bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstructing cancer karyotypes from short read data: the half full and half empty glass
Authors: Eitan Rami , Shamir Ron 
Published: June 2017

AbstractBackgroundDuring cancer progression genomes undergo point mutations as well as larger segmental changes. The latter include, among others, segmental deletions duplications, translocations and inversions. The result is a highly complex, patient-specific cancer karyotype. Using high-throughput technologies of deep sequencing and microarrays it is possible to interrogate a cancer genome and produce chromosomal copy number profiles and a list of breakpoints (“jumps”) relative to the normal genome. This information is very detailed but local, and does not give the overall picture of the cancer genome. One of the basic challenges in cancer genome research is to use such information to infer the cancer karyotype.We present here an algorithmic approach, based on graph theory and integer linear programming, that receives segmental copy number and breakpoint data as input and produces a cancer karyotype that is most concordant with them. We used simulations to evaluate the utility of our approach, and applied it to real data.ResultsBy using a simulation model, we were able to estimate the correctness and robustness of the algorithm in a spectrum of scenarios. Under our base scenario, designed according to observations in real data, the algorithm correctly inferred 69% of the karyotypes. However, when using less stringent correctness metrics that account for incomplete and noisy data, 87% of the reconstructed karyotypes were correct. Furthermore, in scenarios where the data were very clean and complete, accuracy rose to 90%-100%. Some examples of analysis of real data, and the karyotypes reconstructed by our algorithm, are also presented.ConclusionWhile reconstruction of complete, perfect karyotype based on short read data is very hard, a large portion of the reconstruction will still be correct and can provide useful information.
Engineering Cell Sensing and Responses Using a GPCR-Coupled CRISPR-Cas System
Authors: Dingal P. C. Dave P. , Kipniss Nathan H. , Labanieh Louai , Gao Yuchen , Qi Lei S. 
Published: June 2017

AbstractG-protein coupled receptors (GPCRs) are the largest and most diverse group of membrane receptors in eukaryotes, and detects a wide array of physiological cues in the human body. We describe a new molecular device that couples CRISPR-Cas9 programmed genome regulation to natural and synthetic extracellular signals via GPCRs. The design of our synthetic device, named CRISPR ChaCha, displays superior performance over an architecture proposed by the previously reported Tango system. Using a parsimonious mathematical model and gene-reporter assays, we find that CRISPR ChaCha can recruit and activate multiple Cas9 molecules for each GPCR molecule. We also characterize key molecular features that modulate CRISPR ChaCha performance. We adopt the design to diverse GPCRs that sense synthetic and natural ligands including chemokines, mitogens, and fatty acids, and observe efficient conversion of signals to customizable genetic programs in mammalian cells, including regulation of endogenous genes. The new class of CRISPR-coupled GPCRs provides a robust and efficient platform for engineering cells with novel behaviors in response to the diverse GPCR ligand repertoire.
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
Authors: Menschaert Gerben , Wang Xiaojing , Jones Andrew R. , Ghali Fawaz , Fenyö David , Olexiouk Volodimir , Zhang Bing , Deutsch Eric W. , Ternent Tobias , Vizcaíno Juan Antonio 
Published: June 2017

SummaryOn behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI), we are here introducing two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of integrating mass spectrometry based proteomics data with genomics and transcriptomics information in proteogenomics studies. proBAM and proBed are adaptations from the well-defined, widely used file formats SAM/BAM and BED respectively, and both have been extended to meet specific requirements entailed by proteomics data. Therefore, existing popular genomics tools such as SAMtools and Bedtools, and several very popular genome browsers, can be used to manipulate and visualize these formats already out-of-the-box. We also highlight that a number of specific additional software tools, properly supporting the proteomics information available in these formats, are now available providing functionalities such as file generation, file conversion, and data analysis. All the related documentation to the formats, including the detailed file format specifications, and example files are accessible athttp://www.psidev.info/probamandhttp://www.psidev.info/probed.
Sex differences in gene regulation in the dorsal root ganglion after nerve injury
Authors: Stephens Kimberly E. , Zhou Weiqiang , Ji Zhicheng , He Shaoqiu , Ji Hongkai , Guan Yun , Taverna Sean D. 
Published: June 2017

ABSTRACTPain is a subjective experience derived from complex interactions among biological, environmental, and psychosocial pathways. Sex differences in pain sensitivity and chronic pain prevalence are well established. However, the molecular causes underlying these sex dimorphisms are poorly understood particularly with regard to the role of the peripheral nervous system. Here we sought to identify shared and distinct gene networks functioning in the peripheral nervous systems that may contribute to sex differences of pain after nerve injury. We performed RNA-seq on dorsal root ganglia following chronic constriction injury of the sciatic nerve in male and female rats. Analysis from paired naive and injured tissues showed that 1456 genes were differentially expressed between sexes. Appreciating sex-related gene expression differences and similarities in neuropathic pain models may help to improve the translational relevance to clinical populations and efficacy of clinical trials of this major health issue.
Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large scale genetic studies
Authors: Atkinson Jonathan A. , Lobet Guillaume , Noll Manuel , Meyer Patrick E. , Griffiths Marcus , Wells Darren M. 
Published: June 2017

AbstractBackgroundGenetic analyses of plant root system development require large datasets of extracted architectural traits. To quantify such traits from images of root systems, researchers often have to choose between automated tools (that are prone to error and extract only a limited number of architectural traits) or semi-automated ones (that are highly time consuming).FindingsWe trained a Random Forest algorithm to infer architectural traits from automatically-extracted image descriptors. The training was performed on a subset of the dataset, then applied to its entirety. This strategy allowed us to (i) decrease the image analysis time by 73% and (ii) extract meaningful architectural traits based on image descriptors. We also show that these traits are sufficient to identify Quantitative Trait Loci that had previously been discovered using a semi-automated method.ConclusionsWe have shown that combining semi-automated image analysis with machine learning algorithms has the power to increase the throughput in large scale root studies. We expect that such an approach will enable the quantification of more complex root systems for genetic studies. We also believe that our approach could be extended to other area of plant phenotyping.
Olfactory learning primes the heat shock transcription factor HSF-1 to enhance the expression of molecular chaperone genes inC. elegans
Authors: Ooi Felicia K. , Prahlad Veena 
Published: June 2017

AbstractLearning, a process by which animals modify their behavior as a result of experience, allows organisms to synthesize information from their surroundings to acquire resources and predict danger. Here we show that prior encounter with the odor of pathogenic bacteria preparesCaenorhabditis elegansto survive actual exposure to the pathogen by increasing HSF-1-dependent expression of genes encoding molecular chaperones. Learning-mediated enhancement of chaperone gene expression requires serotonin. Serotonin primes HSF-1 to enhance the expression of molecular chaperone genes by promoting its localization to RNA polymerase II–enriched nuclear loci, even prior to transcription. HSF-1-dependent chaperone gene expression ensues, however, only if and when animals encounter the pathogen. Thus, learning equipsC. elegansto better survive environmental dangers by pre-emptively and specifically initiating transcriptional mechanisms throughout the whole organism. These studies provide one plausible basis for the protective role of environmental enrichment in disease.
Striatal fast-spiking interneurons drive habitual behavior
Authors: O’Hare Justin K. , Li Haofang , Kim Namsoo , Gaidis Erin , Ade Kristen K. , Beck Jeffrey M. , Yin Henry H. , Calakos Nicole 
Published: June 2017

AbstractHabit formation is a behavioral adaptation that automates routine actions. Habitual behavior correlates with broad reconfigurations of dorsolateral striatal (DLS) circuit properties that increase gain and shift pathway timing. The mechanism(s) for these circuit adaptations are unknown and could be responsible for habitual behavior. Here we find that a single class of interneuron, fast-spiking interneurons (FSIs), modulates all of these habit-predictive properties. Consistent with a role in habits, FSIs are more excitable in habitual mice compared to goal-directed and acute chemogenetic inhibition of FSIs in DLS prevents the expression of habitual lever pressing.In vivorecordings further reveal a previously unappreciated selective modulation of SPNs based on their firing patterns; FSIs inhibit most SPNs but paradoxically promote the activity of a subset displaying high fractions of gamma-frequency spiking. These results establish a microcircuit mechanism for habits and provide a new example of how interneurons mediate experience-dependent behavior.
Investigating performance indicators disclosure in sustainability reports of large mining companies in Ghana
Authors: Arthur Clement Lamboi , Wu Junjie , Yago Milton , Zhang Jinhua 
Published: June 2017

Purpose
The purpose of this study is to examine the degree, contents and trend development of Global Reporting Initiative (GRI) performance indicators disclosed in sustainability reports of large mining companies in Ghana.

Design/methodology/approach
Content analysis methods are used to analyse 50 sustainability reports of ten large-scale mining companies in Ghana, covering the period 2008-2012.

Findings
The study finds that there has been a widening and increasing trend in the disclosure of performance indicators in sustainability reports of the large mining companies in Ghana, in accordance with GRI guidelines. The findings suggest that good progress in the strategic sector has been made in the voluntary adoption of the GRI guidelines to increase transparency, credibility and comparability in sustainability reporting. The findings also indicate areas to be improved.

Practical implications
The Government of Ghana and the Ghana Chamber of Mines could learn from the findings about the current status of this matter in order for them to formulate policies and regulations which would encourage the mining sector in moving forward in the adoption of international reporting standards.

Originality/value
This paper initializes investigation into the degree, contents and trends of performance indicators in sustainability reports of large mining companies in Ghana using content analysis.
Corporate governance codes of Eurasian Economic Union countries: a comparative investigation
Authors: Nizaeva Mirgul , Uyar Ali 
Published: June 2017

Purpose
The purpose of this paper is to comparatively analyze the corporate governance codes of transition economies, particularly five Eurasian Economic Union (EAEU) members (i.e. Russia, Belarus, Kazakhstan, Kyrgyzstan and Armenia). Specifically, the convergence or divergence of these countries’ corporate governance codes among themselves as well as relative to the best practices of the UK Corporate Governance Code (UK Code) and the OECD Principles of Corporate Governance are investigated.

Design/methodology/approach
Initially, the existing literature on corporate governance with special focus on transition countries is reviewed. Afterwards, benchmarking the international best practices, based on main chapters and contents, the corporate governance codes of all countries in the sample are analyzed.

Findings
The paper finds that even though some principles of the corporate governance codes of the countries in the sample differ in some aspects, they do converge to some extent. However, high misalignments between the UK Code and the OECD Principles and the codes of selected countries in some aspects were found.

Research limitations/implications
The conclusion and implications of the study characterize the corporate governance of selected developing countries; thus, they might not be generalizable to other countries.

Practical implications
The codes of the countries in the sample should be revised, and more specifications regarding the stakeholder, board structure, its subcommittees, independence, diversity and transparency issues need to be addressed.

Originality/value
The paper comprehensively analyzes the contents of corporate governance codes of transition countries; from both practical and academic point of view, it was important gap that needed to be fulfilled.
On-work or off-work relationship? An engagement model of how and when leader–member exchange and leader–memberguanxipromote voice behavior
Authors: Song Xiaoling , Wu Wen , Hao Shengyue , Lu Xiaohua , Zhang Yihua , Liu Yuhuan 
Published: June 2017

PurposeDrawing on engagement theory, this study aims to examine how leader–member relationships, including on-work relationship (leader–member exchange [LMX]) and off-work relationship (leader–memberguanxi[LMG]), influence employees’ promotive and prohibitive voice. Furthermore, the study uses procedural justice as the moderator to distinguish the effects of LMG and LMX on employees’ psychological states and voice through a mediated moderation model.Design/methodology/approachThe authors use a sample from a private and local company in Southern China to test their theoretical model.FindingsThe study finds that both LMG and LMX have positive effects on employees’ voice behavior through employees’ psychological states (psychological meaningfulness and psychological safety).Research limitations/implicationsIn a Chinese context, leaders have a more direct and powerful influence on employees than their counterparts in the Western society. Thus, the findings of LMX and LMG may not be generalizable to a Western context. A possible extension is to examine and compare the effects of social context (e.g., off-work leader–member relationship) on voice between the East and the West.Practical implicationsOne important implication is that off-work relationship should be used by managers to encourage employee voice.Originality/valueThis study enriches the antecedents of voice with a new dimension of leader–member relationship, namely, LMG.
The effect of structure centrality on employees’ performance: evidence from Chinese SMEs
Authors: Cai Meng , Du Haifeng 
Published: June 2017

PurposeThe complicated social relationship in Chinese culture requires human resource management (HRM) practitioners to be aware of the implications of social network. This paper aims to disclose the relevance between social network structure and employees’ performance.Design/methodology/approachAn empirical research is exploited in this paper. Based on cluster sampling method, the authors collected 336 employees’ socio-demographic characteristic data and social network data by means of face-to-face interviews using the structured questionnaire. In addition, employees’ performance data were obtained from the financial department, to support subsequent correlation analysis, grey relational analysis and OLS regression analysis.FindingsThe informal network, rather than the formal network, was observed to contribute more toward employees’ individual performance. We further found that structure centrality has a distinct advantage in delineating an individual’s power and status in the network, success over degree centrality, thus predicting individual performance.Practical implicationsFor the management practice of an organization, the present study’s empirical results demonstrate that informal relations have a more decisive influence on individual performance than formal relations. This research also found that the structure centrality, from the perspective of networks’ structure heterogeneity, is valuable in discovering crucial staff in social networks, especially those in informal network associations.Originality/valueFirst, the relations between network structure and individual performance have been summarized. Second, the different influences between formal and informal networks on individual performance have been discussed. Third, a new index – structure centrality to recapitulate network structure for developing social network theory – introduced. Finally, this paper is an attempt to explore the associations between social network structure and employees’ performance from the perspective of the whole network.
Emergence of organizational routines in entrepreneurial ventures
Authors: Lin Haifen , Murphree Michael , Li Sali 
Published: June 2017

PurposeThe purpose of this paper is to expand the understanding of the process by which organizational routines emerge in entrepreneurial ventures. The emphasis is on the role of management and interaction in shaping shared schemata among members of the enterprise.Design/methodology/approachThis paper uses a longitudinal interpretive and exploratory case study based on semi-structured interviews, archival material and naturalistic observation at a startup enterprise in China.FindingsFocusing on the process through which shared schemata emerge to lay the foundation for routines in new firms, the authors find shared schemata emerge through a three-stage process: individual schemata emergence, partially shared schemata emergence and organizationally shared schemata emergence. Analogical transfer, strong foundational leadership and horizontal interaction among employees facilitate the development of individual schemata and their evolution into the shared schemata underlying organizational routines.Research limitations/implicationsThis paper contributes to the understanding of routine formation in entrepreneurial ventures by creating a framework of the stages of development of organizational routines, as well as the role management plays in each stage. This contribution fits within the emergent field of microfoundations, linking individual actions and cognition to organizational outcomes and adding to this the contribution of social interaction.Practical implicationsManagers in new Chinese enterprises could benefit from understanding the importance of routinization and the managerial approaches which facilitate routine formation. This will increase the likelihood of firm survival as well as the competitive strength of the firm.Originality/valueTo date, there has been little research on how routines arise in entrepreneurial ventures, and none on explicitly the role for management and interaction in fostering routinization.
Numerical simulations of non-stationary distributions of electrochemical potentials in SOFC
Authors: Muramatsu Mayu , Yashiro Keiji , Kawada Tatsuya , Tarada Kenjiro 
Published: June 2017

PurposeThe purpose of this study is to develop a simulation method to calculate non-stationary distributions of the chemical potential of oxygen in a solid oxide fuel cell (SOFC) under operation.Design/methodology/approachThe initial-boundary value problem was appropriately formulated and the appropriate boundary conditions were implemented so that the problem of non-stationary behavior of SOFC can be solved in accordance with actual operational and typical experimental conditions. The dependencies of the material properties on the temperature and partial pressure of oxygen were also elaborately introduced to realize actual material responses. The capability of the proposed simulation method was demonstrated under arbitrary operating conditions.FindingsThe steady state calculated with the open circuit voltage condition was conformable with the analytical solution. In addition, the transient states of the spatial distributions of potentials and currents under the voltage- and current-controlled conditions were successfully differentiated, even though they eventually became the same steady state. Furthermore, the effects of dense materials assumed for interconnects and current collectors were found to not be influential. It is thus safe to conclude that the proposed method enables us to simulate any type of transient simulations regardless of controlling conditions.Practical implicationsAlthough only uniaxial models were tested in the numerical examples in this paper, the proposed method is applicable for arbitrary shapes of SOFC cells.Originality/valueThe value of this paper is that adequate numerical simulations by the proposed method properly captured the electrochemical transient transport phenomena in SOFC under various operational conditions, and that the applicability was confirmed by some numerical examples.
Modelling trajectories of solid particle motion in the cyclone
Authors: Baltrėnas Pranas , Leonavičienė Teresė 
Published: June 2017

Purpose
This purpose of the paper is to examine the multi-channel cyclone created at the Vilnius Gediminas Technical University (VGTU) Research Institute of Environmental Protection. The paper aims to predict the possible trajectories of solid particle motion in the cyclone with reference to the mechanical forces only.

Design/methodology/approach
The numerical calculations were performed on the basis of experimental results. The system of differential equations describing particle motion in the cyclone is analysed and numerically solved using Runge–Kutta–Fehlberg method. Research consists of three examples that illustrate the impact of particle density and velocity on collection and analyses the particle motion trajectories in the first and second channels of the cyclone.

Findings
Numerical calculations were performed according to the data from Vilnius Gediminas Technical University Research Institute of Environmental Protection. The particulate matter of wood ash and granite were used. The collection of solid particles of different size was examined when the air inflow velocity varies from 10 to 20 m/s. The possible motion trajectories of the solid particles are defined and the parameters of collected particles have been discussed.

Research limitations/implications
The obtained results can be used for the analysis of air cleaning efficiency and particulate matter removal from air in a multi-channel cyclone.

Practical implications
The results lead us to improve the structure of the cyclone so as to effectively collect the solid particles of different size.

Originality/value
This paper presents the results obtained for the multi-channel cyclone created at the Vilnius Gediminas Technical University Research Institute of Environmental Protection.