bluuebunny/crossref_metadata_2025_split huggingface dataset:
Independent molecular basis of convergent highland adaptation in maize
Authors: Takuno Shohei , Ralph Peter , Swarts Kelly , Elshire Rob J. , Glaubitz Jeffrey C. , Buckler Edward S. , Hufford Matthew B. , Ross-Ibarra Jeffrey 
Published: January 2015

ABSTRACTConvergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection, and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation, and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.
Merging OpenLifeData with SADI services using Galaxy and Docker
Authors: Aranguren Mikel Egañna 
Published: January 2015

ABSTRACTSemantic Web technologies have been widely applied in Life Sciences, for example by data providers like OpenLifeData and Web Services frameworks like SADI. The recent OpenLifeData2SADI project offers access to the OpenLifeData data store through SADI services. This paper shows how to merge data from OpenLifeData with other extant SADI services in the Galaxy bioinformatics analysis platform, making semantic data amenable to complex analyses, as a worked example demonstrates. The whole setting is reproducible through a Docker image that includes a pre-configured Galaxy server with data and workflows that constitute the worked example.
JAFFA: High sensitivity transcriptome-focused fusion gene detection
Authors: Davidson Nadia M. , Majewski Ian J. , Oshlack Alicia 
Published: January 2015

AbstractGenomic instability is a hallmark of cancer and, as such, structural alterations and fusion genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a powerful method for profiling cancers, but current methods for identifying fusion genes are optimized for short reads. JAFFA (https://code.google.com/p/jaffa-project/) is a sensitive fusion detection method that clearly out-performs other methods with reads of 100bp or greater. JAFFA compares a cancer transcriptome to the reference transcriptome, rather than the genome, where the cancer transcriptome is inferred using long reads directly or byde novoassembling short reads.
Efficient Assembly and Verification of ZFNs and TALENs for Modifying PorcineApoEgene
Authors: Xu H R , Li T , Guo Y , Li H F , Wang L , Zhang Z Y , Wang X 
Published: January 2015

AbstractZinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) are powerful tools for genome engineering. These synthetic nucleases are assembled with programmable, sequence-specific DNA-binding domain and a non-specific FokI cleavage domain. Apolipoprotein E (ApoE) gene polymorphism is associated with cardiovascular outcomes, including ischaemic stroke and coronary heart disease (CHD). So the objective of this study is to create mutations ofAopEgene by ZFNs and TALENs technology. Here, we used the Context-dependent assembly (CoDA) method to design and screen ZFNs specifically targeting withApoEgene. The targeted cleavage capacity of these ZFNs was validated in yeast system and HEK 293T cells. Meanwhile, an efficient assembled TALENs to targetApoEgene in HEK 293T cells was as a control. The results showed that both ZFNs and TALENs worked onApoEgene with similar high-efficiency cleavage capability. The result would provide efficient methods for genome editing, so as to get disease model for gene therapy for the further study.
The Time-Scale of Recombination Rate Evolution in Great Apes
Authors: Stevison Laurie S , Woerner August E , Kidd Jeffrey M , Kelley Joanna L , Veeramah Krishna R , McManus Kimberly F. , Bustamante Carlos D , Hammer Michael F , Wall Jeffrey D ,   Great Ape Genome Project
Published: January 2015

AbstractWe present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequencing data of 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez et al. 2013). Using species-specific PRDM9 sequences to predict potential binding sites, we identified an important role for PRDM9 in predicting recombination rate variation broadly across great apes. Our results are contrary to previous research that PRDM9 is not associated with recombination in western chimpanzees (Auton et al. 2012). Additionally, we show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time-scale of complete hotspot turnover. We quantified the variation in the biased distribution of recombination rates towards recombination hotspots across great apes. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, based on multiple linear regression analysis, we found that various correlates of recombination rate persist throughout primates including repeats, diversity, divergence and local effective population size (Ne). Our study is the first to analyze within-and between-species genome-wide recombination rate variation in several close relatives.
Chromosomal Inversion Symmetry: Generalized Chargaff Rules
Authors: Shporer Sagi , Chor Benny , Horn David 
Published: January 2015

AbstractThe generalization of the second Chargaff rule to values of k larger than 1, states that the frequency of any k-mer on a single strand almost equals that of its inverse (reverse-complement). We demonstrate the validity of the generalized rule up to k=10 for all human chromosomes. Moreover, thisInversion Symmetryholds for many species, both eukaryotes and prokaryotes, for ranges of k which may vary from 7 to 10 as chromosomal lengths vary from 2Mbp up to 200 Mbp. We demonstrate that the statistical distributions of inverted pairs of k-mers are very different from other natral pairings of k-mers, implying that inversion symmetry is a basic principle of chromosomal structure. We suggest that it came into being because genomic evolution employed many rearrangements which conisted of inversions of chromosomal sections; on length scales down to order 1-10Kbp. Model simulations substantiate this claim.Low-scale inversions during chromosomal evolution imply that IS may exist for short sections of human chromosomes. This is indeed the case: we find that chromosome sections of length 5Kbp satisfy IS for k=1 and k=2. The largest value of k for which IS holds,which we call the k-limit of IS, increases logarithmically as the section length increases. The logarithmic dependence of the k-limit on the length of the chromosome is a universal characteristic, observed throughout the tree of life.
From system-wide differential gene expression to perturbed regulatory factors: a combinatorial approach
Authors: Mahajan Gaurang , Mande Shekhar C. 
Published: January 2015

AbstractHigh-throughput experiments such as microarrays and deep sequencing provide large scale information on the pattern of gene expression, which undergoes extensive remodeling as the cell dynamically responds to varying environmental cues or has its function disrupted under pathological conditions. An important initial step in the systematic analysis and interpretation of genome-scale expression alteration involves identification of a set of perturbed transcriptional regulators whose differential activity can provide a proximate hypothesis to account for these transcriptomic changes. In the present work, we propose an unbiased and logically natural approach to transcription factor enrichment. It involves overlaying a list of experimentally determined differentially expressed genes on a background regulatory network coming from e.g. literature curation or computational motif scanning, and identifying thatsubsetof regulators whoseaggregated target setbest discriminates between the altered and the unaffected genes. In other words, our methodology entails testing of all possible regulatorysubnetworks, rather than just the target sets ofindividualregulators as is followed in most standard approaches. We have proposed an iterative search method to efficiently find such a combination, and benchmarked it onE. colimicroarray and regulatory network data available in the public domain. Comparative analysis carried out on simulated differential expression profiles, as well as empirical factor overexpression data forM. tuberculosis, shows that our methodology provides marked improvement in accuracy of regulatory inference relative to the standard method that involves evaluating factor enrichment in an individual manner.
Phosphoenolpyruvate Carboxylase in Arabidopsis Leaves Plays a Crucial Role in Carbon and Nitrogen Metabolism
Authors: Shi Jianghua , Yi Keke , Liu Yu , Xie Li , Zhou Zhongjing , Chen Yue , Hu Zhanghua , Zheng Tao , Liu Renhu , Chen Yunlong , Chen Jinqing 
Published: January 2015

Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a crucial enzyme that catalyzes an irreversible primary metabolic reaction in plants. Previous studies have used transgenic plants expressing ectopic PEPC forms with diminished feedback inhibition to examine the role of PEPC in carbon and nitrogen metabolism. To date, the in vivo role of PEPC in carbon and nitrogen metabolism has not been analyzed in plants. In this study, we examined the role of PEPC in plants, demonstrating that PPC1 and PPC2 were highly expressed genes encoding PEPC in Arabidopsis (Arabidopsis thaliana) leaves and that PPC1 and PPC2 accounted for approximately 93% of total PEPC activity in the leaves. A double mutant, ppc1/ppc2, was constructed that exhibited a severe growth-arrest phenotype. The ppc1/ppc2 mutant accumulated more starch and sucrose than wild-type plants when seedlings were grown under normal conditions. Physiological and metabolic analysis revealed that decreased PEPC activity in the ppc1/ppc2 mutant greatly reduced the synthesis of malate and citrate and severely suppressed ammonium assimilation. Furthermore, nitrate levels in the ppc1/ppc2 mutant were significantly lower than those in wild-type plants due to the suppression of ammonium assimilation. Interestingly, starch and sucrose accumulation could be prevented and nitrate levels could be maintained by supplying the ppc1/ppc2 mutant with exogenous malate and glutamate, suggesting that low nitrogen status resulted in the alteration of carbon metabolism and prompted the accumulation of starch and sucrose in the ppc1/ppc2 mutant. Our results demonstrate that PEPC in leaves plays a crucial role in modulating the balance of carbon and nitrogen metabolism in Arabidopsis.
Academic performance, publishing and peer review: peering into the twilight zone
Authors: Guthrie James , Parker Lee D , Dumay John 
Published: January 2015

Purpose
– The purpose of this paper is to present a critique of published research access and peer review, considering their impacts on accounting scholarship.

Design/methodology/approach
– The paper is based on literature and publishing document review, experiential reflections and argument.

Findings
– The authors reveal changes in publishing formats and accessibility, the challenges of managing research quality and significance and the challenges of avoiding constraint and foreclosure of significant new knowledge and its effective dissemination.

Research limitations/implications
– This paper discusses the research and publishing community’s opening to new, flexible opportunities for knowledge creation and dissemination.

Originality/value
– The discussion challenges the status quo of traditional academic journal publication and points to an innovative future.
The non-destructive examination of cone-beam CT image circuit board based on the new interactive cutting method
Authors: Li Yunjie , Li Kun 
Published: January 2015

Purpose
– The purpose of this paper was to realize a non-destructive examination for printed circuit boards (PCBs) and to obtain an accurate and high-efficient image.

Design/methodology/approach
– This paper provides an approach to realize a non-destructive examination for PCBs and to obtain an accurate and high-efficient image.

Findings
– The result showed that cone-beam computed tomography (CT) image PCB detection based on an interactive cutting method had accuracy and high efficiency and can meet the non-destructive requirement of detection.

Originality/value
– The result showed that cone-beam CT image PCB detection based on an interactive cutting method had accuracy and high efficiency and can meet the non-destructive requirement of detection.
Performance analysis of micro drill bit with asymmetric helix groove
Authors: Shi Hongyan , Ning Jiali , Li Hui 
Published: January 2015

Purpose
– The purpose of this paper is to present a new method to optimize the micro drill bit based on finite element analysis, and analyze the performance of the asymmetric helix groove micro drill bit and provide a way to conduct the optimization of micro drill bits.

Design/methodology/approach
– First, the stress and deform of the micro drills were analyzed in ANSYS. Second, the influence of helix angle, web thickness and ratio of flute to land on stiffness was explored. Combining the former two results, a better set of parameters were optimized. Third, the modal analysis and harmonic response analysis of the optimized micro drill bit were analyzed in ANSYS. Finally, an experiment was carried out to verify the performance of the asymmetric helix groove micro drill bit.

Findings
– The stress and deform of the asymmetric helix groove micro drill bit are not symmetric. The rigidity is getting better with the web thickness increasing in the selected range; while, the rigidity is getting worse with the helix angle and ratio of flute to land increasing in the selected range. The natural frequencies of the optimized micro drill bit are far away from the excitation frequency, and the response displacement is very small under the excitation of the spindle. In the drilling experiment, the optimized micro drill bit performs well.

Research limitations/implications
– In this paper, the diameter of the asymmetric helix groove micro drill bit was 0.3 mm and the cross-section shape was not considered. The future research work should consider different diameters and cross-section shapes.

Originality/value
– Analyzing the influence of three main geometry parameters on the rigidity in ANSYS, a better set of parameters were optimized from the analysis results. The drilling experimental results show that this method is of great significance for obtaining the appropriate parameters of asymmetric helix groove micro drill bits.
Value of IT in supply chain planning
Authors: Fuchs Christoph , Otto Andreas 
Published: January 2015

Purpose
– The purpose of this paper is to understand value creation of information technology (IT) in supply chain planning (SCP). The impact of different IT components in SCP remains unclear and requires some thorough research. In addition, an analysis of the optimization dimension provides insights into intra-functional, inter-functional and cross-company optimization.

Design/methodology/approach
– A survey was conducted among German companies using a continuous production flow. In total, 47 of 193 contacted companies completed the web survey, which corresponds to a response rate of 24 percent.

Findings
– IT functionality for SCP is widely spread. The value of IT functionality in SCP is tremendous. Implementations in demand fulfillment and available-to-promise (ATP) have the biggest value creation potential. Supply chain performance indicators can be improved by investments in certain functional domains. Packaged standard software is widely distributed and should be considered as the first option. IT functionality to improve intra-functional processes is significantly more often implemented than IT functionality for inter-functional or cross-company process optimization although the realized value is comparable.

Research limitations/implications
– Respondents of the survey are limited to the German continuous production flow industry. Future research could be interesting in the discrete manufacturing industry.

Originality/value
– The paper provides empirical insights into the value of IT in SCP where data are less available than in the ERP context. Furthermore, this paper provides first insights into the optimization dimension whether processes are optimized intra-functional, inter-functional or cross-company.
Understanding determinants of cloud computing adoption using an integrated TAM-TOE model
Authors: Gangwar Hemlata , Date Hema , Ramaswamy R 
Published: January 2015

Purpose
– The purpose of this paper is to integrate TAM model and TOE framework for cloud computing adoption at organizational level.

Design/methodology/approach
– A conceptual framework was developed using technological and organizational variables of TOE framework as external variables of TAM model while environmental variables were proposed to have direct impact on cloud computing adoption. A questionnaire was used to collect the data from 280 companies in IT, manufacturing and finance sectors in India. The data were analyzed using exploratory and confirmatory factor analyses. Further, structural equation modeling was used to test the proposed model.

Findings
– The study identified relative advantage, compatibility, complexity, organizational readiness, top management commitment, and training and education as important variables for affecting cloud computing adoption using perceived ease of use (PEOU) and perceived usefulness (PU) as mediating variables. Also, competitive pressure and trading partner support were found directly affecting cloud computing adoption intentions. The model explained 62 percent of cloud computing adoption.

Practical implications
– The model can be used as a guideline to ensure a positive outcome of the cloud computing adoption in organizations. It also provides relevant recommendations to achieve conducive implementation environment for cloud computing adoption.

Originality/value
– This study integrates two of the information technology adoption models to improve predictive power of resulting model.
The impact of knowledge management practices on organizational performance
Authors: Valmohammadi Changiz , Ahmadi Mohsen 
Published: January 2015

Purpose
– The purpose of this paper is to present a holistic approach regarding evaluation of knowledge management (KM) practices on organizational performance. The effects of seven critical success factors (CSFs), namely leadership role, organizational culture, KM strategy, processes and activities, training and education, information technology, and motivation and rewarding system, on organizational performance in the framework of four perspectives of balance scored card (BSC) approach were surveyed.

Design/methodology/approach
– The research hypotheses were raised based on the four perspectives of this approach, namely, growth and learning, internal processes, customer and financial. By literature review, CSFs of KM and organizational performance along with their items were identified in the framework of BSC’s perspectives. Based on these constructs and their items an instrument was designed and distributed among managers and employees of the subsidiary firms of Iran National Petrochemical Company (INPC). Reliability of the instrument was calculated by Chronbach’s α for the two sections of the instrument i.e. KM practices and organizational performance. Also, using factor analysis the construct validity of the questionnaire was approved. Finally, based on the hypotheses of the study and using structural equation modeling the impacts of KM practices on organizational performance were investigated.

Findings
– The results revealed that KM practices positively and meaningfully (though weak) impact overall organizational performance. This impact is significant only regarding growth and learning dimension and on the other dimensions is insignificant. Also, as customer and financial constructs were loaded on one factor based on the entity of their indicators we considered these two constructs as stakeholders construct. In addition, among the above mentioned seven CSFs, motivation and rewarding system obtained the lowest rank among the survey organizations.

Research limitations/implications
– The sample is restricted to only three companies, so gathering data from various parts of Iran including both manufacturing and service industries could increase the generalizability of the results obtained. Also, as in this study the data gathered were cross-sectional, a longitudinal study could help gain deeper understanding of the cause-and-effect relationship among the variables.

Originality/value
– The most significant gap in the literature is the lack of enough application of statistical and comprehensive methods like BSC that KM makes a difference to organizational performance. This study contributes to the field of KM by empirically investigating the impact of KM practices on various measures of organizational performance in order to prove the suitability of a comprehensive approach like BSC.