bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulatingMYCin 3D: Implications for the fitness of cancer cells
Authors: Sumida Noriyuki , Sifakis Emmanouil G , Scholz Barbara A , Fernandez-Woodbridge Alejandro , Kiani Narsis A , Gomez-Cabrero David , Svensson J Peter , Tegner Jesper , Göndör Anita , Ohlsson Rolf 
Published: March 2018

AbstractThe relationship between stochastic transcriptional bursts and dynamic 3D chromatin states is not well understood due to poor sensitivity and/or resolution of current chromatin structure-based assays. Consequently, it is not well established if enhancers operate individually and/or in clusters to coordinate gene transcription. In the current study, we introduce Nodewalk, which uniquely combines high sensitivity with high resolution to enable the analysis of chromatin networks in minute input material. The >10,000-fold increase in sensitivity over other many-to-all competing methods uncovered that active chromatin hubs identified in large input material, corresponding to 10 000 cells, flanking theMYClocus are primarily virtual. Thus, the close agreement between chromatin interactomes generated from aliquots corresponding to less than 10 cells with randomly re-sampled interactomes, we find that numerous distal enhancers positioned within flanking topologically associating domains (TADs) converge onMYCin largely mutually exclusive manners. Moreover, when comparing with several enhancer baits, the assignment of theMYClocus as the node with the highest dynamic importance index, indicates that it isMYCtargeting its enhancers, rather thanvice versa.Dynamic changes in the configuration of the boundary between TADs flankingMYCunderlie numerous stochastic encounters with a diverse set of enhancers to depict the plasticity of its transcriptional regulation. Such an arrangement might increase the fitness of the cancer cell by increasing the probability ofMYCtranscription in response to a wide range of environmental cues encountered by the cell during the neoplastic process.
Bradyrhizobium diazoefficiens USDA 110-Glycine max interactome provides candidate proteins associated with symbiosis
Authors: Zhang Li , Liu Jin-Yang , Gu Huan , Du Yanfang , Zuo Jian-Fang , Zhang Zhibin , Zhang Menglin , Li Pan , Dunwell Jim M. , Cao Yangrong , Zhang Zuxin , Zhang Yuan-Ming 
Published: March 2018

AbstractAlthough the legume-rhizobium symbiosis is a most important biological process, there is a limited knowledge about the protein interaction network between host and symbiont. Using interolog and domain-based approaches, we constructed an inter-species protein interactome with 5115 protein-protein interactions between 2291 Glycine max and 290 Bradyrhizobium diazoefficiens USDA 110 proteins. The interactome was validated by expression pattern analysis in nodules, GO term semantic similarity, and co-expression analysis. One sub-network was further confirmed using luciferase complementation image assay. In the G. max-B. diazoefficiens interactome, bacterial proteins are mainly ion channel and transporters of carbohydrates and cations, while G. max proteins are mainly involved in the processes of metabolism, signal transduction, and transport. We also identified the top ten highly interacting proteins (hubs) for each of the two species. KEGG pathway analysis for each hub showed that two 14-3-3 proteins (SGF14g and SGF14k) and five heat shock proteins in G. max are possibly involved in symbiosis, and ten hubs in B. diazoefficiens may be important symbiotic effectors. Subnetwork analysis showed that 18 symbiosis-related SNARE proteins may play roles in regulating bacterial ion channels, and SGF14g and SGF14k possibly regulate the rhizobium dicarboxylate transport protein DctA. The predicted interactome and symbiosis proteins provide a valuable basis for understanding the molecular mechanism of root nodule symbiosis in soybean.
G2P: Using machine learning to understand and predict genes causing rare neurological disorders
Authors: Botía Juan A. , Guelfi Sebastian , Zhang David , D’Sa Karishma , Reynolds Regina , Onah Daniel , McDonagh Ellen M. , Martin Antonio Rueda , Tucci Arianna , Rendon Augusto , Houlden Henry , Hardy John , Ryten Mina 
Published: March 2018

AbstractTo facilitate precision medicine and neuroscience research, we developed a machine-learning technique that scores the likelihood that a gene, when mutated, will cause a neurological phenotype. We analysed 1126 genes relating to 25 subtypes of Mendelian neurological disease defined by Genomics England (March 2017) together with 154 gene-specific features capturing genetic variation, gene structure and tissue-specific expression and co-expression. We randomly re-sampled genes with no known disease association to develop bootstrapped decision-tree models, which were integrated to generate a decision tree-based ensemble for each disease subtype. Genes generating larger numbers of distinct transcripts and with higher probability of having missense mutations in normal individuals were significantly more likely to cause neurological diseases. Using mouse-mutant phenotypic data we tested the accuracy of gene-phenotype predictions and found that for 88% of all disease subtypes there was a significant enrichment of relevant phenotypic abnormalities when predicted genes were mutated in mice and in many cases mutations produced specific and matching phenotypes. Furthermore, using only newly identified genes included in the Genomics England November 2017 release, we assessed our gene-phenotype predictions and showed an 8.3 fold enrichment relative to chance for correct predictions. Thus, we demonstrate both the explanatory and predictive power of machine-learning-based models in neurological disease.
Current production as a rapid response expression reporter under micro-oxic and anoxic conditions
Authors: Madsen Cody , Barvo Noelia , Fromwiller Ciara , Tyll Serenity , Amburn Brian , Ducat Danny , Hamberger Bjoern , TerAvest Michaela A. 
Published: March 2018

AbstractInducible gene expression is crucial for regulating cellular processes and production of compounds within cellular pathways. Yet, inducing gene expression is only the first step to utilizing cellular processes for an applied purpose such as biosensors. Detecting when gene expression occurs is central to understanding the overall mechanism of the process as well as maximizing the process. Fluorescent proteins have been established as the primary tool for detecting gene expression in inducible systems. This study proposes electricity production as an alternate tool in reporting gene expression. Using a model organism for electricity production, Shewanella oneidensis MR-1, current was shown to be an efficient reporter for gene expression and comparable to superfolder green fluorescent protein (GFP). Through regulation of the lac operator and T7 promoter, current production was induced by isopropyl β-D-1-thiogalactopyranoside (IPTG) addition. IPTG addition induced translation of GFP and the MtrB protein, which complemented a ∆mtrB strain of S. oneidensis MR-1 and restored current production. This inducible system generated reproducible current in 18 minutes in both micro-oxic and anoxic conditions. These results show that current is a fast reporter for gene expression.Financial DisclosureThe team was supported by the following departments and colleges at Michigan State University: College of Natural Science, College of Engineering, Biochemistry and Molecular Biology Department and Plant Research Laboratory. The team also received support from the DOE Great Lakes Bioenergy Research Center (DOE Office of Science BER DE-FC02-07ER64494) and startup funding from the Department of Molecular Biology and Biochemistry, Michigan State University and support from Michigan State University AgBioResearch (MICL02454) (to B.H.). This work was also supported by NSF CAREER (Award #1254238) to T.A.W. MSU Alpha Chi Sigma also supported the team.Competing InterestsThe authors declare that no competing interests exist.Ethics StatementN/AData AvailabilityAll data will be supplied upon request by the corresponding author.This work was assessed during the iGEM/PLOS Realtime Peer Review Jamboree on 23rd February 2018 and has been revised in response to the reviewers’ comments.
Differences between the de novo proteome and its non-functional precursor can result from neutral constraints on its birth process, not necessarily from natural selection alone
Authors: Nielly-Thibault Lou , Landry Christian R 
Published: March 2018

ABSTRACTProteins are among the most important constituents of biological systems. Because all proteins ultimately evolved from previously non-coding DNA, the properties of these non-coding sequences and how they shape the birth of novel proteins are also expected to influence the organization of biological networks. When trying to explain and predict the properties of novel proteins, it is of particular importance to distinguish the contributions of natural selection and other evolutionary forces. Studies in the field typically use non-coding DNA and GC-content-based random-sequence models to generate random expectations for the properties of novel functional proteins. Deviations from these expectations have been interpreted as the result of natural selection. However, interpreting such deviations requires a yet-unattained understanding of the raw material of de novo gene birth and its relation to novel functional proteins. We mathematically show how the importance of the “junk” polypeptides that make up this raw material goes beyond their average properties and their filtering by natural selection. We find that the mean of any property among novel functional proteins also depends on its variance among junk polypeptides and its correlation with their rate of evolutionary turnover. In order to exemplify the use of our general theoretical results, we combine them with a simple model that predicts the means and variances of the properties of junk polypeptides from the genomic GC content alone. Under this model, we predict the effect of GC content on the mean length and mean intrinsic disorder of novel functional proteins as a function of evolutionary parameters. We use these predictions to formulate new evolutionary interpretations of published data on the length and intrinsic disorder of novel functional proteins. This work provides a theoretical framework that can serve as a guide for the prediction and interpretation of past and future results in the study of novel proteins and their properties under various evolutionary models. Our results provide the foundation for a better understanding of the properties of cellular networks through the evolutionary origin of their components.
On the variability of Species Abundance Distributions with trophic guild and community structure
Authors: García-Callejas David 
Published: March 2018

AbstractSpecies Abundance Distributions (SADs) are one of the most studied properties of ecological communities, and their variability has been studied mostly in the context of horizontal communities, i.e. sets of species from a particular trophic guild. However, virtually all ecological communities encompass several trophic guilds, and the trophic interactions between them are key for explaining the persistence and abundance of individual species. Here I ask whether trophic interactions are also important in shaping Species Abundance Distributions of the different guilds of a community. I analyze the variation in SAD shape across trophic guilds in model and empirical communities. For that, I use a theoretical model that allows tracking the variations in abundances across trophic levels. The relationship between SAD shape and (1) trophic level, and (2) degree of predator specialization is analyzed using mixed-effect models. I combine this approach with an analysis of 4676 empirical datasets spanning terrestrial, marine and freshwater habitats, for which the variation in SAD shape is related to (1) trophic guild, and (2) habitat type. The evenness of model SADs is positively correlated to the trophic level of the guild considered, and also to the number of prey species per predator. These findings are confirmed by the empirical data: there is a significant relationship between SAD evenness and trophic guild, whereby primary producers display the most uneven SADs and pure carnivores the most even ones. Furthermore, regardless of trophic guild, SADs from marine habitats are the most even ones, with terrestrial SADs being the most uneven.
Small non-coding RNA expression in developing mouse nephron progenitor cells
Authors: Phua Yu Leng , Clugston Andrew , Chen Kevin Hong , Kostka Dennis , Ho Jacqueline 
Published: March 2018

AbstractMicroRNAs (miRNAs) are small non-coding RNAs that are essential for the regulation of gene expression and play critical roles in human health and disease. Here we present comprehensive miRNA profiling data for mouse nephron progenitors, which give rise to most of the cell-types of the nephron, the functional units of the kidney. We describe a miRNA expression profile for nephron progenitors, with 162 miRNAs differentially expressed in nephron progenitors when compared to whole kidney. We also annotated 52, and experimentally validated 4 novel miRNAs, which are expressed in developing kidney. Our data is available as a public resource, so that it can be integrated into future studies and analyzed in the context of other functional and epigenomic data in kidney development. Specifically, it will be useful in the effort to shed light on molecular mechanisms underlying processes essential for normal kidney development, such as nephron progenitor specification, self-renewal and differentiation.
Apparent oxygen half saturation constant for nitrifiers: genus specific, inherent physiological property, or artefact of colony morphology?
Authors: Law Yingyu , Matysik Artur , Chen Xueming , Thi Sara Swa , Nguyen Thi Quynh Ngoc , Qiu Guang Lei , Natarajan Gayathri , Williams Rohan B.H. , Ni Bing-Jie , Seviour Thomas William , Wuertz Stefan 
Published: March 2018

AbstractWe report that a singleNitrospirasublineage I OTU performs nitrite oxidation in several full-scale domestic wastewater treatment plants (WWTPs) in the tropics (29-31 °C). Contrary to the prevailing theory for the relationship between nitrite oxidizing bacteria (NOB) and ammonia oxidizing bacteria (AOB), members of theNitrospirasublineage I OTU had an apparent half saturation coefficient,Ks(app)lower than that of the full-scale domestic activated sludge cohabitant AOB (0.09 ± 0.02 g O2 m−3versus 0.3 ± 0.03 g O2 m−3). Paradoxically, NOB may thus thrive under conditions of low oxygen supply. Low dissolved oxygen (DO) conditions could enrich for and high aeration inhibit the NOB in a long-term lab-scale reactor. The relative abundance ofNitrospiragradually decreased with increasing DO until it was washed out. Nitritation was sustained even after the DO was lowered subsequently. Based on 3D-fluorescencein situhybridization (FISH) image analysis, the morphologies of AOB and NOB microcolonies responded to DO levels in accordance with their apparent oxygen half saturation constantKs(app). When exposed to the same oxygenation level, NOB formed densely packed spherical clusters with a low surface area-to-volume ratio compared to theNitrosomonas-like AOB clusters, which maintained a porous and non-spherical morphology. Microcolony morphology is thus a way for AOB and NOB to regulate oxygen exposure and sustain the mutualistic interaction. However, short-term high DO exposure can select for AOB and against NOB in full-scale domestic WWTPs and such population dynamics depend on which specific AOB and NOB species predominate under given environmental conditions.
MRI2MRI: A deep convolutional network that accurately transforms between brain MRI contrasts
Authors: Xiao Sa , Wu Yue , Lee Aaron Y. , Rokem Ariel 
Published: March 2018

ABSTRACTDifferent brain MRI contrasts represent different tissue properties and are sensitive to different artifacts. The relationship between different contrasts is therefore complex and nonlinear. We developed a deep convolutional network that learns the mapping between different MRI contrasts. Using a publicly available dataset, we demonstrate that this algorithm accurately transforms between T1- and T2-weighted images, proton density images, time-of-flight angiograms, and diffusion MRI images. We demonstrate that these transformed images can be used to improve spatial registration between MR images of different contrasts.
International business research challenges in Africa
Authors: Ado Abdoulkadre , Wanjiru Roseline 
Published: March 2018

Purpose
This paper aims to explore the challenges researchers in/on Africa face when conducting research on the continent. It examines the reasons behind Africans’ relatively limited contribution to the business literature in the global sphere and why not culturally sensitive and nuanced research on Africa is spreading unchallenged.

Design/methodology/approach
The study combines knowledge creation and institutional theories to explain why African business scholars struggle in researching the continent and in contributing significantly to global knowledge creation. It also explores the debate about why Africa’s narratives in business seem dominated by not culturally sensitive and nuanced voices and approaches. It uses a participant observation method.

Findings
The study found that African scholars have not yet contributed significantly to global knowledge creation because of Africa’s institutional weaknesses and lack of government support for research, coupled with challenges at the interviewing, organizational and scholars’ levels. The study points to the specificities of the continent as well as to African interviewees’ particularities and the type of interactions with the researchers. The paper proposes new avenues to address those multilevel challenges and offers key lessons for future studies.

Originality/value
To the best of the authors’ knowledge, this study is the first to systematically investigate the fundamental reasons behind business research challenges in/on Africa from knowledge creation and institutional standpoints. This study also contributes to the growing debate on Africans’ meager contribution to business literature as well as the controversy regarding culturally sensitive vs not culturally sensitive knowledge creation on Africa. Finally, it proposes avenues to understanding and overcoming those challenges.
In the shiny world of diamonds and jewelry: all that glitters is not gold!
Authors: Azizbekyan Ara , Bodolica Virginia , Spraggon Martin 
Published: March 2018

Subject area
Strategic management.

Study level/applicability
Upper-level undergraduate courses or introductory MBA courses.

Case overview
The need to diversify the financial risks of his scrap metal business based in Georgia led Levan to invest in a diamond trading company in the UAE. He agreed to be a sleeping partner and provide the capital to Kewon, a diamond specialist with a wealth of experience in the field, in their joint attempt to build an international network of diamond trade. Despite several difficulties faced on the way, their company seemed to generate stable returns for more than five years. Yet following the surprising discovery of multiple organizational inconsistencies, Levan decided to end the partnership with Kewon and establish his own retail jewelry store to be managed by the members of his family. Ultimately, he was confronted with two important decisions regarding both his jewelry business and the diamond company in which he had previously invested a significant amount of capital. The decisions he was about to make were of critical importance for the future of these companies and the people who managed them. By walking readers through a series of triggering events, this case offers the opportunity to evaluate the effectiveness of managerial actions through the application of various strategic management tools and frameworks.

Expected learning outcomes
Upon completion of this case study analysis, students should be able to: estimate the complexities associated with the management of a partnership-based venture in the context of emerging markets; perform a detailed diagnosis of an entrepreneurial venture, applying relevant strategic management tools and techniques; evaluate the effectiveness of managerial actions and decisions at different stages of the organizational lifecycle; and demonstrate the importance of the strategic adaptation of organizations through the deployment of viable decision-making skills.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 11: Strategy.
Resource integration for co-creation between marketing agencies and clients
Authors: Hughes Tim , Vafeas Mario , Hilton Toni 
Published: March 2018

Purpose
Resource integration is a central idea within service-dominant logic (S-D logic), but there has been little scholarly research on this aspect of theory. This paper aims to explore resource integration between marketing agencies and their clients.

Design/methodology/approach
In total, nine case studies have been developed using a dyadic approach of interviewing clients and members of their agency teams. This is followed-up with presentations and workshops with over 200 practitioners who validated the findings and added new perspectives.

Findings
The key operant resources in the client/agency context have been identified. The ways the operant resources of the actors developed during the course of resource integration, building potential resources for future co-creation are shown. The differing perspectives of the actors to each other’s contribution are highlighted.

Research limitations/implications
This study suggests that resource enhancement and development, as a result of integration, is important. For agency/client research, resource integration and development brings new perspectives complementing existing relationship approaches to research. The findings have implications for relationship marketing theory across business-to-business (B2B) contexts.

Practical implications
The findings suggest a resource integration approach that could be jointly addressed between agency and client in improving the way they work together. The discourse of co-creation suggests a way for them to talk about how to work together effectively. Suggestions are made for teaching.

Originality/value
This study develops the S-D logic theory through exploring resource enhancement and development in a B2B co-creation context. The dyadic nature of the research is novel in studying how marketing agencies and clients work together and new perspectives emerge from the approach.