bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of theMycobacterium tuberculosiscomplex by whole genome sequencing
Authors: Lipworth S , Jajou R , de Neeling A , Bradley P , van der Hoek W , Maphalala G , Bonnet M , Sanchez-Padilla E , Diel R , Niemann S , Iqbal Z , Smith G , Peto T , Crook D , Walker TM , van Soolingen D 
Published: November 2017

AbstractThe clinical phenotype of zoonotic tuberculosis, its contribution to the global burden of disease and prevalence are poorly understood and probably underestimated. This is partly because currently available laboratory andin silicotools have not been calibrated to accurately identify all subspecies of theMycobacterium tuberculosiscomplex (Mtbc). We here present the first such tool, SNPs to Identify TB (‘SNP-IT’). Applying SNP-IT to a collection of clinical genomes from a UK reference laboratory, we demonstrate an unexpectedly high number ofM. orygisisolates. These are seen at a similar rate toM. boviswhich attracts much health protection resource and yetM. orygiscases have not been previously described in the UK. From an international perspective it is possible thatM. orygisis an underestimated zoonosis. As whole genome sequencing is increasingly integrated into the clinical setting, accurate subspecies identification with SNP-IT will allow the clinical phenotype, host range and transmission mechanisms of subspecies of theMtbcto be studied in greater detail.
APR-246 reactivates mutant p53 by targeting cysteines 124 and 277
Authors: Zhang Qiang , Bykov Vladimir J.N. , Wiman Klas G. , Zawacka-Pankau Joanna 
Published: November 2017

AbstractThe TP53 tumor suppressor gene is frequently inactivated in human tumors by missense mutations in the DNA binding domain. TP53 mutations lead to protein unfolding, decreased thermostability and loss of DNA binding and transcription factor function. Pharmacological targeting of mutant p53 to restore its tumor suppressor function is a promising strategy for cancer therapy. The mutant p53 reactivating compound APR-246 (PRIMA-1Met) has been successfully tested in a phase I/IIa clinical trial. APR-246 is converted to the reactive electrophile methylene quinuclidinone (MQ), which binds covalently to p53 core domain. We identified cysteine 277 as a prime binding target for MQ in p53. Cys277 is also essential for MQ-mediated thermostabilization of wild-type, R175H and R273H mutant p53, while both Cys124 and Cys277 are required for APR-246-mediated functional restoration of R175H mutant p53 in living tumor cells. These findings may open opportunities for rational design of novel mutant p53-targeting compounds.
Boosting Gene Expression Clustering with System-Wide Biological Information: A Robust Autoencoder Approach
Authors: Cui Hongzhu , Zhou Chong , Dai Xinyu , Liang Yuting , Paffenroth Randy , Korkin Dmitry 
Published: November 2017

AbstractGene expression analysis provides genome-wide insights into the transcriptional activity of a cell. One of the first computational steps in exploration and analysis of the gene expression data is clustering. With a number of standard clustering methods routinely used, most of the methods do not take prior biological information into account. In this paper, we propose a new approach for gene expression clustering analysis. The approach benefits from a new deep learning architecture, Robust Autoencoder, which provides a more accurate high-level representation of the feature sets, and from incorporating prior biological information into the clustering process. We tested our approach on two distinct gene expression datasets and compared the performance with two widely used clustering methods, hierarchical clustering and k-means, as well as with a recent deep learning clustering approach. As a result, our approach outperformed all other clustering methods on the labeled yeast gene expression dataset. Furthermore we showed that it is better in identifying the functionally common clusters than k-means on the unlabeled human gene expression dataset. The results demonstrate that our new deep learning architecture could generalize well the specific properties of gene expression profiles. Furthermore, the results confirm our hypothesis that the prior biological network knowledge could be helpful in the gene expression clustering task.
TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution
Authors: Rohwer Robin R. , Hamilton Joshua J. , Newton Ryan J. , McMahon Katherine D. 
Published: November 2017

ABSTRACTTaxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater datasets using the comprehensive Silva database and the freshwater-specific FreshTrain database. TaxAss increased the percent of the dataset classified compared to using only Silva, especially at fine-resolution family-species taxa levels, while across the freshwater test-datasets classifications increased by as much as 11-40 percent of total reads. A similar increase in classifications was not observed in a control mouse gut dataset, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxa-levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxa levels incorrect classifications became significant. We validated TaxAss using simulated amplicon data with known taxonomy and found that 96-99% of test sequences were correctly classified at fine resolution. TaxAss splits a dataset’s sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source, and available at www.github.com/McMahonLab/TaxAss.IMPORTANCEMicrobial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon datasets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at phylum, class, and order level lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are dataset-dependent and cannot be compared between datasets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between datasets.
Imaging-Genomics Study Of Head-Neck Squamous Cell Carcinoma: Associations Between Radiomic Phenotypes And Genomic Mechanisms Via Integration Of TCGA And TCIA
Authors: Zhu Yitan , Mohamed Abdallah S.R. , Lai Stephen Y , Yang Shengjie , Kanwar Aasheesh , Wei Lin , Kamal Mona , Sengupta Subhajit , Elhalawani Hesham , Skinner Heath , Mackin Dennis S , Shiao Jay , Messer Jay , Wong Andrew , Ding Yao , Zhang Joy , Court Laurence , Ji Yuan , Fuller Clifton D , Anderson M.D. 
Published: November 2017

ABSTRACTPurposeRecent data suggest that imaging radiomics features for a tumor could predict important genomic biomarkers. Understanding the relationship between radiomic and genomic features is important for basic cancer research and future patient care. For Head and Neck Squamous Cell Carcinoma (HNSCC), we perform a comprehensive study to discover the imaging-genomics associations and explore the potential of predicting tumor genomic alternations using radiomic features.MethodsOur retrospective study integrates whole-genome multi-omics data from The Cancer Genome Atlas (TCGA) with matched computed tomography imaging data from The Cancer Imaging Archive (TCIA) for the same set of 126 HNSCC patients. Linear regression analysis and gene set enrichment analysis are used to identify statistically significant associations between radiomic imaging features and genomic features. Random forest classifier is used to predict two key HNSCC molecular biomarkers, the status of human papilloma virus (HPV) and disruptive TP53 mutation, based on radiomic features.ResultsWide-spread and statistically significant associations are discovered between genomic features (including miRNA expressions, protein expressions, somatic mutations, and transcriptional activities, copy number variations, and promoter region DNA methylation changes of pathways) and radiomic features characterizing the size, shape, and texture of tumor. Prediction of HPV and TP53 mutation status using radiomic features achieves an area under the receiver operating characteristics curve (AUC) of 0.71 and 0.641, respectively.ConclusionOur analysis suggests that radiomic features are associated with genomic characteristics in HNSCC and provides justification for continued development of radiomics as biomarkers for relevant genomic alterations in HNSCC.
Subtle alteration in microRNA dynamics accounts for differential nature of cellular proliferation
Authors: Sengupta Dola , Govindaraj Vinodhini , Kar Sandip 
Published: November 2017

AbstractIn the G1 phase of the mammalian cell cycle, a bi-stable steady state dynamics of the transcription factor E2F ensures that only a certain threshold level of the growth factor can induce a high expression level (on state) of E2F to initiate either normal or abnormal cellular proliferation or even apoptosis. A group of microRNA’s known as the mir-17-92 cluster, which specifically inhibits E2F, can simultaneously influence the threshold level of growth factor required for E2F activation, and the corresponding expression level of E2F in the on state. However, mir-17-92 cluster can function as either oncogene or tumor suppressor in a cell-type specific manner for reasons that still remain illusive. Here we put forward a deterministic mathematical model for Myc/E2F/mir-17-92 network that demonstrates how the experimentally observed mir-17-92 mediated differential nature of the cellular proliferation can be reconciled by having conflicting steady state dynamics of E2F for different cell types. While a 2-D bifurcation study of the model rationalizes the reason behind the contrasting E2F dynamics, an intuitive sensitivity analysis of the model parameters predicts that by exclusively altering the mir-17-92 related part of the network, it is possible to experimentally manipulate the cellular proliferation in a cell-type specific fashion for therapeutic intervention.
Kombucha as a model system for multispecies microbial cooperation: theoretical promise, methodological challenges and new solutions ‘in solution’
Authors: May Alexander Niall , Medina James , Alcock Joe , Maley Carlo , Aktipis Athena 
Published: November 2017

AbstractKombucha is a sweetened tea fermented by bacteria and yeast into a carbonated, acidic drink, producing a surface biofilm pellicle (colloquially called a SCOBY) during the process. Typically, liquid and a biofilm pellicle from a previously fermented culture is used as a starter for new cultures; however, there is no standard protocol for growing kombucha in the laboratory. In order to establish a standard protocol with low variability between replicates, we tested whether we could begin a kombucha culture with only well-mixed liquid stock. We found that viable kombucha cultures can be grown from low percentages of initial inoculum stock liquid, that new pellicles can form from liquid alone (with no ‘starter’ pellicle), and that the variation in the pellicle characteristics is lower when only a liquid starter is used (p = 0.0004). We also found that blending the pellicle before including it significantly reduces the variation among replicates, though the final pellicle was abnormal. We conclude that growing kombucha from only liquid stock is viable and provides a greater degree of experimental control and reproducibility compared to alternatives. Standardizing methodologies for studying kombucha in the lab can facilitate the use of this system for exploring questions about the evolutionary, ecological and cooperative/competitive dynamics within this multi-species system including resource transfers, functional dependence, genetic divergence, collective defense, and ecological succession. A better understanding of kombucha and other fermented foods may eventually allow us to leverage their pathogen inhibitory properties to develop novel antibiotics and bacteriocins.
Causal Mapping of Emotion Networks in the Human Brain: Framework and Preliminary Findings
Authors: Dubois Julien , Oya Hiroyuki , Tyszka J. Michael , Howard Matthew , Eberhardt Frederick , Adolphs Ralph 
Published: November 2017

AbstractEmotions involve many cortical and subcortical regions, prominently including the amygdala. It remains unknown how these multiple network components interact, and it remains unknown how they cause the behavioral, autonomic, and experiential effects of emotions. Here we describe a framework for combining a novel technique, concurrent electrical stimulation with fMRI (es-fMRI), together with a novel analysis, inferring causal structure from fMRI data (causal discovery). We outline a research program for investigating human emotion with these new tools, and provide initial findings from two large resting-state datasets as well as case studies in neurosurgical patients with electrical stimulation of the amygdala. The overarching goal is to use causal discovery methods on fMRI data to infer causal graphical models of how brain regions interact, and then to further constrain these models with direct stimulation of specific brain regions and concurrent fMRI. We conclude by discussing limitations and future extensions. The approach could yield anatomical hypotheses about brain connectivity, motivate rational strategies for treating mood disorders with deep brain stimulation, and could be extended to animal studies that use combined optogenetic fMRI.
Fixed assets management of Larsen & Toubro: stability vs stagnancy
Authors: Goel Sandeep 
Published: November 2017

Subject area
Accounting and Finance.

Study level/applicability
Postgraduate/graduate.

Case overview
This paper aims to analyse the fixed assets management of Larsen & Toubro Ltd (L&T), a leading Indian construction company for sufficiency and efficiency, and explore its future growth prospects in relation to its capital investments. It also investigates whether the global crisis in 2008 had any impact on the development plans of the company for future orientation as the global recession affected companies in various sectors worldwide. It specifically aims to find out whether L&T was in a better position to face the situation in the industry.

Expected learning outcomes
Expected learning outcomes are as follows: to learn and apply the concept of fixed assets management in a business organization; to evaluate the impact of fixed assets management on the profitability of the company; to appreciate the importance of fixed assets management efficiency in a business organization; and to illustrate the use of financial crisis on the growth prospects of a business.

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 1: Accounting and finance.
Pepsodent: marketing strategy at the bottom of the pyramid
Authors: Tocquer Gerard 
Published: November 2017

Subject area
Marketing in an emerging market.

Study level/applicability
The case is aimed at MBA students in a marketing strategy class on marketing at the bottom of the pyramid or on branding.

Case overview
A young brand manager faced the challenge to increase drastically a brand market share to 8 per cent in 2015 in a context of a new emerging market with large number of consumers living with no more than US$1.25 a day.

Expected learning outcomes
Expected learning outcomes are as follows: to familiarize students with emerging markets characteristics; to illustrate the challenges of marketing a brand to local consumers with limited financial resources to craft a marketing strategy for Pepsodent with a clear positioning, allowing the Pepsodent brand to differentiate itself and to leverage its brand equity; and to develop a marketing-mix aligned with the brand positioning.

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 8: Marketing.
Correlates of mental health and well-being for Mexican female partners of migrants
Authors: Sotomayor-Peterson Marcela , Lucero-Liu Ana A. 
Published: November 2017

Purpose
The purpose of this paper is to assess the associations between familism, frequency of physical contact, and marital satisfaction with mental health and well-being in a sample of 58 female marital partners of migrants who stayed in Mexico when their spouses migrated to the USA.

Design/methodology/approach
In total, 58 women were recruited through word of mouth in Sonora, Mexico. All women had their partner (the father of her children) living in the USA. Survey was administered face-to-face in participants’ homes.

Findings
Hierarchical regression analysis found that higher marital satisfaction and frequency of physical contact predicts mental health and well-being. However, familism was not associated with mental health and well-being for female partners of migrants.

Originality/value
This work is unique in that the current sample of female partners of migrants originate from the Sonora border region and has greater physical contact with their partner than most studies on transnational families assume. Approximately 40 percent of participants residing in the Sonora border state meet with their partners at least once a month. Additionally, this work provides an intimate face to the understanding of the very specific processes distinctive of inhabitants of border regions that are part of international migration. In order to promote health equity, health providers (e.g. counselors) need evidence-based information to tailor services to the specific needs of underserved Mexican transnationals.
Low factual understanding and high anxiety about climate warming impedes university students to become sustainability stewards
Authors: Pfautsch Sebastian , Gray Tonia 
Published: November 2017

PurposeThis study, from Western Sydney University, aims to assess the disposition of students towards climate warming (CW) – a key component of sustainability. CW is a global reality. Any human born after February 1985 has never lived in a world that was not constantly warming, yet little is known about how higher education students perceive their future in a warming world.Design/methodology/approachAn online survey, split into three parts, was used to deliver benchmark data on (I) personal information, (II) factual knowledge and (III) sentiments related to CW.FindingsGender and age of students significantly influenced their perception of CW. While self-rated understanding of CW was generally high, factual knowledge about CW was low. Few students recognized that CW was already under way, and that it was mainly caused by human activity. The most prominent emotions were fear, sadness and anger, foretelling widespread disempowerment and fear for the future.Research limitations/implicationsThe study was based on a single dataset and survey response was relatively low. However, respondents mirrored the composition of the student community very well.Originality/valueThis is the first study revealing large psychological distance to the effects of CW in university students from Australia. Combined with the impression of despondence, the present study suggests that higher education in Australia, and possibly elsewhere, is not providing the prerequisite tools tomorrow’s leaders require for meeting societal, environmental and economic challenges caused by CW. Practical ways to erase these blind spots in sustainability literacy are provided, drawing upon established and novel concepts in higher education.
Curating the infosphere
Authors: Bawden David , Robinson Lyn 
Published: November 2017

PurposeThe purpose of this paper is to re-examine the proposal that Luciano Floridi’s philosphy of information (PI) may be an appropriate conceptual foundation for the discipline of library and information science (LIS).Design/methodology/approachA selective literature review and analysis are carried out.FindingsIt is concluded that LIS is in need of a new conceptual framework, and that PI is appropriate for this purpose.Originality/valueFloridi proposed a close relationship between PI and LIS more than a decade ago. Although various authors have addressed the aspects of this relationship since then, this is the first proposal from an LIS perspective that PI be adopted as a basis for LIS.
Characterization of Leptospira species isolated from soil collected in Japan
Authors: Masuzawa Toshiyuki , Sakakibara Keiko , Saito Mitsumasa , Hidaka Yusuke , Villanueva Sharon Y. A. M. , Yanagihara Yasutake , Yoshida Shin‐ichi 
Published: November 2017

ABSTRACTLeptospira were isolated from soil obtained from Hokkaido, the northernmost island, to Okinawa, the southernmost island, of Japan using sulfamethoxazole, trimethoprim, amphotericin B, fosfomycin, and 5‐ fluorouracil. Fifty of 132 soil samples (37.9%) were culture‐positive. On the basis of 16S‐rDNA sequences, 12 of the isolated Leptospira were classified into a pathogenic species clade that is closely associated with L. alstonii and L. kmetyi. Nine isolates were classified as intermediate species and were found to be similar to L. licerasiae. Twenty‐seven isolates were classified as non‐pathogenic species, of which 23 were found to be related to L. wolbachii. Non‐pathogenic Leptospira are commonly distributed in environmental soil.