bluuebunny/crossref_metadata_2025_split huggingface dataset:
An evolutionary innovation is contingent on maintaining adaptive potential until competition subsides
Authors: Leon Dacia , D'Alton Simon , Quandt Erik M. , Barrick Jeffrey E. 
Published: January 2018

AbstractAfter 15 years of the Lenski experiment one of twelveEscherichia colipopulations evolved the ability to utilize an abundant but previously untapped carbon source, citrate. Mutations responsible for the appearance of rudimentary citrate utilization (Cit+phenotype) and for refining this ability have been characterized. However, the complete nature of the genetic and/or ecological events that set the stage for this key innovation remain unknown. We found that there was a slight fitness benefit for introducing an activatedcitTcassette that mimics the mutation causing Cit+into the ancestor of the evolution experiment and strains isolated from the population close to when it evolved. However, there was no benefit or even a large deleterious effect in intermediate strains. We conclude that achieving Cit+was contingent on both an evolutionary trajectory that maintained a potentiated genetic state and the slowing rate of adaptation in this population late in the experiment.
Global fingerprint of humans on the distribution ofBartonellabacteria in mammals
Authors: Frank Hannah K. , Hadly Elizabeth A. 
Published: January 2018

AbstractAs humans alter habitats and move themselves and their commensal animals around the globe they change the disease risk for themselves, their commensal animals and wildlife.Bartonellabacteria are prevalent in many mammalian taxa, responsible for numerous human infections and presumed to be an important emerging group of zoonoses. Understanding how this genus has evolved and passed between host taxa in the past can reveal not only how current patterns were established but identify potential mechanisms for future cross-species transmission. We analyzed patterns ofBartonellatransmission and likely sources of spillover using the largest collection ofBartonella gltAgenotypes assembled, 860 unique genotypes ofBartonellaglobally. We provide support for the hypothesis that this pathogenic genus originated as an environmental bacterium before becoming an insect commensal and finally vertebrate pathogen. We show that rodents and domestic animals serve as the reservoirs or at least key proximate host for mostBartonellagenotypes in humans. We also find evidence of exchange ofBartonellabetween domestic animals and wildlife and between domestic animals, likely due to increased contact between all groups.Bartonellais a useful infection for tracing potential zoonoses and demonstrates another major impact of humans on the planet. Care should be taken to avoid contact between humans, domestic animals and wildlife to protect the health of all.
Attentional set to safety recruits the medial prefrontal cortex
Authors: Yao Shuxia , Qi Song , Kendrick Keith M. , Mobbs Dean 
Published: January 2018

AbstractDuring threat assessment, the early detection of danger is highly adaptive, yet the fast orientation towards safety is also key to survival. The present study aimed to explore how the human brain searches for safety by manipulating subjects’ attentional set to cues associated with shock probability. Subjects were asked to judge random dots motion (RDM) direction and could be shocked for incorrect responses (RDM task) while keeping alert in detecting the shock probability cues (cue detection task). In contrast to the safe condition, where subjects searched for cues associated with no shock probability, incorrect responses to ‘dangerous+’ (D+) cues would increase the shock probability and correct responses to ‘dangerous-’ (D-) cues would decrease shock probability. In the RDM task, results showed that relative to the D+, the safe attentional set resulted in stronger activation in the ventral medial prefrontal cortex (vmPFC), a core region involved in flexible threat assessment and safety signalling. The vmPFC was also recruited by the D-compared to the D + attentional set. In the cue detection task, shorter response times and greater accuracy were observed for D+ compared to D‐ and safe cues. Correspondingly, at the neural level D+ cues induced increased activity in the frontoparietal attention network including the inferior parietal lobule and intraparietal sulcus. Overall, our findings demonstrate that attentional set for searching safety recruits the vmPFC, while detection of threat elicits activity in the frontoparietal attention network, suggesting a new role for these regions in human defensive survival circuitry.Significance StatementWhile early detection of threat is highly adaptive, the fast orientation towards safety is also key to survival. However, little is known about neural mechanisms underlying attentional set to safety. Using a novel dots motion paradigm combined with fMRI, we explored how human brain prepares for safety searching by manipulating subjects’ attentional set to cues associated with shock probability. Relative to the dangerous attentional set associated with increasing shock probability, the safe attentional set resulted in stronger activity in the ventral medial prefrontal cortex, a core region involved in flexible threat assessment and safety signalling, suggesting a new role for this region in human defensive survival system in encoding stimuli with survival significance.
Partially methylated domains are hallmarks of a cell specific epigenome topology
Authors: Salhab Abdulrahman , Nordström Karl , Kattler Kathrin , Ebert Peter , Ramirez Fidel , Arrigoni Laura , Müller Fabian , Cadenas Cristina , Hengstler Jan G. , Lengauer Thomas , Manke Thomas ,   DEEP Consortium, Walter Jörn 
Published: January 2018

AbstractBackgroundPartially methylated domains, PMDs, are extended regions in the genome exhibiting a reduced average DNA-methylation level. PMDs cover gene-poor and transcriptionally inactive regions and tend to be heterochromatic. Here, we present a first comprehensive comparative analysis of PMDs across more than 190 WGBS methylomes of human and mouse cells providing a deep insight into structural and functional features associated with PMDs.ResultsPMDs are ubiquitous signatures covering up to 75% of the genome in human and mouse cells irrespective of their tissue or cell origin. Additionally, each cell type comes with a distinct set of specific PMDs, and genes expressed in such PMDs show a strong cell type effect. Demethylation strength varies in PMDs with a tendency towards a more pronounced effect in differentiating and replicating cells. The strongest demethylation is observed in highly proliferating and immortal cancer cell lines. A decrease of DNA-methylation within PMDs tends to be linked to an increase in heterochromatic histone marks and a decrease of gene expressions. Characteristic combinations of heterochromatic signatures in PMDs are linked to domains of early, middle and late DNA-replication.ConclusionPMDs are prominent signatures of long-range epigenomic organization. Integrative analysis identifies PMDs as important general, lineage- and cell-type specific topological features. PMD changes are hallmarks of cell differentiation. Demethylation of PMDs combined with increased heterochromatic marks is a feature linked to enhanced cell proliferation. In combination with broad histone marks PMDs demarcate distinct domains of late DNA-replication.
Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing
Authors: Das Sarbashis , Pettersson B. M. Fredrik , Behra Phani Rama Krishna , Mallick Amrita , Cheramie Martin , Shirreff Lisa , DuCote Tanner , Dasgupta Santanu , Ennis Don G. , Kirsebom Leif. A. 
Published: January 2018

AbstractMycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the “M”- and the “Aronson”-type. We suggest that these two clusters should be considered, if not two separate species, at least two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to that M. marinum occupy different ecological niches.
Real-space refinement in Phenix for cryo-EM and crystallography
Authors: Afonine Pavel V. , Poon Billy K. , Read Randy J. , Sobolev Oleg V. , Terwilliger Thomas C. , Urzhumtsev Alexandre , Adams Paul D. 
Published: January 2018

AbstractThis article describes the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite. Use of a simplified refinement target function enables fast calculation, which in turn makes it possible to identify optimal data-restraints weight as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. Re-refinement of 385 cryo-EM derived models available in the PDB at resolutions of 6 Å or better shows significant improvement of models and the fit of these models to the target maps.SynopsisA description of the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite and its application to re-refinement of cryo-EM derived models.
Achieving radical change
Authors: Hyndman Noel , Liguori Mariannunziata 
Published: January 2018

PurposeThe purpose of this paper is to focus on strategies and “spoken discourses” used to construct legitimation around change at the individual level. Comparing changes in financial accounting, budgeting and performance management at two government levels (Westminster and Scotland), it explores the use of legitimation strategies in the implementation of accounting change and its perceived outcomes.Design/methodology/approachDrawing on semi-structured interviews, six legitimation/delegitimation strategies are used to code the transcribed data. Patterns with the perceived outcomes of change are explored.FindingsChanges introduced to enhance “rational” decision making are often received as pushed by some source of authority. Regardless of the interviewees’ background and level, the results suggest that for radical accounting change to embed, it is necessary for it to be perceived as rational, rather than merely driven by authorisation-based pressures. Conversely, incremental change is associated with modest legitimation via rationalisation and delegitimation based on pathos and rationalisation.Research limitations/implicationsThe study deals with actors’ legitimation strategies and perceptions of change. These may not correspond to actual substantial change. Taken-for-granted ideas often remain “under the radar”, therefore care must be taken in interpreting the results. The focus of the empirical study is on the UK, therefore conclusions are restricted to this context.Originality/valueExisting studies struggle to explain organisations’ heterogeneity and practice variation; this study sheds light on how individual legitimation, which may lead to different organisational results, occurs. Differences in how actors interpret changes may be based on their position (central vs devolved administration) and on their ownership of the changes.
Corporate political connection and corporate social responsibility disclosures
Authors: Muttakin Mohammad Badrul , Mihret Dessalegn Getie , Khan Arifur 
Published: January 2018

PurposeThe purpose of this paper is to examine the association of corporate political connection with the level of voluntary corporate social responsibility (CSR) disclosures to determine how the relationships between the state and the corporate sector influence CSR engagement.Design/methodology/approachBased on a neo-pluralist view of legitimacy theory, which conceptualizes the state as a concentration of power amenable to exploitation by the corporate sector, the study develops and empirically tests a hypothesis that CSR disclosures are inversely associated with political connection. A sample of 936 firm-year observations is used with data collected from annual reports of companies listed on the Dhaka Stock Exchange in Bangladesh from 2005 to 2013.FindingsResults indicate that corporate political connection is associated with reduced CSR disclosures. This finding suggests that the perceived need for CSR disclosures as a legitimation strategy diminishes for politically connected firms. The finding supports a neo-pluralist argument that political connection could enable firms to eschew stakeholder pressure associated with potential legitimacy threats originating from poor CSR performance. This conclusion challenges the pluralist view of legitimacy theory that considers the state as a neutral arbiter resolving conflict among stakeholder groups in society.Originality/valueThe study makes a significant contribution to the literature by developing a neo-pluralist theorization of voluntary CSR disclosures within legitimacy theory and empirically testing it. Because prior empirical CSR disclosure research is largely underpinned by the pluralistic conception of society, examining this phenomenon from a neo-pluralist perspective enables a more complete understanding of CSR disclosure behaviors of firms.
Accounting as capital and doxa: exploring power and resistance in World Bank projects in Tonga
Authors: Fukofuka Peni , Jacobs Kerry 
Published: January 2018

Purpose
The purpose of this paper is to explore the fluid role of accounting both as a form of power and resistance in the context of World Bank projects in the Island Kingdom of Tonga.

Design/methodology/approach
Bourdieu’s concepts of doxa and capital provided the framework for problematizing the fluidity of practices of accounting as both a form of power and of resistance. The authors used a qualitative field study design based on a combination of a documentary analysis of these loan agreements and interviews with key actors and informants.

Findings
The role of accounting in relation to subaltern groups is mediated by the doxic rules and existing capital arrangements at the national and the local or village level. Understanding accounting as both capital and as doxa explains why it can be both a form of power and of resistance.

Practical implications
This study provides policy makers and foreign donors of Tonga and other Pacific Islands a deeper understanding on the struggles to implement and the impacts of accounting at local level as accounting is deployed as part of struggles in various social contexts each with its own doxa and capital arrangements.

Originality/value
This study contributes to the growing accounting body of work that seeks to better understand accounting by proposing that role of accounting as a tool for domination is mediated in various social settings by the doxic value and the existing capital arrangements in those settings.
Strategic practices of subsidiary positioning in business networks
Authors: Laari-Salmela Sari , Mainela Tuija , Pernu Elina , Puhakka Vesa 
Published: January 2018

Purpose
The purpose of this paper is to examine subsidiary positioning within the dynamic business networks in the context of multinational companies (MNCs). The research question of the study is: How does the positioning of a subsidiary emerge through strategic practices in the dynamic business networks of an MNC?

Design/methodology/approach
The study relies on the IMP view on strategy with a focus on market positioning activity and the strategy-as-practice approach. Positioning is seen as a question of strategic practices in the interactive spheres of the subsidiaries. In the empirical part of the study, the authors examine the practices of a forest machine industry multinational through longitudinal interview and archival data on three of its sales subsidiaries in Sweden, Russia and the USA.

Findings
The study defines core tensions in subsidiary interactive spheres and the related strategic practices that shape the positioning of the subsidiaries. The study models the practice-based network positioning of MNC subsidiaries as a dynamic play of relationship tensions.

Originality/value
Prior research has focused either on the internal organizing of the MNCs or embeddedness of subsidiaries in their local environment. Less attention has been paid to the practices of positioning through which the subsidiaries deal with the inevitable tensions at the intersection of the internal and external networks.
Academic libraries and student learning outcomes
Authors: Blummer Barbara , Kenton Jeffrey M. 
Published: January 2018

PurposeThe purpose of this paper is to examine the literature on student learning outcomes and academic libraries. An analysis of 81 papers revealed the following themes: outcomes assessment of library skills instruction, tools for assessing students’ achievement of learning outcomes, institutional accreditation and student learning outcomes, academic libraries’ impact on student learning outcomes, and the creation of learning outcomes. An understanding of these themes highlights how student learning outcomes are created, assessed, and valued in the academy.Design/methodology/approachThe methodology centered on a literature review of student learning outcomes and academic libraries from 2001 to the present. To identify relevant articles on this topic, the authors searched the library literature with various combinations of the following keywords: learning outcomes, library, academic, university, college, and higher education.FindingsAn analysis of 81 papers on student learning outcomes and academic libraries revealed the following five themes: outcomes assessment of library skills instruction, assessment tools for student learning outcomes, institutional accreditation and student learning outcomes, academic libraries’ impact on student learning outcomes, and the creation of learning outcomes.Research limitations/implicationsThe research was limited to articles published in English and after 2000.Practical implicationsThe findings can be utilized to inform instructional librarians about creating and assessing student learning outcomes. In addition, the paper can assist librarians in forging partnerships with academic departments and faculty in creating student learning outcomes to support course and departmental outcomes and accreditation efforts.Originality/valueThe research offers librarians opportunities to incorporate student learning outcomes in library instruction as well as collaborate with faculty in creating student learning outcomes.
Regional dynamics of ownership structure and their impact on firm performance and firm valuation
Authors: Ali Awais , Qiang Fu , Ashraf Sadia 
Published: January 2018

Purpose
The purpose of this paper is to analyse the impact of ownership structure on firm valuation and performance across different geographical regions within mainland China.

Design/methodology/approach
The authors classify China in six geographical regions and use cross-sectional data of companies with A-shares listed on domestic stock exchanges in China for the year-end 2015. Using data from CSMAR and Wind database, they use multivariate regression technique and analytically compare the consistency of relationship between operational variables of ownership structure with corporate performance and evaluation.

Findings
The authors find that institutional ownership and state ownership negatively affect market valuation throughout various geographical regions of China. Further, in East, Northwest, South Central and Southwestern parts of China, managerial ownership and concentration of shareholding among top ten shareholders positively influence return on equity (ROE). Interestingly, institutional shareholding negatively affects return on assets (ROA), while institutional ownership has a neutral effect on profitability margin in Northeast China. Although in northern part of China, this relationship is slightly positive. In East China region, state ownership and ownership concentration are directly proportional to profitability margin.

Practical implications
As some of the findings exhibit weak state of market efficiency in some regions, the study may also be useful in identifying arbitrage opportunities across different regions. Moreover, this study suggests that regions with the same business environment and conditions anywhere around the globe invite same or similar ownership structure for better firm performance and valuation.

Originality/value
The study provides unique understanding of relationship between ownership structure, market valuation and firm performance in various parts of China and will be an addition to the relevant literature. Given a change in company’s ownership structure and considering its region of incorporation, this study will help investment analysts in assessing performance and market valuation of the firm. It will also assist several classes of investors, financial institutions and international businesses in making their investment decisions.
HpaP, a novel regulatory protein with ATPase and phosphatase activity, contributes to full virulence in Xanthomonas campestris pv. campestris
Authors: Cui Ping , Li Rui‐Fang , Zhang Da‐Pei , Tang Ji‐Liang , Lu Guang‐Tao 
Published: January 2018

SummaryThe ability of the bacterial phytopathogen Xanthomonas campestris pv. campestris (Xcc) to cause disease is dependent on the type III secretion system (T3SS). Proteins of the Xcc T3SS are encoded by hrp (hypersensitive response and pathogenicity) genes and whose expression is mainly controlled by the regulators HrpG and HrpX. Here, we describe the identification and characterization of a previously unknown regulatory protein (named HpaP), which plays important role in hrp gene expression and virulence in Xcc. Clean deletion of hpaP demonstrated reduced virulence and HR (hypersensitive response) induction of Xcc and alterations in cell motility and stress tolerance. Global transcriptome analyses revealed that most hrp genes were down regulated in the hpaP mutant, suggesting HpaP positively regulates hrp genes. GUS activity assays implied that HpaP regulates the expression of hrp genes via controlling the expression of hrpX. Biochemical analyses revealed that HpaP protein had both ATPase and phosphatase activity. While further site‐directed mutagenesis of conserved residues in the PTP loop (a protein tyrosine phosphatase signature) of HpaP resulted in the loss of both phosphatase activity and regulatory activity in virulence and HR. Taken together, the findings identify a new regulatory protein that controls hrp gene expression and virulence in Xcc.