bluuebunny/crossref_metadata_2025_split huggingface dataset:
IVIM parameters have good scan-rescan reproducibility when evidential motion contaminated and poorly fitted image data are removed
Authors: Chevallier Olivier , Zhou Nan , He Jian , Loffroy Romaric , Wang Yi-Xiáng J. 
Published: August 2017

AbstractBackgroundIntravoxel Incoherent Motion (IVIM) diffusion MRI is a promising technique for liver pathology evaluation, but this technique’s scan-rescan reproducibility has been reported to be unsatisfactory.ObjectiveTo understand whether IVIM MRI parameters for liver parenchyma can be good after removal of motion contaminated and/or poorly fitted image data.Material and MethodsEighteen healthy volunteers had liver scanned twice at the same session to assess scan-rescan repeatability, and again in another session after an average interval of 13 days to assess reproducibility. Diffusion weighted image were acquired with a 3T scanner using respiratory-triggered echo-planar sequence and 16b-values (0 to 800 s/mm2). Measurement was performed on the right liver with segmented-unconstrained least square fitting. Image series with evidential anatomical mismatch, apparent artifacts, and poorly fitted signal intensity vs.b-value curve were excluded. A minimum of three slices was deemed necessary for IVIM parameter estimation of a liver.ResultsWith total 54 examinations, 6 scans did not satisfy inclusion criteria, leading to a success rate of 89%; and 14 volunteers were finally included. With each scan a mean of 5.3 slices (range: 3-10 slices) were utilized for analysis. Using thresholdb-value=80s/mm2, the coefficient of variation and within-subject coefficient of variation for repeatability and reproducibility were: 2.86% and 4.24% for Dslow, 3.81% and 4.24%, for PF, 18.16% and 24.88% for Dfast; and those for reproducibility were 2.48% and 3.24% for Dslow; 4.91% and 5.38% for PF; 21.18% and 30.89% for Dfast.ConclusionIVIM parameter scan-rescan reproducibility can be potentially good.
Genomic and structural features of the Yellow Fever virus from the 2016-2017 Brazilian outbreak
Authors: Gómez Mariela Martínez , de Abreu Filipe Vieira Santos , dos Santos Alexandre Araujo Cunha , de Mello Iasmim Silva , Santos Marta Pereira , Ribeiro Ieda Pereira , Ferreira-de-Brito Anielly , de Miranda Rafaella Moraes , de Castro Marcia Gonçalves , Ribeiro Mario Sergio , Laterrière Roberto da Costa , Aguiar Shirlei Ferreira , Meira Guilherme Louzada Silva , Antunes Deborah , Torres Pedro Henrique Monteiro , Vicente Ana Carolina Paulo , Guimarães Ana Carolina Ramos , Caffarena Ernesto Raul , Bello Gonzalo , Lourenço-de-Oliveira Ricardo , Bonaldo Myrna Cristina 
Published: August 2017

ABSTRACTBrazil has been suffering a severe sylvatic epidemic of yellow fever virus (YFV) since late 2016. Analysis of full-length YFV genomes from all hosts involved in the Brazilian 2017 outbreak reveals that they belong to sub-lineage 1E within modern-lineage, but display several unique amino acid substitutions in highly conserved positions at NS3 and NS5 viral proteins. Evolutionary analyses indicate that YFV carrying that set of amino acid substitution circulates in the Southern Brazilian region for several months before being detected in December 2016. Structural and selection analyses support that some of these substitutions were under positive selection and could impact enzyme structure and function. Altogether, this evidence demonstrated that the current Brazilian YFV carries unique amino acid signatures in the non-structural proteins and support the hypothesis that those substitutions may be affecting the viral fitness and transmissibility.
Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria
Authors: Thorpe Harry A. , Bayliss Sion C. , Sheppard Samuel K. , Feil Edward J. 
Published: August 2017

AbstractDespite overwhelming evidence that variation in intergenic regions (IGRs) in bacteria impacts on phenotypes, most current approaches for analysing pan-genomes focus exclusively on protein-coding sequences. To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on IGRs. We demonstrate the use of Piggy for pan-genome analyses ofStaphylococcus aureusandEscherichia coliusing large genome datasets. ForS. aureus,we show that highly divergent (“switched”) IGRs are associated with differences in gene expression, and we establish a multi-locus reference database of IGR alleles (igMLST; implemented in BIGSdb). Piggy is available athttps://github.com/harry-thorpe/piggy.
Modeling of Epigenetic Modification-Induced Changes in CRX-dependent Genescis-Regulatory Elements
Authors: Hossain Reafa A. , Dunham Nicholas R. , Harris Megan E. , Hutchinson Taylor L. , Kidd Justin M. , Kohler Lindsay R. , Salamon Gregory J. , Schmidt Alexander L. , Thomas Madison D. , Enke Raymond A. , Berndsen Christopher E. 
Published: August 2017

AbstractPurposeDNA methylation is a well characterized epigenetic repressor of mRNA transcription in many plant and vertebrate systems. However, the mechanism of this repression is not fully understood. The process of synthesizing a strand of RNA from DNA, or transcription, is controlled by proteins that regulate RNA polymerase activity by binding to specific gene regulatory sequences. Cone-rod homeobox (CRX) is a well-characterized mammalian transcription factor that controls photoreceptor cell specific gene expression. While much is known about the functions and DNA binding specificity of CRX, less is known about how DNA methylation modulates CRX binding affinity to genomic cis-regulatory elements.MethodsWe used bisulfite pyrosequencing of human ocular tissues to measure DNA methylation levels of the regulatory regions ofRHO,PDE6B, PAX6, andLINE. To describe the molecular mechanism of repression, we used molecular modeling to illustrate the effect of DNA methylation on humanRHOregulatory sequences.ResultsIn this study, we demonstrate an inverse correlation between DNA methylation in regulatory regions adjacent to the humanRHOandPDE6Bgenes and their subsequent transcription in human ocular tissues. Docking of CRX to our DNA models shows that CRX interacts with the grooves of these sequences, suggesting changes in groove structure could regulate binding. Molecular dynamics simulations of theRHOpromoter and enhancer regions show changes in the flexibility and groove width upon epigenetic modification. Models also demonstrate that changes to the local dynamics of CRX binding sites withinRHOregulatory sequences which may account for the repression of CRX dependent transcription.ConclusionCollectively, these data demonstrate epigenetic regulation of CRX binding sites in human retinal tissue and provide insight into the mechanism of this mode of epigenetic regulation to be tested in future experiments.
Zinc detoxification: a functional genomics and transcriptomics analysis inDrosophila melanogastercultured cells
Authors: Mohr Stephanie E. , Rudd Kirstin , Hu Yanhui , Song Wei Roc , Gilly Quentin , Buckner Michael , Housden Benjamin E. , Kelley Colleen , Zirin Jonathan , Tao Rong , Amador Gabriel , Sierzputowska Katarzyna , Comjean Aram , Perrimon Norbert 
Published: August 2017

ABSTRACTCells require some metals, such as zinc and manganese, but excess levels of these metals can be toxic. As a result, cells have evolved complex mechanisms for maintaining metal homeostasis and surviving metal intoxication. Here, we present the results of a large-scale functional genomic screen inDrosophilacultured cells for modifiers of zinc chloride toxicity, together with transcriptomics data for wildtype or genetically zinc-sensitized cells challenged with mild zinc chloride supplementation. Altogether, we identified 47 genes for which knockdown conferred sensitivity or resistance to toxic zinc or manganese chloride treatment, and more than 1800 putative zinc-responsive genes. Analysis of the ‘omics data points to the relevance of ion transporters, glutathione-related factors, and conserved disease-associated genes in zinc detoxification. Specific genes identified in the zinc screen include orthologs of human disease-associated genes CTNS, PTPRN (also known as IA-2), and ATP13A2 (also known as PARK9). We show that knockdown ofred dog mine (rdog; CG11897), a candidate zinc detoxification gene encoding an ABCC-type transporter family protein related to yeast cadmium factor (YCF1), confers sensitivity to zinc intoxication in cultured cells and thatrdogis transcriptionally up-regulated in response to zinc stress. As there are many links between the biology of zinc and other metals and human health, the ‘omics datasets presented here provide a resource that will allow researchers to explore metal biology in the context of diverse health-relevant processes.
Impact of oil volatility shocks on global emerging market stock returns
Authors: Dutta Probal , Noor Md Hasib , Dutta Anupam 
Published: August 2017

Purpose
The purpose of this paper is to investigate whether the crude oil volatility index (OVX) plays any key role in explaining the trend in emerging market stock returns from a global standpoint.

Design/methodology/approach
At the empirical stage, different forms of the GARCH-jump model have been estimated.

Findings
The findings confirm the effects of OVX on equity returns. In addition, the results document that there exist time-varying jumps in the stock market returns. Besides, the impacts of OVX shocks appear to be symmetric. The analysis further shows that the magnitude of OVX impact is marginally bigger than that of the conventional oil price shocks.

Originality/value
Since various financial assets are traded on the basis of oil and equity markets, investors, for instance, could use the findings of this study for taking proper investment decisions and gaining better portfolio diversification benefits. Additionally, policymakers could utilize the results to develop effective measures and strategies in order to minimize the oil price risk.
Comparative process-based life-cycle assessment of bioconcrete and conventional concrete
Authors: Soleimani Milad , Shahandashti Mohsen 
Published: August 2017

Purpose
Bioconcrete is widely believed to be environmentally beneficial over conventional concrete. However, the process of bioconcrete production involves several steps, such as waste recovery and treatment, that potentially present significant environmental impacts. Existing life-cycle assessments of bioconcrete are limited in the inventory and impact analysis; therefore, they do not consider all the steps involved in concrete production and the corresponding impacts. The purpose of this study is to extensively study the cradle-to-gate environmental impacts of all the production stages of two most common bioconcrete types (i.e. sludge-based bioconcrete and cement kiln dust-rice husk ash (CKD-RHA) bioconcrete) as opposed to conventional concrete.

Design/methodology/approach
A cradle-to-gate life-cycle assessment process model is implemented to systematically analyze and quantify the resources consumed and the environmental impacts caused by the production of bioconcrete as opposed to the production of conventional concrete. The impacts analyzed in this assessment include global warming potential, ozone depletion potential, eutrophication, acidification, ecotoxicity, smog, fossil fuel use, human toxicity, particulate air and water consumption.

Findings
The results indicated that sludge-based bioconcrete had higher levels of global warming potential, eutrophication, acidification, ecotoxicity, fossil fuel use, human toxicity and particulate air than both conventional concrete and CKD-RHA bioconcrete.

Originality/value
The contribution of this study to the state of knowledge is that it sheds light on the hidden impacts of bioconcrete. The contribution to the state of practice is that the results of this study inform the bioconcrete production designers about the production processes with the highest impact.
Adverse Childhood Experiences and Criminal Extremity: New Evidence for Sexual Homicide
Authors: DeLisi Matt , Beauregard Eric 
Published: August 2017

AbstractAdverse childhood experiences are associated with a wide range of behavioral, health, and psychiatric deficits and have recently been used to study the development of serious offending careers. Unfortunately, this research paradigm has largely ignored forensic populations. This study utilized the adverse childhood experiences framework to examine the associations between exposure to violence, victimization, and total adverse childhood experiences on sexual homicide using a sample of 616 incarcerated adult male sexual offenders from Canada 85 of whom committed sexual homicide. Epidemiological tables of odds revealed that a gradient of adverse childhood experiences was associated with sexual homicide, but that the most significant risks were for offenders who had the most extensive abuse histories. In adjusted models, exposure to violence, victimization, and total adverse childhood experiences increased the odds of sexual homicide by 334%, 249%, and 546%, respectively. These effects intensified in models adjusted for childhood enuresis, cruelty to animals, parental abandonment, deviant sexual behaviors, poor self‐image, and sexual problems to 559%, 326%, and 849%, respectively. The adverse childhood experiences framework is a systematic way to organize the criminogenic developmental sequela in sexual homicide.
The Physical Effects of Contact and Close‐Distance Gunfire on Sweatshirt Fleece
Authors: Kusluski Michael A. 
Published: August 2017

AbstractPowder stippling caused by the impact of propellant particles during close‐distance gunfire has been previously described on skin and solid objects only. Additionally, radial tearing has been described as clear evidence of a contact‐distance shot, requiring no further testing. Patterns of discrete perforating holes (referred to here as “stippling perforations”) and other physical damage on sweatshirt fleece fabrics were prepared. Using the firearm and ammunition in this study, stippling perforations were observed to a maximum muzzle‐to‐target distance of 35 cm (10 inches). In addition, radial tearing and disintegration were present (and often more extensive) at greater than contact distance. The presence of stippling perforations could augment muzzle‐to‐target distance estimates generated using the Griess test, or allow distance estimates when the Griess test is not feasible. Unlike what has been previously reported, testing on the original evidence (or similar substitute) is warranted when physical damage is used to estimate shooting distance.
Sudden Unexpected Deaths Due to Intracranial Meningioma: Presentation of Six Fatal Cases, Review of the Literature, and A Discussion of the Mechanisms of Death
Authors: Gitto Lorenzo , Bolino Giorgio , Cina Stephen J. 
Published: August 2017

AbstractDeaths due to meningiomas are routinely diagnosed in clinical practice because this neoplasm tends to present with the typical progression of neurological deficits. On the other hand, sudden unexpected deaths due to meningiomas are rarely described in the literature. The study presents six fatal cases of previously undiagnosed intracranial meningiomas from the Cook County Medical Examiner's Office from 1998 to 2014. The most common explanation of the mechanism of sudden death due to intracranial neoplasms is a rapid increase in intracranial pressure produced by the mass effect of the neoplasm. Other mechanisms of death include acute intracranial and intratumoral hemorrhage, and benign neoplasms that grow in the vicinity of vital centers altering neural discharge in autonomic pathways leading to cardiac suppression or lethal arrhythmia. Forensic pathologists must keep in mind that sudden unexpected death caused by intracranial meningiomas, although extremely rare, may be encountered in the forensic setting.
Application of 3D Laser Scanner to Forensic Engineering
Authors: Park Chan‐Seong , Jeon Hong‐Pil , Choi Kwang‐Soo , Kim Jin‐Pyo , Park Nam‐Kyu 
Published: August 2017

AbstractIn the case of building collapses and overturned structures, a three‐dimensional (3D) collapse or overturn model is required to reconstruct the accident. As construction sites become increasingly complex and large, 3D laser scanning is sometimes the best tool to accurately document and store the site conditions. This case report presents one case of a structure collapse and one case of an overturned crane reconstructed by a 3D laser scanner. In the case of structural collapse of a prefabricated shoring system, a 3D model reconstructed all the members successfully, a task that is nearly impossible using a scale such as a tape measure. The reconstructed prefabricated shoring system was verified through a structural analysis through comparison with the construction drawings to investigate faults in construction. In the case of the overturned crane, the jib angle and other major dimensions were successfully acquired through 3D laser scanning and used to estimate the working radius. As a result, the propriety of the working radius with the given lifting load was successfully determined.
Bactericidal Efficacy of Hydrogen Peroxide‐Based Disinfectants Against Gram‐Positive and Gram‐Negative Bacteria on Stainless Steel Surfaces
Authors: Ríos‐Castillo Abel G. , González‐Rivas Fabián , Rodríguez‐Jerez José J. 
Published: August 2017

AbstractIn order to develop disinfectant formulations that leverage the effectiveness of hydrogen peroxide (H2O2), this study evaluated the bactericidal efficacy of hydrogen peroxide‐based disinfectants against Gram‐positive and Gram‐negative bacteria on stainless steel surfaces. Low concentration of hydrogen peroxide as 0.5% with a cationic polymer, ethoxylated fatty alcohol, and ethyl alcohol had bactericidal efficacy (reductions ≥ 4 log10 CFU/mL) against Escherichia coli, Staphylococcus aureus, Enterococcus hirae, and Pseudomonas aeruginosa. Hydrogen peroxide‐based disinfectants were more effective against E. hirae and P. aeruginosa than to S. aureus. However, the efficacy of hydrogen peroxide against catalase positive bacteria such as S. aureus was increased when this compound was formulated with low concentrations of benzalkonium chloride or ethyl alcohol, lactic acid, sodium benzoate, cationic polymer, and salicylic acid. This study demonstrates that the use of hydrogen peroxide with other antimicrobial products, in adequate concentrations, had bactericidal efficacy in Gram‐positive and Gram‐negative bacteria on stainless steel surfaces, enabling to reduce the effective concentration of hydrogen peroxide. In the same way, the use of hydrogen peroxide‐based disinfectants could reduce the concentrations of traditional disinfectants as quaternary ammonium compounds and therefore a reduction of their chemical residues in the environment after being used.Practical ApplicationThe study of the bactericidal properties of environmentally nontoxic disinfectants such as hydrogen peroxide, sole or in formulations with other disinfectants against Gram‐positive and Gram‐negative bacteria can enhance the efficacy of various commonly used disinfectant formulations with the hygiene benefits that it entails. Also, the use of hydrogen peroxide formulations can reduce the concentration levels of products that generate environmental residues.
Control of Native Spoilage Yeast on Dealcoholized Red Wine by Preservatives Alone and in Binary Mixtures
Authors: Sánchez‐Rubio Marta , Guerrouj Kamal , Taboada‐Rodríguez Amaury , López‐Gómez Antonio , Marín‐Iniesta Fulgencio 
Published: August 2017

AbstractIn order to preserve a commercial dealcoholized red wine (DRW), a study with 4 preservatives and binary mixtures of them were performed against 2 native spoilage yeasts: Rhodotorula mucilaginosa and Saccharomyces cerevisiae. Minimal inhibitory concentration (MIC) and minimal fungicidal concentration (MFC) for potassium sorbate, sodium benzoate, sodium metabisulfite and dimethyl dicarbonate (DMDC) were evaluated in DRW stored at 25 °C. MICs of potassium sorbate and sodium metabisulfite were 250 and 60 mg/kg, respectively for both target strains. However for sodium benzoate, differences between yeasts were found; R. mucilaginosa was inhibited at 125 mg/kg, while S. cerevisiae at 250 mg/kg. Regarding MFC, differences between strains were only found for sodium metabisulfite obtaining a MFC of 500 mg/kg for R. mucilaginosa and a MFC of 250 mg/kg for S. cerevisiae. Potassium sorbate and sodium benzoate showed the MFC at 1000 mg/kg and DMDC at 200 mg/kg. Regarding the effect of binary mixtures the Fractional Fungicidal Concentration Index (FFCi) methodology showed that binary mixtures of 100 mg/kg DMDC/200 mg/kg potassium sorbate (FFCi = 0.7) and 50 mg/kg DMDC / 400 mg/kg sodium benzoate (FFCi = 0.65) have both synergistic effect against the 2 target strains. These binary mixtures can control the growth of spoilage yeasts in DRW without metabisulfite addition. The results of this work may be important in preserving the health of DRW consumers by eliminating the use of metabisulfite and reducing the risk of growth of R. mucilagosa, recently recognized as an emerging pathogen.
Discussion of “The Consequences of Audit‐Related Earnings Revisions”
Authors: Hillison Sean M. , Peecher Mark E. 
Published: August 2017

AbstractWe organize our discussion of Haislip, Myers, Scholz, and Seidel (2017) (hereafter HMSS) around three areas: managing auditor business risk, a lack of auditor competence as an alternative story to auditors acting independently for their results, and drawing inferences from archival vis‐à‐vis experimental studies. We conclude our discussion by arguing that the investigation by HMSS sets the stage for future research concerning why earnings revisions occur and why auditors and CFOs appear to bear adverse consequences when they do occur.
Development of an instrument for the evaluation of advanced life support performance
Authors: Peltonen L.‐M. , Peltonen V. , Salanterä S. , Tommila M. 
Published: August 2017

BackgroundAssessing advanced life support (ALS) competence requires validated instruments. Existing instruments include aspects of technical skills (TS), non‐technical skills (NTS) or both, but one instrument for detailed assessment that suits all resuscitation situations is lacking. This study aimed to develop an instrument for the evaluation of the overall ALS performance of the whole team.MethodsThis instrument development study had four phases. First, we reviewed literature and resuscitation guidelines to explore items to include in the instrument. Thereafter, we interviewed resuscitation team professionals (n = 66), using the critical incident technique, to determine possible additional aspects associated with the performance of ALS. Second, we developed an instrument based on the findings. Third, we used an expert panel (n = 20) to assess the validity of the developed instrument. Finally, we revised the instrument based on the experts’ comments and tested it with six experts who evaluated 22 video recorded resuscitations.ResultsThe final version of the developed instrument had 69 items divided into adherence to guidelines (28 items), clinical decision‐making (5 items), workload management (12 items), team behaviour (8 items), information management (6 items), patient integrity and consideration of laymen (4 items) and work routines (6 items). The Cronbach's α values were good, and strong correlations between the overall performance and the instrument were observed.ConclusionThe instrument may be useful for detailed assessment of the team's overall performance, but the numerous items make the use demanding. The instrument is still under development, and more research is needed to determine its psychometric properties.