bluuebunny/crossref_metadata_2025_split huggingface dataset:
UPDtool: a tool for detection of iso- and heterodisomy in parent–child trios using SNP microarrays
Authors: Schroeder Christopher , Sturm Marc , Dufke Andreas , Mau-Holzmann Ulrike , Eggermann Thomas , Poths Sven , Riess Olaf , Bonin Michael 
Published: April 2013

Abstract
Summary: UPDtool is a computational tool for detection and classification of uniparental disomy (UPD) in trio SNP-microarray experiments. UPDs are rare events of chromosomal malsegregation and describe the condition of two homologous chromosomes or homologous chromosomal segments that were inherited from one parent. The occurrence of UPD can be of major clinical relevance. Though high-throughput molecular screening techniques are widely used, detection of UPDs and especially the subclassification remains complex. We developed UPDtool to detect and classify UPDs from SNP microarray data of parent–child trios. The algorithm was tested using five positive controls including both iso- and heterodisomic segmental UPDs and 30 trios from the HapMap project as negative controls. With UPDtool, we were able to correctly identify all occurrences of non-mosaic UPD within our positive controls, whereas no occurrence of UPD was found within our negative controls. In addition, the chromosomal breakage points could be determined more precisely than by microsatellite analysis. Our results were compared with both the gold standard, microsatellite analysis and SNPtrio, another program available for UPD detection. UPDtool is platform independent, light weight and flexible. Because of its simple input format, UPDtool may also be used with other high-throughput technologies (e.g. next-generation sequencing).
Availability and implementation: UPDtool executables, documentation and examples can be downloaded from http://www.uni-tuebingen.de/uni/thk/de/f-genomik-software.html.
Contact: christopher.schroeder@med.uni-tuebingen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Learning gene network structure from time laps cell imaging in RNAi Knock downs
Authors: Failmezger Henrik , Praveen Paurush , Tresch Achim , Fröhlich Holger 
Published: April 2013

Motivation: As RNA interference is becoming a standard method for targeted gene perturbation, computational approaches to reverse engineer parts of biological networks based on measurable effects of RNAi become increasingly relevant. The vast majority of these methods use gene expression data, but little attention has been paid so far to other data types.
Results: Here we present a method, which can infer gene networks from high-dimensional phenotypic perturbation effects on single cells recorded by time-lapse microscopy. We use data from the Mitocheck project to extract multiple shape, intensity and texture features at each frame. Features from different cells and movies are then aligned along the cell cycle time. Subsequently we use Dynamic Nested Effects Models (dynoNEMs) to estimate parts of the network structure between perturbed genes via a Markov Chain Monte Carlo approach. Our simulation results indicate a high reconstruction quality of this method. A reconstruction based on 22 gene knock downs yielded a network, where all edges could be explained via the biological literature.
Availability: The implementation of dynoNEMs is part of the Bioconductor R-package nem.
Contact: frohlich@bit.uni-bonn.de
Supplementary information: Supplementary Data are available at Bioinformatics online.
Deletion of the Transcriptional Regulator cyAbrB2 Deregulates Primary Carbon Metabolism in Synechocystis sp. PCC 6803
Authors: Kaniya Yuki , Kizawa Ayumi , Miyagi Atsuko , Kawai-Yamada Maki , Uchimiya Hirofumi , Kaneko Yasuko , Nishiyama Yoshikata , Hihara Yukako 
Published: April 2013

Abstract
cyAbrB is a transcriptional regulator unique to and highly conserved among cyanobacterial species. A gene-disrupted mutant of cyabrB2 (sll0822) in Synechocystis sp. PCC 6803 exhibited severe growth inhibition and abnormal accumulation of glycogen granules within cells under photomixotrophic conditions. Within 6 h after the shift to photomixotrophic conditions, sodium bicarbonate-dependent oxygen evolution activity markedly declined in the ƊcyabrB2 mutant, but the decrease in methyl viologen-dependent electron transport activity was much smaller, indicating inhibition in carbon dioxide fixation. Decreases in the transcript levels of several genes related to sugar catabolism, carbon dioxide fixation, and nitrogen metabolism were also observed within 6 h. Metabolome analysis by capillary electrophoresis mass spectrometry revealed that several metabolites accumulated differently in the wild-type and mutant strains. For example, the amounts of pyruvate and 2-oxoglutarate (2OG) were significantly lower in the mutant than in the wild type, irrespective of trophic conditions. The growth rate of the ƊcyabrB2 mutant was restored to a level comparable to that under photoautotrophic conditions by addition of 2OG to the growth medium under photomixotrophic conditions. Activities of various metabolic processes, including carbon dioxide fixation, respiration, and nitrogen assimilation, seemed to be enhanced by 2OG addition. These observations suggest that cyAbrB2 is essential for the active transcription of genes related to carbon and nitrogen metabolism upon a shift to photomixotrophic conditions. Deletion of cyAbrB2 is likely to deregulate the partition of carbon between storage forms and soluble forms used for biosynthetic purposes. This disorder may cause inactivation of cellular metabolism, excess accumulation of reducing equivalents, and subsequent loss of viability under photomixotrophic conditions.
Essential elements for recruitment and retention: Generation Y
Authors: Luscombe Jenna , Lewis Ioni , Biggs Herbert C. 
Published: April 2013

PurposeGeneration Y (Gen Y) is the newest and largest generation entering the workforce. Gen Y may differ from previous generations in work‐related characteristics which may have recruitment and retention repercussions. Currently, limited theoretically‐based research exists regarding Gen Y's work expectations and goals in relation to undergraduate students and graduates. The aim of this paper is to attempt to address this gap in the research.Design/methodology/approachThis study conducted a theoretically‐based investigation of the work expectations and goals of Generation Y and, in particular, student Gen Y versus working Gen Y individuals based within a framework incorporating both expectancy‐value and goal setting theories. n=398 provided useable data via an on‐line survey.FindingsOverall, some support was found for predictions with career goals loading on a separate component to daily work expectations and significant differences between students and working Gen Y on career goals. No significant differences were found, however, between the two groups in daily work expectations.Research limitations/implicationsFuture research studies may benefit from adopting a theoretical framework which assesses both daily work expectations and career goals. At a practical level, based on the findings, some examples are provided of the means by which organisations may draw upon daily work expectations and career goals of importance to Gen Y and, in doing so, influence the likelihood that a Gen Y individual will join and remain at their particular organisation.Originality/valueThis research has demonstrated the utility of adopting a sound theoretical framework in furthering understanding about the motivations which influence an organisations’ ability to recruit and retain Gen Y.
The influence of high performance work systems on voluntary turnover of new hires in US state governments
Authors: Selden Sally , Schimmoeller Lee , Thompson Reese 
Published: April 2013

PurposeThis article aims to examine factors associated with new employee turnover in US state governments, where turnover is often highest in organizations. Building on existing studies of high performance work systems (HPWS) turnover, this article develops a set of hypotheses to explain new hire turnover.Design/methodology/approachThe proposed model has been analyzed with a sample of 42 of the 50 US state governments.FindingsPractices associated with HPWS influence turnover of new hires. State governments that operate centralized college recruiting programs, pay higher salaries, offer pay for performance incentives, award group bonuses, invest more in training, and allow job rotation lose significantly fewer new hires.Research limitations/implicationsThis study is limited to specific variables collected in an online survey of states' central human resource departments. Future research may want to focus on other levels of government, include additional practices associated with HPWS, and examine measures of government performance.Practical implicationsThis study stresses the importance of HPWS and how HRM practices impact new employees' decisions to stay or leave an organization. This information will provide an opportunity for actionable knowledge to be created that may help practitioners design and administer programs to reduce new hire turnover.Originality/valueThis study has extended a well‐developed body of knowledge on HPWS to government. Since most HPWS and turnover studies focus on turnover more broadly and since turnover is often highest among new hires, this research extends the HPWS framework to an important outcome, new hire quit rates.
The call center as a revolving door: a Philippine perspective
Authors: Regina M. Hechanova Ma. 
Published: April 2013

PurposeThis study sought to explain the high turnover rates in Philippine call centers using a cultural lens. Specifically, the study looks at the phenomenon of work‐life conflict and its impact on turnover intent. It also examined the moderating role of perceived organization support on the relationship between work‐life conflict and turnover intent.Design/methodology/approachThe study utilized a two‐phased, mixed‐method approach. In the first phase, qualitative data from 30 interviews were obtained to validate the existence of the constructs among Filipino call center agents. In the second phase, 991 surveys were administered to quantitatively test the hypothesized relationships between the study variables.FindingsResults show that work‐life conflict predicts intent to leave over and beyond that explained by job satisfaction. Findings also show that organizational support moderates the relationship between work‐life conflict and intent to leave. The results also reveal the context‐specific sources of work‐life conflict: physical and psychological impact of work schedule, social isolation and lack of social support.Research limitations/implicationsThe study focused on work‐life conflict and perceived organizational support. However, there are other variables that may be examined in future research such as personality, family, and organizational variables.Practical implicationsBeyond the traditional responses to the issue of work‐life conflict, the results suggest the importance of cultural nuanced responses to address work‐life conflict.Social implicationsAlthough outsourcing is a boon to the economy of developing countries, policies encouraging call centers need to be coupled with an understanding of the personal and social costs of call center work.Originality/valueThis study highlights the importance of considering culture in viewing management practices and their impact on workers' behavior and wellbeing. It calls attention to the unique experience of call centers in developing countries and the importance of developing work‐life interventions that are contextualized to local culture.
Agency conflicts and the demand for non‐audit services
Authors: Quick Reiner , Sattler Matthias , Wiemann Daniela 
Published: April 2013

PurposeThe aim of the present paper is to examine the impact of agency costs on the demand for non‐audit services (NAS) in Germany.Design/methodology/approachThis study uses data from German listed companies to test whether audit clients vary their purchases of NAS according to agency costs over time. The paper used multiple regressions and included ownership composition, performance‐based management compensation, and leverage as proxies for agency conflicts.FindingsOverall, the hypothesis that agency costs influence the demand for NAS was not confirmed. None of our proxies for agency conflicts were significantly associated with the purchase of NAS. These findings remain stable when alternative NAS fee measures were applied.Research limitations/implicationsFindings cannot be generalised for smaller, private companies. Particularities of the German setting might have caused the insignificance of agency costs, but this cannot be tested statistically. The contrast between these insignificant results and the significant impact of agency costs on the demand for non‐audit services revealed by many previous studies, in particular from the US and the UK, raises important questions for future research.Practical implicationsThis paper concerns management's perceptions on how stakeholders perceive the effect of NAS provision on auditor independence. Thus, its findings should be of interest to German, European and international regulators when evaluating the impact of the provision of NAS on independence in appearance.Originality/valueThis study is the first to provide evidence on the relationship between agency conflicts and the demand for non‐audit services from Germany and thus from a continental European country. Moreover, it provides evidence for periods after the introduction of stricter standards on the provision of non‐audit services. In addition, it applies a new proxy for agency costs (i.e. performance‐based management compensation).
M×N‐ary chaotic pulse‐width‐position modulation
Authors: Xuan Quyen Nguyen , Van Yem Vu , Manh Hoang Thang , Kyamakya Kyandoghere 
Published: April 2013

PurposeThis paper presents and investigates a method named M×N‐ary chaotic pulse‐width‐position modulation (CPWPM) which is based on the combination of M‐ary chaotic pulse‐position modulation (CPPM) and N‐ary chaotic pulse‐width modulation (CPWM) in order to provide a better performance in noise‐affected environments as well as improve significantly bit rate.Design/methodology/approachAnalysis of schemes for modulator and demodulator are presented in detail through describing the schemes of the individual methods and their combination. Theoretical evaluation of bit‐error rate (BER) performance in presence of additive white Gaussian noise (AWGN) is provided. Chaotic behavior with tent map in variation of modulation parameters is also investigated. In order to verify the theoretical analyses, numerical simulations are carried out and their results are reported.FindingsBoth evaluation and simulation results show that when the number of symbols increases, the bit rate is improved significantly but the BER performance is just slightly worse. This makes M×N‐ary CPWPM become an effective method for chaos‐based digital communication.Originality/valueAlthough CPPM, CPWM and M‐ary modulation methods have been described in the literature separately, their combination is presented and investigated for the first time in this paper.
Determining the active and reactive power range in AC circuits
Authors: Kolev Lubomir 
Published: April 2013

PurposeThe purpose of this paper is to suggest a polynomial complexity method for determining the range of the active and reactive power consumed in AC uncertain parameter circuits whose uncertain parameters are given as intervals.Design/methodology/approachFirst, the original problem is formulated as a corresponding interval quadratic range determination (IQRD) problem. Next, it is shown that the IQRD problem can be transformed equivalently into an interval linear range determination (ILRD) problem.FindingsAn efficient numerical method for solving the associated ILRD problem has been developed, capable of tackling the present active (or reactive) power range problem. It is based on the use of the outer solution y of an associated interval linear system defining the constraints in the ILRD problem.Research limitations/implicationsThe method yields the exact active and reactive power range if the number of the components yi of y containing zero is relatively small (which is most often the case); otherwise, it provides tight outer bounds on the ranges sought.Practical implicationsThe present method can be an alternative to the widely used Monte‐Carlo method since the former method provides exact (within rounding errors) results or tight outer approximations for lesser computation times.Originality/valueTo the best of the author's knowledge, the present paper suggests, for the first time, a simple interval analysis method of polynomial complexity for solving the problem considered which is inherently a NP‐hard problem (of exponential complexity).
Multi‐moment statistical characterization and nonlinear filtering of chaos
Authors: Kontorovich Valeri , Lovtchikova Zinaida 
Published: April 2013

PurposeThe purpose of this paper is to provide the results of investigation of multi‐moment statistical characteristics of chaos and apply them to improve the accuracy of nonlinear algorithms for chaos filtering for real‐time applications.Design/methodology/approachThe approach to find multi‐moment statistical properties of chaos‐multi‐moment cumulant (covariance) functions of higher order is a generalization of the previously proposed (by the authors) “degenerated cumulant equations” method. Those multi‐moment cumulants functions are applied in the generalization of the Stratonovich‐Kushner equations (SKE) for the optimum algorithm of nonlinear filtering of chaos as well as for synthesis of the quasi‐optimum algorithms.FindingsResults are presented to investigate the multi‐moment statistical properties of chaos and formulate the theoretical background for synthesis of multi‐moment optimum and quasi‐optimum algorithms for nonlinear filtering of chaos with the improved accuracy in the presence of additive white noise.Originality/valueThe paper presents new theoretical results of the statistical description of chaos, previously partially reported only from experimental studies. A novel approach for chaos filtering is also presented. The proposed approach is dedicated to further improvement of the filtering accuracy for the case of low (less than one) SNR scenarios and is important for implementation in real‐time processing. As an important practical example, the new modified EKF algorithm is proposed with the rather opportunistic characteristics of the filtering fidelity together with algorithm complexity – practically the same as the “classic” one‐moment EKF algorithm.
MATLAB implementation of the complex power flow
Authors: Granelli Gianpietro , Montagna Mario 
Published: April 2013

PurposeThe purpose of this work is that of providing the guidelines of an efficient implementation of power flow computations using the MATLAB computation environment.Design/methodology/approachThe goal of obtaining high efficiency from MATLAB programs often proves elusive unless special care is taken in exploiting the vectorising capability of MATLAB programming. In the present paper the implementation of Newton‐Raphson power flow in MATLAB is examined with particular emphasis on the way of obtaining a vectorisable code capable of achieving effective numerical performance by exploiting its formulation in terms of complex variables.FindingsTests on actual networks with up to 1,300 buses are presented. They show that the complex power flow is as efficient as the best implementations of the Newton Raphson power flow using real variables, as long as the operations involved are reordered with the aim of exploiting the vectorisation capabilities of the MATLAB environment.Originality/valueIt is shown that improved numerical efficiency in the MATLAB can be obtained through its formulation in terms of complex variables. The complex Newton‐Raphson load flow, not very common in practical uses, is shown to have many desirable qualities from the point of view of MATLAB programming and is presented in detail.
The fuzzy correlation approach in operation of electrical distribution systems
Authors: Grigoras Gheorghe , Cartina Gheorghe 
Published: April 2013

PurposeThe purpose of this paper is to introduce a method based on the fuzzy correlation for modelling of active and reactive powers from the substations of the electrical distribution systems, at the peak load.Design/methodology/approachBased on the correlation theory, the fuzzy models of the loads can be obtained using a new algorithm. If in the case of the principal/connection station there is sufficient database information for a good forecasting of the load, then for those substations where data are missing (there is no continuous monitoring or the measuring system can be broken for a while) the forecasting of the load can be performed using the correlation studies. The starting point of the algorithm is statistical analysis of the active and reactive curves of the substations and utilization of a fuzzy linear regression model. This can be made for different time windows (window 24 h, window 7 h, etc). The window 24 h can be used successfully to estimate the hourly load on any substation. The other time window (7 h) can be used in the peak load estimation of the substations, using the maximum value of the active power recorded in a reference substation.FindingsThe numerical data show that the fuzzy correlation models can be used with very good results for determination of the peak load corresponding distribution substations, and further with the state estimation of the system. In this study, the influence of the time window size is presented in detail, and the fuzzy correlation models for the peak loads from the distribution substations are obtained.Originality/valueStarting from the correlation theory, a method of fuzzy modelling of active and reactive powers from the substations of an electrical distribution system is proposed.