bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signaling Pathway Activities Improve Prognosis for Breast Cancer
Authors: Jiao Yunlong , Hidalgo Marta R. , Çubuk Cankut , Amadoz Alicia , Carbonell-Caballero José , Vert Jean-Philippe , Dopazo Joaquín 
Published: April 2017

AbstractWith the advent of high-throughput technologies for genome-wide expression profiling, a large number of methods have been proposed to discover gene-based signatures as biomarkers to guide cancer prognosis. However, it is often difficult to interpret the list of genes in a prognostic signature regarding the underlying biological processes responsible for disease progression or therapeutic response. A particularly interesting alternative to gene-based biomarkers is mechanistic biomarkers, derived from signaling pathway activities, which are known to play a key role in cancer progression and thus provide more informative insights into cellular functions involved in cancer mechanism. In this study, we demonstrate that pathway-level features, such as the activity of signaling circuits, outperform conventional gene-level features in prediction performance in breast cancer prognosis. We also show that the proposed classification scheme can even suggest, in addition to relevant signaling circuits related to disease outcome, a list of genes that do not code for signaling proteins whose contribution to cancer prognosis potentially supplements the mechanisms detected by pathway analysis.
Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics
Authors: Borowiec Marek L. 
Published: May 2017

AbstractThe evolution of the suite of morphological and behavioral adaptations underlying the ecological success of army ants has been the subject of considerable debate. This “army ant syn-drome” has been argued to have arisen once or multiple times within the ant subfamily Dorylinae. To address this question I generated data from 2,166 loci and a comprehensive taxon sampling for a phylogenetic investigation. Most analyses show strong support for convergent evolution of the army ant syndrome in the Old and New World but certain relationships are sensitive to analytics. I examine the signal present in this data set and find that conflict is diminished when only loci less likely to violate common phylogenetic model assumptions are considered. I also provide a temporal and spatial context for doryline evolution with timecalibrated, biogeographic, and diversification rate shift analyses. This study underscores the need for cautious analysis of phylogenomic data and calls for more efficient algorithms employing better-fitting models of molecular evolution.SignificanceRecent interpretation of army ant evolution holds that army ant behavior and morphology originated only once within the subfamily Dorylinae. An inspection of phylogenetic signal in a large new data set shows that support for this hypothesis may be driven by bias present in the data. Convergent evolution of the army ant syndrome is consistently supported when sequences violating assumptions of a commonly used model of sequence evolution are excluded from the analysis. This hypothesis also fits with a simple scenario of doryline biogeography. These results highlight the importance of careful evaluation of signal and conflict within phylogenomic data sets, even when taxon sampling is comprehensive.
Impact of sequencing depth and read length on single cell RNA sequencing data: lessons from T cells
Authors: Rizzetto Simone , Eltahla Auda A. , Lin Peijie , Bull Rowena , Lloyd Andrew R. , Ho Joshua W. K. , Venturi Vanessa , Luciani Fabio 
Published: May 2017

ABSTRACTSingle cell RNA sequencing (scRNA-seq) has shown great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant sub-populations of T cells, and notably the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, such as RNA library capture, cell quality, and sequencing output have been suggested to affect the quality of scRNA-seq data, but these factors have not been systematically examined.We studied the effect of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCRαβ reconstruction, utilising 1,305 publically available scRNA-seq datasets, and simulation-based analyses. Gene expression was characterised by an increased number of unique genes identified with short read lengths (<50 bp), but these featured higher technical variability compared to profiles from longer reads. TCRαβ were detected in 1,027 cells (79%), with a success rate between 81% and 100% for datasets with at least 250,000 (PE) reads of length >50 bp.Sufficient read length and sequencing depth can control technical noise to enable accurate identification of TCRαβ and gene expression profiles from scRNA-seq data of T cells.
Complex Dynamics From Simple Cognition: The Primary Ratchet Effect in Animal Culture
Authors: Mcelreath Mary Brooke , Boesch Christophe , Kühl Hjalmar , McElreath Richard 
Published: May 2017

AbstractIt is often observed that human culture, unlike most other animal culture, iscumulative: human technology and behavior is more complex than any individual could invent in their own lifetime. Cumulative culture is often explained by appeal to a combination of high-fidelity social learning and innovation, the “ratchet effect.” What is often overlooked is that both human and other animal culture is supported by a more primary ratchet effect that retains and increases the prevalence of adaptive behavior. This primary ratchet can arise without appeal to specialized cognitive adaptations and is plausibly more widespread in animal societies. We use a simple model to highlight how simple forms of contingent social learning can create the primary ratchet effect, dramatically increasing the prevalence of adaptive, hard to invent behavior. We investigate some ways that demography may interact with the primary ratchet to generate patterns of cultural variation. As the primary ratchet may be common to many animal societies, its cognitive components and population dynamics provide a common foundation for the study of animal culture and a necessary foundation for understanding the origins of human cumulative culture.
Seeking “conversations for accountability”
Authors: Agyemang Gloria , O’Dwyer Brendan , Unerman Jeffrey , Awumbila Mariama 
Published: May 2017

PurposeThe purpose of this paper is to ascertain how upward accountability processes can be enabling in, or constraining to, the effective deployment of development aid funding.Design/methodology/approachThe paper derives its primary insights from in-depth interviews and focus groups with non-governmental organization (NGO) fieldworkers working and delivering development aid in Northern Ghana. It analyses inductively the perspectives of fieldworkers to explain their experiences of upward accountability.FindingsThe fieldworkers’ perception of upward accountability was mainly one of external control, in response to which they enacted a skilful form of compliance accountability. This perception of control failed to stifle their initiative and intrinsic commitment to beneficiaries. The fieldworkers craved “conversations for accountability”, in which they had a voice in the development of upward accountability metrics, thereby enabling them to fulfil their sense of felt responsibility to beneficiaries. While aspects of “conversations for accountability” were emerging in fieldworker-funder interactions, it was unclear to what extent funders were committed to further advancing them. Overall, the analysis unveils how felt responsibility mediates for, and partly diminishes, the perceived negative impacts on aid effectiveness of upward accountability processes informed by a focus on control.Originality/valueThe authors examine the potential of upward accountability processes using in-depth analyses of the actual experiences of those involved in delivering NGO services at the grassroots level. The authors contribute to emerging work in this vein by enriching the authors’ understanding of local constituencies’ experiences of accountability processes more generally, especially the impact these mechanisms have on NGO operational activities. The authors also unveil the mediating role fieldworkers’ “felt responsibility” to beneficiaries’ plays in moderating the perceived negative impacts on aid effectiveness of upward accountability processes.
Examining distinct carbon cost structures and climate change abatement strategies in CO2polluting firms
Authors: Cadez Simon , Guilding Chris 
Published: May 2017

PurposeA management accounting perspective that underscores a quest for reducing conventionally appraised costs, negative output costs as well as heightened eco-efficiency has been used in pursuit of the study’s two main study objectives. The purpose of this paper is twofold: first, the study seeks to further understanding of the relationship between product output volume, carbon costs, and CO2emission volume in carbon-intensive firms. Second, it identifies factors affecting climate change abatement strategies pursued by these firms. Heightening appreciation of the climate change challenge, combined with minimal CO2emission research undertaken from a cost management perspective, underscores the significance of the study.Design/methodology/approachA triangulation of quantitative and qualitative data collected from Slovenian firms that operate in the European Union Emissions Trading Scheme has been deployed.FindingsCO2polluting firms exhibit differing carbon cost structures that result from distinctive drivers of carbon consumption (product output vs capacity level). Climate change abatement strategies also differ across carbon-intensive sectors (energy, manufacturing firms transforming non-fossil carbon-based materials, and other manufacturing firms) but are relatively homogeneous within them.Practical implicationsFrom a managerial perspective, the study demonstrates that carbon efficiency improvements are generally not effective in triggering corporate CO2emission reduction when firms pursue a growth strategy.Social implicationsGlobal warming signifies that CO2emissions constitute a social problem. The study has the potential to raise societal awareness that the causality of the manufacturing sector’s CO2emissions is complex. Further, the study highlights that while more efficient use of environmental resources is a prerequisite of enhanced ecological sustainability, in isolation it fails to signify improved ecological sustainability in manufacturing operations.Originality/valueThe paper has high originality as it reports one of the first management accounting studies to explore the distinction between combustion- and process-related CO2emissions. In addition, it provides distinctive support for the view that eco-efficiency is more consistent with the economic than the environmental pillar of sustainability.
Counting to zero: accounting for a green building
Authors: Georg Susse , Justesen Lise 
Published: May 2017

Purpose
The purpose of this paper is to examine how a particular form of environmental accounting, energy accounting, is negotiated in practice and how energy accounting may act as a productive organizing device in organizational contexts. Energy accounting is considered as performative in organizational practices rather than as a representation of resource use.

Design/methodology/approach
This paper is based on a longitudinal case study of the design phase in a construction project. Data collection entailed observational and document studies as well as interviews with those involved in the design processes. This paper draws on actor-network theory, notably the notions of framing and overflowing, in analyzing the role of energy accounting in design processes and in affecting organizational practice.

Findings
The paper provides several insights regarding energy accounting in the making, energy accounting’s performative role in enacting possible futures, the narrative importance of numbers, and the entangled nature of designing, accounting and organizing practices. The findings demonstrate the strong links between accounting and organizing.

Originality/value
This paper adds to the extant literature on environmental accounting by directing attention to how such accounting practices contribute to forming rather than just informing management decisions. By focusing on how the calculative practices of making such accounts mediate ideas and help assemble new entities, this paper provides useful insights into the performative role of environmental accounting.
Bubble characterizations on hydrophobic surface using lattice Boltzmann simulation with large density ratios
Authors: Du Peng , Hu Haibao , Ren Feng , Song Dong 
Published: May 2017

Purpose
The maintenance of the air–water interface is crucial for the drag reduction on hydrophobic surfaces. But the air bubbles become unstable and even washed away under high speed flow, causing the failure of surface hydrophobicity. Thereby, this paper aims to understand the relations between bubble behaviors and surface properties, flow conditions and to discover new methods to maintain the air–water interface.

Design/methodology/approach
Bubble properties on hydrophobic surfaces were characterized using single-component multiphase lattice Boltzmann simulation. Three equations of state (EOSs), including the Peng–Robinson, Carnahan–Starling and modified Kaplun–Meshalkin EOSs, were incorporated to achieve high density ratios.

Findings
Both the static and dynamic properties of bubbles on hydrophobic surfaces were investigated and analyzed under different flow conditions, solid–liquid interactions and surface topology.

Originality/value
By revealing the properties of bubbles on hydrophobic surfaces, the effects of flow conditions and surface properties were characterized. The maintenance method of air–water interface can be proposed according to the bubble properties in the study.
Built asset management climate change adaptation model
Authors: Jones Keith , Desai Api , Brosnan Noel , Cooper Justine , Ali Fuad 
Published: May 2017

PurposeThe purpose of this paper is to present results of an action research addressing climate change adaptation of selected social housing stock in the UK. Climate change continues to pose major challenges to those responsible for the management of built assets. The adaptation required to address long-term building performance affected by climate change rarely get prioritised above more immediate, short-term needs (general built asset management needs).
Design/methodology/approachThe study adopts an in-depth participatory action research with a London-based social landlord and integrates climate change adaptation framework and performance-based model established through author’s previous research projects.
FindingsA staged process for including adaptation measures in built asset management strategy is developed along with metrics to analyse the performance of the housing stock against climate change impact of flooding. The prioritisation of adaptation measure implementation into long-term built asset management plans was examined through cost-based appraisal.
Research limitations/implicationsThe research was carried out with a singular organisation, already acquainted with potential climate change impact, vulnerability and adaptive capacity assessment. The process adopted will differ for similar organisation in the sector with different settings and limited working knowledge of climate change impact assessment.
Practical implicationsThe paper concludes with a ten-step process developed as an aide memoir to guide social landlords through the climate change adaptation planning process.
Originality/valueIn addition to the practical results from the study, the paper outlines a novel process that integrates resilience concepts, risk framing (to climate change impact) and performance management into built asset management (maintenance and refurbishment) planning.
Analysing community needs and skills for enhancing disaster resilience in the built environment
Authors: Perera Srinath , Adeniyi Onaopepo , Babatunde Solomon Olusola 
Published: May 2017

PurposeA better cooperation among all stakeholders working towards enhancing the disaster resilience of societies can only be achieved if the expectations or the needs of each stakeholder are understood. This study attempts to outline the needs of communities affected by disasters for the purpose of aligning the needs and skill requirements with the abilities of built environment professionals serving these communities. Therefore, the study aims to identify and describe community needs and skills requirements for enhancing disaster resilience.
Design/methodology/approachThe study adopted literature review and semi-structured interviews. The semi-structured interviews were conducted with key members of some communities affected by disasters and with some of the professionals who participated in the restoration/reconstruction of those communities. Data obtained were analysed using NVivo 10.
FindingsThe study revealed the current and emerging needs and skills of communities related to the built environment professionals from the viewpoint of enhancing disaster resilience. Thus, 29 classifications of skill and needs were derived and classified under five major disaster resilience dimensions to include social, economic, technological, environmental and institutional aspects.
Research limitations/implicationsThis study focuses only of the needs and skills of the “community”, which is the major stakeholder that is basically the receiver of all that the other stakeholders of disaster resilience have to offer.
Practical implicationsThis study would help the built environment professionals involved in disaster resilience to become aware of the specific needs and skills of the communities affected by disasters for the purpose of developing their competences.
Originality/valueThe study findings would be useful for both the built environment professionals and higher education institutions. Because it is important for professionals to update and upgrade their knowledge towards enhancing their capabilities and meeting stakeholders’ expectations in a bid to enhance societal resilience to disasters across all domains of resilience.
Assessing the legitimacy of HEIs’ contributions to society
Authors: Urdari Claudia , Farcas Teodora Viorica , Tiron-Tudor Adriana 
Published: May 2017

Purpose
This paper aims to inquire about the types of measurements used by international university rankings and their connection to the higher education institutions’ (HEIs) third mission activities, namely, the contribution to society.

Design/methodology/approach
The paper is based on a review of literature and content analysis of nine international rankings.

Findings
This empirical study corroborates that rankings focus on teaching and research activities but rarely measure the HEIs’ connection to practice.

Originality/value
As the measurements used by international university rankings are claimed to have a huge impact on the structuring of the academic environment, this paper shows that international rankings fail to measure the HEIs’ success in developing third mission activities.
Green information technology adoption: influencing factors and extension of theory of planned behavior
Authors: Dezdar Shahin 
Published: May 2017

PurposeThe effect of global warming on our environment has shifted the focus to green technologies worldwide. Subsequently, multiple research studies have attempted to assess awareness around the concept of “Green IT” in different countries. This paper aims to examine the factors that affect the intention to use green information technology (IT) (INT) and their subsequent influence on the actual use of green IT (ACT) among students in the context of a developing country.Design/methodology/approachThe data were collected using survey questionnaires administered to six public university students. A total of 633 valid questionnaires were received and analyzed using structural equation modeling.FindingsA positive relationship of INT with attitude toward green IT, subjective norms toward green IT, perceived behavioral control toward green IT, consideration of future consequences and openness was found, and also, a positive relationship between INT and ACT was found.Originality/valueMany of prior research focused on factors influencing green IT adoption and usage from the organizational point of view, and there is not much literature dedicated to the study of IT users’ belief and behavior about green IT. Moreover, most studies tend to focus on developed nations, while a lesser number of studies gave consideration to developing nations. This study proposes a research framework that incorporated two personality trait factors to the theory of planned behavior to investigate individual factors influencing INT among students in the context of a developing country.
Cruise tourism management: state of the art
Authors: Papathanassis Alexis 
Published: May 2017

PurposeCruise tourism is a dynamic, growing segment of tourism that has long ceased to represent a mere niche and is slowly but steadily entering the domain of mainstream tourism. Yet, cruise tourism represents a minor fraction of tourism-related literature and research (Papathanassis and Beckmann, 2011). This study aims to examine the main trends and state-of-the-art developments in cruise tourism. The intension is to provide a starting point, a basis for non-specialists in this area, for further interdisciplinary research.Design/methodology/approachUsing the author’s previous research and expertise over the past decade, this paper aims at providing a concise overview of the key perspectives and concepts in cruise tourism, whilst highlighting the current and future challenges faced by the sector and its stakeholders.FindingsIn this context, the potential of information and communication technologies for cruise tourism development and research (e-cruising) is underlined.Originality/valueFinally, this paper offers a comprehensive systemic definition of cruise tourism and the corresponding Cruise Entities, inter-Relationships and Themes (CruisERT) framework, highlighting relevant areas and questions for further research.
Social responsibility influence on customer trust in hotels: mediating effects of reputation and word-of-mouth
Authors: Jalilvand Mohammad Reza , Nasrolahi Vosta Leila , Kazemi Mahyari Hamze , Khazaei Pool Javad 
Published: May 2017

PurposeThis paper aims to model and test the relationships between corporate social responsibility (CSR), corporate reputation (CR), word-of-mouth (WOM) behavior and customer trust (CT) within the hotel context.Design/methodology/approachA questionnaire survey was conducted among 300 hotel guests. Following a two-step approach, a measurement model was estimated and then a structural model was analyzed to test six proposed hypotheses.FindingsThe research results show that CSR has a direct and positive effect on CT, CR and WOM; CSR has an indirect and positive influence on CT via CR and WOM as mediating variables; CR is a significant antecedent of WOM; and CR and WOM are positively associated with CT.Originality/valueThe research examines the relationship among CSR, CR, WOM and CT, thus contributing to hospitality management literature theoretically. In addition, relevant implications are provided for managers as to how to improve CT in service industries.