bluuebunny/crossref_metadata_2025 huggingface dataset:
Outcome of TMS-based motor mapping depends on TMS current direction
Authors: Vink Jord JT , Petrov Petar I , Mandija Stefano , Dijkhuizen Rick M , Neggers Sebastiaan FW
Published: July 2018

Navigated transcranial magnetic stimulation (TMS) in combination with electromyography (EMG) recordings can be used to map the brain regions in which TMS evokes motor-evoked potentials (MEPs) in certain muscles. Navigated TMS (nTMS) is used increasingly to identify the functional motor area of different muscles for clinical applications, including neurosurgical planning. However, the accuracy of TMS-based mapping of functional motor areas may depend on the TMS-induced current direction due to anisotropic cortical morphology, complicating association of the functional motor maps with neuroanatomical structures. Furthermore, it is not clear how well nTMS can distinguish nearby muscle representations on the cortical surface. We therefore investigated the functional motor maps obtained with posterior-to-anterior (PA) and lateral-to-medial (LM) TMS-induced currents within a spatially defined area by stimulating targets in a grid of locations over the left primary motor cortex in 8 healthy participants. Results were compared to functional MRI (fMRI) activation maps obtained using a voluntary opposing thumb movement task. We found that TMS applied with PA-induced currents identifies a motor area that is located significantly more anterior (8.7 – 10.4 mm depending on the muscle) with respect to an MEP motor area identified using LM-induced currents for the same muscle. Motor maps obtained with LM-induced currents show more overlap with the motor map identified using fMRI compared to PA-induced currents. In conclusion, the spatial representation of the MEP motor map identified by TMS is dependent on the direction of the induced current. These findings suggest that the application of nTMS using an LM-induced current direction corresponds best with the hand motor area as measured with fMRI.
MetaMaps – Strain-level metagenomic assignment and compositional estimation for long reads
Authors: Dilthey Alexander , Jain Chirag , Koren Sergey , Phillippy Adam M.
Published: July 2018

Metagenomic sequence classification should be fast, accurate and information-rich. Emerging long-read sequencing technologies promise to improve the balance between these factors but most existing methods were designed for short reads. MetaMaps is a new method, specifically developed for long reads, that combines the accuracy of slower alignment-based methods with the scalability of faster k-mer-based methods. Using an approximate mapping algorithm, it is capable of mapping a long-read metagenome to a comprehensive RefSeq database with >12,000 genomes in <30 GB or RAM on a laptop computer. Integrating these mappings with a probabilistic scoring scheme and EM-based estimation of sample composition, MetaMaps achieves >95% accuracy for species-level read assignment and r2 > 0.98 for the estimation of sample composition on both simulated and real data. Uniquely, MetaMaps outputs mapping locations and qualities for all classified reads, enabling functional studies (e.g. gene presence/absence) and the detection of novel species not present in the current database.

Availability and Implementation

MetaMaps is implemented in C++/Perl and freely available from https://github.com/DiltheyLab/MetaMaps (GPL v3).
Evidence for Miocene overwater colonization in CaribbeanCyrtognathaspiders
Authors: Čandek Klemen , Agnarsson Ingi , Binford Greta , Kuntner Matjaž
Published: July 2018

Island systems provide excellent arenas to test evolutionary hypotheses pertaining to gene flow and diversification of dispersal-limited organisms. Here we focus on an orbweaver spider genusCyrtognatha(Tetragnathidae) from the Caribbean, with the aims to reconstruct its evolutionary history, describe its biogeographic history in the archipelago, and to estimate the timing and route of Caribbean colonization. Specifically, we test ifCyrtognathabiogeographic history is consistent with an ancient vicariant scenario (the GAARlandia landbridge hypothesis) or overwater dispersal. We reconstructed a species level phylogeny based on one mitochondrial (CO1) and one nuclear (28S) marker. We then used this topology to constrain a time-calibrated mtDNA phylogeny, for subsequent biogeographical analyses of over 100 originally sampledCyrtognathaindividuals. Our results suggest a monophyletic radiation of CaribbeanCyrtognatha, containing 11 to 14 species that are exclusively single island endemics. Our analyses refute vicariance and instead support an overwater colonization to the Caribbean in mid-Miocene. Having colonized Hispaniola first,Cyrtognathasubsequently dispersed to, and diversified on, the other islands of the Greater, and Lesser Antilles.
Helmsman: fast and efficient generation of input matrices for mutation signature analysis
Authors: Carlson Jedidiah , Li Jun Z , Zöllner Sebastian
Published: July 2018

Motivation

The spectrum of somatic single-nucleotide variants in cancer genomes often reflects the signatures of multiple distinct mutational processes, which can provide clinically actionable insights into cancer etiology. Existing software tools for identifying and evaluating these mutational signatures do not scale to analyze large datasets containing thousands of individuals or millions of variants.

Results

We introduce Helmsman, a program designed to rapidly generate mutation spectra matrices from arbitrarily large datasets. Helmsman is up to 300 times faster than existing methods and can provide more than a 100-fold reduction in memory usage, making mutation signature analysis tractable for any collection of single nucleotide variants, no matter how large.

Availability

Helmsman is freely available for download at https://github.com/carjed/helmsman under the MIT license. Detailed documentation can be found at https://www.jedidiahcarlson.com/docs/helmsman/, and an interactive Jupyter notebook containing a guided tutorial can be accessed at https://mybinder.org/v2/gh/carjed/helmsman/master.

Contact

jedidiah@umich.edu

Supplementary information

Supplementary information for this article is available.
A new lipid force field (FUJI)
Authors: Kamiya Nozomu , Shinoda Keiko , Fujitani Hideaki
Published: July 2018

To explore inhomogeneous and anisotropic systems such as lipid bilayers, the Lennard-Jones particle mesh Ewald (LJ-PME) method was applied without a traditional isotropic dispersion correction. As the popular AMBER and CHARMM lipid force fields were developed using a cutoff scheme, their lipid bilayers unacceptably shrank when using LJ-PME method. A new lipid force field (FUJI) was developed on the basis of the AMBER force field scheme including the Lipid14 van der Waals parameters. Point charges were calculated by the restrained electrostatic potentials of many lipid conformers. The torsion energy profiles were calculated by high level ab initio molecular orbitals (LCCSD(T)/Aug-cc-pVTZ//LMP2/Aug-cc-pVTZ); then, the molecular mechanical dihedral parameters were derived by means of a fast Fourier transform. Incorporating these parameters into a new lipid force field without any fittings to experimental data, desirable lipid characteristics such as the area per lipid and lateral diffusion coefficients were obtained by GROMACS molecular dynamics simulations using the LJ-PME method and hydrogen virtual sites. The stability and structures of large membranes with undulatory fluctuations were studied by a multidrug efflux transporter (AcrABZ-TolC) with inner and outer membranes.
Inferring the nature of missing heritability in human traits
Authors: López-Cortegano Eugenio , Caballero Armando
Published: July 2018

Thousands of genes responsible for many diseases and other common traits in humans have been detected by Genome Wide Association Studies (GWAS) in the last decade. However, candidate causal variants found so far usually explain only a small fraction of the heritability estimated by family data, the rest remaining ‘missing’. The most common explanation for this observation is that the missing heritability corresponds to variants, either rare or common, with very small effect, which pass undetected due to a lack of statistical power. We carried out a meta-analysis using data from the NHGRI-EBI GWAS Catalog in order to explore the distribution of gene effects for a set of 59 complex traits, to investigate the factors related to new gene discovery and to quantify their contributions to heritability. With the data obtained we were able to predict the expected distribution of gene effects for 16 traits and diseases including cancer and immune disorders, the missing number of genes yet to be discovered, and the additive contribution of common variants to heritability. Our results indicate that, for most traits, the additive contribution of hundreds or thousands of genes is able to explain the familiar heritability. However, for some traits, the predicted heritability is lower than the familiar one, so that part of the missing heritability cannot be explained by the contribution of common variants with additive effects, and other phenomena (e.g. dominance or epistasis) should be invoked.

AUTHOR SUMMARY

The heritability of biological traits refers to the fraction of the phenotypic (i.e.visible or diagnosable) variability that is explained by the underlying genetic variability. Despite the efforts made to find the genes responsible for complex traits and diseases, most of the heritability explained by the variants found explains only a small fraction of that measured by population and family studies. The remaining ‘missing’ heritability is usually assumed to be due to the additive effect of undetected variants. Here we carried out a meta-analysis using records from a publicly available database of genome-wide studies on humans. With these data, we were able to investigate and make inferences on the nature of heritability and the factors associated to new gene discovery. Our results indicate that increasing population sample size, as well as its diversity, enhances the discovery of new genes, but these have lower and lower effects, contributing little to heritability. We were also able to predict the distribution of gene effects for many traits and the number of variants needed to fully explain the heritability. For some traits, the additive effects of single variants yet to be discovered cannot explain the heritability, suggesting that other sources of variation are involved.
The taxonomic and functional biogeographies of phytoplankton and zooplankton communities across boreal lakes
Authors: St-Gelais Nicolas F. , Vogt Richard J. , del Giorgio Paul A. , Beisner Beatrix E.
Published: July 2018

Abstract

Strong trophic interactions link primary producers (phytoplankton) and consumers (zooplankton) in lakes. However, the influence of such interactions on the biogeographical distribution of the taxa and functional traits of planktonic organisms in lakes has never been explicitly tested. To better understand the spatial distribution of these two major aquatic groups, we related composition across boreal lakes (104 for zooplankton and 48 for phytoplankton) in relation to a common suite of environmental and spatial factors. We then directly tested the degree of coupling in their taxonomic and functional distributions across the subset of common lakes. Although phytoplankton composition responded mainly to properties related to water quality while zooplankton composition responded more strongly to lake morphometry, we found significant coupling between their spatial distributions at taxonomic and functional levels based on a Procrustes test. This coupling was not significant after removing the effect of environmental drivers (water quality and morphometry) on the spatial distributions of the two groups. This result suggests that top-down and bottom-up effects (e.g. nutrient concentration and predation) drove trophic interactions at the landscape level. We also found a significant effect of dispersal limitation on the distribution of taxa, which could explain why coupling was stronger for taxa than for traits at the scale of this study, with a turnover of species observed between regions, but no trait turnover. Our results indicate that landscape pelagic food web responses to anthropogenic changes in ecosystem parameters should be driven by a combination of top-down and bottom-factors for taxonomic composition, but with a relative resilience in functional trait composition of lake communities.
Evaluating the diversity of maternal age effects upon neonatal survival across animal species
Authors: Ivimey-Cook Edward , Moorad Jacob
Published: July 2018

Maternal effect senescence is the detrimental effect of increased maternal age on offspring performance. Despite much recent interest given to describing this phenomenon, its origins and distribution across the tree-of-life are poorly understood. We find that age affects neonatal survival in 83 of 90 studies across 51 species, but we observed a puzzling difference between groups of animal species. Amongst wild bird populations, the average effect of age was only −0.7% per standardized unit of increasing age, but maternal effects clearly senesced in laboratory invertebrates (−67.1%) and wild mammals (−57.8%). Comparisons amongst demographic predictions derived from evolutionary theory and conventional demographic models suggest that natural selection has shaped maternal effect senescence in the natural world. These results emphasize both the general importance of maternal age effects and the potential for evolutionary genetics to provide a valuable framework for understanding the diversity of this manifestation of ageing in animal species.
Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis
Authors: Manning Cerys S , Biga Veronica , Boyd James , Kursawe Jochen , Ymisson Bodvar , Spiller David G , Sanderson Christopher M , Galla Tobias , Rattray Magnus , Papalopulu Nancy
Published: July 2018

During embryogenesis cells make fate decisions within complex tissue environments. The levels and dynamics of transcription factor expression regulate these decisions. Here we use single cell live imaging of an endogenous HES5 reporter and absolute protein quantification to gain a dynamic view of neurogenesis in the embryonic mammalian spinal cord. We report that dividing neural progenitors show both aperiodic and periodic HES5 protein fluctuations. Mathematical modelling suggests that in progenitor cells the HES5 oscillator operates close to its bifurcation boundary where stochastic conversions between dynamics are possible. HES5 expression becomes more frequently periodic as cells transition to differentiation which, coupled with an overall decline in HES5 expression, creates a transient period of oscillations with higher fold expression change. This increases the decoding capacity of HES5 oscillations and correlates with interneuron versus motor neuron cell fate. Thus, HES5 undergoes complex changes in gene expression dynamics as cells differentiate.
Y-profile evidence: close paternal relatives and mixtures
Authors: Andersen Mikkel M , Balding David J
Published: July 2018

We recently introduced a new approach to the evaluation of weight of evidence (WoE) for Y-chromosome profiles. Rather than attempting to calculate match probabilities, which is particularly problematic for modern Y-profiles with high mutation rates, we proposed using simulation to describe the distribution of the number of males in the population with a matching Y-profile, both the unconditional distribution and conditional on a database frequency of the profile. Here we further validate the new approach by showing that our results are robust to assumptions about the allelic ladder and the founder haplotypes, and we extend the approach in two important directions. Firstly, forensic databases are not the only source of background data relevant to the evaluation of Y-profile evidence: in many cases the Y-profiles of one or more relatives of the accused are also available. To date it has been unclear how to use this additional information, but in our simulation-based approach its effect is readily incorporated. We describe this approach and illustrate how the WoE that a man was the source of an observed Y-profile changes when the Y-profiles of some of his male-line relatives are also available. Secondly, we extend our new approach to mixtures of Y-profiles from two or more males. Surprisingly, our simulation-based approach reveals that observing a 2-male mixture that includes an alleged contributor’s profile is almost as strong evidence as observing a matching single-contributor evidence sample, and even 3-male and 4-male mixtures are only slightly weaker.
Human Cervical Keratinocyte-Derived Monolayer and Organoid Cultures for Disease Modelling and Drug Screening
Authors: Villa Peter L. , Jackson Robert , Eade Statton , Escott Nicholas , Zehbe Ingeborg
Published: July 2018

The successful isolation and propagation of patient-derived keratinocytes from cervical lesions constitute a more appropriate model of cervical disease than traditional cervical cancer-derived cell lines such as SiHa and CaSki. Our aim was to streamline the growth of patient-obtained, cervical keratinocytes into a reproducible process. We performed an observational case series study with 60 women referred to colposcopy for a diagnostic biopsy. Main outcome measures were how many samples could be passaged at least once, and where enough cells could be established, to precisely define their proliferation profile over time. Altering cell culture conditions over those reported by other groups markedly improved outcomes. We were also successful in making freeze backs which could be resuscitated for additional experiments. For best results, biopsy-intrinsic factors such as size and tissue digestion appear to be major variables. This seems to be the first systematic report with a well characterized and defined sample size, detailed protocol, carefully assessed cell yield and performance, and to successfully grow multi-layered, organoid cultures from cervical keratinocytes. This research is particularly impactful for constituting a sample repository-on-demand for appropriate disease modelling and drug screening under the umbrella of personalized health.
An alternative membrane topology permits lipid droplet localization of peroxisomal fatty acyl-CoA reductase 1
Authors: Exner Tarik , Romero-Brey Inés , Yifrach Eden , Rivera-Monroy Jhon , Schrul Bianca , Zouboulis Christos C. , Stremmel Wolfgang , Honsho Masanori , Bartenschlager Ralf , Zalckvar Einat , Poppelreuther Margarete , Füllekrug Joachim
Published: July 2018

Fatty acyl-CoA reductase 1 (Far1) is an ubiquitously expressed peroxisomal membrane protein generating fatty alcohols required for the biosynthesis of ether lipids.

Lipid droplet localization of human Far1 was observed by fluorescence microscopy under conditions of increased triglyceride synthesis in tissue culture cells. This unexpected finding was supported further by correlative light electron microscopy and subcellular fractionation. Selective permeabilization and N-glycosylation tagging suggest that Far1 is able to assume two different membrane topologies, differing in the orientation of the short hydrophilic C-terminus towards the lumen or the cytosol, respectively. Two closely spaced hydrophobic domains are contained within the C-terminal region. When analyzed separately, the second domain was sufficient for the localization of a fluorescent reporter to lipid droplets. Targeting of Far1 to lipid droplets was not impaired in either pex19 or TRC40/ASNA1 CRISPR/Cas9 knockout cells.

In conclusion, our data suggest that Far1 is a novel member of the rather exclusive group of dual topology membrane proteins. At the same time, Far1 shows lipid metabolism-dependent differential subcellular localizations to peroxisomes and lipid droplets.
Pkd2l1 is required for mechanoception in cerebrospinal fluid-contacting neurons and maintenance of spine curvature
Authors: Sternberg Jenna R. , Prendergast Andrew E. , Brosse Lucie , Cantaut-Belarif Yasmine , Thouvenin Olivier , Orts-Del’Immagine Adeline , Castillo Laura , Djenoune Lydia , Kurisu Shusaku , McDearmid Jonathan R. , Bardet Pierre-Luc , Boccara Claude , Okamoto Hitoshi , Delmas Patrick , Wyart Claire
Published: July 2018

Flow of cerebrospinal fluid (CSF) may contribute to spine morphogenesis, as mutations affecting both cilia motility and CSF flow lead to scoliosis1. However, the mechanisms underlying detection of the CSF flow in the central canal of the spinal cord remain elusive. Here we used full-field optical coherence tomography (FF-OCT) and bead tracking to demonstrate that CSF flows bidirectionally along the antero-posterior axis in the central canal of zebrafish embryos. In the zebrafish mutantcfap298tm304, previously known askurly, reduction of cilia motility slows transport down the length of central canal. To investigate downstream mechanisms that could transduce CSF flow, we performed calcium imaging in sensory neurons contacting the CSF (CSF-cNs) and found that disruption in cilia motility impaired the activity of CSF-cNs. CSF-cNs across species express the transient receptor potential channel PKD2L1, also known as TRPP3, which contributes to CSF-cN chemosensory properties. Using calcium imaging and whole-cell patch clamp recordings, we found that the loss of the Pkd2l1 channel inpkd2l1mutant embryos also abolished CSF-cN activity. Whole-cell recordings further demonstrated that opening of a single channel is sufficient to trigger action potentials in wild type CSF-cNs. Recording from isolated cellsin vitro,we showed that CSF-cNs are mechanosensory cells that respond to pressure in a Pkd2l1-dependent manner. Interestingly, adultpkd2l1mutant zebrafish develop an exaggerated spine curvature, reminiscent of kyphosis in humans. Our study indicates that CSF-cNs are mechanosensory cells whose spontaneous activity reflects CSF flowin vivo. Furthermore, Pkd2l1 in CSF-cNs contributes to the maintenance of the natural curvature of the spine.
Coordinative Metabolism of Glutamine Carbon and Nitrogen in proliferating Cancer Cells Under Hypoxia
Authors: Wang Yuanyuan , Bai Changsen , Ruan Yuxia , Liu Miao , Chu Qiaoyun , Qiu Li , Yang Chuanzhen , Li Binghui
Published: July 2018

Under hypoxia, most of glucose is converted to secretory lactate, which leads to the lack of carbon source from glucose and thus the overuse of glutamine-carbon. However, under such a condition how glutamine nitrogen is disposed to avoid releasing potentially toxic ammonia remains to be determined. Here we identify a metabolic flux of glutamine to secretory dihydroorotate under hypoxia. We found that glutamine nitrogen is indispensable to nucleotide biosynthesis, but enriched in dihyroorotate and orotate rather than processing to its downstream uridine monophosphate under hypoxia. Dihyroorotate, not orotate, is then secreted out of cells. The specific metabolic pathway occurs in vivo and is required for tumor growth. Such a metabolic pathway renders glutamine mainly to acetyl coenzyme A for lipogenesis, with the rest carbon and nitrogen being safely removed. Our results reveal how glutamine carbon and nitrogen are coordinatively metabolized under hypoxia, and provide a comprehensive understanding on glutamine metabolism.

Significance

Tumor cells often addict to glutamine, and particularly utilize its carbon for lipogenesis under hypoxia. We reveal that tumor cells package the excessive glutamine-nitrogen into secretory dihydroorotate, instead of toxic ammonia. This specifically reprogrammed pathway supports in vivo tumor growth, and could offer diagnostic markers and therapeutic targets for cancers.
A GYS2/p53 negative feedback loop restricts tumor growth in HBV-related hepatocellular carcinoma
Authors: Chen Shi-Lu , Zhang Chris Zhiyi , Liu Li-Li , Lu Shi-Xun , Pan Ying-Hua , Wang Chun-Hua , He Yang-Fan , Lin Cen-Shan , Yang Xia , Xie Dan , Yun Jing-Ping
Published: July 2018

Hepatocarcinogenesis is attributed to the reprogramming of cellular metabolism as consequence of the alteration in metabolite-related gene regulation. Identifying the mechanism of aberrant metabolism is of great potential to provide novel targets for the treatment of hepatocellular carcinoma (HCC). Here, we demonstrated that glycogen synthase 2 (GYS2) restricted tumor growth in HBV-related HCC via a negative feedback loop with p53. Expression of GYS2 was significantly downregulated in HCC and correlated with decreased glycogen content and unfavorable patient outcomes. GYS2 overexpression suppressed, whereas GYS2 knockdown facilitated cell proliferation in vitro and tumor growth in vivo via modulating p53 expression. GYS2 competitively bound to MDM2 to prevent p53 from MDM2-mediated ubiquitination and degradation. Furthermore, GYS2 enhanced the p300-induced acetylation of p53 at K373/382, which in turn inhibited the transcription of GYS2 in the support of HBx/HDAC1 complex. In summary, our findings suggest that GYS2 serves as a prognostic factor and functions as a tumor suppressor in HCC. The newly identified HBx/GYS2/p53 axis is responsible for the deregulation of glycogen metabolism and represents a promising therapeutic target for the clinical management of HCC.

Synopsis

This study elucidate the role of GYS2 in glycogen metabolism and the progression of HCC. The newly identified HBx/GYS2/p53 axis is responsible for the deregulation of glycogen metabolism and represents a promising therapeutic target for the clinical management of HCC.

Decrease of GYS2 was significantly correlated with decreased glycogen content and unfavorable patient outcomes in a large cohort containing 768 patients with HCC.

GYS2 overexpression suppressed, whereas GYS2 knockdown facilitated cell proliferation in vitro and tumor growth in vivo via modulating p53 signaling pathway.

GYS2 competitively bound to MDM2 to prevent p53 from MDM2-mediated ubiquitination and degradation.

GYS2 enhanced the p300-induced acetylation of p53 at Lys373/382, which in turn inhibited the transcription of GYS2 in the support of HBx/HDAC1 complex.
Double role of metalloporphyrins in catalytic bioinspired supramolecular metal–organic frameworks (SMOFs)
Authors: Fidalgo-Marijuan Arkaitz , Amayuelas Eder , Barandika Gotzone , Larrea Edurne S. , Bazán Begoña , Urtiaga Miren Karmele , Iglesias Marta , Arriortua María Isabel
Published: July 2018

Heterogeneous catalysts are of great interest in many industrial processes for environmental reasons and, during recent years, a great effort has been devoted to obtain metal–organic frameworks (MOFs) with improved catalytic behaviour. Few supramolecular metal–organic frameworks (SMOFs) are stable under ambient conditions and those with anchored catalysts exhibit favourable properties. However, this paper presents an innovative approach that consists of using metal nodes as both structural synthons and catalysts. Regarding the latter, metalloporphyrins are suitable candidates to play both roles simultaneously. In fact, there are a number of papers that report coordination compounds based on metalloporphyrins exhibiting these features. Thus, the aim of this bioinspired work was to obtain stable SMOFs (at room temperature) based on metalloporphyrins and explore their catalytic activity. This work reports the environmentally friendly microwave-assisted synthesis and characterization of the compound [H(bipy)]2[(MnTPPS)(H2O)2]·2bipy·14H2O (TPPS = meso-tetraphenylporphine-4,4′,4′′,4′′′-tetrasulfonic acid and bipy = 4,4′-bipyridine). This compound is the first example of an MnTPPS-based SMOF, as far as we are aware, and has been structurally and thermally characterized through single-crystal X-ray diffraction, IR spectroscopy, thermogravimetry and transmission electron microscopy. Additionally, this work explores not only the catalytic activity of this compound but also of the compounds μ-O-[FeTCPP]2·16DMF and [CoTPPS0.5(bipy)(H2O)2]·6H2O. The structural features of these supramolecular materials, with accessible networks and high thermal stability, are responsible for their excellent behaviour as heterogeneous catalysts for different oxidation, condensation (aldol and Knoevenagel) and one-pot cascade reactions.
Crystal structure of N-allyl-4-methylbenzenesulfonamide
Authors: Patel Zeel S. , Stevens Amanda C. , Bookout Erin C. , Staples Richard J. , Biros Shannon M. , Ngassa Felix N.
Published: July 2018

The title compound, C10H13NO2S, was synthesized by a nucleophilic substitution reaction between allyl amine and p-toluenesulfonyl chloride. The sulfonate S—O bond lengths are 1.4282 (17) and 1.4353 (17) Å, and the C—N—S—C torsion angle involving the sulfonamide moiety is −61.0 (2)°. In the crystal, centrosymmetric dimers of the title compound are present via intermolecular N—H...O hydrogen bonds between sulfonamide groups. These dimers are linked into ribbons along the c-axis direction through offset π–π interactions.
cis-Bromido(n-butylamine-κN)bis(ethene-1,2-diamine-κ2
N,N′)cobalt(III) dibromide
Authors: Manjunathan M. , Manimaran S. , Anbalagan K. , Sambathkumar K. , Govindan E.
Published: July 2018

In the title compound, [CoBr(C2H8N2)2(C4H11N)]Br2, the cobalt(III) ion has a distorted octahedral coordination environment and is surrounded by four N atoms in the equatorial plane made up of three N atoms from the two ethylenediamine ligands and the remaining N from the n-butyl substituent, with the other N atom from the ethylenediamine ligand and the Br atom occupying the axial positions. In the crystal, the complex cation and the two counter-anions are linked via N—H...Br and C—H...Br hydrogen bonds, forming a three-dimensional network. The crystal studied was refined as a two-component inversion twin.
A Study on the Asymmetry of the Human Left and Right Pubic Symphyseal Surfaces Using High‐Definition Data Capture and Computational Shape Methods
Authors: Stoyanova Detelina K. , Algee‐Hewitt Bridget F. B. , Kim Jieun , Slice Dennis E.
Published: July 2018

The pubic symphysis is among the most commonly used bilateral age indicators. Because of potential differences between right and left sides, it is necessary to investigate within‐individual asymmetry, which can inflate age estimation error. This study uses 3D laser scans of paired pubic symphyses for 88 documented White males. Scan data are analyzed by numerical shape algorithms, proposed as an alternative to traditional visual assessment techniques. Results are used to quantify the within‐individual asymmetry, evaluating if one side produces a better age‐estimate. Relationships between the asymmetry and advanced age, weight, and stature are examined. This analysis indicates that the computational, shape‐based techniques are robust to asymmetry (>80% of paired differences are within 10 years and >90% are within 15 years). For notably more asymmetric cases, differences in estimates are not associated with life history factors. Based on this study, either side can be used for age‐at‐death estimation by the computational methods.
The Different Physical and Chemical Composition of Grape Juice and Marc Influence Saccharomyces cerevisiae Strains Distribution During Fermentation
Authors: Bovo Barbara , Nadai Chiara , Lemos Junior Wilson Josè Fernandes , Carlot Milena , Giacomini Alessio , Corich Viviana
Published: July 2018

During white‐grape winemaking, grape marc is separated from juice immediately after crushing. Both mark and juice are obtained from the same grapes, but they differ strongly for their physical and chemical properties. Marc is mainly composed of solid residues. Its pH is usually higher than that of the juice and Saccharomyces cerevisiae strains are largely present. Therefore, it can be considered as a potential alternative environment for the selection of industrial yeasts. In order to evaluate the effect of different pH and physical state of the two matrices on grapes yeast population composition, the isolation of S. cerevisiae, from both grape juice and marc during simultaneous fermentations, was performed. After yeast identification and genotyping, strains present at high frequencies were tested in fermentation at different pH values. Biofilm production was also tested to evaluate strain ability to develop on a solid matrix. Genotype analysis showed that high‐frequency strains were always more abundant in one of the two environments, suggesting the existence of a selective effect. Generally, fermentations at different pH revealed that the best fermentation performance of each strain, in terms of CO2 production, was in the pH range of its original environment. Only one strain, mostly present in grape marc, produced a high biofilm level. Therefore, biofilm production does not seem to favor strain adaptation to grape marc condition.

Practical Application

These results demonstrate that grape juice and marc represent two different environments able to influence yeast strains distribution. The pH level can be included among the selection factors acting on yeast strains distribution. Grape marc can be considered a yeasts reservoir and its fermentation can be used for the development and isolation of new strains, genetically and physiologically different from those present in the grape juice.
First urinary tract infections in children: the role of the risk factors proposed by the Italian recommendations
Authors: Alberici I , La Manna A , Pennesi M , Starc M , Scozzola F , Nicolini G , Toffolo A , Marra G , Chimenz R , Sica F , Maringhini S , Monasta L , Montini G
Published: July 2018

Aim

In 2009, the Italian society for paediatric nephrology suggested the need for cystography, following a first febrile urinary tract infection (UTI), only in children at high risk for dilating vesicoureteral reflux or in the event of a second infection. The aim of this study was to evaluate the adequacy of the risk factors proposed by the Italian guidelines.

Methods

Children aged 2–36 months, managed by 10 Italian hospitals between 2009 and 2013, with a first febrile UTI were retrospectively evaluated.

Results

Four hundred and fourteen children were included: 51% female, mean age eight months. Escherichia coli was responsible of 84% UTIs. 269 children (65%) presented at least one risk factor, thus were further investigated: 44% had a reflux. The presence of a pathogen other than E. coli significantly predicted high‐grade reflux, both in the univariate (Odd Ratio 2.52, 95% Confidence Interval 1.32–4.81, p < 0.005) and multivariate analysis (OR 2.74, 95% CI: 1.39–5.41, p: 0.003). 26/145 children (18%) with no risk factors experienced a second UTI, which prompted the execution of cystography, showing a dilating reflux in 11.

Conclusion

Among the risk factors proposed by the Italian guidelines, only the presence of a pathogen other than E. coli significantly predicted reflux. Cystography can be postponed in children with no risk factors.
Progressive Multi‐Jittered Sample Sequences
Authors: Christensen Per , Kensler Andrew , Kilpatrick Charlie
Published: July 2018

We introduce three new families of stochastic algorithms to generate progressive 2D sample point sequences. This opens a general framework that researchers and practitioners may find useful when developing future sample sequences. Our best sequences have the same low sampling error as the best known sequence (a particular randomization of the Sobol’ (0,2) sequence). The sample points are generated using a simple, diagonally alternating strategy that progressively fills in holes in increasingly fine stratifications. The sequences are progressive (hierarchical): any prefix is well distributed, making them suitable for incremental rendering and adaptive sampling. The first sample family is only jittered in 2D; we call it progressive jittered. It is nearly identical to existing sample sequences. The second family is multi‐jittered: the samples are stratified in both 1D and 2D; we call it progressive multi‐jittered. The third family is stratified in all elementary intervals in base 2, hence we call it progressive multi‐jittered (0,2). We compare sampling error and convergence of our sequences with uniform random, best candidates, randomized quasi‐random sequences (Halton and Sobol'), Ahmed's ART sequences, and Perrier's LDBN sequences. We test the sequences on function integration and in two settings that are typical for computer graphics: pixel sampling and area light sampling. Within this new framework we present variations that generate visually pleasing samples with blue noise spectra, and well‐stratified interleaved multi‐class samples; we also suggest possible future variations.
Deep Adaptive Sampling for Low Sample Count Rendering
Authors: Kuznetsov Alexandr , Kalantari Nima Khademi , Ramamoorthi Ravi
Published: July 2018

Recently, deep learning approaches have proven successful at removing noise from Monte Carlo (MC) rendered images at extremely low sampling rates, e.g., 1–4 samples per pixel (spp). While these methods provide dramatic speedups, they operate on uniformly sampled MC rendered images. However, the full promise of low sample counts requires both adaptive sampling and reconstruction/denoising. Unfortunately, the traditional adaptive sampling techniques fail to handle the cases with low sampling rates, since there is insufficient information to reliably calculate their required features, such as variance and contrast. In this paper, we address this issue by proposing a deep learning approach for joint adaptive sampling and reconstruction of MC rendered images with extremely low sample counts. Our system consists of two convolutional neural networks (CNN), responsible for estimating the sampling map and denoising, separated by a renderer. Specifically, we first render a scene with one spp and then use the first CNN to estimate a sampling map, which is used to distribute three additional samples per pixel on average adaptively. We then filter the resulting render with the second CNN to produce the final denoised image. We train both networks by minimizing the error between the denoised and ground truth images on a set of training scenes. To use backpropagation for training both networks, we propose an approach to effectively compute the gradient of the renderer. We demonstrate that our approach produces better results compared to other sampling techniques. On average, our 4 spp renders are comparable to 6 spp from uniform sampling with deep learning‐based denoising. Therefore, 50% more uniformly distributed samples are required to achieve equal quality without adaptive sampling.
A Composite BRDF Model for Hazy Gloss
Authors: Barla P. , Pacanowski R. , Vangorp P.
Published: July 2018

We introduce a bidirectional reflectance distribution function (BRDF) model for the rendering of materials that exhibit hazy reflections, whereby the specular reflections appear to be flanked by a surrounding halo. The focus of this work is on artistic control and ease of implementation for real‐time and off‐line rendering. We propose relying on a composite material based on a pair of arbitrary BRDF models; however, instead of controlling their physical parameters, we expose perceptual parameters inspired by visual experiments [VBF17]. Our main contribution then consists in a mapping from perceptual to physical parameters that ensures the resulting composite BRDF is valid in terms of reciprocity, positivity and energy conservation. The immediate benefit of our approach is to provide direct artistic control over both the intensity and extent of the haze effect, which is not only necessary for editing purposes, but also essential to vary haziness spatially over an object surface. Our solution is also simple to implement as it requires no new importance sampling strategy and relies on existing BRDF models. Such a simplicity is key to approximating the method for the editing of hazy gloss in real‐time and for compositing.
Thin Structures in Image Based Rendering
Authors: Thonat Theo , Djelouah Abdelaziz , Durand Fredo , Drettakis George
Published: July 2018

We propose a novel method to handle thin structures in Image‐Based Rendering (IBR), and specifically structures supported by simple geometric shapes such as planes, cylinders, etc. These structures, e.g. railings, fences, oven grills etc, are present in many man‐made environments and are extremely challenging for multi‐view 3D reconstruction, representing a major limitation of existing IBR methods. Our key insight is to exploit multi‐view information. After a handful of user clicks to specify the supporting geometry, we compute multi‐view and multi‐layer alpha mattes to extract the thin structures. We use two multi‐view terms in a graph‐cut segmentation, the first based on multi‐view foreground color prediction and the second ensuring multiview consistency of labels. Occlusion of the background can challenge reprojection error calculation and we use multiview median images and variance, with multiple layers of thin structures. Our end‐to‐end solution uses the multi‐layer segmentation to create per‐view mattes and the median colors and variance to create a clean background. We introduce a new multi‐pass IBR algorithm based on depth‐peeling to allow free‐viewpoint navigation of multi‐layer semi‐transparent thin structures. Our results show significant improvement in rendering quality for thin structures compared to previous image‐based rendering solutions.
Evaluation of volumetric wear of abutments on the retention loss of ball attachment systems in implant‐retained overdentures: An in vitro study
Authors: Yabul Ali , Dayan Cagatay , Geckili Onur , Bilhan Hakan , Tuncer Necat
Published: July 2018

Background

There is a lack of studies evaluating the wear of the male components of the ball attachment systems of implant‐retained overdentures.

Purpose

The purpose of this study was to compare the volumetric wear patterns four commercially used ball abutments.

Materials and Methods

Forty‐eight identical polyethylene and acrylic blocks were fabricated and four groups consisting of 12 polyethylene blocks with two implants and 12 acrylic blocks, which were used as overdentures, were generated (two groups with plastic females, one group with gold and one group with titanium females). Every specimen underwent 5000 insertion and removal cycles (~4.5 years) and retention forces were measured. For the evaluation of volumetric wear, all the ball abutments were scanned before and after the 5000 cycles using a three‐dimensional scanner and the data were analyzed using the software supplied by the manufacturer.

Results

Statistically significant retention force differences were observed between the groups at each cycle (P < .05). Among the four groups, retention force was lowest in the group with titanium females (5.59 ± 2.27) and highest in the group with gold females (43.0 ± 6.3) at the end of 5000 cycles. Statistically significant dimensional changes in the male components were observed between the groups (P < .05). Volumetric losses were 11%‐13% in Group I and II, 1% in Group III, and 25% in Group IV. Group III showed significantly lower volumetric wear whereas Group IV showed significantly higher volumetric wear than all the other groups (P < .001). No significance was detected between Group I and II (P > .05).

Conclusion

Within the limitations, it can be concluded that although clinical studies are needed to ensure the findings of the present study, due to severe retention loss and volumetric abutment wear, ball attachments with titanium female components should be used with caution.
Antibiotic prophylaxis in clean head and neck surgery: A prospective randomised controlled trial
Authors: Shkedy Yotam , Stern Sagit , Nachalon Yuval , Levi Dana , Menasherov Inga , Reifen Ella , Shpitzer Thomas
Published: July 2018

Objective

Antibiotic prophylaxis is not indicated for clean head and neck surgery. However, its role in revision cases is not known. The objective was to prospectively test whether antibiotics are useful in this patient group.

Design

This was a prospective, double‐blind, randomised, placebo‐controlled study.

Setting

A single‐centre study in a tertiary care centre.

Participants

The patients were selected from a referred sample of adult patients (>18 years old) who were planned to undergo revision clean head and neck surgery and who had no preoperative indication for prophylactic antibiotics (eg previous radiation therapy, tracheostomy, active infection, immunosuppression). A total of 59 patients were approached for the study. After exclusion, 53 were available for final analysis.

Intervention

The intervention group received a single‐dose cefazolin, while the control group received placebo.

Main outcomes

The primary end‐point was the combined rate of surgical wound infection, bacteremia and sepsis. The secondary end‐points were length of hospital stay and drug‐induced adverse reactions.

Results

A total of 53 patients were randomised to 2 groups: 31 to antibiotics group and 22 to control group. There was no difference between the groups in baseline characteristics. The primary end‐point occurred in both groups at the same rate. There was no difference in secondary end‐point rate, as well.

Conclusion

Prophylactic antibiotics appear to have no benefit in revision, clean head and neck surgery. Further studies in larger populations and other settings are needed.

(ClinicalTrials.gov number NCT01980082, clinicaltrials.gov/ct2/show/NCT01980082).
The treatment of anal fistula: secondACPGBIPosition Statement – 2018
Authors: Williams G. , Williams A. , Tozer P. , Phillips R. , Ahmad A. , Jayne D. , Maxwell‐Armstrong C.
Published: July 2018

It is over 10 years since the firstACPGBIPosition Statement on the management of anal fistula was published in 2007. This second edition is the result of scrutiny of the literature published during this time; it updates the original Position Statement and reviews the published evidence surrounding treatments for anal fistula that have been developed since the original publication.
The neural development of pragmatic inference‐making in natural discourse
Authors: Schwartz Flora , Epinat‐Duclos Justine , Noveck Ira , Prado Jérôme
Published: July 2018

Older interlocutors are more likely than younger ones to make pragmatic inferences, that is, inferences that go beyond the linguistically encoded meaning of a sentence. Here we ask whether pragmatic development is associated with increased activity in brain structures associated with inference‐making or in those associated with Theory of Mind. We employed a reading task that presents vignettes in one of two versions, one of which is expected to prompt more pragmatic processing. Both versions present a major premise containing three possibilities (e.g., Xavier is considering Thursday, Friday or Saturday for inviting his girlfriend out). In theFully‐Deductive(control) condition, the major premise is followed by two disjunction‐elimination premises through two separate lines (one indicating that Saturday is not convenient and another saying that Thursday is not convenient); this is followed by a valid conclusion (e.g., “I'll reserve Friday”). In theImplicated‐Premisecondition, the first disjunction‐elimination premise is followed by a second similar one that eliminates the same disjunction (e.g., both lines explain why Saturday is not convenient). In this condition, readers may pragmatically enrich the conclusion (i.e., “I'll reserve Friday” pragmatically implicates thatXavier is also eliminating Thursday from consideration). Reading times in Experiment 1 showed that processing the speaker's conclusion in theImplicated‐Premisecondition becomes increasingly more effort‐demanding as readers reach adolescence. Experiment 2 showed that this developmental pattern is related to age‐related increases infMRIactivity in fronto‐parietal regions typically involved in inference‐making processes. We found no evidence indicating age effects related to Theory of Mind areas.