bluuebunny/crossref_metadata_2025_split huggingface dataset:
The combinatorics of discrete time-trees: theory and open problems
Authors: Gavryushkin Alex , Whidden Chris , Matsen Frederick A 
Published: July 2016

ABSTRACTAtime-treeis a rooted phylogenetic tree such that all internal nodes are equipped with absolute divergence dates and all leaf nodes are equipped with sampling dates. Such time-trees have become a central object of study in phylogenetics but little is known about the parameter space of such objects. Here we introduce and study a hierarchy of discrete approximations of the space of time-trees from the graph-theoretic and algorithmic point of view. One of the basic and widely used phylogenetic graphs, the NNI graph, is the roughest approximation and bottom level of our hierarchy. More refined approximations discretize the relative timing of evolutionary divergence and sampling dates. We study basic graph-theoretic questions for these graphs, including the size of neighborhoods, diameter upper and lower bounds, and the problem of finding shortest paths. We settle many of these questions by extending the concept of graph grammars introduced by Sleator, Tarjan, and Thurston to our graphs. Although time values greatly increase the number of possible trees, we show that 1-neighborhood sizes remain linear, allowing for efficient local exploration and construction of these graphs. We also obtain upper bounds on ther-neighborhood sizes of these graphs, including a smaller bound than was previously known for NNI.Our results open up a number of possible directions for theoretical investigation of graph-theoretic and algorithmic properties of the time-tree graphs. We discuss the directions that are most valuable for phylogenetic applications and give a list of prominent open problems for those applications. In particular, we conjecture that the split theorem applies to shortest paths in time-tree graphs, a property not shared in the general NNI case.
A conditional likelihood is required to estimate the selection coefficient in ancient DNA
Authors: Valleriani Angelo 
Published: July 2016

AbstractTime-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function built under the hypothesis that the available trajectory spans a sufficiently large portion of the fitness landscape. Especially for ancient DNA, however, often only one single such trajectories is available and the coverage of the fitness landscape is very limited. In fact, one single trajectory is more representative of a process conditioned both in the initial and in the final condition than of a process free to visit the available fitness landscape. Based on two models of population genetics, here we show how to build a likelihood function for the selection coefficient that takes the statistical peculiarity of single trajectories into account. We show that this conditional likelihood delivers a precise estimate of the selection coefficient also when allele frequencies are close to fixation whereas the unconditioned likelihood fails. Finally, we discuss the fact that the traditional, unconditioned likelihood always delivers an answer, which is often unfalsifiable and appears reasonable also when it is not correct.
Abstract spatial, but not body-related, visual information guides bimanual coordination
Authors: Brandes Janina , Rezvani Farhad , Heed Tobias 
Published: July 2016

AbstractVisual spatial information is paramount in guiding bimanual coordination, but anatomical factors, too, modulate performance in bimanual tasks. Vision conveys not only abstract spatial information, but also informs about body-related aspects such as posture. Here, we asked whether, accordingly, visual information induces body-related, or merely abstract, perceptual-spatial constraints in bimanual movement guidance. Human participants made rhythmic, symmetrical and parallel, bimanual index finger movements with the hands held in the same or different orientations. Performance was more accurate for symmetrical than parallel movements in all postures, but additionally when homologous muscles were concurrently active, such as when parallel movements were performed with differently rather than identically oriented hands. Thus, both perceptual and anatomical constraints were evident. We manipulated visual feedback with a mirror between the hands, replacing the image of the left with that of the right hand and creating the visual impression of bimanual symmetry independent of the right hand’s true movement. Symmetrical mirror feedback impaired parallel, but improved symmetrical bimanual performance compared with regular hand view. Critically, these modulations were independent of hand posture and muscle homology. Thus, vision appears to contribute exclusively to spatial, but not to body-related, anatomical movement coding in the guidance of bimanual coordination.
Association of environmental markers with childhood type 1 diabetes mellitus revealed by a long questionnaire on early life exposures and lifestyle in a case-control study
Authors: Balazard F , Le Fur S , Valtat S ,   Isis-Diab collaborative group, Valleron AJ , Bougnères P 
Published: July 2016

AbstractBackgroundThe incidence of childhood type 1 diabetes (T1D) incidence is rising in many countries, supposedly because of changing environmental factors, which are yet largely unknown.PurposeTo unravel environmental markers associated with T1D. Methods: Cases were children with T1D from the French Isis-Diab cohort. Controls were schoolmates or friends of the patients. Parents were asked to fill a 845-item questionnaire investigating the child’s environment before diagnosis. The analysis took into account the matching between cases and controls. A second analysis used propensity score methods.ResultsWe found a negative association of several lifestyle variables, gastroenteritis episodes, dental hygiene, hazelnut cocoa spread consumption, wasp and bee stings with T1D, consumption of vegetables from a farm and death of a pet by old age.ConclusionsThe found statistical association of new environmental markers with T1D calls for replication in other cohorts and investigation of new environmental areas.
Fast genotyping of known SNPs through approximatek-mer matching
Authors: Shajii Ariya , Yorukoglu Deniz , Yu Y. William , Berger Bonnie 
Published: July 2016

AbstractMotivationAs the volume of next-generation sequencing (NGS) data increases, faster algorithms become necessary. Although speeding up individual components of a sequence analysis pipeline (e.g. read mapping) can reduce the computational cost of analysis, such approaches do not take full advantage of the particulars of a given problem. One problem of great interest, genotyping a known set of variants (e.g. dbSNP or Affymetrix SNPs), is important for characterization of known genetic traits and causative disease variants within an individual, as well as the initial stage of many ancestral and population genomic pipelines (e.g. GWAS).ResultsWe introduce LAVA (Lightweight Assignment of Variant Alleles), an NGS-based genotyping algorithm for a given set of SNP loci, which takes advantage of the fact that approximate matching of mid-sizek-mers (withk= 32) can typically uniquely identify loci in the human genome without full read alignment. LAVA accurately calls the vast majority of SNPs in dbSNP and Affymetrix’s Genome-Wide Human SNP Array 6.0 up to about an order of magnitude faster than standard NGS genotyping pipelines. For Affymetrix SNPs, LAVA has significantly higher SNP calling accuracy than existing pipelines while using as low as ~5GB of RAM. As such, LAVA represents a scalable computational method for population-level genotyping studies as well as a flexible NGS-based replacement for SNP arrays.AvailabilityLAVA software is available athttp://lava.csail.mit.edu.Contactbab@mit.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Using qualitative models to define sustainable management for the commons in data poor conditions
Authors: Mancini Francesca , Coghill George M. , Lusseau David 
Published: July 2016

AbstractNearly 50 years after Hardin’s “tragedy of the commons” we have not yet found predictive tools to guide us towards sustainable management of common-pool resources (CPR). We often have a good understanding of the qualitative relationships between the principal actors in socioecological systems (SESs), but classical quantitative approaches require a tremendous amount of data to understand the drivers of SESs sustainability. Here we show that qualitative modelling approaches can provide important governance insights for SESs that are understood but not quantified.We used Loop Analysis to test the outcomes of different management regimes on a simple nature-based tourism SES described by economic, social and environmental variables. We tested the sustainability of different management scenarios on this system and we identified the necessary conditions to achieve it.We found that management regimes where property rights and responsibilities are shared between different stakeholders are more likely to be successful. However, the system is generally highly unstable and it is important to tune each strategy to each particular situation.The conditions for sustainability found across the different systems tested were: a low reinvestment rate of tourist revenues into new infrastructures and a low growth rate of the environment. Management strategies based on maximum sustainable yield, which keep the environment far from its carrying capacity, have less chance to be sustainable.Qualitative models of SESs are powerful diagnostic tools; they can help identifying variables that play an important role in determining socioecological sustainability in data-poor circumstances and guide the design of efficient data collection programmes. Our results highlight the importance of careful planning when designing management strategies for nature-based tourism. The application of one-size-fits-all solutions to every situation is likely to lead to the failure of the commons; however tourism-based SESs can be sustainable if management strategies are tuned to each particular case.
The DELLA-CONSTANS Transcription Factor Cascade Integrates Gibberellic Acid and Photoperiod Signaling to Regulate Flowering
Authors: Wang Houping , Pan Jinjing , Li Yang , Lou Dengji , Hu Yanru , Yu Diqiu 
Published: July 2016

AbstractGibberellin (GA) and photoperiod pathways have recently been demonstrated to collaboratively modulate flowering under long days (LDs). However, the molecular mechanisms underlying this collaboration remain largely unclear. In this study, we found that GA-induced expression of FLOWERING LOCUS T (FT) under LDs was dependent on CONSTANS (CO), a critical transcription factor positively involved in photoperiod signaling. Mechanistic investigation revealed that DELLA proteins, a group of crucial repressors in GA signaling, physically interacted with CO. The DELLA-CO interactions repressed the transcriptional function of CO protein. Genetic analysis demonstrated that CO acts downstream of DELLA proteins to regulate flowering. Disruption of CO rescued the earlier flowering phenotype of the gai-t6 rga-t2 rgl1-1 rgl2-1 mutant (dellap), while a gain-of-function mutation in GA INSENSITIVE (GAI, a member of the DELLA gene) repressed the earlier flowering phenotype of CO-overexpressing plants. In addition, the accumulation of DELLA proteins and mRNAs was rhythmic, and REPRESSOR OF GA1-3 protein was noticeably decreased in the long-day afternoon, a time when CO protein is abundant. Collectively, these results demonstrate that the DELLA-CO cascade inhibits CO/FT-mediated flowering under LDs, which thus provide evidence to directly integrate GA and photoperiod signaling to synergistically modulate flowering under LDs.
The way justice unleashes staff’s compassion toward hotel guests
Authors: Zoghbi-Manrique-de-Lara Pablo , Guerra-Báez Rita M. 
Published: July 2016

PurposeThis paper aims to model staff reactions to a hotel based on the way they perceive hotel’s treatment of customers. It suggests that employees are not motivated to help abused customers in the form of customer-oriented behaviors (COBs) until employees also feel that they are victims of abuse by the hotel. Hence, effects of staff’s unfavorable justice perceptions for customers on employee COBs are expected to be negative until staff’s unfavorable justice perceptions for themselves, interacting in this relationship, turn it positive.Design/methodology/approachDrawing on social exchange and compassion theories, the argument is made that staff members who are also victims of abuse by the hotel can empathize more with guests, turning quid pro quo responses to abuse of customers into compassionate responses.FindingsRegression results from a field study of 280 employees at ten hotels in the Canary Islands provide general support for our hypotheses.Practical implicationsBy understanding when and why (un)fair treatment of guests and staff has consequences for the hotel in the form of COBs, hotel managers can favor a better staff response to hotels’ careful stewardship of the service encounter in terms of COBs. The reversal of the direction in the relationship suggests the unfolding of compassion within a justice framework, which challenges the long-lived perceived incompatibility between compassion and justice in the organizational literature.Originality/valueThe present study is the first one to study COBs stemming either from staff responses to hotels’ abuse of customers or COBs resulting from the interaction between perceived justice for customers and justice perceptions for themselves.
ERP and organizational change
Authors: Hassan Mostafa Kamal , Mouakket Samar 
Published: July 2016

Purpose
The study aims to explore the processes of implementing an enterprise resource planning (ERP) system in a public service organization operating in an emerging market economy, namely, the United Arab Emirates (UAE).

Design/methodology/approach
The study draws on Laughlin’s (1991) model of organizational change to highlight how the introduction of an ERP system, particularly its accounting modules, disrupted the adopting organization’s modes of thinking and its members’ practices. It uses a case study methodology. Data collection methods included semistructured interviews, documentary evidence and personal observation.

Findings
The case study findings show that despite implementation and customization problems, the organization’s employees were forced to use the ERP system. The findings also highlight how the ERP system was acted upon to mobilize the organization’s members toward a new era of information technology. However, the misfit between pre- and post-ERP system accounting practices led to some organizational members to form absorbing groups that questioned accounting-based ERP system organizational changes. The top management’s persistent desire to adopt the ERP system through forcing the organization’s employees to use the system’s modules led the organization to undergo what Laughlin (1991) calls “colonization” organizational change.

Research limitation/implications
The use of a case study methodology inherently limits the generalizability of the study’s findings. The case study was carried out over a relatively short timeframe, namely, ten months. Therefore, the use of a longitudinal case study to examine accounting-based ERP organizational change is recommended.

Practical implications
The study provides insights that can assist top management in formulating organizational change strategies. It also provides insights about emerging economies’ regulatory particularities that influence ERP system implementation.

Originality/value
The study is one of the first studies that utilizes Laughlin’s (1991) model of organizational change to examine accounting-based ERP organizational change in an emerging market economy.
Sensemaking of organizational innovation and change in public research organizations
Authors: Martin-Rios Carlos 
Published: July 2016

PurposeThe purpose of this paper is to examine through a sensemaking lens the transforming nature of scientists’ work role in public research organizations (PROs), resulting from organizational innovations in the form of collaborative culture.Design/methodology/approachBased on a symbolic-functionalist theory of work role transition, the paper uses interview data from a case study to explore scientists’ sensemaking of work role change.FindingsWork role transition and identity processes among scientists in traditional PROs reveal tensions regarding organizational restructuring to the extent that organizational innovations are changing scientific work conflict with organizational norms, procedures and reward structures in hierarchical, bureaucratic PROs.Research limitations/implicationsAs the paper is based on only one case study, further research should be carried out on the difficulties involved in transforming the nature of the scientific work role and the way scientists recognize, contradict and make sense of changes.Originality/valueThe novelty of this paper is in the un-discussed role of organizational innovations in enabling new work roles for scientists in public research centers and how scientists make sense of and react to these innovations. Therefore, this paper could be beneficial for PROs facing pressure to restructure.
Work role stressors and employee outcomes
Authors: Chhabra Bindu 
Published: July 2016

PurposeThe purpose of the present study was to explore the direct effects of work role stressors and subjective fit perceptions on the employee outcomes of job satisfaction, organizational citizenship behavior (OCB) and turnover intentions. The study further aimed to investigate the moderating role of person-organization (P-O) fit, demands-abilities (D-A) fit and needs supplies (N-S) fit in the relationship between work role stressors and the aforementioned employee outcomes.Design/methodology/approachThe study was conducted using structured questionnaires for measuring the aforementioned variables. The sample of the study was 317 professionals from five sectors. Hierarchical multiple regression was used to analyze the data.FindingsHierarchical multiple regression showed that the work role stressors were negatively related to job satisfaction and OCB and positively related to turnover intentions. Subjective fit was seen to be positively related to job satisfaction and OCB and negatively related to turnover intentions. The analysis also found some support for the stress buffering effect of high subjective fit in the prediction of job satisfaction, OCB and turnover intentions.Research limitations/implicationsThis study contributes to the organizational behavior literature by focusing on the fact that the negative effects of work role stressors on employee outcomes can be mitigated by identifying the variables which act as a buffer to weaken this effect. The results of the study highlight the importance of the concept of subjective fit for the managers and the employees to help them in coping up with the demands of the job. They provide support for the fact that matching employees to their organization and job can help in the mitigation of employees’ stress, resulting in positive employee outcomes, hence benefiting the organization in the long run.Originality/valueThe study is the first of its kind to investigate the moderating role of P-O fit, D-A fit and N-S perceptions in the relationship between work role stressors and employee outcomes, especially in the Indian context.
Development of the yield-based process capability index, C

py
, to flexibly and accurately measure conformance
Authors: Kenyon George N , Sale R. Samual , Hozak Kurt , Chiou Paul 
Published: July 2016

Purpose
– The purpose of this paper is to develop an yield-based process capability index (PCI), C

py
, to overcome the shortcomings of existing PCIs that limit their use and lead to inaccurate measures of quality conformance under a variety of common conditions.

Design/methodology/approach
–C

py
is developed conceptually to flexibly and accurately reflect conformance and then used to numerically measure inaccuracies of C

pk
.

Findings
–C

py
overcomes many of the problems associated with existing PCIs, including C

pk
. The degree of process distribution non-normality, level of quality (the sigma level), and whether the process is centered or shifted left or right affect the direction and size of process capability error produced by C

pk
. The accuracy of C

pk
can be greatly affected by process data that deviate even slightly from normality.

Practical implications
–C

py
offers numerous advantages compared to existing PCIs. It accurately reflects process conformance regardless of the process distribution. It is applicable even if the process has multiple characteristics and with both variable and attribute data. Its calculation is relatively simple and the necessary data for it are likely already captured by most organizations.

Originality/value
– The main contributions are the development of a new PCI, C

py
; a conceptual analysis of its advantages; and a numerical analysis of the improved accuracy of C

py
as compared to C

pk
for shifted and non-shifted process means for normal, nearly normal, and highly non-normal distributions over a range of process variability levels.
Modelling satisfaction-commitment relationship in developing country context
Authors: Fatima Johra Kayeser , Razzaque Mohammed Abdur , Di Mascio Rita 
Published: July 2016

Purpose– Considering the significance of customer satisfaction and commitment in the competitive banking industry of developing countries, the purpose of this paper is to investigate the alternative relationships of satisfaction with various types of commitment, benefits, quality and trust. It also attempts to identify the interrelationships among three types of trust, namely, competence, contractual and goodwill, as well as affective, calculative and normative commitment.Design/methodology/approach– Structural equation modelling (AMOS-based) is used to analyse data collected from a survey of 212 bank customers in Bangladesh.Findings– Findings show that satisfaction has a significant impact on affective, calculative and normative commitment, as well as on competence, contractual and goodwill trust. While core and relational service qualities, and confidence and social benefits influence the level of satisfaction, tangible service quality and special treatment benefit seem to have no significant effect on satisfaction. Finally, all three types of trust are found to have a strong influence on affective commitment; however, contractual trust and competence trust are found to have no impact on calculative and normative commitment.Practical implications– The paper provides insights for bank management in order to understand the relative importance of each type of trust, commitment, quality and benefit, and their relationships with satisfaction.Originality/value– It is the first to take the initiative to test a large range of relationships in a single study to better understand customer satisfaction in the banking industry in a developing country context.