bluuebunny/crossref_metadata_2025_split huggingface dataset:
PRESTO, a new tool for integrating large-scale -omics data and discovering disease-specific signatures
Authors: McArdle Sara , Buscher Konrad , Ehinger Erik , Pramod Akula Bala , Riley Nicole , Ley Klaus 
Published: April 2018

AbstractBackgroundCohesive visualization and interpretation of hyperdimensional, large-scale -omics data is an ongoing challenge, particularly for biologists and clinicians involved in current highly complex sequencing studies. Multivariate studies are often better suited towards non-linear network analysis than differential expression testing. Here, we present PRESTO, a ‘PREdictive Stochastic neighbor embedding Tool for Omics’, which allows unsupervised dimensionality reduction of multivariate data matrices with thousands of subjects or conditions. PRESTO is intuitively integrated into an interactive user interface that helps to visualize the multidimensional patterns in genome-wide transcriptomic data from basic science and clinical studies.ResultsPRESTO was tested with multiple input omics’ platforms, including microarray and proteomics from both mouse and human clinical datasets. PRESTO can analyze up to tens of thousands of genes and shows no increase in processing time with a large number of samples or patients. In complex datasets, such as those with multiple time points, several patient groups, or diverse mouse strains, PRESTO outperformed conventional methods. Core co-expressed gene networks were intuitively grouped in clusters, or gates, after dimensionality reduction and remained consistent across users. Networks were identified and assigned to physiological and pathological functions that cannot be gleaned from conventional bioinformatics analyses. PRESTO detected gene networks from the natural variations among mouse macrophages and human blood leukocytes. We applied PRESTO to clinical transcriptomic and proteomic data from large patient cohorts and detected disease-defining signatures in antibody-mediated kidney transplant rejection, renal cell carcinoma, and relapsing acute myeloid leukemia (AML). In AML, PRESTO confirmed a previously described gene signature and found a new signature of 10 genes that is highly predictive of patient outcome.ConclusionsPRESTO offers an important integration of powerful bioinformatics tools with an interactive user interface that increases data analysis accessibility beyond bioinformaticians and ‘coders’. Here, we show that PRESTO out performs conventional methods, such as DE analysis, in multi-dimensional datasets and can identify biologically relevant co-expression gene networks. In paired samples or time points, co-expression networks could be compared for insight into longitudinal regulatory mechanisms. Additionally, PRESTO identified disease-specific signatures in clinical datasets with highly significant diagnostic and prognostic potential.
Discovering epistatic feature interactions from neural network models of regulatory DNA sequences
Authors: Greenside Peyton , Shimko Tyler , Fordyce Polly , Kundaje Anshul 
Published: April 2018

AbstractMotivationTranscription factors bind regulatory DNA sequences in a combinatorial manner to modulate gene expression. Deep neural networks (DNNs) can learn the cis-regulatory grammars encoded in regulatory DNA sequences associated with transcription factor binding and chromatin accessibility. Several feature attribution methods have been developed for estimating the predictive importance of individual features (nucleotides or motifs) in any input DNA sequence to its associated output prediction from a DNN model. However, these methods do not reveal higher-order feature interactions encoded by the models.ResultsWe present a new method called Deep Feature Interaction Maps (DFIM) to efficiently estimate interactions between all pairs of features in any input DNA sequence. DFIM accurately identifies ground truth motif interactions embedded in simulated regulatory DNA sequences. DFIM identifies synergistic interactions between GATA1 and TAL1 motifs from in vivo TF binding models. DFIM reveals epistatic interactions involving nucleotides flanking the core motif of the Cbf1 TF in yeast from in vitro TF binding models. We also apply DFIM to regulatory sequence models of in vivo chromatin accessibility to reveal interactions between regulatory genetic variants and proximal motifs of target TFs as validated by TF binding quantitative trait loci. Our approach makes significant strides in improving the interpretability of deep learning models for genomics.AvailabilityCode is available at: https://github.com/kundajelab/dfim.Contact: akundaje@stanford.edu
Six species of non-tuberculosis mycobacteria carry non-identical 16S rRNA gene copies
Authors: Takeda Keita , Chikamatsu Kinuyo , Igarashi Yuriko , Morishige Yuta , Murase Yoshiro , Aono Akio , Yamada Hiroyuki , Takaki Akiko , Mitarai Satoshi 
Published: April 2018

AbstractNon-tuberculosis mycobacteria (NTM) can carry two or more 16S rRNA gene copies that are, in some instances, non-identical. In this study, we used a combined cloning and sequencing approach to analyze the 16S rRNA gene sequences of six NTM species,Mycobacterium cosmeticum, M. pallens, M. hodleri, M. crocinum, M. flavescens, andM. xenopi. The approach facilitated the identification of two distinct gene copies in each species. The twoM. cosmeticumgenes had a single nucleotide difference, whereas two nucleotide polymorphisms were identified inM. hodleri, M. flavescens, andM. xenopi. M. pallenshad a difference in four nucleotides andM. crocinumin 23. Hence, we showed that the six NTM species possess at least two non-identical 16S rRNA gene copies.ImportanceThe presence of multiple 16S rRNA gene copies with nucleotide polymorphisms represents a challenge for species identification using 16S rRNA as the target sequence. Our analysis was focused on six NTM species,M. cosmeticum, M. pallens, M. hodleri, M. crocinum, M. flavescens, andM. xenopi. As a result, we generated the full-length sequences of two non-identical 16S rRNA copies for each NTM species. The data will be helpful for the sequence analysis of specimens or other samples.
Fusion expression and anti-Aspergillus flavusactivity of a novel inhibitory protein DN-AflR
Authors: Liang Yuan , Kong Qing , Yao Yao , Xu Shujing , Xie Xiang 
Published: April 2018

ABSTRACTThe regulatory gene (aflR) of aflatoxin encodes AflR, a positive regulator that activates transcriptional pathway of genes in aflatoxin biosynthesis. New L-Asp-L-Asn (DN) extracted fromBacillus megateriuminhibited the growth ofA. flavushad been elucidated in our laboratory. The genes encoding DN and binuclear zinc finger cluster protein of AflR were fused, then fusion protein could compete with the AflS-AflR complex for the AflR binding site and significantly improve anti-A. flavusactivity of DN. The fusion genedn-aflRwas cloned into pET32a and recombinant plasmid was introduced intoEscherichia coliBL21. The highest expression was observed after 10 h induction and purified by affinity chromatography column. Compared with DN, the novel fusion protein DN-AflR significantly inhibited the growth ofA. flavusand biosynthesis of aflatoxin B1. This study promoted the use of competitive inhibition of fusion proteins to reduce the expression of regulatory genes in the biosynthetic pathway of aflatoxin. Moreover, it provided more supports for deep research and industrialization of such novel, anti-A. flavusbio-inhibitors.IMPORTANCEAflatoxin contamination has seriously influence on export of agricultural products, income of farmers and economic development. Biological methods, especially using antagonistic microorganisms to inhibit aflatoxin biosynthesis gradually become the hot spot in recent years. DN (L-Asp-L-Asn) fromBacillus megaterium, which could inhibit growth ofAspergillus flavusand synthesis of aflatoxin, has been identified. In this report, we fused the genes encoding inhibitory peptides (DN) and specific zinc finger cluster protein, and expressed the novel anti-A.flavusprotein inEscherichia coli. Compared with DN, the inhibitory ability of novel protein has been improved significantly. This research showed fusion expression of anti-fungal proteins, such as DN-AflR, is a promising method to economically improve the inhibitory activity of bio-inhibitors forA. flavus.
Sequencing and de novo assembly reveals genomic variations associated with differential responses of Candida albicans ATCC 10231 towards fluconazole, pH and non-invasive growth
Authors: Zore Gajanan , Thakre Archana , Patil Rajendra , Pradeep Chaithra , Balan Bipin 
Published: April 2018

AbstractThe whole genome sequencing generated 8.09 million paired-end reads, which were assembled into 2,262 scaffolds totaling 17,113,050 bp in length. We predict 7,654 coding regions and 7,647 genes, and annotated the coding regions with gene ontology terms based on similarity to other annotated genomes. Genome comparisons revealed variations (including SNP and indels in genes involved in pH response, fluconazole resistance and invasive growth) compared to C. albicans SC5314 and WO1.
Chromosomal scale length variation of germline DNA can predict individual cancer risk
Authors: Toh Chris , Brody James P. 
Published: April 2018

AbstractInherited factors are thought to be responsible for a substantial fraction of many different forms of cancer. However, individual cancer risk cannot currently be well quantified by analyzing germ line DNA. Most analyses of germline DNA focus on the additive effects of single nucleotide polymorphisms (SNPs) found. Here we show that chromosomal-scale length variation of germline DNA can be used to predict whether a person will develop cancer. In two independent datasets, the Cancer Genome Atlas (TCGA) project and the UK Biobank, we could classify whether or not a patient had a certain cancer based solely on chromosomal scale length variation. In the TCGA data, we found that all 32 different types of cancer could be predicted better than chance using chromosomal scale length variation data. We found a model that could predict ovarian cancer in women with an area under the receiver operator curve, AUC=0.89. In the UK Biobank data, we could predict breast cancer in women with an AUC=0.83. This method could be used to develop genetic risk scores for other conditions known to have a substantial genetic component and complements genetic risk scores derived from SNPs.
IRES-mediated ribosome repositioning directs translation of a +1 overlapping ORF that enhances viral infection
Authors: Kerr Craig H , Wang Qing S , Moon Kyung-Mee , Keatings Kathleen , Allan Douglas W , Foster Leonard J , Jan Eric 
Published: April 2018

AbstractRNA structures can interact with the ribosome to alter translational reading frame maintenance and promote recoding that result in alternative protein products. Here, we show that the internal ribosome entry site (IRES) from the dicistrovirus Cricket paralysis virus drives translation of the 0-frame viral polyprotein and an overlapping +1 open reading frame, called ORFx, via a novel mechanism whereby a subset of ribosomes recruited to the IRES bypasses downstream to resume translation at the +1-frame 13th non-AUG codon. A mutant of CrPV containing a stop codon in the +1 frame ORFx sequence, yet synonymous in the 0-frame, is attenuated compared to wild-type virus in aDrosophilainfection model, indicating the importance of +1 ORFx expression in promoting viral pathogenesis. This work demonstrates a novel programmed IRES-mediated recoding strategy to increase viral coding capacity and impact virus infection, highlighting the diversity of RNA-driven translation initiation mechanisms in eukaryotes.Significance StatementViruses use alternate mechanisms to increase the coding capacity of their viral genomes. Here, we provide biochemical evidence that ribosomes recruited to the dicistrovirus cricket paralysis virus IRES undergo a bypass event to direct translation of a downstream +1 frame overlapping open reading frame, called ORFx. Mutations that block ORFx expression inhibit +1 frame translation and infection in fruit flies. These findings highlight the diversity of RNA-driven translation initiation mechanisms in eukaryotes.
Political connections and stock price crash risk
Authors: Hu Guoliu , Wang Yu 
Published: April 2018

Purpose
The purpose of this paper is to research the impact of firms’ political connections on the stock price crash risk.

Design/methodology/approach
Empirical methodology is used in this study.

Findings
Using a large sample of Chinese firms for the period 2008-2013, the authors find that corporate political connections can reduce the stock price crash risk. When managers are still in politics or firms are in high financial transparency of local governments, the relationship between political connections and the stock price crash risk is weakened. In addition, the authors’ research shows that the corporate political connections influence the stock price crash risk by affecting the speed of confirmation of bad news.

Research limitations/implications
The findings in this study suggest that political connections will affect corporate disclosure.

Practical implications
These results can help senior executives and investors make better decisions to prevent the stock price crash risk.

Originality/value
This paper empirically analyzes the impact of different types of political connections on the stock price crash risk for the first time.
Optimal overcurrent relay coordination in distribution network based on Lightning Flash Algorithm
Authors: Kheshti Mostafa , Kang Xiaoning 
Published: April 2018

Purpose
Distribution network protection is a complicated problem and mal-operation of the protective relays due to false settings make the operation of the network unreliable. Besides, obtaining proper settings could be very complicated. This paper aims to discuss an innovative evolutionary Lightning Flash Algorithm (LFA) which is developed for solving the relay coordination problems in distribution networks. The proposed method is inspired from the movements of cloud to ground lightning strikes in a thunderstorm phenomenon. LFA is applied on three case study systems including ring, interconnected and radial distribution networks. The power flow analysis is performed in Digsilent Power Factory software; then the collected data are sent to MATLAB software for optimization process. The proposed algorithm provides optimum time multiplier setting and plug setting of all digital overcurrent relays in each system. The results are compared with other methods such as particle swarm optimization and genetic algorithm. The result comparisons demonstrate that the proposed LFA can successfully obtain proper relay settings in distribution networks with faster speed of convergence and lower total operation time of relays. Also, it shows the superiority and effectiveness of this method against other algorithms.

Design/methodology/approach
A novel LFA is designed based on the movements of cloud to ground lightning strikes in a thunderstorm. This method is used to optimally adjust the time multiplier setting and plug setting of the relays in distribution system to provide a proper coordination scheme.

Findings
The proposed algorithm was tested on three case study systems, and the results were compared with other methods. The results confirmed that the proposed method could optimally adjust the relay settings in the electric distribution system to provide a proper protection scheme.

Practical implications
The practical implications can be conducted on distribution networks. The studies provided in this paper approve the practical application of the proposed method in providing proper relay protection in real power system.

Originality/value
This paper proposes a new evolutionary method derived from the movements of cloud to ground lightning strikes in thunderstorm. The proposed method can be used as an optimization toolbox to solve complex optimization problems in practical engineering systems.
Controllable velocity moment and prediction model for inlet guide vanes of a centrifugal pump
Authors: Liu Ming , Tan Lei , Liu Yabin , Xu Yun , Cao Shuliang 
Published: April 2018

Purpose
This paper aims to investigate the effect of three-dimensional (3D) inlet guide vanes (IGVs) on performance of a centrifugal pump.

Design/methodology/approach
A design method for 3D IGVs is proposed based on the controllable velocity moment, which is determined by a fourth-order dimensionless function. Numerical simulation of the centrifugal pump with IGVs is carried out by solving the Reynolds-averaged Navier–Stokes equations. The method of frozen rotor is applied to couple the stationary and rotational domain.

Findings
The efficiency of pump with 3D IGVs is higher than that with 2D IGVs for most prewhirl angles, which validate the advancement of 3D IGVs on prewhirl regulation. The effect of prewhirl regulation at small flow rate is more significant than that at large flow rate.

Originality/value
A prediction model of velocity moment based on the Oseen vortex is proposed to describe the flow pattern downstream the IGVs.
Application of smooth transition regression (STR) model on the relationship between natural gas consumption and economic growth in Nigeria
Authors: Galadima Mukhtar Danladi , Aminu Abubakar Wambai 
Published: April 2018

Purpose
The purpose of this paper is to identify the level of natural gas consumption that can be adjudged as capable of improving the growth of the Nigerian economy, to investigate whether natural gas consumption is at optimal level in Nigeria and to examine the nature and rate to which natural gas consumption affects economic growth in Nigeria at low and high regimes.

Design/methodology/approach
The tool used to achieve the objectives of the paper is the smooth transition regression (STR) model.

Findings
The findings of the paper are that the relationship between natural gas consumption and economic growth in Nigeria is asymmetric, where the natural gas consumption threshold value in the country is 9085.36 standard cubic meters, whereas the level of its consumption in the country is below the optimal level. Further, in both low and high regimes, natural gas consumption has been found to have a positive and significant impact on economic growth in Nigeria.

Practical implications
The policy implication of the paper is that natural gas consumption in Nigeria should not be less than 9085.36 standard cubic meters and the country should intensify efforts to increase the level of natural gas consumption, as it is below the optimal level and its consumption bolsters the growth of Nigerian economy.

Originality/value
What is new in this paper is its ability to use the STR model. To the best of the authors’ knowledge, such methodology has not been adopted before in such a relation.
Developing the capability to terminate IT projects when they can no longer deliver business value
Authors: Thornley Clare Victoria , Crowley Catherine Anne 
Published: April 2018

Purpose
The purpose of this paper is to address the problem of ensuring that the capabilities are in place to identify when a project can no longer deliver value and to take appropriate action to terminate the project.

Design/methodology/approach
Focus groups with project management practitioners were used to collect in-depth qualitative data. This was then supplemented with a questionnaire, which included both closed questions and the opportunity for free text answers.

Findings
The problem of getting better at stopping projects is both common and difficult to solve. It has many facets, which include complex people and cultural issues, processes and procedures as well as financial reporting and project governance. In order to improve, therefore, it is useful to address these different facets in a coordinated way using a capability approach with a focus on business value.

Research limitations/implications
The data from practitioners are retrospective, as their actions were not actually observed by the researchers as they were happening. This means that faulty recollection may influence the results but, it also allows for insights from reflection to be incorporated.

Practical implications
An organizational capability approach focusing on all three aspects of capability; people, processes and technology, can help organizations get better at stopping projects. Specific recommendations are provided and analyzed in terms of their respective capability focus.

Social implications
If performance in terminating projects is improved, it has the potential for significant benefits and cost saving for society in terms of improved government services and the ability to halt projects around new policy initiatives when emerging evidence shows they will not work.

Originality/value
It provides detailed practitioner input on the problem of stopping projects and suggests recommendations for improvement in the context of a structured organizational capability approach with reference to a particular framework, IT-CMF.
“Superfast!” managing the urgent: case study of telecommunications infrastructure project in Algeria
Authors: Zidane Youcef J-T. , Klakegg Ole Jonny , Andersen Bjorn , Hussein Bassam 
Published: April 2018

Purpose
With the aim of furthering the understanding of project speed and how to manage the urgent project, the purpose of this paper is to investigate the management challenges involved in delivering a telecommunications infrastructure project in a period of much shorter duration than a similar project. The authors wanted to understand the reasons behind the urgency and how the project management team succeeds in delivering in such a tight time window. Finally, the authors assessed the consequences (negative and positive, during and after the project delivery), knowing that the project was considered a success at its delivery, but not that it was successful at the post-project evaluation.

Design/methodology/approach
A case study based on qualitative research interviews with management team including the client, the main contractor and some related stakeholders, combined with case archives and internal documentation from the case project.

Findings
The urgency of a project or programme may lead to some negative consequences and impacts. The success seen in a short- and mid-term view is not enough to justify making acceleration decisions: thus holistic thinking and a long-term sustainable approach are needed to ensure continuity and profits.

Research limitations/implications
This research is based on a single case study. There are some limitations regarding how urgent and unexpected the case was managed in comparing to normal case. A second limitation is that there is no clear definition of what are normal practices such that we can say what are a normal case and an urgent case.

Practical implications
There are some lessons learned from this case study about managing the unexpected and the urgent. Practitioners can obtain insight into positive and negative consequences of fast project delivery from this case.

Originality/value
This study is unique in its content and context, since it presents the first-hand insight into a case study that seemed to be successful to some extent (short-term impact); however, negative consequences appeared within a few years of its delivery.