bluuebunny/crossref_metadata_2025 huggingface dataset:
Spontaneous mutations and transmission distortions of genic copy number variants shape the standing genetic variation inPicea glauca
Authors: Sahli Atef , Giguére Isabelle , Bousquet Jean , MacKay John
Published: January 2017

Copy number variations (CNVs) are large genetic variations detected among the individuals of every multicellular organism examined so far. These variations are believed to play an important role in the evolution and adaptation of species. In plants, little is known about the characteristics of CNVs, particularly regarding the rates at which they are generated and the mechanics of their transmission from a generation to the next. Here, we used SNP-array raw intensity data for 55 two-generations families (3663 individuals) to scan the gene space of the conifer treePicea glauca(Moench) Voss for CNVs. We were particularly interested in the abundance, inheritance, spontaneous mutation rate spectrum and the evolutionary consequences they may have on the standing genetic variation of white spruce. Our findings show that CNVs affect a small proportion of the gene space and are predominantly copy number losses. CNVs were either inherited or generated throughde novoevents.De novoCNVs present high rates of spontaneous mutations that vary for different genes and alleles and are correlated with gene expression levels. Most of the inherited CNVs (70%) are transmitted from the parents in violation of Mendelian expectations. These transmission distortions can cause considerable frequency changes between generations and be dependent on whether the heterozygote parents contribute as male or female. Transmission distortions were also influenced by the partner genotype and the parents’ genetic background. This study provides new insights into the effects of different evolutionary forces on copy number variations based on the analysis of a perennial plant.
Escape Excel: a tool for preventing gene symbol and accession conversion errors
Authors: Welsh Eric A. , Stewart Paul A. , Kuenzi Brent M.
Published: January 2017

Background

Microsoft Excel automatically converts certain gene symbols, database accessions, and other alphanumeric text and numbers into dates, scientific notation, and other numerical representations, which may lead to subsequent, irreversible corruption of the imported text. A recent survey of popular genomic literature estimates that one-fifth of all papers with supplementary data containing gene lists in Excel format suffer from this issue.

Results

Here, we present an open-source tool, Escape Excel, which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel. Escape Excel is available in the Galaxy web environment and can be installed through the Galaxy ToolShed. Escape Excel is also available as a stand-alone, command line Perl script on GitHub (http://www.github.com/pstew/escape_excel). A Galaxy test server implementation is accessible athttp://apostl.moffitt.org.

Conclusions

Escape Excel detects and escapes a wide variety of problematic text strings so that they are not erroneously converted into other representations upon importation into Excel. Examples of problematic strings include date-like strings, time-like strings, leading zeroes in front of numbers, and long numeric and alpha-numeric identifiers that should not be automatically converted into scientific notation. It is hoped that greater awareness of these potential data-corruption issues, together with diligent escaping of text files prior to importation into Excel, will help to reduce the amount of Excel-corrupted data in scientific analyses and publications.
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm
Authors: Zimin Aleksey V. , Puiu Daniela , Luo Ming-Cheng , Zhu Tingting , Koren Sergey , Marçais Guillaume , Yorke James A. , Dvořák Jan , Salzberg Steven L.
Published: January 2017

Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data alone, particularly with highly repetitive plant genomes. Errors in the raw data can lead to insertion or deletion errors (indels) in the consensus genome sequence, which in turn create significant problems for downstream analysis; for example, a single indel may shift the reading frame and incorrectly truncate a protein sequence. Here, we describe an algorithm that solves the high error rate problem by combining long, high-error reads with shorter but much more accurate Illumina sequencing reads, whose error rates average <1%. Our hybrid assembly algorithm combines these two types of reads to construct mega-reads, which are both long and accurate, and then assembles the mega-reads using the CABOG assembler, which was designed for long reads. We apply this technique to a large data set of Illumina and PacBio sequences from the species Aegilops tauschii, a large and extremely repetitive plant genome that has resisted previous attempts at assembly. We show that the resulting assembled contigs are far larger than in any previous assembly, with an N50 contig size of 486,807 nucleotides. We compare the contigs to independently produced optical maps to evaluate their large-scale accuracy, and to a set of high-quality bacterial artificial chromosome (BAC)-based assemblies to evaluate base-level accuracy.
Polymorphism‐aware protein databases – a prerequisite for an unbiased proteomic analysis of natural populations
Authors: Otte Kathrin A. , Schlötterer Christian
Published: January 2017

Recent technological advances have increased the throughput of proteomics, facilitating the characterization of molecular phenotypes on the population level, thus bearing the potential to complement transcriptomic analyses. Reference protein databases are crucial for the analysis and quantification, because only peptides in the protein database can be identified. Any peptide carrying an amino acid variant cannot be identified. Because most proteomic studies, even of natural populations, do not account for polymorphisms, we analysed the influence of variant peptides on quantitative proteomic analyses. We used transcriptomic and proteomic data of two Drosophila melanogaster genotypes and identified genotype‐specific variants from RNA‐seq data. We introduce a simple pipeline to include these variants in a polymorphism‐aware protein database and compared the results to an unmodified reference database. The polymorphism‐aware database not only identifies more peptides, but the quantitative values also changed when peptide variants were included. We conclude that proteomic quantification is likely to be biased, in particular for small genes, when polymorphisms are being ignored. Polymorphism‐aware databases may be therefore a key step towards improved proteomic data analyses, especially for the analysis of pooled individuals and the comparison of population samples.
Haplostrips: revealing population structure through haplotype visualization
Authors: Marnetto Davide , Huerta‐Sánchez Emilia
Published: January 2017

Population genetic analyses often identify polymorphic variants in regions of the genome that indicate the effect of non‐neutral evolutionary processes. However, in order to obtain deeper insights into the evolutionary processes at play, we often resort to summary statistics, sacrificing the information encoded in the complexity of the original data.

Here, we present haplostrips, a tool to visualize polymorphisms of a given region of the genome in the form of independently clustered and sorted haplotypes. Haplostrips is a command‐line tool written in Python and R, that uses variant call format files as input and generates a heatmap view.

Haplostrips is available at: https://bitbucket.org/dmarnetto/haplostrips. It can be applied in several fields and in all living systems for which a phased haplotype is available to visualize complex effects of, among others: introgression, domestication, selection, demographic events.

Haplostrips can reveal hidden patterns of genetic variation without losing the basic information encoded in variant sequences.
Neil Smith's Long Revolutionary Imperative
Authors: Heynen Nik , Kent Andrew , McKittrick Katherine , Gidwani Vinay , Larner Wendy
Published: January 2017

Whether writing about gentrification or nature, the production of space or the politics of scale, uneven development or public space, globalization or revolution, the geographer Neil Smith was nothing if not provocative. Neither Festschrift nor hagiography, this special issue of Antipode critically engages Smith's work—not to unpick the rich tapestry, but to draw the threads out and spin them on in new directions. Consisting of newly commissioned essays by comrades from across the human sciences, it considers the entire range of Smith's oeuvre. This paper introduces the essays by offering not only some thoughts about Smith's intellectual contributions generally, but also new insight into the role he played in Antipode.
Use of antenatal corticosteroids in special circumstances: a comprehensive review
Authors: Magann Everett F. , Haram Kjell , Ounpraseuth Songthip , Mortensen Jan H. , Spencer Horace J. , Morrison John C.
Published: January 2017

The aim of this study was to determine, in pregnancies complicated by preterm premature rupture of membranes (PPROM), hypertension, intrauterine growth restriction, multi‐fetal gestations and pregnancies 23–26 weeks and ≥34 weeks’ gestation, whether antenatal corticosteroids benefit the fetus.

Literature review using PubMed, Web of Science, Clinical trials.gov, Cochrane Database of Systematic Reviews (1990–2015).

Search terms linked special circumstances with corticosteroids. Randomized clinical trials, retrospective and prospective cohort studies, and case control studies were reviewed.

In all, 468 abstracts were identified and 84 added from selected article bibliographies; of these, 503 abstracts were excluded, leaving 49 articles as the basis of review.

The literature supports corticosteroids for PPROM up to 32–34 weeks without chorioamnionitis. Antenatal corticosteroids are beneficial for preterm infants of women with HELLP (hemolysis, elevated liver enzymes, low platelets) syndrome/severe preeclampsia. Postpartum corticosteroid treatment of HELLP patients results in more rapid correction of liver enzymes, platelet counts, and urinary output, which can reduce maternal morbidity. Corticosteroids in twin pregnancies decrease respiratory distress syndrome but the effect is less than in singleton pregnancies. Corticosteroid effects on intrauterine growth restriction pregnancies are conflicting and steroid use should be individualized. Corticosteroid use for 23–26 weeks reduces neonatal mortality but not morbidity. In pregnancies of 34 weeks to 366/7 weeks, corticosteroids reduce respiratory distress syndrome, but follow‐up studies are unavailable. No long‐term adverse child developmental effects have been observed with one or two courses of corticosteroids, but three or more steroid courses lowers birthweight and organ weight, and there may be an increase in neurodevelopmental abnormalities. Longer follow up of corticosteroid‐treated fetuses is required.
Antibiotic prophylaxis does not reduce the infection rate following percutaneous endoscopic gastrostomy in infants and children
Authors: van Els Anne L. , van Driel J Joris , Kneepkens CM Frank , de Meij Tim G. J.
Published: January 2017

Aim

Percutaneous endoscopic gastrostomy (PEG) is the standard for placing gastrostomy in children needing long‐term enteral nutrition, with major and minor complications reported in up to 19% and 47.7% of children, respectively. We reviewed our experience with PEG, concentrating on the efficacy of antibiotic prophylaxis in reducing infectious complications.

Methods

We performed a retrospective, single‐centre study that comprised all children up to 18 years of age who underwent a first PEG procedure in the VU University Medical Centre, Amsterdam, from 2008 to 2012. All complications up to one month after PEG were recorded. Infection rates with and without antibiotic prophylaxis could be compared as a new protocol requiring the preprocedure administration of cefazolin was not followed consistently.

Results

We enrolled 129 patients (78 male) with a mean age of 4.9 ± 4.8 years and median age of 2.9 years. Major complications were seen in seven patients (5.4%) and minor complications in 23 patients (17.8%). Antibiotic prophylaxis was administered to 99 of 129 children (76.7%). Infections occurred in 15 of 129 patients (11.6%); 14 of 99 with and 1 of 30 without prophylaxis developed infections (p = 0.106). Peristomal infections were the most frequent complication (10.1%).

Conclusion

Percutaneous endoscopic gastrostomy was a safe procedure and antibiotic prophylaxis did not seem to decrease infectious complications.
Nephrologists need to play a key role in improving annual influenza vaccination rates in children with kidney disease
Authors: Scheuerman Oded , Zilber Eyal , Davidovits Miriam , Chodick Gabriel , Levy Itzhak
Published: January 2017

Aim

This study investigated the under‐researched area of annual influenza vaccination rates in children with chronic kidney disease and identified reasons for nonimmunisation.

Methods

A prospective cross‐sectional study was conducted in the nephrology clinic and dialysis unit of a tertiary paediatric medical centre from August to October 2011 and September to October 2012. Parents were asked to complete a questionnaire on their child's immunisation against influenza.

Results

Of the 217 children studied, 45.6% were vaccinated against influenza. The major reason for nonimmunisation was because the parents had not received the necessary information from the primary physician or treating nephrologist. The nonvaccinated children were significantly more likely to be less than two years old and female and to have parents who did not believe in the benefits of vaccination (p < 0.05). Of the parents who did not vaccinate their child, 38% claimed they would have done so if the vaccine had been offered in the nephrology clinic.

Conclusion

Children with kidney disease had a higher annual influenza vaccination rate than the general population, but it was still suboptimal. Nephrologists should be alerted to the need to provide parents with information on influenza vaccinations and they should be available in nephrology clinics.
First‐time success with needle procedures was higher with a warm lidocaine and tetracaine patch than an eutectic mixture of lidocaine and prilocaine cream
Authors: Cozzi Giorgio , Borrometi Fabio , Benini Franca , Neri Elena , Rusalen Francesca , Celentano Loredana , Zanon Davide , Schreiber Silvana , Ronfani Luca , Barbi Egidio
Published: January 2017

Aim

More than 50% of children report apian during venepuncture or intravenous cannulation and using local anaesthetics before needle procedures can lead to different success rates. This study examined how many needle procedures were successful at the first attempt when children received either a warm lidocaine and tetracaine patch or an eutectic mixture of lidocaine and prilocaine (EMLA) cream.

Methods

We conducted this multicentre randomised controlled trial at three tertiary‐level children's hospitals in Italy in 2015. Children aged three to 10 years were enrolled in an emergency department, paediatric day hospital and paediatric ward and randomly allocated to receive a warm lidocaine and tetracaine patch or EMLA cream. The primary outcome was the success rate at the first attempt.

Results

The analysis included 172 children who received a warm lidocaine and tetracaine patch and 167 who received an EMLA cream. The needle procedure was successful at the first attempt in 158 children (92.4%) who received the warm patch and in 142 children (85.0%) who received the cream (p = 0.03). The pain scores were similar in both groups.

Conclusion

This study showed that the first‐time needle procedure success was 7.4% higher in children receiving a warm lidocaine and tetracaine patch than EMLA cream.
Optimum Designs for Non-Linear Mixed Effects Models in the Presence of Covariates
Authors: Bogacka Barbara , Latif Mahbub A. H. M. , Gilmour Steven G. , Youdim Kuresh
Published: January 2017

In this article, we present a new method for optimizing designs of experiments for non-linear mixed effects models, where a categorical factor with covariate information is a design variable combined with another design factor. The work is motivated by the need to efficiently design preclinical experiments in enzyme kinetics for a set of Human Liver Microsomes. However, the results are general and can be applied to other experimental situations where the variation in the response due to a categorical factor can be partially accounted for by a covariate. The covariate included in the model explains some systematic variability in a random model parameter. This approach allows better understanding of the population variation as well as estimation of the model parameters with higher precision.
Developing new online calibration methods for multidimensional computerized adaptive testing
Authors: Chen Ping , Wang Chun , Xin Tao , Chang Hua‐Hua
Published: January 2017

Multidimensional computerized adaptive testing (MCAT) has received increasing attention over the past few years in educational measurement. Like all other formats of CAT, item replenishment is an essential part of MCAT for its item bank maintenance and management, which governs retiring overexposed or obsolete items over time and replacing them with new ones. Moreover, calibration precision of the new items will directly affect the estimation accuracy of examinees’ ability vectors. In unidimensional CAT (UCAT) and cognitive diagnostic CAT, online calibration techniques have been developed to effectively calibrate new items. However, there has been very little discussion of online calibration in MCAT in the literature. Thus, this paper proposes new online calibration methods for MCAT based upon some popular methods used in UCAT. Three representative methods, Method A, the ‘one EM cycle’ method and the ‘multiple EM cycles’ method, are generalized to MCAT. Three simulation studies were conducted to compare the three new methods by manipulating three factors (test length, item bank design, and level of correlation between coordinate dimensions). The results showed that all the new methods were able to recover the item parameters accurately, and the adaptive online calibration designs showed some improvements compared to the random design under most conditions.
Meta‐CART: A tool to identify interactions between moderators in meta‐analysis
Authors: Li Xinru , Dusseldorp Elise , Meulman Jacqueline J.
Published: January 2017

In the framework of meta‐analysis, moderator analysis is usually performed only univariately. When several study characteristics are available that may account for treatment effect, standard meta‐regression has difficulties in identifying interactions between them. To overcome this problem, meta‐CART has been proposed: an approach that applies classification and regression trees (CART) to identify interactions, and then subgroup meta‐analysis to test the significance of moderator effects. The previous version of meta‐CART has its shortcomings: when applying CART, the sample sizes of studies are not taken into account, and the effect sizes are dichotomized around the median value. Therefore, this article proposes new meta‐CART extensions, weighting study effect sizes by their accuracy, and using a regression tree to avoid dichotomization. In addition, new pruning rules are proposed. The performance of all versions of meta‐CART was evaluated via a Monte Carlo simulation study. The simulation results revealed that meta‐regression trees with random‐effects weights and a 0.5‐standard‐error pruning rule perform best. The required sample size for meta‐CART to achieve satisfactory performance depends on the number of study characteristics, the magnitude of the interactions, and the residual heterogeneity.
MicroRNA‐155‐5p promotes hepatocellular carcinoma progression by suppressing PTEN through the PI3K/Akt pathway
Authors: Fu Xiao , Wen Hongqing , Jing Li , Yang Yujuan , Wang Wenjuan , Liang Xuan , Nan Kejun , Yao Yu , Tian Tao
Published: January 2017

MicroRNA‐155‐5p (miR‐155‐5p) has been reported to play an oncogenic role in different human malignancies; however, its role in hepatocellular carcinoma (HCC) progression is not clearly understood. In this study, we used real‐time PCR in 20 rats with chemically‐induced HCC, 28 human HCC tissues, and the matched paracarcinoma tissues, and HCC cell lines to determine the expression patterns of miR‐155‐5p and PTEN mRNA. Algorithm‐based and experimental strategies, such as dual luciferase gene reporter assays, real‐time PCR and western blots were used to identify PTEN as a candidate miR‐155‐5p target. Gain‐ and loss‐of‐function experiments and administration of a PI3K/Akt pathway inhibitor (wortmannin) were used to identify the effects of miR‐155‐5p and PTEN in MTT assays, flow cytometric analysis, wound healing assays and transwell assays. The results showed that miR‐155‐5p was highly overexpressed; however, PTEN was underexpressed in the HCC rat models, human HCC tissues and cell lines. In addition, miR‐155‐5p upregulation and PTEN downregulation were significantly associated with TNM stage (P < 0.05). Through in vitro experiments, we found that miR‐155‐5p promoted proliferation, invasion and migration, but inhibited apoptosis in HCC by directly targeting the 3′‐UTR of PTEN. Western blots showed that miR‐155‐5p inactivated Bax and caspase‐9, but activated Bcl‐2 to inhibit apoptosis, and it activated MMP to promote migration and invasion via the PI3K/Akt pathway. A xenograft tumor model was used to demonstrate that miR‐155‐5p targets PTEN and activates the PI3K/Akt pathway in vivo as well. Our study highlighted the importance of miR‐155‐5p and PTEN associated with aggressive HCC both in vitro and in vivo.
Glymphatic stasis at the site of the lamina cribrosa as a potential mechanism underlying open‐angle glaucoma
Authors: Wostyn Peter , Killer Hanspeter Esriel , De Deyn Peter Paul
Published: January 2017

The underlying pathophysiology of primary open‐angle glaucoma remains unclear, but the lamina cribrosa seems to be the primary site of injury, and raised intraocular pressure is a major risk factor. In recent years, a decreased intracranial pressure, leading to an abnormally high trans‐lamina cribrosa pressure difference, has gained interest as a new risk factor for glaucoma. New research now lends support to the hypothesis that a paravascular transport system is present in the eye analogous to the recently discovered ‘glymphatic system’ in the brain, which is a functional waste clearance pathway that promotes elimination of interstitial solutes, including β‐amyloid, from the brain along paravascular channels. Given that β‐amyloid has been reported to increase by chronic elevation of intraocular pressure in glaucomatous animal models and to cause retinal ganglion cell death, the discovery of a paravascular clearance system in the eye may provide powerful new insights into the pathophysiology of primary open‐angle glaucoma. In this review, we provide a new conceptual framework for understanding the pathogenesis of primary open‐angle glaucoma, present supporting preliminary data from our own post‐mortem study and hypothesize that the disease may result from restriction of normal glymphatic flow at the level of the lamina cribrosa owing to a low intracranial pressure and/or a high trans‐lamina cribrosa pressure gradient. If confirmed, this viewpoint could offer new perspectives for the development of novel diagnostic and therapeutic strategies for this devastating disorder.
The importance of incorporating functional habitats into conservation planning for highly mobile species in dynamic systems
Authors: Webb Matthew H. , Terauds Aleks , Tulloch Ayesha , Bell Phil , Stojanovic Dejan , Heinsohn Robert
Published: January 2017

The distribution of mobile species in dynamic systems can vary greatly over time and space. Estimating their population size and geographic range can be problematic and affect the accuracy of conservation assessments. Scarce data on mobile species and the resources they need can also limit the type of analytical approaches available to derive such estimates. We quantified change in availability and use of key ecological resources required for breeding for a critically endangered nomadic habitat specialist, the Swift Parrot (Lathamus discolor). We compared estimates of occupied habitat derived from dynamic presence‐background (i.e., presence‐only data) climatic models with estimates derived from dynamic occupancy models that included a direct measure of food availability. We then compared estimates that incorporate fine‐resolution spatial data on the availability of key ecological resources (i.e., functional habitats) with more common approaches that focus on broader climatic suitability or vegetation cover (due to the absence of fine‐resolution data). The occupancy models produced significantly (P < 0.001) smaller (up to an order of magnitude) and more spatially discrete estimates of the total occupied area than climate‐based models. The spatial location and extent of the total area occupied with the occupancy models was highly variable between years (131 and 1498 km2). Estimates accounting for the area of functional habitats were significantly smaller (2–58% [SD 16]) than estimates based only on the total area occupied. An increase or decrease in the area of one functional habitat (foraging or nesting) did not necessarily correspond to an increase or decrease in the other. Thus, an increase in the extent of occupied area may not equate to improved habitat quality or function. We argue these patterns are typical for mobile resource specialists but often go unnoticed because of limited data over relevant spatial and temporal scales and lack of spatial data on the availability of key resources. Understanding changes in the relative availability of functional habitats is crucial to informing conservation planning and accurately assessing extinction risk for mobile resource specialists.
Multiple unruptured aortic sinus of Valsalva aneurysms: A rare presentation
Authors: Chigurupati Keerthi , Kumaresan Balaji , Gadhinglajkar Shrinivas , Sreedhar Rupa
Published: January 2017

Aneurysms of sinus of Valsalva, usually a rare presentation, account for 0.1%–3.5% of congenital heart defects. They rarely present unless rupture occurs. There are very few cases of unruptured sinus of Valsalva aneurysms that presented with myocardial ischemia, symptomatic cardiac dysfunction, and conduction abnormalities. We present a case of multiple unruptured sinus of Valsalva aneurysms with particular emphasis on the transesophageal echocardiography.
Mitral annular motion in patients after transcatheter MitraClip and mitral valve surgery
Authors: Toyama Kentaro , Rader Florian , Ayabe Kengo , Kar Saibal , Trento Alfredo , Nishioka Toshihiko , De Robertis Michele A. , Siegel Robert J.
Published: January 2017

Background

Longitudinal motion of the mitral annulus is an index that reflects left ventricular (LV) function. The aim of this study was to evaluate and compare the effects of transcatheter mitral valve (MV) repair and open heart surgery for mitral regurgitation (MR) on mitral annular motion (MAM).

Methods

We retrospectively analyzed in total 115 patients who underwent isolated transcatheter MV repair using MitraClip (n=50) or surgical MV interventions (n=65, 50 repairs and 15 replacements) for MR. MAM was assessed by two‐dimensional B‐mode echocardiography in the four‐ and two‐chamber views. MAM was measured before and within 1 month after the mitral procedure.

Results

Compared with patients undergoing MV surgery, patients undergoing the MitraClip procedure were older and had more comorbidities. MR grade improved significantly in both groups after MV intervention. MAM decreased significantly in the surgery group (12.0±3.1 to 8.1±2.2 mm, P<.01), whereas MAM did not change in the MitraClip group (8.8±2.6 to 8.6±2.5 mm, P=.59). In multivariate analysis, mitral surgery was associated with a decrease in MAM when compared to the MitraClip procedure. Furthermore, LV ejection fraction (EF) decreased to a greater degree in patients undergoing surgery than those undergoing MitraClip placement (MV surgery; −10.1±7.6% vs MitraClip; −3.0±10.5%, P<.01).

Conclusions

MitraClip therapy does not adversely influence MAM and is associated with less postprocedural EF reduction compared to surgical intervention. Our results suggest that patients with reduced LV systolic function may benefit from the MitraClip procedure compared to mitral surgery.
Time to electroencephalography is independently associated with outcome in critically ill neonates and children
Authors: Sánchez Fernández Iván , Sansevere Arnold J. , Guerriero Rejean M. , Buraniqi Ersida , Pearl Phillip L. , Tasker Robert C. , Loddenkemper Tobias
Published: January 2017

Objective

To identify factors associated with in‐hospital mortality in neonates and children undergoing continuous electroencephalography (cEEG) monitoring in the intensive care unit (ICU).

Methods

We performed a retrospective observational study in patients from birth to 21 years of age who underwent clinically indicated cEEG in the ICU from 2011 to 2013. The main outcome measure was in‐hospital mortality.

Results

Six‐hundred and twenty‐five patients (54.2% male) met eligibility criteria, of whom 211 were neonates (55% male, 24.8% premature) and 414 were pediatric patients (53.9% male). Electrographic seizures occurred in 176 patients (28.2%) and status epilepticus (SE) occurred in 20 (11.4%). The time from ICU admission to cEEG initiation was 16.7 (5.1–94.4) h. Eighty‐nine patients (14.2%) (30 [14.2%] neonates, and 59 [14.3%] pediatric patients) died in the hospital. In neonates—after controlling for gender and prematurity—independent factors associated with mortality were prematurity (odds ratio [OR] 2.63. 95% confidence interval [CI] 1.06–6.5, p = 0.037), presence of status epilepticus (SE); OR 8.82, 95% CI 1.74–44.57, p = 0.008), and time from ICU admission to initiation of cEEG (OR 1.002, 95% CI 1.001–1.004 per hour, p = 0.008]. In pediatric patients—after controlling for gender and age—independent factors associated with mortality were the absence of seizures factors associated with mortality were absence of seizures (OR = 4.3, (95% CI: 1.5–12.4), p = 0.007), the presence of SE (OR 7.76, 95% CI 1.47–40.91, p = 0.016), and the time from ICU admission to initiation of cEEG (OR 1.001, 95% CI 1.0002–1.001, per hour, p = 0.005].

Significance

Both presence of electrographic SE and time from ICU admission to cEEG initiation were independent factors associated with mortality in neonates and pediatric patients with cEEG in the ICU.
Identification, distribution, and quantification of biominerals in a deciduous forest
Authors: Krieger C. , Calvaruso C. , Morlot C. , Uroz S. , Salsi L. , Turpault M.‐P.
Published: January 2017

Biomineralization is a common process in most vascular plants, but poorly investigated for trees. Although the presence of calcium oxalate and silica accumulation has been reported for some tree species, the chemical composition, abundance, and quantification of biominerals remain poorly documented. However, biominerals may play important physiological and structural roles in trees, especially in forest ecosystems, which are characterized by nutrient‐poor soils. In this context, our study aimed at investigating the morphology, distribution, and relative abundance of biominerals in the different vegetative compartments (foliage, branch, trunk, and root) of Fagus sylvatica L. and Acer pseudoplatanus L. using a combination of scanning electron microscopy and tomography analyses. Biomineral crystallochemistry was assessed by X‐ray diffraction and energy‐dispersive X‐ray analyses, while calcium, silicon, and oxalic acid were quantified in the compartments and at the forest scale. Our analyses revealed that biominerals occurred as crystals or coating layers mostly in bark and leaves and were identified as opal, whewellite, and complex biominerals. In both tree species, opal was mostly found in the external tissues of trunk, branch, and leaves, but also in the roots of beech. In the stand, opal represents around 170 kg/ha. Whewellite was found to suit to conductive tissues (i.e., axial phloem parenchyma, vascular bundles, vessel element) in all investigated compartments of the two tree species. The shape of whewellite was prismatic and druses in beech, and almost all described shapes were seen in sycamore maple. Notably, the amount of whewellite was strongly correlated with the total calcium in all investigated compartments whatever the tree species is, suggesting a biologic control of whewellite precipitation. The amount of whewellite in the aboveground biomass of Montiers forest was more important than that of opal and was around 1170 kg/ha. Therefore, biominerals contribute in a substantial way to the biogeochemical cycles of silicon and calcium.
Aspartate transaminase–platelet ratio and Fibrosis‐4 indices as effective markers for monitoring esophageal varices in HIV/hepatitis C virus co‐infected patients due to contaminated blood products for hemophilia
Authors: Natsuda Koji , Takatsuki Mitsuhisa , Tanaka Takayuki , Soyama Akihiko , Adachi Tomohiko , Ono Shinichiro , Hara Takanobu , Baimakhanov Zhassulan , Imamura Hajime , Okada Satomi , Hidaka Masaaki , Eguchi Susumu
Published: January 2017

Aim

We examined the feasibility of the aspartate transaminase (AST)–platelet ratio index (APRI) and Fibrosis‐4 (FIB4) score, which are well‐established markers for liver fibrosis, as indicators for monitoring esophageal varices in patients who were co‐infected with HIV and hepatitis C virus (HCV) due to contaminated blood products for hemophilia in Japan.

Methods

Forty‐three HIV/HCV co‐infected patients were enrolled. All were hemophilic men (median age 41 years; range, 29–66 years). We analyzed the correlations between fibrosis indices (APRI, FIB4) and various liver function tests, fibrosis markers, liver stiffness measured by acoustic radiation force impulse elastography, and the findings of gastrointestinal endoscopy.

Results

Both APRI and FIB4 were well correlated with several of the factors related to liver fibrosis and the existence of esophageal varices in the patients. The cut‐off values for detecting esophageal varices estimated as the area under the receiver operating characteristic curve were 0.85 for APRI and 1.85 for FIB4.

Conclusion

In patients co‐infected with HIV/HCV due to contaminated blood products for hemophilia, APRI and FIB4 are effective for monitoring esophageal varices, even among patients who are apparently doing well with good liver function as Child–Pugh grade A.
Colloidal processing: enabling complex shaped ceramics with unique multiscale structures
Authors: Franks George V. , Tallon Carolina , Studart André R. , Sesso Mitchell L. , Leo Silvia
Published: January 2017

Colloidal processing of fine ceramic powders enables the production of complex shaped ceramics with unique micro and macro structures which are not possible to produce via conventional dry processing routes. Because of this enhanced structural control and shaping capabilities, colloidal processing has been exploited to produce ceramic components with ever increasing complexity and functionalities. In this review, we revisit some of the research efforts on this topic to highlight its relevance and growing importance for the advanced manufacturing of functional ceramics. Selected examples of colloidal systems with increasing level of complexity are discussed to showcase the wide range of structures that can be generated through wet processing approaches. The historical development and background knowledge pertaining to colloids and surface interactions is first briefly reviewed. The major colloidal shape forming and additive manufacturing processes that utilize colloidal pastes and inks are then reviewed, highlighting the control of suspension rheology needed in these techniques. Next, methodologies that combine suspended particles with a pore‐forming phase are discussed as a means to produce porous ceramic materials. Further control over the interactions between anisotropic particles and their alignment in suspensions can be gained via externally applied fields (such as magnetic) to produce texturally aligned green bodies. This leads to bioinspired ceramics that can programmably morph into complex shaped objects upon sintering. Hierarchical porous structures with high mechanical efficiency are also shown as an example of the multiscale designs that can be generated through advanced colloidal processing. As drying of ceramic bodies is an inevitable consequence of wet colloidal processing, the current understanding of this critical processing step is reviewed. Finally, the gaps in knowledge in these fields are discussed to provide our perspective on where the field may support advances in ceramics in the future.
Population‐based cross‐sectional study on insulin resistance and insulin‐secretory capacity in Japanese school children
Authors: Nishimura Rimei , Sano Hironari , Onda Yoshiko , Tsujino Daisuke , Ando Kiyotaka , Ebara Futoshi , Matsudaira Toru , Ishikawa Shinichiro , Sakamoto Takuya , Tajima Naoko , Utsunomiya Kazunori
Published: January 2017

Aims/Introduction

Little information is available regarding the status of insulin resistance (IR) and insulin deficiency (ID), as well as their relationship with obesity in children using the homeostasis model assessment (HOMA) in a population‐based setting.

Materials and Methods

The study included a total of 445 ninth‐grade children participating in health check‐up programs implemented in Tsunan Town, Niigata, Japan (boys/girls, 252/193 [participation rates: 98.1/95.5%]). HOMA of insulin resistance ≥2.5 was defined as IR, and HOMA of β‐cell function <40 defined as ID.

Results

The medians (25–75th percentiles) of HOMA of insulin resistance, HOMA of β‐cell function, Disposition Index and body mass index in boys were 1.2 (0.8–1.7), 64 (44–93), 52 (43–64) and 19.2 (18.0–20.7) kg/m2, respectively, vs 1.5 (1.0–2.0), 86 (63–120), 60 (50–74) and 20.4 (18.9–22.0) kg/m2, respectively, in girls. The HOMA of insulin resistance, HOMA of β‐cell function and Disposition Index values were significantly higher in the girls (P = 0.002, P < 0.001 and P < 0.001, respectively). Those with IR accounted for a significantly higher proportion of girls than boys (15.5/8.7%; P = 0.027); those with obesity accounted for 9.9/10.7% (boys/girls); and those with IR and obesity accounted for 2.4/4.7%. Those with ID accounted for a significantly higher proportion of boys than girls (20.6/8.8%; P = 0.001), whereas those with ID and obesity accounted for a very small proportion of either group (0.4/0.5%).

Conclusions

The presence of IR was higher among the girls. In contrast, ID was more frequent among the boys. The infrequent presence of ID among children might support the presence of non‐obese type 2 diabetes adults in Japan.
Bee visitation rates to cultivated sunflowers increase with the amount and accessibility of nectar sugars
Authors: Mallinger R. E. , Prasifka J. R.
Published: January 2017

Pollinators make foraging decisions based on numerous floral traits, including nectar and pollen rewards, and associated visual and olfactory cues. For insect‐pollinated crops, identifying and breeding for attractive floral traits may increase yields. In this study, we examined floral trait variation within cultivated sunflowers and its effects on bee foraging behaviours. Over 2 years, we planted different sunflower inbred lines, including male‐fertile and male‐sterile lines, and measured nectar volume, nectar sugar concentration and composition, and corolla length. During bloom, we recorded visits by both managed honey bees and wild bees. We then examined consistency in relative nectar production by comparing field results to those from a greenhouse experiment. Sunflower inbred lines varied significantly in all floral traits, including the amount and composition of nectar sugars, and in corolla length. Both wild bee and honey bee visits significantly increased with nectar sugar amount and decreased with corolla length, but appeared unaffected by nectar sugar composition. While wild bees made more visits to sunflowers providing pollen (male‐fertile), honey bees preferred plants without pollen (male‐sterile). Differences in nectar quantity among greenhouse‐grown sunflower lines were similar to those measured in the field, and bumble bees preferentially visited lines with more nectar in greenhouse observations. Our results show that sunflowers with greater quantities of nectar sugar and shorter corollas receive greater pollination services from both managed and wild bees. Selecting for these traits could thus increase sunflower crop yields and provide greater floral resources for bees.
Evaluation and Allocation of Greenhouse Gas Reductions in Industrial Symbiosis
Authors: Kim Hyeong‐Woo , Ohnishi Satoshi , Fujii Minoru , Fujita Tsuyoshi , Park Hung‐Suck
Published: January 2017

Industrial symbiosis (IS) exchanges have been recognized to reduce greenhouse gas (GHG) emission, though methods for quantification of GHG emissions in IS exchanges are varied, and no standardized methods are available. This article proposes a practical approach to quantify total and allocated GHG emissions from IS exchanges by integrating the GHG protocol and life cycle assessment. The proposed method expands the system boundaries to include all IS companies, and the functional flow is set to be the sum of the main products. The total impact of a company is allocated to the main product. Three by‐product impact allocation methods of cutoff, avoidance, and 50/50 are proposed, and the total and distributed impacts of the IS systems in an industrial park are theoretically derived. The proposed method was tested to quantify GHG reduction in a real IS exchange developed between Korea Zinc (a zinc smelter) and Hankook Paper (a paper mill company) in the Ulsan Eco‐Industrial Park initiative. The total reduction of GHG emissions in this IS exchange, 60,522 tonnes of carbon dioxide per year, was the same in the GHG protocol, whereas GHG distribution between two companies depended on the allocation method. Given that the reduction of GHG emissions from IS exchanges is the product of the collaboration of giving companies and receiving companies, the 50/50 allocation method is best from an equivalent‐responsibility and benefit‐sharing perspective. However, this study suggests a more practical implementation approach based on a flexible and negotiable method of allocating the total GHG reduction between stakeholders.
Social Life Cycle Assessment of a Concentrated Solar Power Plant in Spain: A Methodological Proposal
Authors: Corona Blanca , Bozhilova‐Kisheva Kossara P. , Olsen Stig I. , San Miguel Guillermo
Published: January 2017

Measuring the sustainability of goods and services in a systematic and objective manner has become an issue of paramount importance. Life cycle sustainability assessment (LCSA) is a holistic methodology whose aim is to integrate into a compatible format the analysis of the three pillars of sustainability, namely, economy, environment, and society. Social life cycle assessment (S‐LCA) is a novel methodology still under development, used to cover the social aspects of sustainability within LCSA. The aim of this article is to provide additional discussion on the practical application of S‐LCA by suggesting a new classification and characterization model that builds upon previous methodological developments. The structure of the social analysis has been adapted to maintain coherence with that of standard LCA. The application of this methodology is demonstrated using a case study—the analysis of power generation in a concentrated solar power plant in Spain. The inventory phase was completed by using the indicators proposed by the United Nations Environment Program/Society for Environmental Toxicology and Chemistry (UNEP/SETAC) Guidelines on S‐LCA. The impact assessment phase was approached by developing a social performance indicator that builds on performance reference points, an activity variable, and a numeric scale with positive and negative values. The social performance indicator obtained (+0.42 over a range of –2 to +2) shows that the deployment of the solar power plant increases the social welfare of Spain, especially in the impact categories of socioeconomic sustainability and fairness of relationships, whose results were 1.38 and 0.29, respectively.
What seals the I‐deal? Exploring the role of employees' behaviours and managers' emotions
Authors: Rofcanin Yasin , Kiefer Tina , Strauss Karoline
Published: January 2017

Idiosyncratic deals (I‐deals) are work arrangements between an employee and a manager, aimed at meeting the employee's specific work‐related needs (Rousseau,,I‐deals: Idiosyncratic deals employees bargain for themselves, M. E. Sharpe, New York, NY). Studies to date have focused on the effects of successful I‐deal negotiations, but have paid little attention to what determines whether negotiated I‐deals are also obtained. We propose that managers play a crucial role in this process, and explore the role of managers' emotions in translating negotiation into obtainment. We suggest that I‐deals are more likely to be obtained when managers feel more positive and less negative about an employee's I‐deal process in the aftermath of the negotiation. We then aim to determine what shapes managers' emotions about the I‐deal process. Given that I‐deals are intended to be beneficial for the entire team (Rousseau,,I‐deals: Idiosyncratic deals employees bargain for themselves, M. E. Sharpe, New York, NY), we expect that managers feel more positive about the I‐deal process of employees who engage in socially connecting behaviours following their I‐deal negotiation. In contrast, managers feel more negative about the I‐deal process of employees who engage in socially disconnecting behaviours. Results from a two‐wave study of employees and their managers supported our hypotheses. Our findings contribute to research on I‐deals by distinguishing between the negotiation and obtainment of I‐deals and by highlighting the role of managers' emotions in translating negotiated I‐deals into obtainment and the importance of employees' socially connecting and disconnecting behaviours following I‐deal negotiations.

Practitioner points

I‐deals are individually negotiated work agreements between an employee and an employer about parts of their jobs or specific tasks. Previous research has predominantly focused on the negotiation of I‐deals.

Yet, negotiated I‐deals may not always materialize. How managers feel about the I‐deal process of employees in the aftermath of the negotiation is a crucial factor in translating successfully negotiated I‐deals into obtained I‐deals.

When managers feel more positive and less negative about the I‐deal process, they are more likely to facilitate the obtainment of employees' deals.

Because I‐deals are supposed to benefit the entire team, managers' emotions about the I‐deal process are influenced by employees' behaviours following the negotiation. Managers are likely to feel more positive about an employee's I‐deal process if he/she displays socially connecting behaviours and more negative when the employee disconnects from others in the aftermath of I‐deal negotiations.