bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
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.
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

ABSTRACTHaemoglobinopathies 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

AbstractBackgroundThe 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.ResultsWe 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.ConclusionsRhizosphere 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

AbstractLD-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

AbstractBackgroundStressful 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.MethodsA 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.ResultsPast 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).ConclusionsThese 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

ABSTRACTObjectiveTo understand the effect of peripheral hearing loss on the representation of speech in noise in the aging midbrain and cortex.MethodsSubjects 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).ResultsBoth 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.ConclusionsThe 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.SignificanceClinical devices, such as hearing aids, should not ignore age-related temporal processing deficits in the design of algorithms to maximize user benefit.HIGHLIGHTSMild 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

AbstractTissue-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.
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

AbstractAustralasian 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

AbstractHumankind 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

AbstractDiversity 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.