bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of organic matter source and quality on living benthic foraminiferal distribution on a river‐dominated continental margin: A study of the Portuguese margin
Authors: Dessandier Pierre‐Antoine , Bonnin Jérôme , Kim Jung‐Hyun , Bichon Sabrina , Deflandre Bruno , Grémare Antoine , Sinninghe Damsté Jaap S.
Published: June 2016

Living (rose Bengal stained) benthic foraminifera were investigated on surface sediments from 23 stations from the river‐dominated northwestern Portuguese margin. Samples were collected in March 2011, following the period of the maximum rainfall over the Iberian Peninsula, between 20 and 2000 m water depth along five cross‐margin transects. Four of them are located off the Douro, Mondego, Tagus, and Sado Rivers and one off the Estremadura coast. The major objectives of this study are (1) to assess the impact of organic matter of various origin and quality on the benthic foraminifera and (2) to investigate the spatial differences of faunal distribution from coastal waters to the deep sea under river influences. To do this, sedimentological and biogeochemical characteristics of the sediments were identified by measuring grain size, oxygen penetration depth, total organic carbon (TOC) content, stable carbon isotopic composition of TOC (δ13CTOC) and concentration of pigments and amino acids. Based on the principal component and cluster analyses of the environmental data, three major geographical groups are identified: (1) deep stations, (2) coastal and middle slope stations, and (3) shelf stations under river influence. At the deepest stations, species are associated with high organic matter (OM) quantity but low OM quality, where Uvigerina mediterranea, Hoeglundina elegans, and agglutinated species such as Reophax scorpiurus or Bigenerina nodosaria are dominant. All stations off the Sado River, which is the most affected area by the anthropogenic influence, are also characterized by high quantity but low quality of OM with the minimum faunal density and diversity within the study area. Middle slope stations are associated with low OM content and coarse sediments (Q50) with the predominance of N. scaphum. Shallow shelf stations close to the Douro and Tagus River mouths show a dominance of taxa (e.g., Ammonia beccarii, Bulimina aculeata, Eggerelloides scaber, Nonion scaphum, Cancris auriculus, and Quinqueloculina seminula) adapted to environments characterized by high OM quality (high fresh chlorophyll (Chl a/Phaeo)) and available amino acids (enzymatically hydrolyzable amino acid (EHAA)/total enzymatically hydrolyzable amino acid (THAA)). The Biotic and Environmental linking analysis suggests that the benthic foraminiferal distribution is mostly controlled by three environmental parameters, i.e., TOC (quantity), EHAA/THAA (quality), and δ13CTOC (source). Hence, this study clearly highlights that the quantitative and qualitative inputs of OM and its source are the most important factors controlling the living benthic foraminiferal distribution with clear influences between the different rivers. This study also suggests a good tolerance of several species for river discharges where the OM quality is high.
A trajectory‐based classification of ERA‐Interim ice clouds in the region of the North Atlantic storm track
Authors: Wernli Heini , Boettcher Maxi , Joos Hanna , Miltenberger Annette K. , Spichtinger Peter
Published: June 2016

A two‐type classification of ice clouds (cirrus) is introduced, based on the liquid and ice water content, LWC and IWC, along air parcel backward trajectories from the clouds. In situ cirrus has no LWC along the trajectory segment containing IWC; it forms via nucleation from the gas phase. In contrast, liquid‐origin cirrus has both LWC and IWC along their backward trajectories; it forms via lifting from the lower troposphere and freezing of mixed‐phase clouds. This classification is applied to 12 years of ERA‐Interim ice clouds in the North Atlantic region. Between 400 and 500 hPa more than 50% are liquid‐origin cirrus, whereas this frequency decreases strongly with altitude (<10% at 200 hPa). The relative frequencies of the two categories vary only weakly with season. More than 50% of in situ cirrus occur on top of liquid‐origin cirrus, indicating that they often form in response to the strong lifting accompanying the formation of liquid‐origin cirrus.
Polyamide‐Based Fibers Containing Microwave‐Exfoliated Graphite Nanoplatelets
Authors: Nasillo Giorgio , Arrigo Rossella , Dintcheva Nadka Tzankova , Morici Elisabetta , Chillura Martino Delia , Caponetti Eugenio
Published: June 2016

Exfoliated Graphite NanoPlatelets (GNP) have been obtained from Graphite Intercalation Compounds (GIC) subjected to thermal and microwave treatments. Accurate morphological and structural characterization of obtained GNP, performed to compare the degree of exfoliation, show that microwave‐treated GNP, exhibit well‐exfoliated structure, without any reduction in dimensions compared with the native GIC, differently to the thermal‐treated ones. Microwave‐treated GNP have been introduced in polyamide (PA) through melt‐mixing to obtain nanocomposite that has been subjected to elongational flow, with the aim to improve the nanofiller dispersion and induce GNP orientation along the fiber direction. Upon extensional flow, really, GNP are able to further exfoliate and to align along the flow direction, leading to obtain advanced nanocomposite with excellent mechanical performance. Finally, both GNP loading and stretching lead to a significant variation in crystalline PA phase, detected by thermal and nuclear magnetic resonance analysis in the solid state.
Van der Woude and Popliteal Pterygium Syndromes: Broad intrafamilial variability in a three generation family with mutation in IRF6
Authors: Busche Andreas , Hehr Ute , Sieg Peter , Gillessen‐Kaesbach Gabriele
Published: June 2016

Patients with Van der Woude syndrome typically present with cleft lip, cleft lip and palate, or with cleft palate only. In contrast to non‐syndromic cleft lip and/or palate, Van der Woude syndrome typically is characterized by bilateral, paramedian lower‐lip pits. Popliteal pterygium syndrome shares features with Van der Woude syndrome, but, in addition, is characterized by a popliteal pterygium, genital anomalies, cutaneous syndactyly of the fingers and the toes, and a characteristic pyramidal fold of skin overlying the nail of the hallux. In some patients oral synechiae or eyelid synechiae are present. Van der Woude Syndrome and Popliteal pterygium syndrome are autosomal dominantly inherited disorders caused by heterozygous mutations in IRF6. We present a three generation family with tremendous intrafamilial phenotypic variability. The newborn index patient had a diagnosis of Popliteal pterygium syndrome. The mother presented with a classic Van der Woude Syndrome, while the maternal grandfather had Van der Woude Syndrome as well as minor signs of Popliteal pterygium syndrome. In all three affecteds the known pathogenic mutation c.265A>G, p.Lys89Glu in IRF6 was identified. While inter‐ as well as intra‐familial variability has been described in IRF6‐related disorders, the occurrence of a typical Van der Woude Syndrome without any other anomalies as well as a diagnosis of Popliteal pterygium syndrome in the same family is rare. © 2016 Wiley Periodicals, Inc.
Hybrid organosiloxane coatings containing epoxide precursors for protecting mild steel against corrosion in a saline medium
Authors: Suleiman Rami , Estaitie Mohammed , Mizanurahman Mohammad
Published: June 2016

Hybrid organic–inorganic materials made from sol–gel precursors can be used as anticorrosion barriers on metal substrates. The modification of epoxy resins with silicones is an interesting approach toward the synthesis of hybrid materials that combine the advantages offered by epoxy resins with those of silicones. In this study, novel hybrid epoxy‐silicon materials were synthesized using sol–gel chemistry and subsequently functionalized with 4,4′‐methylenebis(phenyl isocyanate), incorporating urethane functionality into the final polymer. The study screened five different epoxide precursors for use in the synthesis of the new hybrid materials and optimizing their anticorrosion properties. Spectral characterization confirms the proposed chemical structures of the newly synthesized polymers. The newly developed polymers were painted on mild steel panels, thermally cured, and their thermal, surface morphological, adhesion, and anticorrosion properties were fully characterized. The new coatings were found to have excellent thermal stability and adherence properties to steel surface. The results of corrosion testing on coated steel panels following long‐term immersion in a 3.5 wt % aqueous NaCl medium revealed that the polymer prepared using the epoxide precursor bisphenol A diglycidyl ether provided the best anticorrosion protection property among the synthesized polymers. This could be attributed to the excellent integrity and crosslink density properties in addition to the lack of microdefects in the surface of this coated sample as confirmed by scanning electron microscopy analyses. The newly prepared hybrid coatings reported in this study are very promising as an alternative to toxic chromate‐based coatings. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43947.
Long‐Term Fiscal Sustainability in Advanced Economies
Authors: Auerbach Alan J
Published: June 2016

With the Great Recession leaving nearly all advanced economies with substantially higher debt–gross domestic product ratios, this paper re‐evaluates the long‐term fiscal sustainability of these economies based on current estimates of their current‐policy fiscal trajectories. Through measuring fiscal imbalance, we find that for many countries, short‐term fiscal measures such as the debt–gross domestic product ratio and current budget deficits as a share of gross domestic product bear little relationship to the sustainability of policy. The longer‐term challenges these countries face are related much more to the future fiscal challenge of growing primary deficits, associated with the cost of providing pensions and health care in the face of growing old‐age dependency ratios. While focusing on managing the short‐term debt burden may help avoid crises like the one being played out in Greece, attention and policy actions must eventually turn to the longer‐term fiscal problem.
Fiscal Sustainability in Japan
Authors: Armstrong Shiro , Okimoto Tatsuyoshi
Published: June 2016

Japanese government debt is at unprecedented levels with a gross debt to gross domestic product ratio of over 230 per cent and a net debt to gross domestic product ratio of 150 per cent. There are three big challenges to fiscal sustainability: the huge amount of government bonds outstanding; continued budget deficits; and the growing age‐related spending. The debt is sustainable as long as the market as a whole believes it is. The path to fiscal consolidation requires increasing the tax rate, reducing spending, broadening the tax base and growing the economy out of trouble. The longer the delay before moving to a more sustainable consolidation path, the larger the risks and closer Japan moves towards a financial crisis. The policy goal is to keep government debt sustainable, not to repay it all. Just as Japan has done since the burst of the asset bubble in the early 1990s, there is every likelihood that the Japanese economy will muddle through.
Making the Transition to a Low‐Carbon Economy: The Key Challenges for China
Authors: Zhang ZhongXiang
Published: June 2016

China has realised that for its own sake and from the international community's perspective, it cannot afford to continue on the conventional path of encouraging economic growth at the expense of the environment. Accordingly, the country has placed ecological goals at the same level of priority as policies on economic, political, cultural and social development. Specifically, meeting the grand goal involves not only capping China's nationwide coal consumption to let it peak before 2020 and carbon emissions peak around 2030, but also putting in place a variety of flagship programs and policies. This article argues that the 2030 carbon emissions peak goal is ambitious but achievable and concludes by arguing why there is reason to be optimistic about China's ‘green push’.
The effect of social media promotion on academic article uptake
Authors: Botting Nicola , Dipper Lucy , Hilari Katerina
Published: June 2016

Important emerging measures of academic impact are article download and citation rates. Yet little is known about the influences on these and ways in which academics might manage this approach to dissemination. Three groups of papers by academics in a center for speech‐language‐science (available through a university repository) were compared. The first group of target papers were blogged, and the blogs were systematically tweeted. The second group of connected control papers were nonblogged papers that we carefully matched for author, topic, and year of publication. The third group were papers by different staff members on a variety of topics—Unrelated Control Papers. The results suggest an effect of social media on download rate, which was limited not just to Target Papers but also generalized to Connected Control Papers. Unrelated Control Papers showed no increase over the same amount of time (main effect of time, F(1,27) = 55.6, p < .001); Significant Group×Time Interaction, F(2,27) = 7.9, p = .002). The effect on citation rates was less clear but followed the same trend. The only predictor of the 2015 citation rate was downloads after blogging (r = 0.450, p = .012). These preliminary results suggest that promotion of academic articles via social media may enhance download and citation rate and that this has implications for impact strategies.
Is collaboration among scientists related to the citation impact of papers because their quality increases with collaboration? An analysis based on data from F1000Prime and normalized citation scores
Authors: Bornmann Lutz
Published: June 2016

In recent years, the relationship of collaboration among scientists and the citation impact of papers have been frequently investigated. Most of the studies show that the two variables are closely related: An increasing collaboration activity (measured in terms of number of authors, number of affiliations, and number of countries) is associated with an increased citation impact. However, it is not clear whether the increased citation impact is based on the higher quality of papers that profit from more than one scientist giving expert input or other (citation‐specific) factors. Thus, the current study addresses this question by using two comprehensive data sets with publications (in the biomedical area) including quality assessments by experts (F1000Prime member scores) and citation data for the publications. The study is based on more than 15,000 papers. Robust regression models are used to investigate the relationship between number of authors, number of affiliations, and number of countries, respectively, and citation impact—controlling for the papers' quality (measured by F1000Prime expert ratings). The results point out that the effect of collaboration activities on impact is largely independent of the papers' quality. The citation advantage is apparently not quality related; citation‐specific factors (e.g., self‐citations) seem to be important here.
Antimicrobial Compounds from Drypetes staudtii
Authors: Grace David , Khan Madiha S. , Friesen Kenneth , Ata Athar
Published: June 2016

Antimicrobial‐directed phytochemical investigation of the MeOH extract of Drypetes staudtii afforded two new compounds, 4,5‐(methylenedioxy)‐o‐coumaroylputrescine (1), 4,5‐(methylenedioxy)‐o‐coumaroyl‐4′‐N‐methylputrescine (2), along with seven known natural products 4α‐hydroxyeremophila‐1,9‐diene‐3,8‐dione (3), drypemolundein B (4), friedelan‐3β‐ol (5), erythrodiol (6), ursolic acid (7), p‐coumaric acid (8), and β‐sitosterol (9). Structures of compounds 1 – 9 were elucidated with the aid of extensive NMR and mass spectral studies. All of the isolates exhibited antibacterial activity against Gram‐positive and Gram‐negative bacteria with minimum inhibitory concentration (MIC) in the range of 8 – 128 μg/ml. Compounds 1 – 2 were also moderately active against Candida albicans with an MIC value of 32 μg/ml.
Random‐effects models for meta‐analytic structural equation modeling: review, issues, and illustrations
Authors: Cheung Mike W.‐L. , Cheung Shu Fai
Published: June 2016

Meta‐analytic structural equation modeling (MASEM) combines the techniques of meta‐analysis and structural equation modeling for the purpose of synthesizing correlation or covariance matrices and fitting structural equation models on the pooled correlation or covariance matrix. Both fixed‐effects and random‐effects models can be defined in MASEM. Random‐effects models are well known in conventional meta‐analysis but are less studied in MASEM. The primary objective of this paper was to address issues related to random‐effects models in MASEM. Specifically, we compared two different random‐effects models in MASEM—correlation‐based MASEM and parameter‐based MASEM—and explored their strengths and limitations. Two examples were used to illustrate the similarities and differences between these models. We offered some practical guidelines for choosing between these two models. Future directions for research on random‐effects models in MASEM were also discussed. Copyright © 2016 John Wiley & Sons, Ltd.
Maximum likelihood estimation in meta‐analytic structural equation modeling
Authors: Oort Frans J. , Jak Suzanne
Published: June 2016

Meta‐analytic structural equation modeling (MASEM) involves fitting models to a common population correlation matrix that is estimated on the basis of correlation coefficients that are reported by a number of independent studies. MASEM typically consist of two stages. The method that has been found to perform best in terms of statistical properties is the two‐stage structural equation modeling, in which maximum likelihood analysis is used to estimate the common correlation matrix in the first stage, and weighted least squares analysis is used to fit structural equation models to the common correlation matrix in the second stage. In the present paper, we propose an alternative method, ML MASEM, that uses ML estimation throughout. In a simulation study, we use both methods and compare chi‐square distributions, bias in parameter estimates, false positive rates, and true positive rates. Both methods appear to yield unbiased parameter estimates and false and true positive rates that are close to the expected values. ML MASEM parameter estimates are found to be significantly less bias than two‐stage structural equation modeling estimates, but the differences are very small. The choice between the two methods may therefore be based on other fundamental or practical arguments. Copyright © 2016 John Wiley & Sons, Ltd.
Analyzing matrices of meta‐analytic correlations: current practices and recommendations
Authors: Sheng Zitong , Kong Wenmo , Cortina Jose M. , Hou Shuofei
Published: June 2016

Researchers have become increasingly interested in conducting analyses on meta‐analytic correlation matrices. Methodologists have provided guidance and recommended practices for the application of this technique. The purpose of this article is to review current practices regarding analyzing meta‐analytic correlation matrices, to identify the gaps between current and best practices, and to offer a comprehensive set of recommendations regarding the planning, collection, analysis, and interpretation of studies that utilize meta‐analytic correlation matrices. Copyright © 2016 John Wiley & Sons, Ltd.
Implications of applying methodological shortcuts to expedite systematic reviews: three case studies using systematic reviews from agri‐food public health
Authors: Pham Mai T. , Waddell Lisa , Rajić Andrijana , Sargeant Jan M. , Papadopoulos Andrew , McEwen Scott A.
Published: June 2016

Background

The rapid review is an approach to synthesizing research evidence when a shorter timeframe is required. The implications of what is lost in terms of rigour, increased bias and accuracy when conducting a rapid review have not yet been elucidated.

Methods

We assessed the potential implications of methodological shortcuts on the outcomes of three completed systematic reviews addressing agri‐food public health topics. For each review, shortcuts were applied individually to assess the impact on the number of relevant studies included and whether omitted studies affected the direction, magnitude or precision of summary estimates from meta‐analyses.

Results

In most instances, the shortcuts resulted in at least one relevant study being omitted from the review. The omission of studies affected 39 of 143 possible meta‐analyses, of which 14 were no longer possible because of insufficient studies (<2). When meta‐analysis was possible, the omission of studies generally resulted in less precise pooled estimates (i.e. wider confidence intervals) that did not differ in direction from the original estimate.

Conclusions

The three case studies demonstrated the risk of missing relevant literature and its impact on summary estimates when methodological shortcuts are applied in rapid reviews. © 2016 The Authors. Research Synthesis Methods Published by John Wiley & Sons Ltd.
Preparation of poly(glycidylmethacrylate‐divinylbenzene) weak acid cation exchange stationary phases with succinic anhydride, phthalic anhydride, and maleic anhydride for ion chromatography
Authors: Liu Junwei , Wang Yong , Wu Shuchao , Zhang Peimin , Zhu Yan
Published: June 2016

In this work, poly(glycidylmethacrylate‐divinylbenzene) microspheres were prepared and applied for the preparation of weak acid cation exchange stationary phases. Succinic anhydride, phthalic anhydride, and maleic anhydride were selected as carboxylation reagents to prepare three weak acid cation exchangers by direct chemical derivatization reaction without solvent or catalyst. The diameters and dispersity of the microspheres were characterized by scanning electron microscopy; the amount of accessible epoxy groups and mechanical stability were also measured. The weak acid cation exchangers were characterized by Fourier transform infrared spectroscopy; the content of carboxyl groups was measured by traditional acid base titration method. The chromatographic properties were characterized and compared by separating alkali, alkaline earth metal ions and ammonium and polar amines. The separation properties enhanced in the order of succinic anhydride, phthalic anhydride, and maleic anhydride modified poly(glycidylmethacrylate‐divinylbenzene) cation exchangers.
Synthesis and functional features of wood fiber‐polypropylene materials: Based on wood fibers with assembling nano‐coating via adopting simple in situ‐hydrothermal mechanism
Authors: Ye Xianzhu , Wang Hua , Wu Zhaofeng , Zhou Haifeng , Tian Xingyou
Published: June 2016

Wood plastic composites (WPCs) are experiencing a dynamic boom. High performance WPCs with excellent mechanical properties, thermal properties, water resistance and ultraviolet absorption features of wood fiber–polypropylene‐composites had been fabricated based on wood fibers assembled with nano‐SiO2 via hydrothermal method in this research. Coating morphology and assembling ratio were influenced notably by the pH values, Tetra‐Ethyl‐Ortho‐Silicate (TEOS) concentrations and coupling effect of Triethoxysilane (KH550). Tensile strength, flexural strength and thermal transition temperature (Tg) of polypropylene were enhanced due to strong interfacial adhesion and sufficient load transfer. In addition, the initial decomposition temperature of WPCs moved to high‐temperature area for shielded nano‐network. Besides, for electronic transition and shielding network, it is also noted that ultraviolet absorption and dimensional stability were improved efficiently if adopting coupling nano‐coating. After soaking with 24 h, value of water absorption decreased from 12.28 wt% to 2.20 wt%. POLYM. COMPOS., 39:5–13, 2018. © 2016 Society of Plastics Engineers
Imidazolium‐based poly(ionic liquid)s with poly(ethylene oxide) main chains: Effects of spacer and tail structures on ionic conductivity
Authors: Ikeda Taichi , Moriyama Satoshi , Kim Jedeok
Published: June 2016

Ten types of cationic glycidyl triazole polymers (GTPs) are prepared from combinations of five alkyl‐imidazolium units (methyl‐, ethyl‐, n‐propyl‐, iso‐propyl‐, and n‐butyl‐imidazoliums) and two spacers [di‐ and tri(ethylene glycol)s]. Since these poly(ionic liquid)s are prepared from the same sample of glycidyl azide polymer by postfunctionalization method, they have the same degree of polymerization. Therefore, the structure–property relationship can be discussed without influence of molecular weight difference. The samples are characterized by NMR, differential scanning calorimetry, and thermogravimetric analysis. The ionic conductivity data are obtained by impedance measurements. The GTPs with the tri(ethylene glycol) spacer and ethyl‐ and n‐butyl‐imidazolium units afford the highest anhydrous conductivity of 1.5 × 10−5 S cm−1 at 30 °C. Based on electrode polarization (EP) analysis, we calculate the conducting ion (carrier) concentration and mobility. We discuss the effect of the spacer and N‐alkyl tail structures on the ionic conductivity using the data obtained by EP analysis and X‐ray diffraction. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 2896–2906
Biological control of chestnut blight in Croatia: an interaction between host sweet chestnut, its pathogen Cryphonectria parasitica and the biocontrol agent Cryphonectria hypovirus 1
Authors: Krstin Ljiljana , Katanić Zorana , Ježić Marin , Poljak Igor , Nuskern Lucija , Matković Ivana , Idžojtić Marilena , Ćurković‐Perica Mirna
Published: June 2016

BACKGROUND

Chestnut blight, caused by the fungus Cryphonectria parasitica, is a severe chestnut disease that can be controlled with naturally occurring hypoviruses in many areas of Europe. The aim of this research was to measure the effect of different Cryphonectria hypovirus 1 (CHV1) strains on the growth of the fungal host and select strains that could potentially be used for human‐mediated biocontrol in forests and orchards, and to investigate whether and how chestnut–fungus–virus interactions affect the development and growth of the lesion area on cut stems.

RESULTS

Two Croatian CHV1 strains (CR23 and M56/1) were selected as potential biocontrol agents. The sequencing of CHV1/ORF‐A showed that both of these virus strains belonged to the Italian subtype of CHV1. In vitro transfection of selected virus strains from hypovirulent to genetically diverse virus‐free fungal isolates and subsequent inoculation of all virus/fungus combinations on stems of genetically diverse sweet chestnut trees revealed that Croatian virus strain CR23 had an equally hypovirulent effect on the host as the strong French strain CHV1‐EP713, while M56/1 had a weaker effect. Furthermore, it was shown that in some cases the same hypovirus/fungus combinations induced various degrees of canker development on different chestnut genotypes.

CONCLUSION

Some CHV1 strains belonging to the Italian subtype have similar hypovirulent effects on C. parasitica to those belonging to the French subtype. Furthermore, chestnut susceptibility and recovery could be influenced by the response of chestnut trees to particular hypovirulent C. parasitica isolates, and virus–fungus–chestnut interactions could have significant implications for the success of chestnut blight biocontrol. © 2016 Society of Chemical Industry
Publicación científica de asesores de tesis de pregrado en una escuela de medicina de Cusco, Perú
Authors: Atamari-Anahui Noé , Sucasaca-Rodríguez Cristian , Marroquin-Santa Cruz Jhonatan A.
Published: June 2016

La producción científica es considerada la expresión del conocimiento, producto de la investigación en determinadas áreas, contribuyendo de esta manera al desarrollo de la ciencia, siendo función primordial de las universidades incentivarla y promoverla en sus docentes y estudiantes.
Car Windshield Wiper in the Brain: Case Report
Authors: Liu Zhenpeng , Hou Xianzeng , Fan Xiaoyong , Hu Yuanyuan , Liu Guangcun
Published: June 2016

Background Transorbital intracranial penetrating injury is rare. Damage caused by a huge metallic foreign body is very critical and life-threatening.

Method We report an extremely rare case of transorbital intracranial penetrating metal strip (a car windshield wiper), which has not previously been reported in the literature.

Results Emergency craniotomy was performed; the object was removed successfully, and the patient's life was saved.

Conclusion With the life-threatening penetrating brain injury caused by a huge foreign body, prompt surgical treatment and comprehensive postoperative treatment are important to save patients' lives.
Structure of a low-population binding intermediate in protein-RNA recognition
Authors: Borkar Aditi N. , Bardaro Michael F. , Camilloni Carlo , Aprile Francesco A. , Varani Gabriele , Vendruscolo Michele
Published: June 2016

Significance

All biochemical reactions in living organisms require molecular recognition events. In particular, the interactions between protein and RNA molecules are crucial in the regulation of gene expression. However, the transient nature of the conformations populated during the recognition process has prevented a detailed characterization of the mechanisms by which these interactions take place. To address this problem, we report a high-resolution structure of an intermediate state in protein-RNA recognition. We determined this structure by using NMR measurements as ensemble-averaged structural restraints in metadynamics simulations, and validated it by performing a structure-based design of two mutants with rationally modified binding rates.
Prediction of conserved long-range RNA-RNA interactions in full viral genomes
Authors: Fricke Markus , Marz Manja
Published: June 2016

Motivation: Long-range RNA-RNA interactions (LRIs) play an important role in viral replication, however, only a few of these interactions are known and only for a small number of viral species. Up to now, it has been impossible to screen a full viral genome for LRIs experimentally or in silico. Most known LRIs are cross-reacting structures (pseudoknots) undetectable by most bioinformatical tools.

Results: We present LRIscan, a tool for the LRI prediction in full viral genomes based on a multiple genome alignment. We confirmed 14 out of 16 experimentally known and evolutionary conserved LRIs in genome alignments of HCV, Tombusviruses, Flaviviruses and HIV-1. We provide several promising new interactions, which include compensatory mutations and are highly conserved in all considered viral sequences. Furthermore, we provide reactivity plots highlighting the hot spots of predicted LRIs.

Availability and Implementation: Source code and binaries of LRIscan freely available for download at http://www.rna.uni-jena.de/en/supplements/lriscan/, implemented in Ruby/C ++ and supported on Linux and Windows.

Contact:  manja@uni-jena.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
GenVisR: Genomic Visualizations in R
Authors: Skidmore Zachary L. , Wagner Alex H. , Lesurf Robert , Campbell Katie M. , Kunisaki Jason , Griffith Obi L. , Griffith Malachi
Published: June 2016

Summary: Visualizing and summarizing data from genomic studies continues to be a challenge. Here, we introduce the GenVisR package to addresses this challenge by providing highly customizable, publication-quality graphics focused on cohort level genome analyses. GenVisR provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and Bioconductor.

Availability and Implementation: GenVisR is an R package available via Bioconductor (https://bioconductor.org/packages/GenVisR) under GPLv3. Support is available via GitHub (https://github.com/griffithlab/GenVisR/issues) and the Bioconductor support website.

Contacts:  obigriffith@wustl.edu or mgriffit@wustl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Inferring the perturbation time from biological time course data
Authors: Yang Jing , Penfold Christopher A. , Grant Murray R. , Rattray Magnus
Published: June 2016

Motivation: Time course data are often used to study the changes to a biological process after perturbation. Statistical methods have been developed to determine whether such a perturbation induces changes over time, e.g. comparing a perturbed and unperturbed time course dataset to uncover differences. However, existing methods do not provide a principled statistical approach to identify the specific time when the two time course datasets first begin to diverge after a perturbation; we call this the perturbation time. Estimation of the perturbation time for different variables in a biological process allows us to identify the sequence of events following a perturbation and therefore provides valuable insights into likely causal relationships.

Results: We propose a Bayesian method to infer the perturbation time given time course data from a wild-type and perturbed system. We use a non-parametric approach based on Gaussian Process regression. We derive a probabilistic model of noise-corrupted and replicated time course data coming from the same profile before the perturbation time and diverging after the perturbation time. The likelihood function can be worked out exactly for this model and the posterior distribution of the perturbation time is obtained by a simple histogram approach, without recourse to complex approximate inference algorithms. We validate the method on simulated data and apply it to study the transcriptional change occurring in Arabidopsis following inoculation with Pseudomonas syringae pv. tomato DC3000 versus the disarmed strain DC3000hrpA.

Availability and Implementation: An R package, DEtime, implementing the method is available at https://github.com/ManchesterBioinference/DEtime along with the data and code required to reproduce all the results.

Contact:  Jing.Yang@manchester.ac.uk or Magnus.Rattray@manchester.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
RTFBSDB: an integrated framework for transcription factor binding site analysis
Authors: Wang Zhong , Martins André L. , Danko Charles G.
Published: June 2016

Summary: Transcription factors (TFs) regulate complex programs of gene transcription by binding to short DNA sequence motifs. Here, we introduce rtfbsdb, a unified framework that integrates a database of more than 65 000 TF binding motifs with tools to easily and efficiently scan target genome sequences. Rtfbsdb clusters motifs with similar DNA sequence specificities and integrates RNA-seq or PRO-seq data to restrict analyses to motifs recognized by TFs expressed in the cell type of interest. Our package allows common analyses to be performed rapidly in an integrated environment.

Availability and Implementation:  rtfbsdb available at (https://github.com/Danko-Lab/rtfbs_db).

Contact:  dankoc@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data
Authors: Stokowy Tomasz , Garbulowski Mateusz , Fiskerstrand Torunn , Holdhus Rita , Labun Kornel , Sztromwasser Pawel , Gilissen Christian , Hoischen Alexander , Houge Gunnar , Petersen Kjell , Jonassen Inge , Steen Vidar M.
Published: June 2016

Motivation: The search for causative genetic variants in rare diseases of presumed monogenic inheritance has been boosted by the implementation of whole exome (WES) and whole genome (WGS) sequencing. In many cases, WGS seems to be superior to WES, but the analysis and visualization of the vast amounts of data is demanding.

Results: To aid this challenge, we have developed a new tool—RareVariantVis—for analysis of genome sequence data (including non-coding regions) for both germ line and somatic variants. It visualizes variants along their respective chromosomes, providing information about exact chromosomal position, zygosity and frequency, with point-and-click information regarding dbSNP IDs, gene association and variant inheritance. Rare variants as well as de novo variants can be flagged in different colors. We show the performance of the RareVariantVis tool in the Genome in a Bottle WGS data set.

Availability and implementation:  https://www.bioconductor.org/packages/3.3/bioc/html/RareVariantVis.html

Contact:  tomasz.stokowy@k2.uib.no

Supplementary information:  Supplementary data are available at Bioinformatics online.
Quark deconfinement in the proto-magnetar model of long gamma-ray bursts
Authors: Pili A. G. , Bucciantini N. , Drago A. , Pagliara G. , Del Zanna L.
Published: June 2016

We investigate the possible implications of quark deconfinement on the phenomenology of long gamma-ray bursts focusing, in particular, on the possibility to describe multiple prompt emission phases in the context of the proto-magnetar model. Starting from numerical models of rotating Hadron Stars and Quark Stars in full general relativity we track the electromagnetic spin-down evolution in both the hadronic and quark phase, linking the two families through conservation of baryon number and angular momentum. We give estimates of the time-scales and the energetics involved in the spin-down process deriving, in the relevant spin range, the relation between the initial and the final masses and rotational energies, whenever hadron-quark conversion is possible. We show how the results can be used in relevant astrophysical cases such as the double burst GRB 110709B.
Immunopathogenesis and risk factors for allopurinol severe cutaneous adverse reactions
Authors: Wang Chuang-Wei , Dao Ro-Lan , Chung Wen-Hung
Published: June 2016

Purpose of review

The article reviews the immunopathogenesis and risk factors related to allopurinol-induced severe cutaneous adverse reactions (SCARs).

Recent findings

For years, allopurinol remains one of the leading cause for SCARs worldwide. The pathogenesis of allopurinol-induced SCARs have been discovered in recent years. HLA-B∗58 : 01 has been found to be strongly associated with allopurinol-SCARs with functional interactions between allopurinol/its metabolite-oxypurinol and the T-cell receptor (TCR). However, the genetic strength of HLA-B∗58 : 01 may vary among different ethnic populations. In addition to HLA-B∗58 : 01, specific T cells with preferential TCR clonotypes, which have no cross-reactivity with new xanthine oxidase inhibitors structurally different from allopurinol, are found to play a crucial role for allopurinol-induced SCARs. Furthermore, other nongenetic factors such as renal impairment are also found to be an important factor resulting in allopurinol-induced SCARs of greater severity and poorer prognosis.

There are multiple risk factors for allopurinol-induced SCARs, including genetic and nongenetic factors. Activation of specific T cells with preferential TCR and its functional interaction of HLA-B∗58 : 01 molecule and allopurinol/oxypurinol are involved in the immune mechanism of allopurinol-induced SCAR. Patients with allopurinol-induced SCARs with renal impairment have significantly higher risk of mortality. A structurally different new generation xanthine oxidase inhibitor can provide a safer alternative for patients intolerant to allopurinol.
A meta-analysis of flexible intramedullary nailing versus external fixation for pediatric femoral shaft fractures
Authors: Guo Yong Cheng , Feng Guo Ming , Xing Guang Wei , Yin Jin Neng , Xia Bing , Dong Yan Zhao , Niu Xue Qiang , He Qianyi , Hu Pengfei
Published: June 2016

To compare the difference in efficacy following flexible intramedullary nailing (FIN) and external fixation (EF) for pediatric femoral shaft fractures. A systematic search was performed on PubMed, Embase, Medline, and Cochrane library for relevant studies. We included controlled trials comparing complications between FIN and EF for pediatric femoral shaft fractures published before 25 November 2014. Modified Jadad scores were utilized to assess the methodological quality of the studies included. The meta-analysis was carried out using Stata 12.0 software. Six studies involving 237 patients were included. On comparison of EF, a low incidence of overall complications [relative risk (RR)=0.30, 95% confidence interval (CI): 0.19–0.46; P<0.001] and pin-tract infection (RR=0.286, 95% CI: 0.13–0.61; P=0.001), but a high risk of soft tissue irritation (RR=1.86, 95% CI: 1.35–2.56; P<0.001) were found in patients treated with the FIN approach. No significant differences in other complications were found. On the basis of current evidence, the use of FIN leads to fewer complications than EF and may be considered as the first-line approach in the treatment of femoral shaft fractures.
Discovering Healthcare Missions
Authors: Leonard Diane Beth
Published: June 2016

Embarking on a pilgrimage to Lourdes, France, to serve as a nurse, I believed I failed because my experience wasn't clinical. On a second mission trip to Lourdes, learning ways to spiritually connect with clients transformed my definition of nursing care and understanding of what gifts I can offer in service to others.
Ebola
Authors: Kiser Erin
Published: June 2016

Two U.S. nurses relay their experience of deciding to serve and work in Sierra Leone during the 2015 Ebola crisis. The nurses' heartbreaking experiences convey the devastation of Ebola in West Africa and the privilege of answering God's call to serve. Learn about the current status and known outcomes of Ebola Virus Disease (EVD) as of March 2016 for infected patients and the people of West Africa.
Reciprocal Service-Learning Benefits Students, Educators, and the University
Authors: Forehand Jeffery W. , Vardaman Shellye A. , Outlaw Kerri L.
Published: June 2016

Service-learning offers an opportunity to educate nursing students and foster important personal and professional characteristics. A different kind of service-learning project was developed and implemented in a nursing school. Community/public health nursing students and nurse educators taught cardiopulmonary resuscitation (CPR) and epilepsy training to faculty and staff members of another university department in a Good Samaritan Training project. The multiple benefits of the project to nursing students, educators, and the project recipients are discussed.
Salvaging the Infected Breast Tissue Expander: A Standardized Multidisciplinary Approach
Authors: Viola George M. , Selber Jesse C. , Crosby Melissa , Raad Issam I. , Butler Charles E. , Villa Mark T. , Kronowitz Steven J. , Clemens Mark W. , Garvey Patrick , Yang Wei , Baumann Donald P.
Published: June 2016

Background:

Infections of breast tissue expander (TE) are complex, often requiring TE removal and hospitalization, which can delay further adjuvant therapy and add to the overall costs of breast reconstruction. Therefore, to reduce the rate of TE removal, hospitalization, and costs, we created a standardized same-day multidisciplinary outpatient quality improvement protocol for diagnosing and treating patients with early signs of TE infection.

Methods:

We prospectively evaluated 26 consecutive patients who developed a surgical site infection between February 2013 and April 2014. On the same day, patients were seen in the Plastic Surgery and Infectious Diseases clinics, underwent breast ultrasonography with or without periprosthetic fluid aspiration, and were prescribed a standardized empiric oral or intravenous antimicrobial regimen active against biofilm-embedded microorganisms. All patients were managed as per our established treatment algorithm and were followed up for a minimum of 1 year.

Results:

TEs were salvaged in 19 of 26 patients (73%). Compared with TE-salvaged patients, TE-explanted patients had a shorter median time to infection (20 vs 40 days; P = 0.09), a significantly higher median temperature at initial presentation [99.8°F; interquartile range (IQR) = 2.1 vs 98.3°F; IQR = 0.4°F; P = 0.01], and a significantly longer median antimicrobial treatment duration (28 days; IQR = 27 vs 21 days; IQR = 14 days; P = 0.05). The TE salvage rates of patients whose specimen cultures yielded no microbial growth, Staphylococcus species, and Pseudomonas were 92%, 75%, and 0%, respectively. Patients who had developed a deep-seated pocket infection were significantly more likely than those with superficial cellulitis to undergo TE explantation (P = 0.021).

Conclusions:

Our same-day multidisciplinary diagnostic and treatment algorithm not only yielded a TE salvage rate higher than those previously reported but also decreased the rate of hospitalization, decreased overall costs, and identified several clinical scenarios in which TE explantation was likely.
Cardiovascular diseases in mega-countries: the challenges of the nutrition, physical activity and epidemiologic transitions, and the double burden of disease
Authors: Barquera Simon , Pedroza-Tobias Andrea , Medina Catalina
Published: June 2016

Purpose of review

There are today 11 mega-countries with more than 100 million inhabitants. Together these countries represent more than 60% of the world's population. All are facing noncommunicable chronic disease (NCD) epidemic where high cholesterol, obesity, diabetes, and cardiovascular diseases are becoming the main public health concerns. Most of these countries are facing the double burden of malnutrition where undernutrition and obesity coexist, increasing the complexity for policy design and implementation. The purpose of this study is to describe diverse sociodemographic characteristics of these countries and the challenges for prevention and control in the context of the nutrition transition.

Recent findings

Mega-countries are mostly low or middle-income and are facing important epidemiologic, nutrition, and physical activity transitions because of changes in food systems and unhealthy lifestyles. NCDs are responsible of two-thirds of the 57 million global deaths annually. Approximately, 80% of these are in low and middle-income countries. Only developed countries have been able to reduce mortality rates attributable to recognized risk factors for NCDs, in particular high cholesterol and blood pressure.

Mega-countries share common characteristics such as complex bureaucracies, internal ethnic, cultural and socioeconomic heterogeneity, and complexities to implement effective health promotion and education policies across population. Priorities for action must be identified and successful lessons and experiences should be carefully analyzed and replicated.
Diagnostic scoring for familial hypercholesterolaemia in practice
Authors: Haralambos Kate , Ashfield-Watt Pauline , McDowell Ian F.W.
Published: June 2016

Purpose of review

Diagnostic scoring for familial hypercholesterolaemia (FH) can be used either to screen for possible FH or guide the selection of patients for genetic (DNA) testing. We review the published diagnostic criteria and discuss the options for future development.

Recent findings

Scoring systems have been developed internationally based on lipid values and various combinations of clinical signs and cardiovascular history. The predictive value varies according to the test population, be it lipid clinic referrals, general population, or relatives of patients with FH. Also, there is increasing recognition of genetic heterogeneity in FH so that criteria are of differing predictive value depending on the genetic variant of FH.

These clinical scoring systems are increasingly used to guide selection of patients for FH genetic testing but no single approach has yet emerged as the system of choice. Further refinement of these scoring tools using more sophisticated calculators are superseding the more manual approaches. These are well suited to web-based tools or smartphone applications.