bluuebunny/crossref_metadata_2025 huggingface dataset:
pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information
Authors: Cheng Xiang , Xiao Xuan , Chou Kuo-Chen
Published: November 2017

Motivation

For in-depth understanding the functions of proteins in a cell, the knowledge of their subcellular localization is indispensable. The current study is focused on human protein subcellular location prediction based on the sequence information alone. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions that are particularly important for both basic research and drug design.

Results

Using the multi-label theory, we present a new predictor called ‘pLoc-mHum’ by extracting the crucial GO (Gene Ontology) information into the general PseAAC (Pseudo Amino Acid Composition). Rigorous cross-validations on a same stringent benchmark dataset have indicated that the proposed pLoc-mHum predictor is remarkably superior to iLoc-Hum, the state-of-the-art method in predicting the human protein subcellular localization.

Availability and implementation

To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mHum/, by which users can easily get their desired results without the need to go through the complicated mathematics involved.

Supplementary information

Supplementary data are available at Bioinformatics online.
Creating a ‘Suspect Community’: Monitoring and Controlling the Cypriot Community in Inter-War London
Authors: Smith Evan , Varnava Andrekos
Published: November 2017

This article offers a critical assessment of British policing and government monitoring and controlling of a ‘suspect community’ in inter-war London, which was also the subject of emigration control, the only colonial group to be thus treated prior to the Commonwealth Immigration Act 1962. The case is that of the Cypriots, who began to emigrate to the imperial metropolis in significant numbers in the late 1920s and largely settled in and around Soho. Their concentrated geographical location made them easy to police, monitor and control once their criminality and deviant communist politics made them a ‘suspect community’. They were also subjected to immigration control at their homeland by the Cypriot Colonial Government. There was significant co-operation between the Home and Colonial Offices to achieve the controls in both London and Cyprus. The immigration controls served as a prototype for the subsequent restrictions on other groups after the Second World War (namely those from India and Pakistan) and formed the basis of the Commonwealth Immigration Act.
CBP-1 Acts in GABAergic Neurons to Double Life Span in Axenically Cultured Caenorhabditis elegans
Authors: Cai Huaihan , Dhondt Ineke , Vandemeulebroucke Lieselot , Vlaeminck Caroline , Rasulova Madina , Braeckman Bart P
Published: November 2017

When cultured in axenic medium, Caenorhabditis elegans shows the largest life-span extension compared with other dietary restriction regimens. However, the underlying molecular mechanism still remains elusive. The gene cbp-1, encoding the worm ortholog of p300/CBP (CREB-binding protein), is one of the very few key genes known to be essential for life span doubling under axenic dietary restriction (ADR). By using tissue-specific RNAi, we found that cbp-1 expression in the germline is essential for fertility, whereas this gene functions specifically in the GABAergic neurons to support the full life span–doubling effect of ADR. Surprisingly, GABA itself is not required for ADR-induced longevity, suggesting a role of neuropeptide signaling. In addition, chemotaxis assays illustrate that neuronal inactivation of CBP-1 affects the animals’ food sensing behavior. Together, our results show that the strong life-span extension in axenic medium is under strict control of GABAergic neurons and may be linked to food sensing.
Open-Access Physical Activity Programs for Older Adults: A Pragmatic and Systematic Review
Authors: Balis Laura E , Strayer Thomas , Ramalingam NithyaPriya , Wilson Meghan , Harden Samantha M
Published: November 2017

Background and Objectives

Open-access, community-based programs are recommended to assist older adults in meeting physical activity guidelines, but the characteristics, impact, and scalability of these programs is less understood. The Land-Grant University Cooperative Extension System, an organization providing education through county-based educators, functions as a delivery system for these programs. A systematic review was conducted to determine characteristics of effective older adult physical activity programs and the extent to which programs delivered in Extension employ these characteristics.

Research Design and Methods

A systematic review of peer-reviewed and grey literature was conducted from August 2016 to February 2017. The review was limited to open-access (available to all), community-based physical activity interventions for older adults (≥65 years of age). The peer-reviewed literature search was conducted in PubMed and EBSCOhost; the grey literature search for Extension interventions was conducted through Extension websites, Land-Grant Impacts, and the Journal of Extension.

Results

Sixteen peer-reviewed studies and 17 grey literature sources met inclusion criteria and were analyzed. Peer-reviewed and Extension programs were similar in their limited use of behavioral theories and group-based strategies. Compared to Extension programs, those in the peer-reviewed literature were more likely to use a combination of physical activity components and be delivered by trained professionals.

Discussion and Implications

The results indicate notable differences between peer-reviewed literature and Extension programs and present an opportunity for Extension programs to more effectively use evidence-based program characteristics, including behavioral theories and group dynamics, a combination of physical activity components, and educator/agent-trained delivery agents.
Draft genome of the reindeer (Rangifer tarandus)
Authors: Li Zhipeng , Lin Zeshan , Ba Hengxing , Chen Lei , Yang Yongzhi , Wang Kun , Qiu Qiang , Wang Wen , Li Guangyu
Published: November 2017

Background

The reindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and it is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer, as well as males, regularly grow cranial appendages (antlers, the defining characteristics of cervids). Moreover, reindeer milk contains more protein and less lactose than bovids' milk. A high-quality reference genome of this species will assist efforts to elucidate these and other important features in the reindeer.

Findings

We obtained 615 Gb (Gigabase) of usable sequences by filtering the low-quality reads of the raw data generated from the Illumina Hiseq 4000 platform, and a 2.64-Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21 555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1339 snRNA, and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus and ancestors of Bos taurus and Capra hircus is estimated to be about 29.5 million years ago.

Conclusions

Our results provide the first high-quality reference genome for the reindeer and a valuable resource for studying the evolution, domestication, and other unusual characteristics of the reindeer.
A pro-inflammatory role of Fcα/μR on marginal zone B cells in sepsis
Authors: Shibuya Akira , Honda Shin-ichiro , Shibuya Kazuko
Published: November 2017

Fc receptors play important roles for a wide array of immune responses. In contrast to the well-defined Fcγ and Fcε receptors, the molecular and functional characteristics of Fc receptors for IgA and IgM have remained incompletely understood for years. Recent progress has unveiled the characteristics of Fc receptors for IgA and IgM, including Fcα/μ receptor (Fcα/μR) (CD351), polymeric immunoglobulin receptor (poly-IgR), Fcα receptor (FcαRI) (CD89) and Fcμ receptor (FcμR). In this review, we summarize the molecular and functional characteristics of Fcα/μR in comparison with poly-IgR, FcμR and FcαRI, and focus particularly on the pro-inflammatory function of Fcα/μR expressed on marginal zone B cells in sepsis.
Processing of intended and unintended strategic issues and integration into the strategic agenda
Authors: Ridder Hans-Gerd , Schrader Jan Simon
Published: November 2017

Background:

Strategic change is needed in hospitals due to external and internal pressures. However, research on strategic change, as a combination of management and medical expertise in hospitals, remains scarce.

Purpose:

We analyze how intended strategic issues are processed into deliberate strategies and how unintended strategic issues are processed into emergent strategies in the management of strategy formation in hospitals. This study empirically investigates the integration of medical and management expertise in strategy formation.

Methodology:

The longitudinal character of the case study enabled us to track patterns of intended and unintended strategic issues over 2 years. We triangulated data from interviews, observations, and documents. In accordance with the quality standards of qualitative research procedures, we analyzed the data by pattern matching and provided analytical generalization regarding strategy formation in hospitals.

Results:

Our findings suggest that strategic issues are particularly successful within the strategy formation process if interest groups are concerned with the strategic issue, prospective profits are estimated, and relevant decisions makers are involved early on. Structure and interaction processes require clear criteria and transparent procedures for effective strategy formation.

Conclusion:

There is systematic neglect of medical expertise in processes of generating strategies.

Practice Implications:

Our study reveals that the decentralized structure of medical centers is an adequate template for both the operationalization of intended strategic issues and the development of unintended strategic issues. However, tasks, roles, responsibility, resources, and administrative support are necessary for effective management of strategy formation. Similarly, criteria, procedures, and decision-making are prerequisites for effective strategy formation.
Double-Docking Technique for Femtosecond Laser-Assisted Deep Anterior Lamellar Keratoplasty
Authors: Guindolet Damien , Nguyen Diem T. , Bergin Ciara , Doan Serge , Cochereau Isabelle , Gabison Eric E.
Published: November 2017

Purpose:

To describe a new and safe surgical technique of deep anterior lamellar keratoplasty (DALK) using the femtosecond laser (FSL) and intraoperative optical coherence tomography (iOCT) for surgical management of corneal thinning and/or opacities. The technique was coined the double-docking procedure for DALK (DD-DALK).

Methods:

FSL-integrated iOCT was used for direct visualization and calibration to perform precise anterior lamellar and side cuts for the removal of the anterior stroma. Air was then injected in the residual posterior stroma to detach Descemet membrane [big-bubble (BB) formation]. Returning the residual posterior stroma into the docked position, a cylindrical vertical cut was made with the FSL to securely open the BB roof. Next, the stromal roof of the BB was removed with forceps leaving Descemet membrane intact, followed by a lamellar corneal graft.

Results:

Anterior stroma resection, BB formation, and residual stromal resection were achieved in every case without perforation. The curved applanation surface helped to limit the formation of folds on the posterior stroma (ie, advanced thinning).

Conclusions:

DD-DALK is a reproducible and safe procedure for surgical management of corneal thinning and/or opacities. The precision of stromal cuts made by the FSL and iOCT guidance for air injection increases success in DD-DALK preparation.
Contribution of Co-detected Respiratory Viruses and Patient Age to the Clinical Manifestations of Mycoplasma Pneumoniae Pneumonia in Children
Authors: Han Mi Seon , Yun Ki Wook , Lee Hoan Jong , Park Ji Young , Rhie Kyuyol , Lee Joon Kee , Lee Hyunju , Kwak Young Ho , Kim Do Kyun , Suh Dong In , Choi Eun Hwa
Published: November 2017

Background:

The clinical spectrum of Mycoplasma pneumoniae pneumonia is widely variable. This study evaluated the clinical manifestations of M. pneumoniae pneumonia in children of different age groups and by the presence of co-detected respiratory virus.

Methods:

This study included children hospitalized with M. pneumoniae pneumonia between 2010 and 2015. At the time of pneumonia diagnosis, a nasopharyngeal aspirate was analyzed for respiratory viruses by reverse transcription-polymerase chain reaction (RT-PCR). The clinical manifestations and laboratory findings were reviewed from medical records.

Results:

Of the 286 children with M. pneumoniae pneumonia, 84 (29.4%) had a co-detected respiratory virus, with the highest co-detection rate in young children (51.9% of children <2 years; P = 0.002). In children <2 years, with and without co-detected virus, wheezing occurred in 35.7% and 15.4%, respectively. Among the 202 children without any virus detected, only 6.4% were <2 years. These young children showed fewer median days of fever than the children ≥2 years (8 vs. 11 days; P = 0.022). Children ≥2 years tended to have accompanying skin rashes (21.7% vs.7.7%; P = 0.310) and elevated liver enzymes (21.7% vs. 0%; P = 0.075) more frequently than children <2 years. Only 53.8% of the patients <2 years were treated with macrolide compared with 94.1% of the patients ≥2 years (P < 0.001).

Conclusions:

The clinical manifestations of M. pneumoniae pneumonia in young children are milder than those in older children. A high prevalence of co-detected respiratory virus in young children suggests that virus might play a role in making pneumonia clinically apparent in this age group.
Use of Nutrition and Physical Activity Modules to Promote Continuing Professional Development
Authors: Olson Karin , Avdagovska Melita , Bistritz Lana , Kovacs Burns Katharina , Cui Ying , Gramlich Leah
Published: November 2017

Background: The authors developed five online modules about physical activity and nutrition. Methods: Registered nurses completed surveys before and after each module. Results: Evaluations showed an increase in knowledge and skill, but the psychometric parameters of the evaluation tool were poor. The low participation rate was associated with module length and technological difficulties. Conclusions: Given busy schedules of health professionals, online education approaches need to be feasible and be easy to access and use.
The Influence of the Art of Clinical Supervision Program on Nurses’ Knowledge and Attitude About Working With Students
Authors: Russell Kylie , Alliex Selma , Gluyas Heather
Published: November 2017

The Art of Clinical Supervision program was developed, implemented, and evaluated to determine nursing staff knowledge of and attitudes toward nursing students and the clinical supervision thereof. A key point of the program was the inclusion of strategies to promote one’s attitude toward working with students. A mixed methods approach of surveys, online reflections, and interviews was used to determine the program’s effect. The findings highlighted a positive impact on participants’ self-knowledge and attitudes toward students and student clinical supervision.
Looking Back and Looking Forward Through the Lens of the Nursing Professional Development
Authors: Harper Mary G. , Maloney Patsy , Shinners Jean
Published: November 2017

This final column in the Nursing Professional Development (NPD) Scope and Standards department provides five exemplars of incorporation of the scope and standards into NPD practice and ends with a call to action for all NPD practitioners.
Intravenous Push Cephalosporin Antibiotics in the Emergency Department
Authors: McLaughlin Julie M. , Scott Robin A. , Koenig Stephanie L. , Mueller Scott W.
Published: November 2017

Delays in administration of appropriate antibiotics to patients with septic shock are associated with increased mortality. To improve the care of patients with sepsis within our 73-bed emergency department (ED), a “first-dose” intravenous push (IVP) cephalosporin antibiotic protocol was initiated. This project was aimed at improving the time from provider order of antibiotic to administration, which follows the Sepsis Core Measure of timely antibiotic administration.

This was a single-center, retrospective analysis of a practice improvement study. Time from provider order of an IV cephalosporin antibiotic to administration was compared between postprotocol dates of March to May 2016 (n = 1110) and preprotocol dates of November 2015 to January 2016 (n = 1146). The cost of supplies for IVP was compared with traditional infusion. Prior to implementation of the IVP protocol, ED nursing staff completed a survey of administration preferences and then received one-on-one instruction about the protocol from the clinical nurse specialist and clinical nurse educator. In addition, a tip sheet was developed and IVP kits complete with all needed supplies were made available in the automated medication dispensing system.

Median time from IV cephalosporin antibiotic order to administration significantly decreased by 8, 12, 14, and 13 min for ceftriaxone, ceftazidime, cefepime, and cefazolin, respectively (p < 0.007 for all). This was true for all indications of antibiotic use. Nursing staff favored IVP administration over traditional IV infusion (87%). Supply cost to administer IVP antibiotics was $0.83 compared with $9.53 for traditional IV infusion.

A “first-dose IVP” protocol decreased time to administration by eliminating the need for procurement of an infusion pump, setup, and documentation of a secondary infusion. It was also preferred by ED nursing staff and associated with cost savings.
Cellular v-ATPase is required for virion assembly compartment formation in human cytomegalovirus infection
Authors: Pavelin Jonathan , McCormick Dominique , Chiweshe Stephen , Ramachandran Saranya , Lin Yao-Tang , Grey Finn
Published: November 2017

Successful generation of virions from infected cells is a complex process requiring orchestrated regulation of host and viral genes. Cells infected with human cytomegalovirus (HCMV) undergo a dramatic reorganization of membrane organelles resulting in the formation of the virion assembly compartment, a process that is not fully understood. Here we show that acidification of vacuoles by the cellular v-ATPase is a crucial step in the formation of the virion assembly compartment and disruption of acidification results in mis-localization of virion components and a profound reduction in infectious virus levels. In addition, knockdown of ATP6V0C blocks the increase in nuclear size, normally associated with HCMV infection. Inhibition of the v-ATPase does not affect intracellular levels of viral DNA synthesis or gene expression, consistent with a defect in assembly and egress. These studies identify a novel host factor involved in virion production and a potential target for antiviral therapy.
Host–parasite fluctuating selection in the absence of specificity
Authors: Best Alex , Ashby Ben , White Andy , Bowers Roger , Buckling Angus , Koskella Britt , Boots Mike
Published: November 2017

Fluctuating selection driven by coevolution between hosts and parasites is important for the generation of host and parasite diversity across space and time. Theory has focused primarily on infection genetics, with highly specific ‘matching-allele’ frameworks more likely to generate fluctuating selection dynamics (FSD) than ‘gene-for-gene’ (generalist–specialist) frameworks. However, the environment, ecological feedbacks and life-history characteristics may all play a role in determining when FSD occurs. Here, we develop eco-evolutionary models with explicit ecological dynamics to explore the ecological, epidemiological and host life-history drivers of FSD. Our key result is to demonstrate for the first time, to our knowledge, that specificity between hosts and parasites is not required to generate FSD. Furthermore, highly specific host–parasite interactions produce unstable, less robust stochastic fluctuations in contrast to interactions that lack specificity altogether or those that vary from generalist to specialist, which produce predictable limit cycles. Given the ubiquity of ecological feedbacks and the variation in the nature of specificity in host–parasite interactions, our work emphasizes the underestimated potential for host–parasite coevolution to generate fluctuating selection.
ITHANET: Information and database community portal for haemoglobinopathies
Authors: Kountouris Petros , Stephanou Coralea , Bento Celeste , Fanis Pavlos , Elion Jacques , Ramesar Raj S , Zilfalil Bin Alwi , Robinson Helen M , Traeger-Synodinos Joanne ,   Human Variome Project Global Globin 2020 Challenge, Lederer Carsten W , Kleanthous Marina
Published: November 2017

Haemoglobinopathies are the commonest monogenic diseases, with millions of carriers and patients worldwide. Online resources for haemoglobinopathies are largely divided into specialised sites catering for patients, researchers and clinicians separately. However, the severity, ubiquity and surprising genetic complexity of the haemoglobinopathies call for an integrated website to serve as a free and comprehensive repository and tool for patients, scientists and health professionals alike. This paper presents the ITHANET community portal, an expanding resource for clinicians and researchers dealing with haemoglobinopathies. It integrates information on news, events, publications, clinical trials and haemoglobinopathy-related organisations and experts and, most importantly, databases of variations, epidemiology and diagnostic and clinical data. Specifically, ITHANET provides annotation for 2690 haemoglobinopathy-related variations, epidemiological data for more than 180 countries and information for more than 600 HPLC diagnostic reports. The ITHANET portal accepts and incorporates contributions to its content by local experts from any country in the world and is freely available for the public at http://www.ithanet.eu.
Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon
Authors: Starr Evan P. , Shi Shengjing , Blazewicz Steven J. , Probst Alexander J. , Herman Donald J. , Firestone Mary A. , Banfield Jillian F.
Published: November 2017

Background

The transformation of plant photosynthate into soil organic carbon and its recycling to CO2 by soil microorganisms is one of the central components of the terrestrial carbon cycle. There are currently large knowledge gaps related to which soil-associated microorganisms take up plant carbon in the rhizosphere and the fate of that carbon.

Results

We conducted an experiment in which common wild oats (Avena fatua) were grown in a 13CO2 atmosphere and the rhizosphere and non-rhizosphere soil was sampled for genomic analyses. Density gradient centrifugation of DNA extracted from soil samples enabled distinction of microbes that did and did not incorporate the 13C into their DNA. A 1.45 Mbp genome of a Saccharibacteria (TM7) was identified and, despite the microbial complexity of rhizosphere soil, curated to completion. The genome lacks many biosynthetic pathways, including genes required to synthesize DNA de novo. Rather, it requires externally-derived nucleotides for DNA and RNA synthesis. Given this, we conclude that rhizosphere-associated Saccharibacteria recycle DNA from bacteria that live off plant exudates and/or phage that acquired 13C because they preyed upon these bacteria and/or directly from the labelled plant DNA. Isotopic labeling indicates that the population was replicating during the six-week period of plant growth. Interestingly, the genome is ~30% larger than other complete Saccharibacteria genomes from non-soil environments, largely due to more genes for complex carbon utilization and amino acid metabolism. Given the ability to degrade cellulose, hemicellulose, pectin, starch and 1,3-β-glucan, we predict that this Saccharibacteria generates energy by fermentation of soil necromass and plant root exudates to acetate or lactate. The genome encodes a linear electron transport chain featuring a terminal oxidase, suggesting that this Saccharibacteria may respire aerobically. The genome encodes a hydrolase that could breakdown salicylic acid, a plant defense signaling molecule, and genes to make a variety of isoprenoids, including the plant hormone zeatin.

Conclusions

Rhizosphere Saccharibacteria likely depend on other bacteria for basic cellular building blocks. We propose that isotopically labeled CO2 is incorporated into plant-derived carbon and then into the DNA of rhizosphere organisms capable of nucleotide synthesis, and the nucleotides are recycled into Saccharibacterial genomes.
Equivalence of LD-Score Regression and Individual-Level-Data Methods
Authors: de Vlaming Ronald , Johannesson Magnus , Magnusson Patrik K.E. , Ikram M. Arfan , Visscher Peter M.
Published: November 2017

LD-score (LDSC) regression disentangles the contribution of polygenic signal, in terms of SNP-based heritability, and population stratification, in terms of a so-called intercept, to GWAS test statistics. Whereas LDSC regression uses summary statistics, methods like Haseman-Elston (HE) regression and genomic-relatedness-matrix (GRM) restricted maximum likelihood infer parameters such as SNP-based heritability from individual-level data directly. Therefore, these two types of methods are typically considered to be profoundly different. Nevertheless, recent work has revealed that LDSC and HE regression yield near-identical SNP-based heritability estimates when confounding stratification is absent. We now extend the equivalence; under the stratification assumed by LDSC regression, we show that the intercept can be estimated from individual-level data by transforming the coefficients of a regression of the phenotype on the leading principal components from the GRM. Using simulations, considering various degrees and forms of population stratification, we find that intercept estimates obtained from individual-level data are nearly equivalent to estimates from LDSC regression (R2> 99%). An empirical application corroborates these findings. Hence, LDSC regression is not profoundly different from methods using individual-level data; parameters that are identified by LDSC regression are also identified by methods using individual-level data. In addition, our results indicate that, under strong stratification, there is misattribution of stratification to the slope of LDSC regression, inflating estimates of SNP-based heritability from LDSC regression ceteris paribus. Hence, the intercept is not a panacea for population stratification. Consequently, LDSC-regression estimates should be interpreted with caution, especially when the intercept estimate is significantly greater than one.
Genetic and environmental determinants of stressful life events and their overlap with depression and neuroticism
Authors: Clarke Toni-Kim , Zeng Yanni , Navrady Lauren , Xia Charley , Haley Chris , Campbell Archie , Navarro Pau , Amador Carmen , Adams Mark J. , Howard David M. , Arnau Soler Aleix , Hayward Caroline , Thomson Pippa A. , Smith Blair H. , Padmanabhan Sandosh , Hocking Lynne J. , Hall Lynsey S. , Porteous David J. , Deary Ian J. , McIntosh Andrew M.
Published: November 2017

Background

Stressful life events (SLEs) and neuroticism are risk factors for major depressive disorder (MDD). However, SLEs and neuroticism are heritable traits that are correlated with genetic risk for MDD. In the current study, we sought to investigate the genetic and environmental contributions to SLEs in a large family-based sample, and quantify any genetic overlap with MDD and neuroticism.

Methods

A subset of Generation Scotland: the Scottish Family Health Study, consisting of 9618 individuals comprise the present study. We estimated the heritability of SLEs using pedigree-based and molecular genetic data. The environment was assessed by modelling familial, couple and sibling components. Using polygenic risk scores (PRS) and LD score regression we analysed the genetic overlap between MDD, neuroticism and SLEs.

Results

Past 6-month life events were positively correlated with lifetime MDD status (β=0.21, r2=1.1%, p=2.5 × 10−25) and neuroticism (β =0.13, r2=1.9%, p=1.04 × 10−37). Common SNPs explained 8% of the variance in personal life events (those directly affecting the individual) (S.E.=0.03, p=9 × 10−4). A significant effect of couple environment accounted for 13% (S.E.=0.03, p=0.016) of variation in SLEs. PRS analyses found that individuals with higher PRS for MDD reported more SLEs (β =0.05, r2=0.3%, p=3 × 10−5). LD score regression demonstrated genetic correlations between MDD and both SLEs (rG=0.33, S.E.=0.08) and neuroticism (rG=0.15, S.E.=0.07).

Conclusions

These findings suggest that SLEs are partially heritable and this heritability is shared with risk for MDD and neuroticism. Further work should determine the causal direction and source of these associations.
Representation of speech in noise in the aging midbrain and cortex: aging may dominate over hearing-loss
Authors: Presacco Alessandro , Simon Jonathan Z. , Anderson Samira
Published: November 2017

Objective

To understand the effect of peripheral hearing loss on the representation of speech in noise in the aging midbrain and cortex.

Methods

Subjects comprised 17 normal-hearing younger adults, 15 normal-hearing older adults and 14 hearing-impaired older adults. The midbrain response, measured with Frequency-Following Responses (FFRs), and the cortical response, measured with magnetoencephalography (MEG) responses, were recorded from subjects listening to speech in quiet and noise at varying signal to noise ratios (SNRs).

Results

Both groups of older listeners showed both weaker midbrain response amplitudes and overrepresentation of cortical responses compared to younger listeners. However, significant differences between the older groups were found in both midbrain-cortex relationships and in cortical processing durations, suggesting that hearing loss may alter reciprocal connections between lower and higher levels of the auditory pathway.

Conclusions

The paucity of differences in midbrain or cortical responses between the two older groups suggest that age-related temporal processing deficits may contribute to older adults’ communication difficulties beyond what might be predicted from peripheral hearing loss alone.

Significance

Clinical devices, such as hearing aids, should not ignore age-related temporal processing deficits in the design of algorithms to maximize user benefit.

HIGHLIGHTS

Mild sensorineural hearing loss does not appear to significantly exacerbate already appreciable age-related deficits in midbrain speech-in-noise encoding.

Mild sensorineural hearing loss also does not appear to significantly exacerbate already appreciable age-related deficits in most measures of cortical speech-in-noise encoding.

Central processing deficits caused by peripheral hearing loss in older adults are seen only in more subtle measures, including altered relationships between midbrain and cortex.
Hypermethylation of human DNA: Fine-tuning transcription associated with development
Authors: Baribault Carl , Ehrlich Kenneth C. , Ponnaluri V. K. Chaithanya , Pradhan Sriharsa , Lacey Michelle , Ehrlich Melanie
Published: November 2017

Tissue-specific gene transcription can be affected by DNA methylation in ways that are difficult to discern from studies focused on genome-wide analyses of differentially methylated regions (DMRs). We studied 95 genes in detail using available epigenetic and transcription databases to detect and elucidate less obvious associations between development-linked hypermethylated DMRs in myoblasts (Mb) and cell-and tissue-specific expression. Many of these genes encode developmental transcription factors and display DNA hypermethylation also in skeletal muscle (SkM) and a few heterologous samples (e.g., aorta, mammary epithelial cells, or brain) among the 38 types of human cell cultures or tissues examined. Most of the DMRs overlapped transcription regulatory elements, including canonical, alternative, or cryptic promoters; enhancers; CTCF binding sites; and long-noncoding RNA (lncRNA) gene regions. Among the prominent relationships between DMRs and expression was promoter-region hypermethylation accompanying repression in Mb but not in many other repressed samples (26 genes). Another surprising relationship was down-modulated (but not silenced) expression in Mb associated with DNA hypermethylation at cryptic enhancers in Mb although such methylation was absent in both non-expressing samples and highly expressing samples (24 genes). The tissue-specificity of DNA hypermethylation can be explained for many of the genes by their roles in prenatal development or by the tissue-specific expression of neighboring genes. Besides elucidating developmental epigenetics, our study provides insights into the roles of abnormal DNA methylation in disease, e.g., cancer, Duchenne muscular dystrophy, and congenital heart malformations.
XenopusTadpole Tissue Harvest
Authors: Patmann Matthew D. , Shewade Leena H. , Schneider Katelin A. , Buchholz Daniel R.
Published: November 2017

The procedures described here apply toXenopustadpoles from the beginning of feeding through the major changes of metamorphosis and are appropriate for downstream postoperative snap freezing for molecular analysis, fixation for histological analysis, and sterile organ culture. To the uninitiated, the most difficult aspects of tadpole tissue dissections are likely knowing the appearance and location of organs, and the difficulty manipulating and holding tadpoles in place to carry out the oftentimes fine and precise dissections. Therefore, images and stepwise instructions are given for the harvest of external organs (tail, head, eyes, tail skin, back skin, gills, thymus, hind limbs, forelimbs) and peritoneal organs (intestine, pancreas, liver, spleen, lungs, fat bodies, kidney/gonad complex), as well as brain, heart, and blood. Dissections are typically done under a dissection stereomicroscope, and two pairs of fine straight forceps, one pair of fine curved forceps, and one pair of microdissection scissors are sufficient for most tissue harvests.
Sampling and Preparation of Mouse and Rat Serum
Authors: Greenfield Edward A.
Published: November 2017

After immunization, samples of serum are taken to check the production of specific antibodies. Serum is collected from clotted blood or plasma without the fibrinogen and other clotting factors. Serum contains fewer proteins than plasma and is preferred for use in many clinical assays because some of the proteins in plasma or the addition of anticoagulants can interfere with the test results. Methods for obtaining blood samples and preparing serum are described here. Blood collection should not exceed 7%–9% of the animal's total blood volume or 1% of total body weight every 2–4 wk.
Characterizing Antibodies
Authors: Weis-Garcia Frances , Carnahan Robert H.
Published: November 2017

Perhaps because they are such commonly used tools, many researchers view antibodies one-dimensionally: Antibody Y binds antigen X. Although few techniques require a comprehensive understanding of any particular antibody’s characteristics, well-executed experiments do require a basic appreciation of what is known and, equally as important, what is not known about the antibody being used. Ignorance of the relevant antibody characteristics critical for a particular assay can easily lead to loss of precious resources (time, money, and limiting amounts of sample) and, in worst-case scenarios, erroneous conclusions. Here, we describe various antibody characteristics to provide a more well-rounded perspective of these critical reagents. With this information, it will be easier to make informed decisions on how best to choose and use the available antibodies, as well as knowing when it is essential and how to determine a particular as yet-undefined characteristic.
3D printing the future: scenarios for supply chains reviewed
Authors: Ryan Michael J. , Eyers Daniel R. , Potter Andrew T. , Purvis Laura , Gosling Jonathan
Published: November 2017

Purpose

The purpose of this paper is to evaluate the existing scenarios for 3D printing (3DP) in order to identify the “white space” where future opportunities have not been proposed or developed to date. Based around aspects of order penetration points, geographical scope and type of manufacturing, these gaps are identified.

Design/methodology/approach

A structured literature review has been carried out on both academic and trade publications. As of the end of May 2016, this identified 128 relevant articles containing 201 future scenarios. Coding these against aspects of existing manufacturing and supply chain theory has led to the development of a framework to identify “white space” in the existing thinking.

Findings

The coding shows that existing future scenarios are particularly concentrated on job shop applications and pull-based supply chain processes, although there are fewer constraints on geographical scope. Five distinct areas of “white space” are proposed, reflecting various opportunities for future 3DP supply chain development.

Research limitations/implications

Being a structured literature review, there are potentially articles not identified through the search criteria used. The nature of the findings is also dependent upon the coding criteria selected. However, these are theoretically derived and reflect important aspect of strategic supply chain management.

Practical implications

Practitioners may wish to explore the development of business models within the “white space” areas.

Originality/value

Currently, existing future 3DP scenarios are scattered over a wide, multi-disciplinary literature base. By providing a consolidated view of these scenarios, it is possible to identify gaps in current thinking. These gaps are multi-disciplinary in nature and represent opportunities for both academics and practitioners to exploit.
Why change the name of the College from Australasian to Australian and New Zealand?
Authors: Ardagh Michael
Published: November 2017

Australasian is the adjectival version of the name of a geographical region. The region is defined differently by different people. It includes islands other than Australia and New Zealand and variably includes or excludes New Guinea. It has nothing to do with Asia. The adjective is often misunderstood, it leaves New Zealand invisible to many readers and it is an incorrect description of who we are as a college. Australian and New Zealand describes who we are – fellows from two sovereign nations – Australia and New Zealand. Changing the name is not about secession, division nor ingratitude and does not undermine the College's commitment to helping other nations in the greater region. It is a positive acknowledgement of who we are and a strong foundation for a united College's future growth.
Predation pressure in maize across Europe and in Argentina: an intercontinental comparison
Authors: Ferrante Marco , Lövei Gábor L. , Magagnoli Serena , Minarcikova Lenka , Tomescu Elena Larisa , Burgio Giovanni , Cagan Ludovit , Ichim Mihael Cristin
Published: November 2017

Humankind draws important benefits from large‐scale ecological processes termed ecosystem services, yet the status of several of them is declining. Reliable monitoring methods are essential for tracking the status of ecosystem services. Predation is the mainstay of natural pest control, a key ecosystem service. We used green plasticine caterpillars to monitor predation pressure, and to obtain baseline data on predator activity in transgenic Bt versus non‐Bt maize fields in Old and New World countries. Predation pressure was measured at ground and canopy levels using an identical, small‐plot experimental design in four European countries (Denmark, Slovakia, Romania and Italy) and Argentina. Total predation rate in maize was 11.7%d−1 (min. 7.2%d−1 in Argentina, max. 29.0%d−1 in Romania). Artificial caterpillars were attacked both by invertebrates (mostly chewing insects with 42.0% of the attack marks, and ants with 7.1%, but also predatory and parasitoid wasps, spiders and slugs), and vertebrates (small mammals 25.5%, and birds 20.2%). Total predation at ground level (15.7%d−1) was significantly higher than in maize canopies (6.0%d−1) in all countries, except Argentina. We found no significant differences between predator pressure in Bt versus non‐Bt maize plots. The artificial caterpillar method provided comparable, quantitative data on predation intensity, and proved to be suitable for monitoring natural pest control. This method usefully expands the existing toolkit by directly measuring ecological function rather than structure.
Evidence for a conserved microbiota across the different developmental stages of Plodia interpunctella
Authors: Mereghetti Valeria , Chouaia Bessem , Limonta Lidia , Locatelli Daria Patrizia , Montagna Matteo
Published: November 2017

Diversity and composition of lepidopteran microbiotas are poorly investigated, especially across the different developmental stages. To improve this knowledge, we characterize the microbiota among different developmental stages of the Indian meal moth, Plodia interpunctella, which is considered one of the major pest of commodities worldwide. Using culture‐independent approach based on Illumina 16S rRNA gene sequencing we characterized the microbiota of four developmental stages: eggs, first‐, and last‐instar larvae, and adult. A total of 1022 bacterial OTUs were obtained, showing a quite diversified microbiota associated to all the analyzed stages. The microbiotas associated with P. interpunctella resulted almost constant throughout the developmental stages, with approximately 77% of bacterial OTUs belonging to the phylum of Proteobacteria. The dominant bacterial genus is represented by Burkholderia (∼64%), followed by Propionibacterium, Delftia, Pseudomonas, and Stenotrophomonas. A core bacterial community, composed of 139 OTUs, was detected in all the developmental stages, among which 112 OTUs were assigned to the genus Burkholderia. A phylogenetic reconstruction, based on the 16S rRNA, revealed that our Burkholderia OTUs clustered with Burkholderia cepacia complex, in the same group of those isolated from the hemipterans Gossyparia spuria and Acanthococcus aceris. The functional profiling, predicted on the base of the bacterial 16S rRNA, indicates differences in the metabolic pathways related to metabolism of amino acids between preimaginal and adult stages. We can hypothesize that bacteria may support the insect host during preimaginal stages.
Detection and analysis of circulating large intergenic non‐coding RNA regulator of reprogramming in plasma for breast cancer
Authors: Zhang Kaijiong , Luo Zhenglian , Zhang Yi , Wang Yuzhi , Cui Meng , Liu Lian , Zhang Li , Liu Jinbo
Published: November 2017

Background

Previous studies have indicated that large intergenic non‐coding RNA regulator of reprogramming (lincRNA‐ROR) plays an important role in regulating tumor carcinogenesis and metastasis; however, whether circulating lincRNA‐ROR could function as a potential biomarker for breast cancer (BC) diagnosis and monitoring is unknown. This study was conducted to investigate circulating lincRNA‐ROR in plasma as a potential biomarker for BC diagnosis and monitoring.

Methods

We performed reverse transcription‐quantitative‐PCR to examine lincRNA‐ROR expression levels in cell lines, 24 pairs of BC tissue samples, and 94 plasma samples from BC patients. Potential correlations between plasma lincRNA‐ROR levels and clinicopathological characteristics were analyzed. A receiver operating characteristic curve was calculated to evaluate the diagnostic values for BC. Pearson correlation analysis of lincRNA‐ROR in plasma samples and the corresponding tissues of the same patients was performed to explore tumor monitoring values.

Results

LincRNA‐ROR expression was significantly increased in BC cell lines, tissues, and plasma (all P < 0.01). Plasma lincRNA‐ROR levels were associated with estrogen receptors (P = 0.042) and lymph node metastasis (P = 0.046). The area under the receiver operating characteristic curve of plasma lincRNA‐ROR was 0.844 (sensitivity 80.0%, specificity 56.7%), which was higher than carcinoembryonic and carbohydrate antigen 15‐3 values. Moreover, plasma lincRNA‐ROR levels were decreased in postoperative compared to preoperative samples (P < 0.0001). Plasma lincRNA‐ROR levels moderately correlated with the corresponding tissue level in the same patients (r2 = 0.638, P < 0.0001).

Conclusion

Plasma lincRNA‐ROR may be a potential biomarker for BC diagnosis and a dynamic monitor.
Definition and estimation of vital rates from repeated censuses: Choices, comparisons and bias corrections focusing on trees
Authors: Kohyama Takashi S. , Kohyama Tetsuo I. , Sheil Douglas
Published: November 2017

Mortality and recruitment rates are fundamental measures of population dynamics. Ecologists and others have defined and estimated these vital rates in various ways. We review these alternatives focusing on tree population census data in fixed area plots, though many aspects have wider application when similar data characteristics and assumptions apply: our goal is to guide choices and facilitate comparisons.

We divide our estimates into “instantaneous” and “annual” rates, corresponding to continuous or discrete time dynamics, respectively. In each case, vital rate estimates can be further divided into those based on population density (“per‐capita” rates) and those based on census area (“per‐area” rates). We also examine how all such rate estimates relate to each other and can thus be interconverted and compared.

In a heterogeneous population (e.g. trees in a forest stand) comprising subpopulations (e.g. species, locations, exposure classes), estimates of vital rates that assume homogeneity (equal likelihood of mortality and equal likelihood of recruitment for all individuals) are biased towards lower vital rates in stable mixed populations (due to survivorship bias) and towards lower absolute values of population change rate (due to changing‐frequency bias).

We describe and illustrate an individual‐based Bayesian procedure for estimating vital rates that reduces biases by accounting for demographic heterogeneity and sampling errors among and within subpopulations.