holistic, analytical, relational, entrepreneurial and dynamic. Each of these principles covers one central dimension of management that has recently been affected by a new logic of sharing. Real-life examples of selected companies are given, and many other firms’ managerial challenges in applying and profiting from these principles are described.

Originality/value
The six principles indicate that the idea of sharing applies to multiple facets of management, which challenge conventional strategy wisdom. They play a particularly important role in a sharing economy, which involves the collaborative production and consumption of goods and services by multiple persons and organizations. Altogether, the principles provide the basis for the shared management framework, which may serve as a step toward an up-to-date picture and realistic guideline for today’s management in many organizations.