bluuebunny/crossref_metadata_2025 huggingface dataset:
ProteomeGenerator: A framework for comprehensive proteomics based on de novo transcriptome assembly and high-accuracy peptide mass spectral matching
Authors: Cifani Paolo , Dhabaria Avantika , Yoshimi Akihide , Abdel-Wahab Omar , Poirier John T. , Kentsis Alex
Published: December 2017

Modern mass spectrometry now permits genome-scale and quantitative measurements of biological proteomes. However, analyses of specific specimens are currently hindered by the incomplete representation of biological variability of protein sequences in canonical reference proteomes, and the technical demands for their construction. Here, we report ProteomeGenerator, a framework for de novo and reference-assisted proteogenomic database construction and analysis based on sample-specific transcriptome sequencing and high-resolution and high-accuracy mass spectrometry proteomics. This enables assembly of proteomes encoded by actively transcribed genes, including sample-specific protein isoforms resulting from non-canonical mRNA transcription, splicing, or editing. To improve the accuracy of protein isoform identification in non-canonical proteomes, ProteomeGenerator relies on statistical target-decoy database matching augmented with spectral-match calibrated sample-specific controls. We applied this method for the proteogenomic discovery of splicing factor SRSF2-mutant leukemia cells, demonstrating high-confidence identification of non-canonical protein isoforms arising from alternative transcriptional start sites, intron retention, and cryptic exon splicing, as well as improved accuracy of genome-scale proteome discovery. Additionally, we report proteogenomic performance metrics for the current state-of-the-art implementations of SEQUEST HT, Proteome Discoverer, MaxQuant, Byonic, and PEAKS mass spectral analysis algorithms. Finally, ProteomeGenerator is implemented as a Snakemake workflow, enabling open, scalable, and facile discovery of sample-specific, non-canonical and neomorphic biological proteomes (https://github.com/jtpoirier/proteomegenerator).
Synthetic hormone-responsive transcription factors can monitor and reprogram plant development
Authors: Khakhar Arjun , Leydon Alexander R. , Lemmex Andrew C. , Klavins Eric , Nemhauser Jennifer L.
Published: December 2017

Developmental programs continuously sculpt plant morphology to meet environmental challenges, and these same programs have been manipulated to increase agricultural productivity1,2. Small molecule phytohormones act as signals within these programs creating chemical circuitry3 that, in many cases, has been represented in mathematical models4,5. To date, model validation and forward engineering of plant morphology has been largely restricted to adding or subtracting genes, as more nuanced tools to modulate key control parameters identified by such models in vivo are severely limited6,7. Here, we use Arabidopsis thaliana to validate a novel set of synthetic and modular hormone activated Cas9-based repressors (HACRs) that respond to three phytohormones: auxin, gibberellins and jasmonates. We demonstrate that HACRs can regulate genes in response to both exogenous hormone treatments, as well as in response to local differences in endogenous hormone levels associated with developmental events. We further show that HACRs can be used to reprogram the agriculturally relevant traits of shoot branching and phyllotaxy by tuning canalization strength, a critical control parameter predicted by mathematical models. By deploying a HACR to re-parameterize the threshold for induction of the auxin transporter PIN-FORMED1 (PIN1), we observed a decrease in shoot branching and phyllotactic noise as predicted by existing models4,5. The approach described here provides a framework for improved mapping of developmental circuitry, as well as a means to better leverage model predictions to engineer development.
Exploring Single-Cell Data with Deep Multitasking Neural Networks
Authors: Amodio Matthew , van Dijk David , Srinivasan Krishnan , Chen William S , Mohsen Hussein , Moon Kevin R. , Campbell Allison , Zhao Yujiao , Wang Xiaomei , Venkataswamy Manjunatha , Desai Anita , Ravi V. , Kumar Priti , Montgomery Ruth , Wolf Guy , Krishnaswamy Smita
Published: December 2017

Biomedical researchers are generating high-throughput, high-dimensional single-cell data at a staggering rate. As costs of data generation decrease, experimental design is moving towards measurement of many different single-cell samples in the same dataset. These samples can correspond to different patients, conditions, or treatments. While scalability of methods to datasets of these sizes is a challenge on its own, dealing with large-scale experimental design presents a whole new set of problems, including batch effects and sample comparison issues. Currently, there are no computational tools that can both handle large amounts of data in a scalable manner (many cells) and at the same time deal with many samples (many patients or conditions). Moreover, data analysis currently involves the use of different tools that each operate on their own data representation, not guaranteeing a synchronized analysis pipeline. For instance, data visualization methods can be disjoint and mismatched with the clustering method. For this purpose, we present SAUCIE, a deep neural network that leverages the high degree of parallelization and scalability offered by neural networks, as well as the deep representation of data that can be learned by them to perform many single-cell data analysis tasks, all on a unified representation.

A well-known limitation of neural networks is their interpretability. Our key contribution here are newly formulated regularizations (penalties) that render features learned in hidden layers of the neural network interpretable. When large multi-patient datasets are fed into SAUCIE, the various hidden layers contain denoised and batch-corrected data, a low dimensional visualization, unsupervised clustering, as well as other information that can be used to explore the data. We show this capability by analyzing a newly generated 180-sample dataset consisting of T cells from dengue patients in India, measured with mass cytometry. We show that SAUCIE, for the first time, can batch correct and process this 11-million cell data to identify cluster-based signatures of acute dengue infection and create a patient manifold, stratifying immune response to dengue on the basis of single-cell measurements.
Deep sequencing reveals two Jurkat subpopulations with distinct miRNA profiles during camptothecin-induced apoptosis
Authors: Erdoğan İpek , Coşacak Mehmet İlyas , Aldanmaz Ayten Nalbant , Akgül Bünyamin
Published: December 2017

microRNAs (miRNAs) are small non-coding RNAs of about 19-25 nt that regulate gene expression post-transcriptionally under various cellular conditions, including apoptosis. The miRNAs involved in modulation of apoptotic events in T cells are partially known. However, heterogeneity associated with cell lines makes it difficult to interpret gene expression signatures especially in cancer-related cell lines. Treatment of Jurkat T cell leukemia cell line with the universal apoptotic drug, camptothecin, resulted in identification of two Jurkat sub-populations: one that is sensitive to camptothecin and the other being rather intrinsically resistant. We sorted apoptotic Jurkat cells from the non-apoptotic ones prior to profiling miRNAs through deep sequencing. Our data showed that a total of 184 miRNAs were dysregulated. Interestingly, apoptotic and non-apoptotic sub-populations exhibited a distinct miRNA expression profile. In particular, 6 miRNAs were inversely expressed in these two sub-populations. The pyrosequencing results were validated by real time qPCR. Altogether these results suggest that miRNAs modulate apoptotic events in T cells and that cellular heterogeneity requires careful interpretation of miRNA expression profiles obtained from drug-treated cell lines.
A series of (E)-5-(arylideneamino)-1-tert-butyl-1H-pyrrole-3-carbonitriles and their reduction products to secondary amines: syntheses and X-ray structural studies
Authors: Macías Mario A. , Castillo Juan-Carlos , Portilla Jaime
Published: December 2017

An efficent access to a series of N-(pyrrol-2-yl)amines, namely (E)-1-tert-butyl-5-[(4-chlorobenzylidene)amino]-1H-pyrrole-3-carbonitrile, C16H16ClN3, (7a), (E)-1-tert-butyl-5-[(2,4-dichlorobenzylidene)amino]-1H-pyrrole-3-carbonitrile, C16H15Cl2N3, (7b), (E)-1-tert-butyl-5-[(pyridin-4-ylmethylene)amino]-1H-pyrrole-3-carbonitrile, C15H16N4, (7c), 1-tert-butyl-5-[(4-chlorobenzyl)amino]-1H-pyrrole-3-carbonitrile, C16H18ClN3, (8a), and 1-tert-butyl-5-[(2,4-dichlorobenzyl)amino]-1H-pyrrole-3-carbonitrile, C16H17Cl2N3, (8b), by a two-step synthesis sequence (solvent-free condensation and reduction) starting from 5-amino-1-tert-butyl-1H-pyrrole-3-carbonitrile is described. The syntheses proceed via isolated N-(pyrrol-2-yl)imines, which are also key synthetic intermediates of other valuable compounds. The crystal structures of the reduced compounds showed a reduction in the symmetry compared with the corresponding precursors, viz. Pbcm to P\overline{1} from compound (7a) to (8a) and P21/c to P\overline{1} from compound (7b) to (8b), probably due to a severe change in the molecular conformations, resulting in the loss of planarity observed in the nonreduced compounds. In all of the crystals, the supramolecular assembly is controlled mainly by strong (N,C)—H...N hydrogen bonds. However, in the case of (7a)–(7c), C—H...Cl interactions are strong enough to help in the three-dimensional architecture, as observed in Hirshfeld surface maps.
Corporate governance and firm risk
Authors: Mathew Sudha , Ibrahim Salma , Archbold Stuart
Published: December 2017

Purpose

This study aims to explore the relationship between board governance structure and firm risk. In particular, this study develops a “governance index” based on four aspects of the board: board composition, board leadership structure, board member characteristics and board processes, and it examines how the overall index relates to firm risk.

Design/methodology/approach

The study is conducted using a sample of 268 UK firms from the FTSE 350 index over the period from 2005 to 2010. An index is constructed to capture the overall governance structure of the firm. Regressions of the index on three risk measures are examined.

Findings

This study finds that the governance index that aggregates the four sets of board attributes is significantly and negatively related to firm risk. Robustness tests confirm this result.

Research limitations/implications

A large number of studies have explored the relationship between the attributes of corporate boards and firm performance with mixed results. A much smaller number of studies have looked at board attributes and firm risk, but these have either focused on financial sector firms alone or have included only a single or a limited number of attributes. This study, using a broad agency framework, seeks to extend the work on firm risk and board attributes by both expanding industry sectors examined and using a comprehensive set of board attributes.

Originality value

The findings have policy and practical implications for investors, regulators and chairmen of boards of governors to the extent that they inform these constituencies about the set of board attributes that are associated with firm risk. This study is the first to use a comprehensive measure of governance and relate it to firm risk.
The chairperson and CEO roles interaction and responses to strategic tensions
Authors: Morais Filipe , Kakabadse Andrew , Kakabadse Nada
Published: December 2017

Purpose

The purpose of this paper is to use Stewart’s model of role as a lense from which to explore chairperson and CEO role dynamics in addressing strategic paradox and tension.

Design/methodology/approach

The paper draws on 29 semi-structured, in-depth interviews with chairpersons and CEOs of UK-listed companies. Interview data are subjected to role analysis using Stewart’s (1982) Demands-Constraints-Choice (DCC) model of role.

Findings

Findings indicate that relationship levels of trust, communication and chairperson time enable strategic tensions to be raised and confronted in the relationship reducing defensiveness. Two distinct approaches to handle strategic tensions are found. The CEO-led approach predominates and rests on less flexible role boundaries, requiring the chairperson to proactively identify strategic tensions and perform an advisory/mentoring role. The shared leadership approach, less prevalent, rests on highly flexible role boundaries where the skills and experience of each incumbent become more relevant, enabling the separation of efforts and integration of strategic tensions in the relationship in a “dynamic complementarity of function”.

Research limitations/implications

The paper only applies to the UK context and is limited to contexts where CEO and chairperson roles are separate. The paper draws on individual perceptions of chairperson and CEOs (i.e. not pairs).

Practical implications

The paper provides insights to practicing CEOs and chairperson on two distinct ways of working through strategic paradox and tensions.

Originality/value

The paper adds to the scarce literature at chairperson and CEO roles and strategic paradox and tension.
The curse of the #1 carmaker: Toyota’s crisis
Authors: Chikudate Nobuyuki , Alpaslan Can M.
Published: December 2017

Purpose

Using as many perspectives as possible to understand large-scale industrial crises can be a daunting task. This paper aims to demonstrate a reasonably complex yet systemic, analytical and critical approach to analyzing what causes crises.

Design/methodology/approach

The authors use a multi-perspective methodology within which each perspective uses a substantially different ontology and epistemology, offering a deeper understanding of the causes of large-scale crises. The methodology utilizes extant theory and findings, archival data from English and Japanese sources, including narratives of focal people such as Toyota President Akio Toyoda.

Findings

The analysis suggests that what caused Toyota’s crisis was not just Toyota’s failure to solve its technical problems. It was Toyota’s collective myopia, interactively complex new technologies and misunderstanding of corporate citizenship.

Practical implications

The authors argue that crises are complex situations best understood from multiple perspectives and that easily observable aspects of crises are often not the most significant causes of crises. In most cases, causes of crises are hidden and taken-for-granted assumptions of managers. Thus, managers must view crises critically from multiple yet distinct viewpoints.

Originality/value

The authors use Alpaslan and Mitroff’s multi-disciplinary methodology to outline several critical perspectives on Toyota’s messy recall crisis.
Organizational innovation: the role of leadership and organizational culture
Authors: Li Wenjing , Bhutto Tahseen Ahmed , Nasiri Ali Reza , Shaikh Hamid Ali , Samo Fayaz Ali
Published: December 2017

Purpose

The purpose of this paper is to approach the issue of how organizational innovation can be accelerated with the support of leadership structures and the organizational climate, specifically taking into account the top innovative universities of the world, which has not been found in previous empirical studies.

Design/methodology/approach

A survey, based on a deductive approach, is adopted since the questionnaire for organizational innovation is designed for organizations in order to measure organizational innovation, widely used by experienced employees from senior managers to all kind of employees (Caird et al., 2013) facilitating the European Commission work, whereas for transformational leadership, a Multifactor Leadership Questionnaire (Bass and Avolio, 1994) is utilized. A complete online questionnaire was developed for collecting data, and the PLS-SEM statistical technique is used for analysis and results.

Findings

Top innovative universities of the world mostly have a transformational leadership style directly triggering organizational innovation which is consistent with the previous studies, while transactional leadership is having a positive relationship with organizational culture and innovation, but the results were statistically insignificant.

Research limitations/implications

Based on this research and other previous studies, it is suggested that universities across the world ought to imply transformational leadership traits and style which have fostered organizational innovation in the top-ranked innovative universities in developed nations, whereas more factors needed to be studied so that comprehensive guidelines should be provided to universities and research institutes where innovation is stagnant and passive.

Practical implications

The finding has practical implications, suggesting that universities and research institutes should draft and implement guidelines where leaders with certain traits and norms can play a role to nourish an environment where stakeholders think outside the box, with learning and knowledge creation, and proactive contribution beyond responsibilities, obligations, and compulsion.

Social implications

This study has suggested that less innovative universities should draft and design leadership and cultural enriching plans so that society, organizations, and commercial firms could foster innovation, ultimately benefiting general public and society.

Originality/value

Very few of the scholars have investigated from the perspective of innovative universities, where knowledge is created and flows into organizations, either governmental or private, and society in general. As a result, this study aims to investigate how leadership has impacted the culture of knowledge creation and innovativeness in the top 100 innovative universities. So, this is among rare studies where universities are suggested to adopt innovation supporting culture and leadership.
Human behavior analysis under financial information science
Authors: Hsu Feng Jui , Chen Yu-Cheng
Published: December 2017

Purpose

The purpose of this paper is to investigate the relationships among corporate social responsibility (CSR), analyst forecast accuracy and firms’ earnings management behavior using US-based firms.

Design/methodology/approach

The authors use the Kinder, Lydenberg, Domini (KLD) database to construct CSR performance scores and divide all firms into ten groups from high to low as a proxy for CSR performance. The authors obtained an initial sample of 33,364 firm-year observations from 1991 to 2012. Filtering for records which exist in the KLD, Compustat, and Center for Research in Security Prices databases lefts a total of 16,807 firm-year observations and CSR evaluation reports for 5,896 firms.

Findings

The authors find that high CSR-score firms have lower rates of analyst forecast error than their low CSR-score counterparts, suggesting that CSR performance is a useful means of forecasting earnings. Furthermore, firms with better CSR performance have significantly lower accrual-based earnings management behavior. However, the level of the manipulation behavior of real earnings management (REM) activities increased significantly in better CSR firms, suggesting that high CSR-score firms substituted REM methods for accrual-based methods. REM methods are consistent with the stipulations of the Sarbanes-Oxley Act and allow high CSR-score firms to better manipulate earnings behavior. These results hold after the authors control for various factors related to firm financial characteristics.

Originality/value

Overall, the findings have important implications for investors and regulators to more easily assess firms’ earnings manipulation behavior and earnings stability under CSR performance and financial information in financial markets.
An emergent understanding of influences on managers’ voices in SMEs
Authors: Cumberland Denise M. , Shuck Brad , Immekus Jason , Alagaraja Meera
Published: December 2017

Purpose

The purpose of this paper is to highlight the effect of supervisor openness on employee voice among middle management employees in small and medium-sized enterprises (SMEs). The authors develop a model to examine the mediating role of job satisfaction and employee engagement in the SME context.

Design/methodology/approach

A cross-sectional survey design was used to gather data from respondents who worked in SMEs (N=202). Exploratory factor analysis was used for dimensionality assessment of the voice measure. Mediation analysis was used to examine a two-mediator model to investigate the effects of engagement and job satisfaction on voice, and the degree these variables mediated the relationship of supervisor openness to ideas with employee voice.

Findings

Results revealed that supervisor openness is positively associated with job satisfaction and employee engagement, but only engagement was a facilitating variable that stimulated employee voice.

Research limitations/implications

Middle management members can be a conduit or inhibitor of the free flow of information. Yet, research has tended to ignore the role of middle managers in voice research. Moreover, within the specific organizational context of SMEs, greater understanding of both the antecedents and mediators to voice behavior is likely to impact the development of specific HR practices that focus on engagement and better facilitate two-way communication between supervisors and employees.

Originality/value

This work refines the understanding of the role employee engagement has on employee voice in the context of SMEs.
Effects of increased specialization on revenue of Alaskan salmon fishers over four decades
Authors: Ward Eric J. , Anderson Sean C. , Shelton Andrew O. , Brenner Richard E. , Adkison Milo D. , Beaudreau Anne H. , Watson Jordan T. , Shriver Jennifer C. , Haynie Alan C. , Williams Benjamin C.
Published: December 2017

Theory and previous studies have shown that commercial fishers with a diversified catch across multiple species may experience benefits such as increased revenue and reduced variability in revenue. However, fishers can only increase the species diversity of their catch if they own fishing permits that allow multiple species to be targeted, or if they own multiple single‐species permits. Individuals holding a single permit can only increase catch diversity within the confines of their permit (e.g. by fishing longer or over a broader spatial area).

Using a large dataset of individual salmon fishers in Alaska, we build a Bayesian variance function regression model to understand how diversification impacts revenue and revenue variability, and how these effects have evolved since the 1970s.

Applying these models to six salmon fisheries that encompass a broad geographic range and a variety of harvesting methods and species, we find that the majority of these fisheries have experienced reduced catch diversity through time and increasing benefits of specialization on mean individual revenues.

One factor that has been hypothesized to reduce catch diversity in salmon fisheries is large‐scale hatchery production. While our results suggest negative correlations between hatchery returns and catch diversity for some fisheries, we find little evidence for a change in variability of annual catches associated with increased hatchery production.

Synthesis and applications. Despite general trends towards more specialization among commercial fishers in Alaska, and more fishers exclusively targeting salmon, we find that catching fewer species can have positive effects on revenue. With increasing specialization, it is important to understand how individuals buffer against risk, as well as any barriers that prevent diversification. In addition to being affected by environmental variability, fishers are also affected by economic factors including demand and prices offered by processors. Life‐history variation in the species targeted may also play a role. Individuals participating in Alaskan fisheries with high contributions of pink salmon — which have the shortest life cycles of all Pacific salmon — also have the highest variability in year‐to‐year revenue.
Impact of adjusting for inter‐rater variability in conference abstract ranking and selection processes
Authors: Scanlan Justin Newton , Lannin Natasha A. , Hoffmann Tammy , Stanley Mandy , McDonald Rachael
Published: December 2017

Background/aim

Scientific conferences provide a forum for clinicians, educators, students and researchers to share research findings. To be selected to present at a scientific conference, authors must submit a short abstract which is then rated on its scientific quality and professional merit and is accepted or rejected based on these ratings. Previous research has indicated that inter‐rater variability can have a substantial impact on abstract selection decisions. For their 2015 conference, the Occupational Therapy Australia National Conference introduced a system to identify and adjust for inter‐rater variability in the abstract ranking and selection process.

Method

Ratings for 1340 abstracts submitted for the 2015 and 2017 conferences were analysed using many‐faceted Rasch analysis to identify and adjust for inter‐rater variability. Analyses of the construct validity of the abstract rating instrument and rater consistency were completed. To quantify the influence of inter‐rater variability of abstract selection decisions, comparisons were made between decisions made using Rasch‐calibrated measure scores and decisions that would have been made based purely on raw average scores derived from the abstract ratings.

Results

Construct validity and measurement properties of the abstract rating tool were good to excellent (item fit MnSq scores ranged from 0.8 to 1.2; item reliability index = 1.0). Most raters (24 of 27, 89%) were consistent in their use of the rating instrument. When comparing abstract allocations under the two conditions, 25% of abstracts (n = 341) would have been allocated differently if inter‐rater variability was not accounted for.

Conclusion

This study demonstrates that, even with a strong abstract rating instrument and a small rater pool, inter‐rater variability still exerts a substantial influence on abstract selection decisions. It is recommended that all occupational therapy conferences internationally, and scientific conferences more generally, adopt systems to identify and adjust for the impact of inter‐rater variability in abstract selection processes.
Pregnancy leisure physical activity and children's neurodevelopment: a narrative review
Authors: Álvarez‐Bueno C , Cavero‐Redondo I , Sánchez‐López M , Garrido‐Miguel M , Martínez‐Hortelano JA , Martínez‐Vizcaíno V
Published: December 2017

In recent years, interest in the relation between maternal physical activity during pregnancy and children's neurocognitive development has been growing. Several observational studies and clinical trials have analysed this relation and they differ in the findings, especially for children's language‐related skills and IQ. Physical activity assessment, amount of physical activity and the test used for measuring children's cognition could affect this relation, as well as other factors that should be considered. This article will review the evidence on the effects of physical activity during pregnancy on children's different cognitive domains.

Tweetable abstract

Leisure physical during pregnancy positively affects offspring's general intelligence and language skills.
Predicting re‐presentation following discharge from the emergency department with non‐specific chest pain
Authors: Potezny Tessa M , Horwood Christopher M , Hakendorf Paul , Papendick Cynthia , Thompson Campbell H
Published: December 2017

Objective

To determine the 30 day major adverse cardiac events (MACE) and re‐presentation rates of non‐specific chest pain (NSCP) patients following four different disposition pathways and to contrast re‐presentation rates of patients with NSCP with those for all other patients presenting to the ED.

Methods

Cases were derived from the ED database for two large teaching hospitals where patients aged 18 or over were triaged between 2009 and 2016, and their diagnosis on leaving the ED was NSCP. Statewide 30 day rates of MACE and ED re‐presentations were calculated, and multivariable logistic regression analysis identified significant predictors of both.

Results

A total of 40 183 cases were included; 16 014 discharged directly from the ED, while the remainder were admitted under Cardiology (n = 7286), General Medicine (n = 7739) or an ED observation unit (n = 4086). Compared to discharge directly from the ED, admission was associated with a decreased 30 day re‐presentation rate (OR = 0.857; 95% CI 0.795–0.923; P < 0.001). However, there was no significant difference in adjusted re‐presentation between admitting units. The rates of 30 day MACE were higher in admitted patients, particularly in those admitted to general medicine; however, this difference was accounted for by differing patient characteristics.

Conclusion

Despite a slightly increased rate of re‐presentation in patients with NSCP sent home from the ED, we conclude that there is minimal advantage in admitting many patients who lack a diagnosis for their chest pain. For a selected patient population, discharge from the ED may become a safe and cost‐effective approach. A prospective randomised study is required.
Achieving the four dimensions of food security for resettled refugees in Australia: A systematic review
Authors: Lawlis Tanya , Islam Wasima , Upton Penney
Published: December 2017

Aim

Food security is defined by four dimensions: food availability, access, utilisation and stability. Resettled refugees face unique struggles securing these dimensions and, thus, food security when moving to a new country. This systematic review aimed to identify the challenges Australian refugees experience in achieving the four dimensions of food security.

Methods

The Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) guidelines were followed; the SPIDER tool was used to determine eligibility criteria. Three databases were searched using terms relating to food in/security and refugees from 2000 to 20 May 2017.

Results

Seven articles were retained for analysis. Studies were categorised against the four dimensions, with four studies identifying challenges against all dimensions. Challenges contributing to high levels of food insecurity in each dimension included: availability and cost of traditional foods, difficulty in accessing preferred food outlets, limited food knowledge and preparation skills and food stability due to low income and social support.

Conclusions

Food insecurity adversely impacts refugee health and integration. Methodical research framed by the four dimensions of food security is imperative to address challenges to securing food security in refugee groups and assisting in the development of sustainable interventions.
Specific changes of enteric mycobiota and virome in inflammatory bowel disease
Authors: Chu Yi , Jiang Ming Zuo , Xu Bing , Wang Wei Jie , Chen Di , Li Xiao Wei , Zhang Yu Jie , Liang Jie
Published: December 2017

One of the important features of inflammatory bowel disease (IBD) is dysbiosis of the gut microbiota. It has been well documented that changes in the commensal bacterial population are involved in IBD development. However, the function of the fungal and viral communities in IBD remains unclear. Moreover, the optimal treatment for IBD patients with opportunistic infections is still undecided. This review focused on how the enteric mycobiota and virome changes during the pathogenesis of IBD and discussed potential treatment strategies that open new insights into the managements of IBD.
dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing
Authors: Gruber Bernd , Unmack Peter J. , Berry Oliver F. , Georges Arthur
Published: December 2017

Although vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new r package, dartr, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. dartr provides user‐friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy–Weinberg equilibrium, gametic‐phase disequilibrium and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis and conducts standard F‐statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g., newhybrids, faststructure and phylogeny applications) outside of the r environment. The package serves two main purposes: first, a user‐friendly approach to lower the hurdle to analyse such data—therefore, the package comes with a detailed tutorial targeted to the r beginner to allow data analysis without requiring deep knowledge of r. Second, we use a single, well‐established format—genlight from the adegenet package—as input for all our functions to avoid data reformatting. By strictly using the genlight format, we hope to facilitate this format as the de facto standard of future software developments and hence reduce the format jungle of genetic data sets. The dartr package is available via the r CRAN network and GitHub.
Identification of differential protein‐coding gene expressions in early phase lung adenocarcinoma
Authors: Zhou Li‐Na , Li Shi‐Cheng , Li Xue‐Ying , Ge Hong , Li Hong‐Mei
Published: December 2017

Background

The diagnosis of early phase lung adenocarcinoma (LADC) is associated with therapeutic strategy, effect, and survival time. However, the sensitive biomarkers of early phase LADC are still unclear. This study aimed to identify protein‐coding genes that can be used as biomarkers of early stage LADC.

Methods

Gene microarray analysis was performed to identify key hub genes that show different expression in lung adenocarcinoma compared to normal tissues. The microarray data of lung adenocarcinoma in stages IA, IB, IIA, IIB, and normal tissues (GSE10072) were downloaded from a free online database, Gene Expression Omnibus (GEO).

Results

A total of 572 differentially expressed genes (DEGs) were identified between early phase lung adenocarcinoma and normal tissues using R software. Database for Annotation, Visualization and Integrated Discovery online tools were used to obtain Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to analyze DEGs. Cytoscape software was used to express the protein‐protein interaction network. We found that some cancer‐related Gene Ontology terms and pathways (e.g. cell adhesion, cell surface receptor signaling pathway, PI3K‐Akt signaling pathway) were significantly enriched in DEGs.

Conclusion

Protein‐coding genes JUN, FYN, CAV1, and SFN may play vital roles in the progress of early‐stage lung adenocarcinoma. Consequently, through bioinformatics analysis, the key genes could be established to provide more potential references for the therapeutic targets of lung adenocarcinoma.
Survival analysis of patients with advanced non‐small cell lung cancer receiving tyrosine kinase inhibitor (TKI) treatment: A multi‐center retrospective study
Authors: Shi Qingming , Guan Maojing , Wang Yong , Xu Congjing , Tang Lei , Fu Wenhua , Bi Minghong , Sun Xiang , Gu Kangsheng , Pang Dongsheng
Published: December 2017

Background

The study was conducted to assess differences in overall survival (OS) in patients with non‐small cell lung cancer (NSCLC) receiving different treatment modalities of tyrosine kinase inhibitors (TKIs).

Methods

A total of 463 NSCLC patients receiving TKI treatment were included. OS was compared according to treatment timing in all patients, the elderly, and patients positive for EGFR mutations.

Results

One hundred and seventy two patients received TKIs as first‐line treatment, 220 as second‐line, and 67 as third‐line. The results between the three groups were not statistically significant: the one, two, and three‐year OS rates were: 55.3%, 22.3%, and 11.3% (first‐line); 59.6%, 27.8%, and 14.9% (second‐line); and 53.8%, 41.3%, and 29.5% (third‐line), respectively (P = 0.095). Results between the three groups of elderly patients were also not statistically significant (P = 0.469). The one and two‐year OS rates in EGFR mutation‐positive patients receiving first‐line treatment were 48% and 17.5%, respectively. The one, two, and three‐year OS rates of patients receiving second‐line treatment were: 54.2%, 30.3%, and 20.2%, respectively. There were no statistically significant differences between the groups with EGFR mutations receiving first‐line or second‐line treatment. Thirteen EGFR mutation‐positive patients received third‐line TKI treatment for a median duration of 7 months. Their one and two‐year OS rates were 69.8% and 58.2%, respectively, which were higher than in the other two groups (P = 0.015).

Conclusion

Three lines of TKI therapy can prolong survival in NSCLC patients. Elderly patients can benefit from TKI therapy. EGFR mutation‐positive patients can benefit from second‐line or third‐line TKI therapy.
Canine Conundrum: domestic dogs as an invasive species and their impacts on wildlife in India
Authors: Home C. , Bhatnagar Y. V. , Vanak A. T.
Published: December 2017

Domestic dogs are increasingly being recognized as a conservation threat for native species. In many places, their impacts may be as severe as other invasive predators such as cats and rats. We conducted the first ever sub‐continent scale assessment of the impacts of dogs on native species in India using an online key informant survey and reports from national print media. Dogs reportedly attacked 80 species, of which 31 were IUCN Red list threatened species, including four Critically Endangered species. Larger bodied mammals such as ungulates and carnivores, were most commonly reported to be attacked, although this may be an observation bias. Approximately 68% of the attacks were carried out by dogs unaccompanied by humans. Most of the attacks were carried out by packs of dogs with 45% of these attacks leading to the death of the prey. Nearly 48% of the incidents were reported in and around wildlife protected areas, suggesting that dogs are an important large‐scale edge effect around protected areas in India. For Critically Endangered species that are already suffering from serious population declines due to other causes, the impact of dogs may seriously impede population recovery efforts. Mitigating the impacts of dogs on wildlife requires a multi‐pronged approach of responsible dog ownership, restriction in free‐ranging behaviour, and strong population control measures, especially around sensitive conservation areas.
Application of three‐dimensional print in minor hepatectomy following liver partition between anterior and posterior sectors
Authors: Igami Tsuyoshi , Nakamura Yoshihiko , Oda Masahiro , Tanaka Hiroshi , Nojiri Motoi , Ebata Tomoki , Yokoyama Yukihiro , Sugawara Gen , Mizuno Takashi , Yamaguchi Junpei , Mori Kensaku , Nagino Masato
Published: December 2017

Background

Minor hepatectomy following liver partition between the right anterior and posterior sectors requires technical ingenuities. In such hepatectomy, we used three‐dimensional (3D) print; therefore, our procedure was introduced.

Methods

Digital segmentation of anatomical structures from multidetector‐row computed tomography images utilized the original software ‘PLUTO’, which was developed by Graduate School of Information Science, Nagoya University. After changing the final segmentation data to the stereolithography files, 3D‐printed liver at 70% scale was produced. The support material was washed and mould charge was removed from 3D‐printed hepatic veins. The surface of 3D‐printed model was abraded and coated with urethane resin paint. After natural drying, 3D‐printed hepatic veins were coloured by injection of a dye. The 3D‐printed portal veins were whitish because mould charge remained. All procedures after 3D printing were performed by hand work. A 3D‐printed model of the right posterior sector and a 3D‐printed model of other parenchyma were produced, respectively. Measuring the length between the main structures on the liver surface and the planned partition line on the 3D‐printed model, land mark between the right anterior and posterior sectors on the real liver surface was produced with scale adjustment.

Results

Minor hepatectomy following liver partition between the right anterior and posterior sectors was performed referring to 3D‐printed model. The planned liver partition and resection were successful.

Conclusions

Application of 3D‐printed liver to minor hepatectomy following liver partition between the right anterior and posterior sectors is easy and a suitable procedure.
Neutrophil Gelatinase‐Associated Lipocalin as a Biomarker of Allograft Function After Renal Transplantation: Evaluation of the Current Status and Future Insights
Authors: Cappuccilli Maria , Capelli Irene , Comai Giorgia , Cianciolo Giuseppe , La Manna Gaetano
Published: December 2017

Neutrophil gelatinase‐associated lipocalin (NGAL), a protein belonging to the lipocalin superfamily initially found in activated neutrophils, is expressed by several cell types, including kidney tubule. The increase in NGAL production and release from tubular cells in response to various insults has been proven to predict acute kidney injury (AKI). For this reason, it has emerged as a valuable noninvasive biomarker of AKI in clinical nephrology. Also in the renal transplant setting, different studies have indicated NGAL as a valuable tool, especially in the early postoperative period, since the currently available clinical and laboratory parameters remain poorly sensitive to monitor immediate posttransplant graft function. This is an analysis of the recent literature to assess the utility of plasma and urinary NGAL, exosomal mRNA for NGAL, and NGAL levels in the perfusate of machine‐perfused kidneys for the prediction of graft function recovery in the early postsurgery phase after renal transplantation. We found that NGAL appears as a promising troponin‐like biomarker to detect short‐term impairment of graft function after renal transplant, but there are still some limitations in its clinical application, essentially related to its low specificity. Moreover, comparing NGAL assayed in serum, urine, machine‐perfusate, or as exosomal mRNA, each one has shown limitations and benefits in terms of predictive performance for DGF, according to various existing studies, feasibly due to different cut‐off levels, designs and patient sample sizes.
The Performance of Pre‐Founding Entrepreneurial Teams: The Importance of Learning and Leadership
Authors: Knipfer Kristin , Schreiner Emanuel , Schmid Ellen , Peus Claudia
Published: December 2017

Entrepreneurial teams often struggle with simultaneous task and team challenges at an early stage of new venture creation. The way in which teams shape their teamwork is key in leveraging performance in the pre‐founding phase. Learning should help the team in establishing good teamwork and in expanding its members’ entrepreneurial capabilities. Leadership is needed to facilitate and guide this learning. Accordingly, we investigated learning and leadership as facilitators of performance in the pre‐founding phase. Specifically, we examined team reflexivity as a collective internal learning process and boundary spanning behaviour as an externally directed individual activity, operating at different levels in fostering team and individual performance. Charismatic team leadership was examined as a catalyst of learning, shaping team and individual performance ultimately. The multilevel mediation model was tested based on data from 196 members of 58 teams of a venture creation programme. Team reflexivity predicted team and individual performance. Boundary spanning behaviour was not related to performance. As hypothesised, charismatic team leadership predicted team and individual performance, both mediated by team reflexivity. This research highlights the relevance of team learning in pre‐founding teams and emphasises leadership in shaping learning and moving new ventures forward.
Pediatric femoral hernia in the laparoscopic era
Authors: Aneiros Castro Belén , Cano Novillo Indalecio , García Vázquez Araceli , López Díaz María , Benavent Gordo María Isabel , Gómez Fraile Andrés
Published: December 2017

Introduction

Femoral hernia is a rare and often misdiagnosed condition in childhood. The aim of our study was to demonstrate that the laparoscopic approach improves diagnostic accuracy and offers a safe and effective treatment.

Methods

A retrospective study of 687 pediatric patients who underwent laparoscopic inguinal hernia repair from January 2000 to December 2015 was performed.

Results

Femoral hernias were identified in 16 patients (2.3%). The right side was affected in 10 cases (62.5%), the left side in 5 (31.2%), and 1 case was bilateral (6.2%). The mean age of patients was 8.00 ± 3.81 years, and there was a male predominance. Preoperative diagnosis was femoral hernia in eight cases (50%) and indirect inguinal hernia in the remaining eight (50%). Seven children (43.8%) presented with hernia recurrence after having undergone an open ipsilateral indirect hernia repair. A modified laparoscopic McVay technique was performed in 12 cases (70.6%). An epigastric artery injury by trocar occurred in one patient. All operations were completed laparoscopically. The mean surgical time was 45.6 ± 22.9 min for unilateral cases and 110 ± 10.0 min for bilateral cases. No immediate postoperative complications were noted. The mean postoperative hospital stay was 0.6 ± 0.4 days. No recurrence was observed after a median follow‐up of 11 years (range, 4–16 years).

Conclusion

Femoral hernia is a rare pathology in pediatric patients that is often difficult to diagnose. The laparoscopic approach is effective in the diagnosing and treating these hernias, and it allows for the simultaneous repair of multiple groin defects.
Comerciar con la sangre de nuestros hermanos: Early Abolitionist Discourses in Spain's Empire
Authors: SANJURJO JESÚS
Published: December 2017

The proposal ofAgustín deArgüelles to abolish the slave trade in 1811 was crucial in defining a new ideological stance within theSpanish political debate by adopting the moral condemnation elaborated by theBritish abolitionist movement. His initiative was the result of a coordinated strategy with theBritish authorities and was key in the construction of early abolitionist discourses inSpain. This article explores the political, ideological and diplomatic influence ofBritain in the development of early anti‐slavery and anti‐slave trade discourses inSpain and the centrality ofArgüelles' proposal.
Phages of life – the path to pharma
Authors: Forde Amanda , Hill Colin
Published: December 2017

Bacteriophage (phage) therapy has encountered both enthusiasm and scepticism in the past century. New antimicrobial strategies against lethal pathogens are now a top priority for the World Health Organization, and although compassionate use of phages recently met with significant success, regulated clinical interventions seem unlikely in the near future. The hundredth anniversary of their discovery seems an appropriate time for a revival of phage therapy, particularly as the dilemma of antibiotic resistance grows. Phages are ubiquitous in the environment, on our food and in and on our bodies. Their influence on human health is currently being evaluated, and in this mini‐review, we examine data from recent metagenomic studies that propose a role for phages in the structure of the microbiome and in health and disease. We assess evidence for phages as vehicles for gene transfer in the context of antibiotic resistance and discuss challenges and opportunities along the critical path from phage discovery to a patient‐focused pharmaceutical intervention.