bluuebunny/crossref_metadata_2025 huggingface dataset:
Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control
Authors: Cuscó Pol , Filion Guillaume J.
Published: June 2016

Motivation: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the standard method to investigate chromatin protein composition. As the number of community-available ChIP-seq profiles increases, it becomes more common to use data from different sources, which makes joint analysis challenging. Issues such as lack of reproducibility, heterogeneous quality and conflicts between replicates become evident when comparing datasets, especially when they are produced by different laboratories.

Results: Here, we present Zerone, a ChIP-seq discretizer with built-in quality control. Zerone is powered by a Hidden Markov Model with zero-inflated negative multinomial emissions, which allows it to merge several replicates into a single discretized profile. To identify low quality or irreproducible data, we trained a Support Vector Machine and integrated it as part of the discretization process. The result is a classifier reaching 95% accuracy in detecting low quality profiles. We also introduce a graphical representation to compare discretization quality and we show that Zerone achieves outstanding accuracy. Finally, on current hardware, Zerone discretizes a ChIP-seq experiment on mammalian genomes in about 5 min using less than 700 MB of memory.

Availability and Implementation: Zerone is available as a command line tool and as an R package. The C source code and R scripts can be downloaded from https://github.com/nanakiksc/zerone. The information to reproduce the benchmark and the figures is stored in a public Docker image that can be downloaded from https://hub.docker.com/r/nanakiksc/zerone/.

Contact: guillaume.filion@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.
The Glycome Analytics Platform: an integrative framework for glycobioinformatics
Authors: Barnett Christopher B. , Aoki-Kinoshita Kiyoko F. , Naidoo Kevin J.
Published: June 2016

Motivation: Complex carbohydrates play a central role in cellular communication and in disease development. O- and N-glycans, which are post-translationally attached to proteins and lipids, are sugar chains that are rooted, tree structures. Independent efforts to develop computational tools for analyzing complex carbohydrate structures have been designed to exploit specific databases requiring unique formatting and limited transferability. Attempts have been made at integrating these resources, yet it remains difficult to communicate and share data across several online resources. A disadvantage of the lack of coordination between development efforts is the inability of the user community to create reproducible analyses (workflows). The latter results in the more serious unreliability of glycomics metadata.

Results: In this paper, we realize the significance of connecting multiple online glycan resources that can be used to design reproducible experiments for obtaining, generating and analyzing cell glycomes. To address this, a suite of tools and utilities, have been integrated into the analytic functionality of the Galaxy bioinformatics platform to provide a Glycome Analytics Platform (GAP).

Using this platform, users can design in silico workflows to manipulate various formats of glycan sequences and analyze glycomes through access to web data and services. We illustrate the central functionality and features of the GAP by way of example; we analyze and compare the features of the N-glycan glycome of monocytic cells sourced from two separate data depositions.

This paper highlights the use of reproducible research methods for glycomics analysis and the GAP presents an opportunity for integrating tools in glycobioinformatics.

Availability and Implementation: This software is open-source and available online at https://bitbucket.org/scientificomputing/glycome-analytics-platform

Contacts:  chris.barnett@uct.ac.za or kevin.naidoo@uct.ac.za

Supplementary information:  Supplementary data are available at Bioinformatics online.
Professional nurses and the dark side of work passion
Authors: Bushardt Stephen C. , Beal Brent D. , Young Marilyn , Khosla Sanjana
Published: June 2016

Obsessive passion can lead to burnout and work-life imbalance, harming your personal life, as well as causing negative effects for your organization.
Biologic therapy in the management of asthma
Authors: McCracken Jennifer L. , Tripple Julia W. , Calhoun William J.
Published: June 2016

Purpose of review

Current asthma management relies on inhaled corticosteroids, but some asthma is not well controlled with inhaled steroids alone or in combination with long-acting bronchodilators or leukotriene pathway inhibitors. The field of biologic therapy has grown dramatically in the past two decades, with current availability of three molecules, with two distinct and highly selective approaches to interfering with the allergic and eosinophilic airway inflammation common to most asthma. This review summarizes current and future options for incorporating biologic therapy into the overall management of asthma.

Recent findings

Two new biologic agents have been recently introduced in the United States market, supported by well controlled, randomized clinical trials. These trials have provided insight into the types of patients who are most likely to benefit from these novel agents.

In asthma patients with frequent exacerbations, the addition of a biologic agent targeting the interleukin-5 pathway, or immunoglobulin E, can significantly reduce exacerbations and improve asthma control. The clinical predictors of utility of specific agents overlap with one another, highlighting the importance of clinical judgment in the overall management of this complex disorder.
Comparisons of outcomes with food immunotherapy strategies: efficacy, dosing, adverse effects, and tolerance
Authors: Yanagida Noriyuki , Sato Sakura , Asaumi Tomoyuki , Ebisawa Motohiro
Published: June 2016

Purpose of review

In the recent decade, oral immunotherapy has been studied in many clinical trials and entails many problems including a low efficacy for real tolerance and a high rate of induced symptoms. The optimal dose for inducing tolerance is unknown. The aim of this review was to clarify the efficacy and safety of oral immunotherapy, focusing on low doses.

Recent findings

We reviewed articles published in a few years or articles dealing with oral immunotherapy focusing on a low dose. We summarize recent articles on oral immunotherapy and those focusing on low doses.

Although lower doses for oral immunotherapy appear to cause fewer adverse reactions and be more effective than strict elimination, this strategy may be less effective than oral immunotherapy involving larger doses. The optimal dose for inducing tolerance is still unknown.
Tears for the City
Authors: Dunlap Ruby
Published: June 2016

Most nurses can describe a memorable patient, one who moved them deeply, and one who made them remember why they chose nursing as a calling. Thinking of a population with an emotional connection is usually more difficult. Current nursing practice includes the ability to serve a population or community as client. This article describes core functions of public health—assessment, policy development, and assurance, while offering biblical resources the Christian nurse has to consider a population with the same compassion as one does an individual.
From Checklist to Awareness
Authors: Snead Victoria , Moss Julie A.
Published: June 2016

This student experience of international community health nursing in Cape Town, South Africa, illustrates the value of missions that provide health training and education to lay persons, and the calling of God to serve him through nursing.
Bioengineered Self-assembled Skin as an Alternative to Skin Grafts
Authors: Climov Mihail , Medeiros Erika , Farkash Evan A. , Qiao Jizeng , Rousseau Cecile F. , Dong Shumin , Zawadzka Agatha , Racki Waldemar J. , Al-Musa Ahmad , Sachs David H. , Randolph Mark A. , Huang Christene A. , Bollenbach Thomas J.
Published: June 2016

For patients with extensive burns or donor site scarring, the limited availability of autologous and the inevitable rejection of allogeneic skin drive the need for new alternatives. Existing engineered biologic and synthetic skin analogs serve as temporary coverage until sufficient autologous skin is available. Here we report successful engraftment of a self-assembled bilayered skin construct derived from autologous skin punch biopsies in a porcine model. Dermal fibroblasts were stimulated to produce an extracellular matrix and were then seeded with epidermal progenitor cells to generate an epidermis. Autologous constructs were grafted onto partial- and full-thickness wounds. By gross examination and histology, skin construct vascularization and healing were comparable to autologous skin grafts and were superior to an autologous bilayered living cellular construct fabricated with fibroblasts cast in bovine collagen. This is the first demonstration of spontaneous vascularization and permanent engraftment of a self-assembled bilayered bioengineered skin that could supplement existing methods of reconstruction.
The use of β-blockers is associated with a lower risk of developing hepatocellular carcinoma in patients with cirrhosis
Authors: Herrera Iván , Pascual Sonia , Zapater Pedro , Carnicer Fernando , Bellot Pablo , María Palazón José
Published: June 2016

Introduction

Patients with cirrhosis by hepatitis C virus infection treated with β-blockers (BB) have been shown to have a reduced incidence of hepatocellular carcinoma (HCC). Also, an association between propranolol therapy and lower incidence of other tumors has been described.

Aim

To analyze the incidence of HCC according to BB treatment in cirrhosis of any cause.

Patients and methods

Cirrhotic patients included in the program for early detection of HCC were followed. Patients’ data were prospectively registered, including transplantation and death. Patients were classified as chronically taken or not BB and the proportions of patients who remained free of tumor from the diagnosis of cirrhosis until the end of follow-up were compared using Kaplan–Meier analysis and the Breslow test.

Results

A total of 173 patients (73 treated and 100 untreated BB) were followed. The median duration of follow-up was 11 years. There were no differences between both groups in the overall survival, number of deaths, or liver transplant.

Overall, 28 patients developed HCC during the follow-up, 20 patients who were untreated and eight patients treated with BB. The cumulative proportion of cases of HCC between untreated and treated with BB from the diagnosis of cirrhosis was statistically significant (6 vs. 3%, at 5 years; 19 vs. 6% at 10 years; 24 vs. 16% at 15 years; P=0.048). Multivariate analyses showed BB intake as the only significant variable associated with the development of HCC.

Conclusion

Cirrhotic patients treated with BB have a lower cumulative probability of developing HCC during the 10 years after the diagnosis of cirrhosis.
Control of the onset of puberty
Authors: Livadas Sarantis , Chrousos George P.
Published: June 2016

Purpose of review

The mechanism of puberty initiation remains an enigma, despite extensive research in the field. Pulsatile pituitary gonadotropin secretion under the guidance of hypothalamic gonadotropin-releasing hormone (GnRH) constitutes a sine qua non for pubertal onset. In turn, the secretion of GnRH in the human hypothalamus is regulated by kisspeptin and its receptor as well as by permissive or opposing signals mediated by neurokinin B and dynorphin acting on their respective receptors. These three supra-GnRH regulators compose the Kisspeptin, Neurokinin B and Dynorhin neurons (KNDy) system, a key player in pubertal onset and progression.

Recent findings

The recent discovery that makorin ring finger protein 3 is also involved in puberty initiation provided further insights into the regulation of the KNDy pathway. In fact, the inhibitory (γ-amino butyric acid, neuropeptide Y, and RFamide-related peptide-3) and stimulatory signals (glutamate) acting upstream of KNDy called into question the role of makorin ring finger protein 3 as the gatekeeper of puberty. Meanwhile, the findings that ‘neuroestradiol’ produced locally and endocrine disruptors from the environment may influence GnRH secretion is intriguing. Finally, epigenetic mechanisms have been implicated in pubertal onset through recently discovered mechanisms.

The exact molecular machinery underlying puberty initiation in humans is under intensive investigation. In this review, we summarize research evidence in the field, while emphasizing the areas of uncertainty and underlining the impact of current information on the evolving theory regarding this fascinating phenomenon.
Resilience in Patients With Recent Diagnosis of a Schizophrenia Spectrum Disorder
Authors: Bozikas Vasilis P. , Parlapani Eleni , Holeva Vasiliki , Skemperi Eleni , Bargiota Stavroula I. , Kirla Danai , Rera Eirini , Garyfallos Georgios
Published: June 2016

This study focused on resilience in patients who recently received a diagnosis of schizophrenia spectrum disorder (SSD). Psychopathological symptoms, depressive symptoms, and hopelessness were considered as sources of stress in the context of psychosis. Forty-eight SSD patients (mean period between diagnosis and recruitment, 20.79 months) were enrolled. Psychopathological symptoms were assessed by the Positive and Negative Syndrome Scale, depression by the Calgary Depression Scale for Schizophrenia, hopelessness by the Beck Hopelessness Scale, and functioning by the Social and Occupational Functioning Scale. Resilience was evaluated by the Connor-Davidson Resilience Scale, which was additionally completed by 81 healthy controls. Patients demonstrated less resilience than did healthy participants. Female patients showed higher resilience levels and functioning than did males. High resilience levels were associated with less severe positive symptoms, general psychopathological symptoms, depression, and hopelessness. Apart from negative symptoms, results indicated that resilience may be a potential moderator of functioning. Thus, resilience-oriented interventions might constitute an additional therapeutic approach for SSD patients.
Primary Langerhans Cell Histiocytosis of the Vulva: Case Report and Review of the Literature
Authors: Zudaire Tamara , Guarch Rosa , Valcayo Ana , García Kelly , Resano Miguel Ángel , Requena Diego , Rodríguez Mercedes
Published: June 2016

Langerhans cell histiocytosis (LCH) of the vulva is rare and even moreso in postmenopausal women. Twenty-six cases of primary vulvar LCH have been described in the current literature, and only 8 cases are in postmenopausal women. We report an additional case of primary vulvar LCH in a 59-yr-old woman with subsequent multiorgan involvement. In this article, we briefly describe the clinical presentation, histopathological findings, and immunohistochemistry results of vulvar LCH. We want to emphasize the importance of recognizing this entity in a woman with vulvar lesions both for the clinician and the pathologist.
Gene-tree reconciliation with MUL-trees to resolve polyploidy events
Authors: Thomas Gregg W.C. , Hussain Ather S. , Hahn Matthew W.
Published: June 2016

Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids - autopolyploids and allopolyploids - differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker’s yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy.
Hipk is required for JAK/STAT activity and promotes hemocyte-derived tumorigenesis
Authors: Blaquiere Jessica A. , Wray Nathan B. , Verheyen Esther M.
Published: June 2016

Dysregulation of key signaling molecules and pathways are causative of many Human diseases and cancers. A point mutation in the Drosophila Janus kinase (calledhop) causes constitutive activation of the JAK/STAT pathway and results in blood cell tumours. We provide robust genetic evidence that Hipk is required for endogenous JAK/STAT activity. Overexpression of Hipk can phenocopy the effects of overactive JAK/STAT mutations and lead to melanized tumors and loss of Hipk can suppress the effects of hyperactive JAK/STAT. Furthermore, Hipk expression in blood cell progenitors causes tumors. PLA experiments show that Hipk can interact with the pathway effector Stat92E. Together our results show that Hipk is a novel factor required for effective JAK/STAT signaling.

Summary Statement

Loss ofhipkimpairs JAK/STAT activity in multiple tissue types and elevated Hipk leads to the formation of blood cell tumors in Drosophila.
Differential analysis of RNA-Seq incorporating quantification uncertainty
Authors: Pimentel Harold , Nicolas L. Bray , Puente Suzette , Melsted Páll , Pachter Lior
Published: June 2016

We describe a novel method for the differential analysis of RNA-Seq data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. The method is implemented in an interactive shiny app called sleuth that utilizes kallisto quantifications and bootstraps for fast and accurate analysis of RNA-Seq experiments.
Controlling the Rate of GWAS False Discoveries
Authors: Brzyski Damian , Peterson Christine B. , Sobczyk Piotr , Candés Emmanuel J. , Bogdan Malgorzata , Sabatti Chiara
Published: June 2016

With the rise of both the number and the complexity of traits of interest, control of the false discovery rate (FDR) in genetic association studies has become an increasingly appealing and accepted target for multiple comparison adjustment. While a number of robust FDR controlling strategies exist, the nature of this error rate is intimately tied to the precise way in which discoveries are counted, and the performance of FDR controlling procedures is satisfactory only if there is a one-to-one correspondence between what scientists describe as unique discoveries and the number of rejected hypotheses. The presence of linkage disequilibrium between markers in genome-wide association studies (GWAS) often leads researchers to consider the signal associated to multiple neighboring SNPs as indicating the existence of a single genomic locus with possible influence on the phenotype. This a posteriori aggregation of rejected hypotheses results in inflation of the relevant FDR. We propose a novel approach to FDR control that is based on pre-screening to identify the level of resolution of distinct hypotheses. We show how FDR controlling strategies can be adapted to account for this initial selection both with theoretical results and simulations that mimic the dependence structure to be expected in GWAS. We demonstrate that our approach is versatile and useful when the data are analyzed using both tests based on single marker and multivariate regression. We provide an R package that allows practitioners to apply our procedure on standard GWAS format data, and illustrate its performance on lipid traits in the NFBC66 cohort study.
Thanatotranscriptome: genes actively expressed after organismal death
Authors: Pozhitkov Alex E. , Neme Rafik , Domazet-Lošo Tomislav , Leroux Brian G. , Soni Shivani , Tautz Diethard , Noble Peter A.
Published: June 2016

A continuing enigma in the study of biological systems is what happens to highly ordered structures, far from equilibrium, when their regulatory systems suddenly become disabled. In life, genetic and epigenetic networks precisely coordinate the expression of genes -- but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes are involved. We investigated the unwinding of the clock by identifying upregulated genes, assessing their functions, and comparing their transcriptional profiles through postmortem time in two species, mouse and zebrafish. We found transcriptional abundance profiles of 1,063 genes were significantly changed after death of healthy adult animals in a time series spanning from life to 48 or 96 h postmortem. Ordination plots revealed non-random patterns in profiles by time. While most thanatotranscriptome (thanatos-, Greekdefn. death) transcript levels increased within 0.5 h postmortem, some increased only at 24 and 48 h. Functional characterization of the most abundant transcripts revealed the following categories: stress, immunity, inflammation, apoptosis, transport, development, epigenetic regulation, and cancer. The increase of transcript abundance was presumably due to thermodynamic and kinetic controls encountered such as the activation of epigenetic modification genes responsible for unraveling the nucleosomes, which enabled transcription of previously silenced genes (e.g., development genes). The fact that new molecules were synthesized at 48 to 96 h postmortem suggests sufficient energy and resources to maintain self-organizing processes. A step-wise shutdown occurs in organismal death that is manifested by the apparent upregulation of genes with various abundance maxima and durations. The results are of significance to transplantology and molecular biology.
Temporal development and spatial scale of coastal fish indicators in reference ecosystems: hydroclimate and anthropogenic drivers
Authors: Östman Örjan , Lingman Anna , Bergström Lena , Olsson Jens
Published: June 2016

Indicators of ecosystem status are of increasing importance for management. Many studies infer associations between the environment and fish communities, but little is known about how fish community indicators are related to temporal variation in anthropogenic and hydroclimate drivers, and on what geographical scale, these indicators are representative.

Here, we investigate the spatial synchrony of seven indicators of coastal fish community status among eleven reference sites 2002–2014 in the Baltic Sea. At three of these sites, we study the temporal covariation between indicators and anthropogenic and hydroclimate drivers over 25 years.

The indicators (abundance of) – Perch, Large Piscivores and Non‐perch Piscivores – showed spatial synchrony over the study scale (100–1000 km), whereas temporal dynamics of other indicators reflected changes at scales <100 km.

At the studied reference sites, temporal changes of indicators were mainly associated with climate‐related hydrological variables, but nutrient‐related variables were important in the northern Baltic Sea. Landings showed no associations with any indicator. Four of the indicators showed evident temporal autocorrelation reflecting an influence of internal population/community processes.

Synthesis and applications. Environmental status of coastal fish communities in the Baltic Sea should be assessed and managed at a local scale. The main drivers of fish community indicators of ecosystem status tend to differ between coastal areas, but among the reference sites assessed in this study, hydroclimatic variation and internal processes seem to be of greater importance for the temporal development of indicators than anthropogenic pressures. Therefore, when assessing the status of coastal fish communities and evaluating management measures in areas impacted by anthropogenic activities, it is important to account for variation in salinity, temperature and time lags.
Decomposing trends in Swedish bird populations using generalized additive mixed models
Authors: Knape Jonas
Published: June 2016

Estimating trends of populations distributed across wide areas is important for conservation and management of animals. Surveys in the form of annually repeated counts across a number of sites are used in many monitoring programmes, and from these, nonlinear trends may be estimated using generalized additive models (GAM).

I use generalized additive mixed models (GAMM) to decompose population change into a long‐term, smooth, trend component and a component for short‐term fluctuations. The long‐term population trend is modelled as a smooth function of time and short‐term fluctuations as temporal random effects. The methods are applied to analyse trends in goldcrest and greenfinch populations in Sweden using data from the Swedish Breeding Bird Survey. I use simulations to investigate statistical properties of the model.

The model separates short‐term fluctuations from longer term population change. Depending on the amount of noise in the population fluctuations, estimated long‐term trends can differ markedly from estimates based on standard GAMs. For the goldcrest with wide among‐year fluctuations, trends estimated with GAMs suggest that the population has in recent years recovered from a decline. When filtering out, short‐term fluctuations analyses suggest that the population has been in steady decline since the beginning of the survey.

Simulations suggest that trend estimation using the GAMM model reduces spurious detection of long‐term population change found with estimates from a GAM model, but gives similar mean square errors. The simulations therefore suggest that the GAMM model, which decomposes population change, estimates uncertainty of long‐term trends more accurately at little cost in detecting them.

Policy implications. Filtering out short‐term fluctuations in the estimation of long‐term smooth trends using temporal random effects in a generalized additive mixed model provides more robust inference about the long‐term trends compared to when such random effects are not used. This can have profound effects on management decisions, as illustrated in an example for goldcrest in the Swedish breeding bird survey. In the example, if temporal random effects were not used, red listing would be highly influenced by the specific year in which it was done. When temporal random effects are used, red listing is stable over time. The methods are available in an R‐package, poptrend.
Quercus suber dieback alters soil respiration and nutrient availability in Mediterranean forests
Authors: Avila José M. , Gallardo Antonio , Ibáñez Beatriz , Gómez‐Aparicio Lorena
Published: June 2016

An increase in tree mortality rates has been recently detected in forests world‐wide. However, few works have focused on the potential consequences of forest dieback for ecosystem functioning.

Here we assessed the effect of Quercus suber dieback on carbon, nitrogen and phosphorus cycles in two types of Mediterranean forests (woodlands and closed forests) affected by the aggressive pathogen Phytophthora cinnamomi. We used a spatially explicit neighbourhood approach to analyse the direct effects of Q. suber dieback on soil variables, comparing the impact of Q. suber trees with different health status, as well as its potential long‐term indirect effects, comparing the impact of non‐declining coexistent species.

Quercus suber dieback translated into lower soil respiration rates and phosphorus availability, whereas its effects on nitrogen varied depending on forest type. Coexistent species differed strongly from Q. suber in their effects on nutrient availability, but not on soil respiration rates. Our models showed low interannual but high intra‐annual variation in the ecosystem impacts of tree dieback.

Synthesis. Our results support that tree dieback might have important short‐ and long‐term impacts on ecosystem processes in Mediterranean forests. With this work, we provide valuable insights to fill the existent gap in knowledge on the ecosystem‐level impacts of forest dieback in general and P. cinnamomi‐driven mortality in particular. Because the activity and range of this pathogen is predicted to increase due to climate warming, these impacts could also increase in the near future altering ecosystem functioning world‐wide.
ddradseqtools: a software package for in silico simulation and testing of double‐digest RADseq experiments
Authors: Mora‐Márquez F. , García‐Olivares V. , Emerson B. C. , López de Heredia U.
Published: June 2016

Double‐digested RADseq (ddRADseq) is a NGS methodology that generates reads from thousands of loci targeted by restriction enzyme cut sites, across multiple individuals. To be statistically sound and economically optimal, a ddRADseq experiment has a preliminary design stage that needs to consider issues related to the selection of enzymes, particular features of the genome of the focal species, possible modifications to the library construction protocol, coverage needed to minimize missing data, and the potential sources of error that may impact upon the coverage. We present ddradseqtools, a software package to help ddRADseq experimental design by (i) the generation of in silico double‐digested fragments; (ii) the construction of modified ddRADseq libraries using adapters with either one or two indexes and degenerate base regions (DBRs) to quantify PCR duplicates; and (iii) the initial steps of the bioinformatics preprocessing of reads. ddradseqtools generates single‐end (SE) or paired‐end (PE) reads that may bear SNPs and/or indels. The effect of allele dropout and PCR duplicates on coverage is also simulated. The resulting output files can be submitted to pipelines of alignment and variant calling, to allow the fine‐tuning of parameters. The software was validated with specific tests for the correct operability of the program. The correspondence between in silico settings and parameters from ddRADseq in vitro experiments was assessed to provide guidelines for the reliable performance of the software. ddradseqtools is cost‐efficient in terms of execution time, and can be run on computers with standard CPU and RAM configuration.
Identification and qualification of 500 nuclear, single‐copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture
Authors: Teasdale Luisa C. , Köhler Frank , Murray Kevin D. , O'Hara Tim , Moussalli Adnan
Published: June 2016

The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis‐indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single‐copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein‐coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete phylogenetic data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon capture targeting 490 of the 500 genes (those with at least one exon >120 bp) from 22 species of Australian Camaenidae successfully captured sequences of 2825 exons (representing all targeted genes), with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single‐copy gene set and identified a further 375 putative single‐copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness when considering the original 500 genes. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and ‘Agalma‐equivalent’ data set (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a range of evolutionary depths and highlights the importance of addressing fragmentation at the homolog alignment stage for probe design.
Testis‐specific RNA‐Seq of Calligrapha (Chrysomelidae) as a transcriptomic resource for male‐biased gene inquiry in Coleoptera
Authors: Vizán‐Rico Helena I. , Gómez‐Zurita Jesús
Published: June 2016

We report the architecture of testis transcriptomes of four closely related species of Calligrapha (Chrysomelidae) beetles, which diverged during the last 3 million years. Five cDNA libraries were sequenced using Illumina HiSeq technology, retrieving 102 884–176 514 assembled contigs, of which ~33–45% of these longer than 499 nt were functionally annotated. Annotation and sequence similarity comparisons of these libraries revealed high homogeneity in gene composition and the presence of several functional candidates related to reproduction or reproductive processes (0.72–1.08% of annotated sequences). Stringent sequence similarity analyses of these transcriptomes against empirically demonstrated male‐biased genes in Drosophila melanogaster and Tribolium castaneum allowed the identification of 77 homologues in Calligrapha, possible candidates of male‐biased expression. Some of these genes – including CG9313, Tektin‐A or tomboy40 – were confirmed as orthologs of these male‐biased genes using phylogenetic inference and available model insect data, increasing our confidence that they represent functional homologues too. Our transcriptomes are a valuable transcriptomic resource for the analysis of male‐biased genes in Calligrapha, which has the added interest of including several female‐only species. But it simultaneously represents a landmark for similar studies in Coleoptera, broadening the taxonomic diversity currently represented by the model species T. castaneum, and incipient genomic data in other herbivorous lineages, including weevils, longhorn beetles and leaf beetles.
The Role of United Nations Secretary‐General in the Climate Change Process
Authors: Pasztor Janos
Published: June 2016

Ban Ki‐moon, the UN Secretary‐General (SG) has been visibly engaged throughout the year on preparations for and during the Paris Conference, but his role in contributing to achieving this agreement has been little understood. The SG has no specific mandate to deal with climate change issues. Yet without his intensive engagement it would not have been possible to reach the agreement we had in Paris. The role played by the SG and its outcomes will be the focus of this paper. Particular attention will be paid to events in 2015, but the paper also looks at some earlier events during the entire mandate of this Secretary‐General, covering 2007–2016.
Systematic Molecular Phenotyping: A Path Toward Precision Emergency Medicine?
Authors: Limkakeng Alexander T. , Monte Andrew A. , Kabrhel Christopher , Puskarich Michael , Heitsch Laura , Tsalik Ephraim L. , Shapiro Nathan I.
Published: June 2016

Precision medicine is an emerging approach to disease treatment and prevention that considers variability in patient genes, environment, and lifestyle. However, little has been written about how such research impacts emergency care. Recent advances in analytical techniques have made it possible to characterize patients in a more comprehensive and sophisticated fashion at the molecular level, promising highly individualized diagnosis and treatment. Among these techniques are various systematic molecular phenotyping analyses (e.g., genomics, transcriptomics, proteomics, and metabolomics). Although a number of emergency physicians use such techniques in their research, widespread discussion of these approaches has been lacking in the emergency care literature and many emergency physicians may be unfamiliar with them. In this article, we briefly review the underpinnings of such studies, note how they already impact acute care, discuss areas in which they might soon be applied, and identify challenges in translation to the emergency department (ED). While such techniques hold much promise, it is unclear whether the obstacles to translating their findings to the ED will be overcome in the near future. Such obstacles include validation, cost, turnaround time, user interface, decision support, standardization, and adoption by end‐users.
Pregnancy outcomes following maternal kidney transplantation: a national cohort study
Authors: Majak Guri B. , Sandven Irene , Lorentzen Bjørg , Vangen Siri , Reisæter Anna V. , Henriksen Tore , Michelsen Trond M.
Published: June 2016

Introduction

Internal design flaws in previous reports of pregnancies following kidney transplantation have been outlined, and the need for a validation has been stated. The aim of this study was to collect information about obstetrical and neonatal outcomes in all Norwegian pregnancies following maternal kidney transplantation, and to compare these data with the general Norwegian population.

Material and methods

A retrospective cohort study based on 1 272 000 deliveries in Norway between 1969 and 2013. All data were collected from medical records. From the source population, we compared 119 first deliveries in kidney transplanted women with 238 first deliveries in nontransplanted women. An explanatory strategy was used in the analysis.

Results

The risk of preeclampsia was significantly increased in kidney‐transplanted women compared with nontransplanted women (adjusted incidence rate ratio: 6.06, 95% confidence interval 3.18–11.55). Additionally, preeclampsia in kidney‐transplanted women was early onset (diagnosed <34 gestational weeks) in half of the cases. There were also persistent risks of cesarean delivery (adjusted incidence rate ratio 4.14, 95% confidence interval 2.56–6.66), preterm delivery (adjusted incidence rate ratio 4.45, 95% confidence interval 2.13–9.30) and a birthweight below the 10th centile (22.7% vs. 9.7%) in the kidney‐transplanted group. A high proportion (63%) of the kidney‐transplanted women with chronic hypertension developed preeclampsia.

Conclusions

Using consistent diagnostic criteria, this study shows high rates of maternal and neonatal complications in pregnancies following kidney transplantation. In particular, we reveal a high rate of early‐onset preeclampsia requiring operative preterm delivery, conferring long‐term risks on both the mother and child.
Attenuation of iron‐binding proteins in ARPE‐19 cells reduces their resistance to oxidative stress
Authors: Karlsson Markus , Kurz Tino
Published: June 2016

Purpose

Oxidative stress‐related damage to retinal pigment epithelial (RPE) cells is an important feature in the development of age‐related macular degeneration. Iron‐catalysed intralysosomal production of hydroxyl radicals is considered a major pathogenic factor, leading to lipofuscin formation with ensuing depressed cellular autophagic capacity, lysosomal membrane permeabilization and apoptosis. Previously, we have shown that cultured immortalized human RPE (ARPE‐19) cells are extremely resistant to exposure to bolus doses of hydrogen peroxide and contain considerable amounts of the iron‐binding proteins metallothionein (MT), heat‐shock protein 70 (HSP70) and ferritin (FT). According to previous findings, autophagy of these proteins depresses lysosomal redox‐active iron. The aim of this study was to investigate whether up‐ or downregulation of these proteins would affect the resistance of ARPE‐19 cells to oxidative stress.

Methods

The sensitivity of ARPE‐19 cells to H2O2 exposure was tested following upregulation of MT, HSP70 and/or FT by pretreatment with ZnSO4, heat shock or FeCl3, as well as siRNA‐mediated downregulation of the same proteins.

Results

Upregulation of MT, HSP70 and FT did not improve survival following exposure to H2O2. This was interpreted as existence of an already maximal protection. Combined siRNA‐mediated attenuation of both FT chains (H and L), or simultaneous downregulation of all three proteins, made the cells significantly more susceptible to oxidative stress confirming the importance of iron‐binding proteins.

Conclusion

The findings support our hypothesis that the oxidative stress resistance exhibited by RPE cells may be explained by a high autophagic influx of iron‐binding proteins that would keep levels of redox‐active lysosomal iron low.
Inhibition of HIF‐1α decreases expression of pro‐inflammatory IL‐6 and TNF‐α in diabetic retinopathy
Authors: Gao Xiuhua , Li Yonghua , Wang Hongxia , Li Chuanbao , Ding Jianguang
Published: June 2016

Purpose

Recent studies demonstrate that pro‐inflammatory cytokines (PICs, i.e. IL‐1β, IL‐6 and TNF‐α) in retinal tissues are likely involved in the development of diabetic retinopathy (DR). In this report, we particularly examined contributions of hypoxia inducible factor subtype 1α (HIF‐1α) to the expression of PICs and their receptors in diabetic retina.

Methods

Streptozotocin (STZ) was systemically injected to induce hyperglycaemia in rats. ELISA and Western blot analysis were employed to determine the levels of HIF‐1α and PICs as well as PIC receptors in retinal tissues of control rats and STZ rats.

Results

The levels of retinal HIF‐1α were significantly increased in STZ rats 4–10 weeks after induction of hyperglycaemia as compared with control animals. With increasing HIF‐1α retinal PICs including IL‐1β, IL‐6 and TNF‐α, their respective receptors, namely IL‐1R, IL‐6R and TNFR1, were also elevated in STZ rats. Moreover, inhibition of HIF‐1α by injection of 2‐methoxyestradiol (2‐MET) significantly decreased the amplified expression IL‐6, TNF‐α, IL‐6R and TNFR1 in diabetic retina, but did not modify IL‐1β pathway. In addition, we examined protein expression of Caspase‐3 indicating cell apoptosis in the retina of STZ rats after infusing 2‐MET, demonstrating that 2‐MET attenuated an increase in Caspase‐3 evoked by STZ.

Conclusion

Hypoxia inducible factor subtype 1α (HIF‐1α) activated in diabetic retina is likely to play a role in regulating pathophysiological process via IL‐6 and TNF‐α mechanism. This has pharmacological implications to target specific HIF‐1α, IL‐6 and TNF‐α signalling pathway for dysfunction and vulnerability related to DR.
Silencing Op18/stathmin by RNA Interference Promotes the Sensitivity of Nasopharyngeal Carcinoma Cells to Taxol and High‐Grade Differentiation of Xenografted Tumours in Nude Mice
Authors: Lin Xuechi , Yu Ting , Zhang Lingxi , Chen Sangyan , Chen Xian , Liao Ying , Long Dan , Shen Fang
Published: June 2016

Nasopharyngeal carcinoma (NPC) is a refractory tumour, and chemotherapy is one of the primary treatment modalities. Oncoprotein 18 (Op18)/stathmin is a conserved small cytosolic phosphoprotein and highly expressed in tumours, which plays a vital role in maintaining the malignant phenotype of tumours. Taxol is a clinically widely used chemotherapeutic agent for a broad range of taxol‐resistant tumours. This study showed that Op18/stathmin silencing by RNA interference (RNAi) combined taxol cooperatively improved cellular apoptosis in CNE1 cells mainly via initiating endogenous death receptor pathway, impaired the capabilities of cellular proliferation and cellular migration and down‐regulated the half maximal inhibitory concentration (IC50) of taxol, meanwhile decreased the expression of the upstream extracellular regulated kinase 1 (ERK1) in vitro. Evidence also showed that taxol cytotoxicity was markedly augmented for Op18/stathmin RNAi in other NPC cells. In vivo animal experiments have demonstrated that early combination of Op18/stathmin silencing and taxol evidently inhibited tumourigenicity of CNE1 cells and growth of xenografted tumours in nude mice. Remarkably, silencing Op18/stathmin by RNAi still promoted transformation of late‐stage CNE1 cells in NPC‐xenografted tumours from moderately to highly differentiated and inhibited the pleiotropic cytokine interleukin‐10 (IL‐10) autocrine by transplanted tumours. These findings suggest that silencing Op18/stathmin by RNAi promotes chemosensitization of NPC to taxol and reverses malignant phenotypes of NPC, which provides a new clue for treating drug‐resistant tumours.
Controversies in the management of deep neck space infection in children: an evidence‐based review
Authors: Lawrence R. , Bateman N.
Published: June 2016

Background

Deep neck space infection (DNSI) is defined as infection in the potential spaces and fascial planes of the neck. Early recognition of DNSI can be challenging due to the complex head and neck anatomy; hence, a high index of suspicion is required to prevent a delay in diagnosis and appropriate management.

Objective of review

There remains a lack of consensus on the management of paediatric DNSI with many advocating a more aggressive approach with immediate surgical drainage, while others favour a more conservative approach with medical management in the first instance. The current literature on the management of paediatric DNSI is reviewed.

Type of review and search strategy

A literature review performed in November 2015 searched PubMed using the terms ‘deep neck space’, ‘infection’, ‘paediatric’, ‘pediatric’, ‘children’, ‘imaging’, ‘conservative’, ‘antibiotic’ and ‘surgery’. Articles not in the English language were excluded.

Results

(i) Clinical presentation: Management of a compromised airway is the priority. Clinical history and examination enables the identification of the primary source of infection and presence of complications. (ii) Investigations: Laboratory and microbiological investigations should be appropriately targeted, and CT imaging is the modality utilised in most cases. The presence of specific complications may warrant other imaging modalities. (iii) Antibiotics: An evidence‐based antibiotic regime is proposed. (iv) Conservative treatment: In children lacking indications for surgical intervention, a trial 48 h of intravenous antibiotics (IV Abx) should be commenced. v) Surgical intervention: Indications include signs of airway compromise, presence of complications, no clinical improvement after 48 h of IV Abx, abscess >2.2 cm on CT imaging, age <4 years and ITU admission.

Conclusions

An appreciation of head and neck anatomy is vital to understanding disease pathology and potential complications of DNSI, which may be life threatening. Both conservative and surgical approaches are viable treatment options and may compliment each other. Current evidence suggests that clinical management should be targeted towards the individual patient as factors such as age of the child may influence the balance of a conservative versus a surgical approach.
Fine needle aspiration cytology aided categorisation of neuroblastic tumours: a report of two cases
Authors: Das S. , Majumder B. , Islam N. , Das R. N. , Chatterjee U. , Saha K. , Datta C. , Ghosh D.
Published: June 2016

Pre‐treatment diagnosis of neuroblastic tumours is important, as they are known to undergo maturation following chemotherapy. Fine needle aspiration cytology (FNAC) plays a vital role in making pre‐operative diagnosis and categorisation of these tumours. Here we present two cases, one of ganglioneuroblastoma and the other of ganglioneuroma, diagnosed on FNAC.