bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic prediction informed by biological processes expands our understanding of the genetic architecture underlying free amino acid traits in dryArabidopsisseeds
Authors: Turner-Hissong Sarah D. , Bird Kevin A. , Lipka Alexander E. , King Elizabeth G. , Beissinger Timothy M. , Angelovici Ruthie 
Published: February 2018

ABSTRACTPlant growth, development, and nutritional quality depends upon amino acid homeostasis, especially in seeds. However, our understanding of the underlying genetics influencing amino acid content and composition remains limited, with only a few candidate genes and quantitative trait loci identified to date. Improved knowledge of the genetics and biological processes that determine amino acid levels will enable researchers to use this information for plant breeding and biological discovery. Towards this goal, we used genomic prediction to identify biological processes that are associated with, and therefore potentially influence, free amino acid (FAA) composition in seeds of the model plantArabidopsis thaliana. Markers were split into categories based on metabolic pathway annotations and fit using a genomic partitioning model to evaluate the influence of each pathway on heritability explained, model fit, and predictive ability. Selected pathways included processes known to influence FAA composition, albeit to an unknown degree, and spanned four categories: amino acid, core, specialized, and protein metabolism. Using this approach, we identified associations for pathways containing known variants for FAA traits, in addition to finding new trait-pathway associations. Markers related to amino acid metabolism, which are directly involved in the FAA regulation, improved predictive ability for branched chain amino acids and histidine. The use of genomic partitioning also revealed patterns across biochemical families, in which serine-derived FAAs were associated with protein related annotations and aromatic FAAs were associated with specialized metabolic pathways. Taken together, these findings provide evidence that genomic partitioning is a viable strategy to uncover the relative contributions of biological processes to FAA traits in seeds, offering a promising framework to guide hypothesis testing and narrow the search space for candidate genes.
A novel environmental DNA (eDNA) sampling method for aye-ayes from their feeding traces
Authors: Aylward Megan L. , Sullivan Alexis P. , Perry George H. , Johnson Steig E. , Louis Edward E. 
Published: February 2018

AbstractNon-invasive sampling is an important development in population genetic monitoring of wild animals. Particularly, the collection of environmental DNA (eDNA) which can be collected without needing to encounter the target animal, facilitates the genetic analysis of cryptic and threatened species. One method that has been applied to these types of sample is target capture and enrichment which overcomes the issue of high proportions of exogenous (non-host) DNA from these lower quality samples. We tested whether target capture of mitochondrial DNA from sampled feeding traces of wild aye-ayes would yield mitochondrial DNA sequences for population genetic monitoring. We sampled gnawed wood from feeding traces where aye-ayes excavate wood-boring insect larvae from trees. We designed RNA probes complementary to the aye-aye’s mitochondrial genome and used these to isolate aye-aye DNA from other non-target DNA in these samples. We successfully retrieved six near-complete mitochondrial genomes from two sites within the aye-aye’s geographic range that had not been sampled previously. This method can likely be applied to alternative foraged remains to sample species other than aye-ayes. Our method demonstrates the application to next-generation molecular techniques to species of conservation concern.
GenFam: A web application and database for gene family-based classification and functional enrichment analysis
Authors: Bedre Renesh , Mandadi Kranthi 
Published: February 2018

ABSTRACTGenome-scale studies using high-throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user-defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new approach, GenFam, which allows classification and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query. GenFam and its integrated database comprises of three-hundred and eighty-four unique gene families and supports gene family classification and enrichment analyses for sixty plant genomes. Four comparative case studies with plant species belonging to different clades and families were performed using GenFam which demonstrated its robustness and comprehensiveness over preexisting functional enrichment tools. To make it readily accessible for plant biologists, GenFam is available as a web-based application where users can input gene IDs and export enrichment results in both tabular and graphical formats. Users can also customize analysis parameters by choosing from the various statistical enrichment tests and multiple testing correction methods. Additionally, the web-based application, source code and database are freely available to use and download. Website:http://mandadilab.webfactional.com/home/. Source code and database:http://mandadilab.webfactional.com/home/dload/.
Most regulatory interactions are not in linkage disequilibrium
Authors: Whalen Sean , Pollard Katherine S. 
Published: February 2018

AbstractLinkage disequilibrium (LD) and genomic proximity are commonly used to map non-coding variants to genes, despite increasing examples of causal variants outside the LD block of the gene they regulate. We compared chromatin contacts in 22 cell types to LD across billions of pairs of loci in the human genome and found no concordance, even at genomic distances below 25 kilobases where both tend to be high. Gene expression and ontology data suggest that chromatin contacts identify regulatory variants more reliably than do LD and genomic proximity. We conclude that the genomic architectures of genetic and physical interactions are independent, with important implications for gene regulatory evolution and precision medicine.
α-proteobacterial RNA degradosomes assemble liquid-liquid phase separated RNP bodies
Authors: Al-Husini Nadra , Tomares Dylan T. , Childers W. Seth , Schrader Jared M. 
Published: February 2018

AbstractRibonucleoprotein (RNP) granules play an important role in organizing eukaryotic mRNA metabolism via liquid-liquid phase separation (LLPS) of mRNA decay factors into membrane-less “droplet” organelles in the cytoplasm. Here we show that the bacterium Caulobacter crescentus Ribonuclease (RNase) E assembles RNP LLPS droplets that we term bacterial RNP-bodies (BR-bodies) similar to eukaryotic P-bodies and stress granules. RNase E requires RNA to assemble a BR-body, and disassembly requires RNA cleavage, suggesting BR-bodies provide localized sites of RNA degradation. The unstructured C-terminal domain of RNase E is both necessary and sufficient to assemble the core of the BR-body, is functionally conserved in related α-proteobacteria, and influences mRNA degradation. BR-bodies are rapidly induced under cellular stresses and provide enhanced cell growth under stress. To our knowledge, Caulobacter RNase E is the first bacterial protein identified that forms LLPS droplets, providing an effective strategy for subcellular organization in cells lacking membrane bound compartments.
A prize-collecting Steiner tree application for signature selection to stratify diffuse large B-cell lymphoma subtypes
Authors: Akhmedov Murodzhon , Galbusera Luca , Montemanni Roberto , Bertoni Francesco , Kwee Ivo 
Published: February 2018

ABSTRACTBackground:With the explosion of high-throughput data available in biology, the bottleneck is shifted to effective data interpretation. By taking advantage of the available data, it is possible to identify the biomarkers and signatures to distinguish subtypes of a specific cancer in the context of clinical trials. This requires sophisticated methods to retrieve the information out of the data, and various algorithms have been recently devised.Results:Here, we applied the prize-collecting Steiner tree (PCST) approach to obtain a gene expression signature for the classification of diffuse large B-cell lymphoma (DLBCL). The PCST is a network-based approach to capture new insights about genomic data by incorporating an interaction network landscape. Moreover, we adopted the ElasticNet incorporating PCA as a classification method. We used seven public gene expression profiling datasets (three for training, and four for testing) available in the literature, and obtained 10 genes as signature. We tested these genes by employing ElasticNet, and compared the performance with the DAC algorithm as current golden standard. The performance of the PCST signature with ElasticNet outperformed the DAC in distinguishing the subtypes. In addition, the gene expression signature was able to accurately stratify DLBCL patients on survival data.Conclusions:We developed a network-based optimization technique that performs unbiased signature selection by integrating genomic data with biological networks. Our classifier trained with the obtained signature outperformed the state-of-the-art method in subtype distinction and survival data stratification in DLBCL. The proposed method is a general approach that can be applied on other classification problems.
MYC Dysregulates Mitotic Spindle Function Creating a Dependency on TPX2
Authors: Rohrberg Julia , Corella Alexandra , Taileb Moufida , Kilinc Seda , Jokisch Marie-Lena , Camarda Roman , Zhou Alicia , Balakrishnan Sanjeev , Chang Aaron N. , Goga Andrei 
Published: February 2018

AbstractThe MYC oncogene promotes tumorigenesis in part by facilitating cell cycle entry thus driving cellular proliferation. Tumors that overexpress MYC frequently demonstrate aneuploidy, numerical chromosome alterations associated with highly aggressive cancers, rapid tumor evolution, and poor patient outcome. While the role of MYC in overcoming the G1/S checkpoint is well established, it remains poorly understood whether MYC induces chromosomal instability (CIN). Here, we identify a direct influence of MYC on mitotic progression. MYC overexpression induces defects in microtubule nucleation and spindle assembly promoting chromosome segregation defects, micronuclei and CIN. We examined which mitotic regulators are required for the survival of MYC-overexpressing cells and found a reliance on high TPX2 expression. TPX2, a master microtubule regulator, is overexpressed together with MYC in multiple cell lines, in mouse tumor models and in aggressive human breast cancers. High TPX2 expression is permissive for mitotic spindle assembly and chromosome segregation in cells with deregulated MYC, whereas TPX2 depletion blocks mitotic progression, induces cell death and prevents tumor growth. Importantly, attenuation of MYC expression reverses the mitotic defects observed, even in established tumor cell lines, implicating an ongoing role for high MYC in the persistence of a CIN phenotype in tumors. Here, we implicate the MYC oncogene as a regulator of spindle assembly and dynamics and identify a new MYC-TPX2 synthetic-lethal interaction that could represent a future therapeutic strategy in MYC-overexpressing cancers. Our studies suggest that blocking MYC activity can attenuate the emergence of CIN and tumor evolution.
Computing Signal Transduction in Signaling Networks modeled as Boolean Networks, Petri Nets, and Hypergraphs
Authors: Vieira Luis Sordo , Vera-Licona Paola 
Published: February 2018

AbstractMathematical frameworks circumventing the need of mechanistic detail to build models of signal transduction networks include graphs, hypergraphs, Boolean Networks, and Petri Nets. Predicting how a signal transduces in a signaling network is essential to understand cellular functions and disease. Different formalisms exist to describe how a signal transduces in a given intracellular signaling network represented in the aforementioned modeling frameworks: elementary signaling modes, T-invariants, extreme pathway analysis, elementary flux modes, and simple paths. How do these formalisms compare?We present an overview of how signal transduction networks have been modelled using graphs, hypergraphs, Boolean Networks, and Petri Nets in the literature. We provide a review of the different formalisms for capturing signal transduction in a given model of an intracellular signaling network. We also discuss the existing translations between the different modeling frameworks, and the relationships between their corresponding signal transduction representations that have been described in the literature. Furthermore, as a new formalism of signal transduction, we show how minimal functional routes proposed for signaling networks modeled as Boolean Networks can be captured by computing topological factories, a methodology found in the metabolic networks literature. We further show that in the case of signaling networks represented with an acyclic B-hypergraph structure, the definitions are equivalent. In signaling networks represented as directed graphs, it has been shown that computations of elementary modes via its incidence matrix correspond to computations of simple paths and feedback loops. We show that computing elementary modes based on the incidence matrix of a B-hypergraph fails to capture minimal functional routes.
Numerical simulation of transient flow field in a mixed-flow pump during starting period
Authors: Li Wei , Zhang Yang , Shi Weidong , Ji Leilei , Yang Yongfei , Ping Yuanfeng 
Published: February 2018

Purpose
This paper aims to study the transient flow characteristics in a mixed-flow pump during the start-up period.

Design/methodology/approach
In this study, numerical calculation of the internal flow field in a mixed-flow pump using the sliding mesh method was carried out. The regulation of the pressure, streamline and the relative speed during the start-up period was analyzed.

Findings
The trend of the simulated head is consistent with the experimental results, and the calculated head is around 0.3 m higher than the experimental head when the rotation speed reached the stable stage, indicating that the numerical method for the start-up process simulation of the mixed-flow pump has a high accuracy. At the beginning, the velocity inside the impeller changes little along the radius direction and the flow rate increases slowly during the start-up process. As the rotation speed reached the stable stage, the flow inside the impeller became steady, the vortex reduced and transient effects disappeared gradually.

Originality/value
The study results have significant value for revealing the internal unsteady flow characteristics of the mixed-flow pump and providing the reference for the design optimization of the mixed-flow pump.
Researching corporate social responsibility in developing-countries context
Authors: Amos Gideon Jojo 
Published: February 2018

PurposeThis paper aims to present a systematic review of scholarly articles focused on corporate social responsibility (CSR) in developing countries and published during the period 2004 to 2014 in international journals.Design/methodology/approachThis paper applied a bibliometric analysis to 101 articles on CSR research focused on developing countries.FindingsThe study confirms that the most prevalent CSR themes addressed in journals have been social issues, followed by environmental issues in a distant second, with ethics-related issues receiving the least attention. Also, as CSR research in developing countries constitutes an emerging stream of literature, an overwhelming dominance of empirical (qualitative) papers aimed at exploring and/or seeking interpretations to CSR motivations have been confirmed.Research limitations/implicationsAn important limitation of this study is in relation to the methods applied. In the first place, this review is based on two electronic databases: ABI/INFORM Global (ProQuest) and Web of Science Core Collection: Social Sciences Citation Index (SSCI) and Science Citation Index Expanded (SCI-EXPANDED). This means that research published in international journals that are not included in either of these databases will be omitted.Practical implicationsThis review provides useful guidance for future CSR research focused on developing countries thereby providing a foundation for future research in this stream of CSR research.Social implicationsThe findings of this study suggest that much CSR knowledge in developing countries reflects the unique social issues that call for companies to adopt different CSR interventions when operating in developing countries.Originality/valueAlthough this paper is not the first to systematically review CSR research, but it is one of the initial attempts, to the best of the knowledge, to systematically review the state of CSR knowledge in the context of developing countries.
Seeking specific relief in cases of Islamic banking in Malaysia – an analysis
Authors: Muneeza Aishath 
Published: February 2018

Purpose
Often, the application of specific relief to Islamic banking is unspoken and unwritten. However, few studies suggest that legislation on specific relief needs amendment to cater for the effective application of Islamic banking and finance in the country and proposing the idea to introduce an Islamic Specific Relief Act. This paper aims to understand the application of specific relief to Islamic banking in Malaysia. This paper will look at the application of specific relief in Malaysia and discuss the extent of its application to Islamic banking cases reported in Malaysia from 1983 to 2015. The study will shed light on the general types of specific relief from Malaysian and Islamic law perspectives to conclude whether the provisions of Malaysian specific relief law invoked in courts in Islamic banking cases are in line with the general principles of Sharīcah. To further support this, evidence from various commercial civil codes of Muslim countries have been discussed to analyse these provisions from a more practical perspective.

Design/methodology/approach
This is a legal exploratory study primarily focussed on library research.

Findings
When it comes to Islamic banking, federal legislations dealing with commercial matters are applicable. For example, in Islamic banking products, if the land is the subject matter, then National Land Code 1965 shall be applied, and when dealing with Islamic banking agreements, the provisions of Contracts Act 1950 shall be followed. This has been highlighted as a problem faced by Islamic financial services in the case of Tan Sri Abdul Khalid Ibrahim v. Bank Islam Malaysia Berhad and other cases where the judge referred Engku Rabiah and quoted that in Islamic banking transactions, “the transactions entered by the parties may be Sharīcah-compliant in the first place, but upon enforcement of the contracts, the court may make orders and decisions that may side line the Islamic legal principles”. This happens when the substantive laws applicable to Islamic banking are incompatible with Islamic law. Fortunately, the analysis of the relevant sections of Specific Relief Act 1950 in this research proves that the provisions reviewed are in line with Sharīcah. However, to further enhance the operation of specific relief, the granting of specific relief could be made a general rule rather than an exceptional rule available with stringent rules. The research revealed that Specific Relief Act (1950) is expressly referred and discussed only in three cases reported from 1983 to 2015. There are only two specific sections of Specific Relief Act (1950) that have been deliberated in the reported case law on Islamic banking: provisions related to granting of a mandatory injunction and specific performance of contracts.

Originality/value
It is anticipated that this paper will assist to comprehend the importance of converging law and Sharīcah in legislations to attain Sharīcah compliance and will help to realise that not all conventional legislations are Sharīcah non-compliant.
Counterproductive hiring discrimination against women
Authors: Duguet Emmanuel , du Parquet Loïc , L’Horty Yannick , Petit Pascale 
Published: February 2018

PurposeMentioning car and motorcycle licences on a resume sends a signal of strong mobility, which should increase the chances of getting a job in congested traffic areas. The purpose of this paper is to examine whether this is the case for both women and men.Design/methodology/approachThe authors implement an experimental design in order to test for the existence of gender discrimination. The authors use the first-order stochastic dominance (FOSD) criterion and estimate components models.FindingsThe authors find that holding a motorcycle licence leads to a counterproductive selection of female candidates, since the highest commuting mobility meets the lowest hiring rate.Research limitations/implicationsThe methodology developed in the paper can be used for all correspondence test data.Originality/valueThe authors examine effects that have not been observed thus far in the literature, namely, the effects of gender crossed with the effects of the class of driving licence that is mentioned on the resume. The authors also advocate the use of the FOSD criterion to discrimination studies.
The relationship between flexible employment arrangements and workplace performance in Great Britain
Authors: Giovanis Eleftherios 
Published: February 2018

PurposeThere is an increasing concern on the quality of jobs and productivity witnessed in the flexible employment arrangements. The purpose of this paper is to examine the relationship between various flexible employment arrangements and the workplace performance.Design/methodology/approachHome-based working, teleworking, flexible timing and compressed hours are the main employment types examined using the Workplace Employee Relations Survey (WERS) over the years 2004 and 2011 in Great Britain. The workplace performance is measured by two outcomes – the financial performance and labour productivity. First, the determinants of these flexible employment types are explored. Second, the ordinary least squares (OLS) method is followed. Third, an instrumental variable (IV) approach is applied to account for plausible endogeneity and to estimate the causal effects of flexible employment types on firm performance.FindingsThe findings show a significant and positive relationship between the flexible employment arrangements and the workplace performance. Education, age, wage, quality of relations between managers-employees, years of experience, the area of the market the workplace is operated and the competition are significant factors and are positively associated with the propensity of the implementation of flexible employment arrangements.Social implicationsThe insights derived from the study can have various profound policy implications for employees, employers and the society overall, including family-work balance, coping with family demands, improving the firm performance, reducing traffic congestion and stress among others.Originality/valueIt is the first study that explores the relationship between flexible employment types and workplace performance using an IV approach. This allows us to estimate the causal effects of flexible employment types and the possible associated social implications.