bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lesions of the Parotid Gland and Buccal Artery After Buccal Fat Pad Reduction
Authors: Vieira Giovanni Modesto , Jorge Fabrício David , Franco Eduardo Jacomino , Dias Leandro da Cunha , Guimarães Maria do Carmo Machado , Oliveira Laudimar Alves de 
Published: November 2018

Abstract
The significant increase in esthetic surgery, especially buccal fat pad reduction, has led to a corresponding increase in lesions and postoperatory after-effects from this surgical procedure. The aim of this study is to discuss the immediate and mediate risks of removing the Bichat ball, as well as describing a clinical study in which this surgical procedure resulted in lesions of the parotid gland and buccal artery, which was confirmed via nuclear magnetic resonance. The facial lesions were remedied via exploratory surgery by opening a new orifice of the glandular duct in the buccal cavity followed by drainage and compressive surgical bandages.
Dissipative structures induced by photoisomerization in a dye-doped nematic liquid crystal layer
Authors: Andrade-Silva I. , Bortolozzo U. , Castillo-Pinto C. , Clerc M. G. , González-Cortés G. , Residori S. , Wilson M. 
Published: November 2018

Order–disorder phase transitions driven by temperature or light in soft matter materials exhibit complex dissipative structures. Here, we investigate the spatio-temporal phenomena induced by light in a dye-doped nematic liquid crystal layer. Experimentally, for planar anchoring of the nematic layer and high enough input power, photoisomerization processes induce a nematic–isotropic phase transition mediated by interface propagation between the two phases. In the case of a twisted nematic layer and for intermediate input power, the light induces a spatially modulated phase, which exhibits stripe patterns. The pattern originates as an instability mediated by interface propagation between the modulated and the homogeneous nematic states. Theoretically, the phase transition, emergence of stripe patterns and front dynamics are described on the basis of a proposed model for the dopant concentration coupled with the nematic order parameter. Numerical simulations show quite a fair agreement with the experimental observations.
This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 2)’.
Fluctuations out of equilibrium
Authors: Belyi V. V. 
Published: November 2018

A generalized fluctuation–dissipation theorem involving slowly varying parameters is presented. Application of the Langevin method, the method of moments and of a multiscale technique reveal that not only dissipation but also dispersive contributions determine the spectral functions of fluctuations in arbitrary statistical systems. The non-Joule dispersive contribution is characterized by a novel non-local effect due to the additional phase shift between the force and the response of the system. This phase shift occurs as a result of parametric control to the system. The general formalism is illustrated by concrete examples and applications.
This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 2)’.
Stationary localized structures and the effect of the delayed feedback in the Brusselator model
Authors: Kostet B. , Tlidi M. , Tabbert F. , Frohoff-Hülsmann T. , Gurevich S. V. , Averlant E. , Rojas R. , Sonnino G. , Panajotov K. 
Published: November 2018

The Brusselator reaction–diffusion model is a paradigm for the understanding of dissipative structures in systems out of equilibrium. In the first part of this paper, we investigate the formation of stationary localized structures in the Brusselator model. By using numerical continuation methods in two spatial dimensions, we establish a bifurcation diagram showing the emergence of localized spots. We characterize the transition from a single spot to an extended pattern in the form of squares. In the second part, we incorporate delayed feedback control and show that delayed feedback can induce a spontaneous motion of both localized and periodic dissipative structures. We characterize this motion by estimating the threshold and the velocity of the moving dissipative structures.This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 2)’.
Observation and modelling of vegetation spirals and arcs in isotropic environmental conditions: dissipative structures in arid landscapes
Authors: Tlidi M. , Clerc M. G. , Escaff D. , Couteron P. , Messaoudi M. , Khaffou M. , Makhoute A. 
Published: November 2018

We report for the first time on the formation of spirals like vegetation patterns in isotropic and uniform environmental conditions. The vegetation spirals are not waves and they do not rotate. They belong to the class of dissipative structures found out of equilibrium. Isolated or interacting spirals and arcs observed in South America (Bolivia) and North Africa (Morocco) are interpreted as a result of curvature instability that affects the circular shape of localized patches. The biomass exhibits a dynamical behaviour with arcs that transform into spirals. Interpretation of observations and of the predictions provided by the theory is illustrated by recent measurements of peculiar plant morphology (the alfa plant, orStipa tenacissimaL.) originated from northwestern Africa and the southern part of the Iberian Peninsula.This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 2)’.
Dams have varying impacts on fish communities across latitudes: A quantitative synthesis
Authors: Turgeon Katrine , Turpin Christian , Gregory-Eaves Irene 
Published: November 2018

AbstractDams are recognized to impact aquatic biodiversity and ecosystem functions, but the magnitude of effects vary across studies. By using a meta-analytical approach, we examined the effects of impoundment on fish community across three large biomes. The impacts of dams on richness and diversity differed across biomes, with significant declines in the tropics, lower amplitude but similar directional changes in temperate reservoirs, and no changes in boreal reservoirs. Our analysis also showed that non-native species increased significantly in tropical and temperate reservoirs, but not in boreal reservoirs. In contrast, temporal trajectories in fish assemblage metrics were common across regions, with all biomes showing an increase in mean trophic position and in the proportion of generalist species after impoundment. Such changes in fish assemblages may affect food web stability and merit closer study. Across the literature examined, predominant factors or mechanisms that render fish assemblages susceptible to impacts from dams were: 1) the transformation of the lotic environment into a lentic environment; 2) habitat fragmentation and 3) invasive or non-native species. Collectively our results highlight that an understanding of the regional context and a suite of metrics are needed to make robust predictions about how fish will respond to river impoundments.
Mapping the Computational Similarity of Individual Neurons within Large-scale Ensemble Recordings using the SIMNETS analysis framework
Authors: Hynes Jacqueline B. , Brandman David M. , Zimmermann Jonas B. , Donoghue John P. , Vargas-Irwin Carlos E. 
Published: November 2018

AbstractThe expansion of large-scale neural recording capabilities has provided new opportunities to examine multi-scale cortical network activity at single neuron resolution. At the same time, the growing scale and complexity of these datasets introduce new conceptual and technical challenges beyond what can be addressed using traditional analysis techniques. Here, we present SIMNETS, a mathematically rigorous and efficient unsupervised relational analysis framework designed to generate intuitive, low-dimensional neuron maps that support a multi-scale view of the computational similarity (CS) relations among individual neurons. The critical innovation is the use of a novel measure of computational similarity that is based on comparing the intrinsic structure of latent spaces representing the spiking output of individual neurons. We use three publicly available neural population test datasets from the visual, motor, and hippocampal CA1 brain regions to validate the SIMNETS framework and demonstrate how it can be used to identify putative subnetworks (i.e., clusters of neurons with similar computational properties). Our analysis pipeline includes a novel statistical test designed to evaluate the likelihood of detecting spurious neuron clusters to validate network structure results. The SIMNETS framework can facilitate linking computational geometry representations across scales, from single neurons to subnetworks, within large-scale neural recording data.
New players in the regulatory network of Vibrio parahaemolyticus Type VI secretion system 1
Authors: Ben-Yaakov Rotem , Salomon Dor 
Published: November 2018

SUMMARYType VI secretion systems (T6SSs) are widespread, tightly regulated, protein delivery apparatuses used by Gram-negative bacteria to outcompete their neighbors. The pathogen, Vibrio parahaemolyticus, encodes two T6SSs. These T6SSs are differentially regulated by external conditions. T6SS1, an antibacterial system predominantly found in pathogenic isolates, requires warm marine-like conditions and surface sensing for activation. The regulatory network that governs this activation is not well understood. In this work, we devised a screening methodology that allows us to easily monitor the outcome of bacterial competitions and thus, to identify mutants that are defective in T6SS1-mediated bacterial killing. The methodology, termed Bacterial Competition Fluorescence (BaCoF), relies on detection of a fluorescent signal as an indicator of the survival and growth of a T6SS-sensitive, GFP-expressing prey that has been co-cultured with mutants derived from a T6SS+ attacker of interest. Using BaCoF, we screened a random transposon insertion mutant library and identified genes required for V. parahaemolyticus T6SS1 activation, among them TfoY and Tmk. We used epistasis experiments to determine the relationships between the newly identified components and other regulators that were previously described. Thus, we present here a detailed biological understanding of the T6SS1 regulatory network.
Integrating water, sanitation, handwashing, and nutrition interventions to reduce child soil-transmitted helminth andGiardiainfections: a cluster-randomized controlled trial in rural Kenya
Authors: Pickering Amy J. , Njenga Sammy M. , Steinbaum Lauren , Swarthout Jenna , Lin Audrie , Arnold Benjamin F. , Stewart Christine P. , Dentz Holly N. , Mureithi MaryAnne , Chieng Benard , Wolfe Marlene , Mahoney Ryan , Kihara Jimmy , Byrd Kendra , Rao Gouthami , Meerkerk Theodora , Cheruiyot Priscah , Papaiakovou Marina , Pilotte Nils , Williams Steven A. , Colford John M. , Null Clair 
Published: November 2018

AbstractBackground.Helminth and protozoan infections affect >1 billion children globally. Improved water, sanitation, handwashing, and nutrition could be more sustainable control strategies for parasite infections than mass drug administration (MDA), while providing other quality of life benefits.Methods and Findings.We enrolled geographic clusters of pregnant women into a cluster-randomized controlled trial that tested six interventions: disinfecting drinking water(W), improved sanitation(S), handwashing with soap(H), combined WSH, improved nutrition(N), and combined WSHN. We assessed intervention effects on parasite infections by measuringAscaris lumbricoides,Trichuris trichiura, hookworm, andGiardia duodenalisamong individual children born to enrolled mothers and their older siblings (ClinicalTrials.govNCT01704105). We collected stool specimens from 9077 total children in 622 clusters, including 2346 children in control, 1117 in water, 1160 in sanitation, 1141 in handwashing, 1064 in WSH, 1072 in nutrition, and 1177 in WSHN. In the control group, 23% of children were infected withAscaris lumbricoides, 1% withTrichuris trichuria, 2% with hookworm and 39% withGiardia duodenalis. After two years of intervention exposure,Ascarisinfection prevalence was 18% lower in the water treatment arm (95% confidence interval (CI) 0%, 33%), 22% lower in the WSH arm (CI 4%, 37%), and 22% lower in the WSHN arm (CI 4%, 36%) compared to control. Individual sanitation, handwashing, and nutrition did not significantly reduceAscarisinfection on their own, and integrating nutrition with WSH did not provide additional benefit.Trichurisand hookworm were rarely detected, resulting in imprecise effect estimates. No intervention reducedGiardia. Reanalysis of stool samples by quantitative polymerase chain reaction (qPCR) confirmed the reductions inAscarisinfections measured by microscopy in the WSH and WSHN groups. Lab technicians and data analysts were blinded to treatment assignment, but participants and sample collectors were not blinded. The trial was funded by the Bill & Melinda Gates Foundation and USAID.Conclusions.Our results suggest integration of improved water quality, sanitation, and handwashing could contribute to sustainable control strategies forAscarisinfections, particularly in similar settings with recent or ongoing deworming programs. Water treatment alone was similarly effective to integrated WSH, providing new evidence that drinking water should be given increased attention as a transmission pathway forAscaris.
7-Transmembrane Helical (7TMH) Proteins: Pseudo-Symmetry and Conformational Plasticity
Authors: Youkharibache Philippe , Tran Alexander , Abrol Ravinder 
Published: November 2018

AbstractMembrane proteins sharing 7 transmembrane helices (7-TMH) dominate the polytopic TMH proteome. They cannot be grouped under a monolithic fold or superfold, however, a parallel structural analysis of folds around that magic number of 7-TMH in distinct 6/7/8-TMH protein superfamilies (SWEET, PnuC, TRIC, FocA, Aquaporin, GPCRs, AND MFS), reveals a common homology, not in their structural fold, but in their systematic pseudo-symmetric construction. Our analysis leads to guiding principles of intragenic duplication and pseudo-symmetric assembly of ancestral 3 or 4 Transmembrane Helix (3/4-TMH) protodomains/protofolds. A parallel deconstruction and reconstruction of these domains provides a structural and mechanistic framework for the evolution path of current pseudo-symmetrical transmembrane helical (TMH) proteins. It highlights the conformational plasticity inherent to fold formation itself. The sequence/structure analysis of different 6/7/8-TMH superfamilies provides a unifying theme of their evolutionary process involving the intragenic duplication of protodomains with varying degrees of sequence and fold divergence under conformational and functional constraints.
Leafhopper Viral Pathogens: Ultrastructure of salivary gland infection of Taastrup-like virus inPsammotettix alienusDahlbom; and a novel Rhabdovirus inHomalodisca vitripennis(Germar) Hemiptera: Cicadellidae
Authors: Lundsgaard Thorben , Hunter Wayne B. , Adkins Scott 
Published: November 2018

AbstractViruses that are pathogenic to insect pests can be exploited as biological control agents. Viruses that are pathogenic to beneficial insects and other arthropods, as in honey bees, silk worms, and shrimp, cause millions of dollars of losses to those industries. Current advances in next generation sequencing technologies along with molecular and cellular biology have produced a wealth of information about insect viruses and their potential applications. Leafhoppers cause economic losses as vectors of plant pathogens which significantly reduce the worlds’ food crops. Each year more viruses are discovered primarily through the use of next generation sequencing of the leafhopper hosts. The diversity of viruses from leafhoppers demonstrates a wide range of taxonomic members that includes genomes of DNA or RNA from families like: Reoviridae, Iridoviridae, Dicistroviridae, Iflaviridae, and others yet to be classified. Discussed is a recent viral pathogen isolated from the leafhopperPsammotettix alienus, name Taastrup Virus. Taastrup virus (TV) is a novel virus with a RNA genome, a Filovirus-like morphology, being tentatively placed within theMononegavirales. AdultPsammotettix alienusinfected with TV, showed the highest concentration of virions in salivary glands, consisting of a principal gland (type I-VI-cells) and an accessory gland. Examination of thin sections revealed enveloped particles, about 1300 nm long and 62 nm in diameter, located singly or in paracrystalline arrays in canaliculi of type III- and IV-cells. In gland cells with TV particles in canaliculi, granular masses up to 15 μm in diameter were present in the cytoplasm. These masses are believed to be viroplasms, the sites for viral replication. TV particles were observed at the connection between a canaliculus and the salivary duct system. A TV-like virus with strongly similar morphology was discovered in the ornamental plant,Liriope, near Fort Pierce, Florida, USA. When the virus was inoculated to a leafhopper cell culture, HvWH, made from the glassy-winged sharpshooter,Homalodisca vitripennis(Germar), the cells rapidly degraded with 100% mortality in 48 hours. These two instances are the only reported cases of this newly discovered viral pathogen of leafhoppers.
Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria
Authors: Probst Alexander J. , Elling Felix J. , Castelle Cindy J. , Zhu Qingzeng , Elvert Marcus , Birarda Giovanni , Holman Hoi-Ying , Lane Katherine R. , Ladd Bethany , Ryan M. Cathryn , Woyke Tanja , Hinrichs Kai-Uwe , Banfield Jillian F. 
Published: November 2018

ABSTRACTSediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community.
The landscape of viral associations in human cancers
Authors: Zapatka Marc , Borozan Ivan , Brewer Daniel S. , Iskar Murat , Grundhoff Adam , Alawi Malik , Desai Nikita , Sültmann Holger , Moch Holger ,   PCAWG Pathogens Working Group,   ICGC/TCGA Pan-cancer Analysis of Whole Genomes Network, Cooper Colin S. , Eils Roland , Ferretti Vincent , Lichter Peter 
Published: November 2018

AbstractPotential viral pathogens were systematically investigated in the whole-genome and transcriptome sequencing of 2,656 donors as part of the Pan-Cancer Analysis of Whole Genomes using a consensus approach integrating three independent pathogen detection pipelines. Viruses were detected in 382 genomic and 68 transcriptome data sets. We extensively searched and characterized numerous features of virus-positive cancers integrating various PCAWG datasets. We show the high prevalence of known tumor associated viruses such as EBV, HBV and several HPV types. Our systematic analysis revealed that HPV presence was significantly exclusive with well-known driver mutations in head/neck cancer. A strong association was observed between HPV infection and the APOBEC mutational signatures, suggesting the role of impaired mechanism of antiviral cellular defense as a driving force in the development of cervical, bladder and head neck carcinoma. Viral integration into the host genome was observed for HBV, HPV16, HPV18 and AAV2 and associated with a local increase in copy number variations. The recurrent viral integrations at theTERTpromoter were coupled to high telomerase expression uncovering a further mechanism to activate this tumor driving process. High levels of endogenous retrovirus ERV1 expression is linked to worse survival outcome in kidney cancer.
Orc4 spatiotemporally stabilizes centromeric chromatin
Authors: Sreekumar Lakshmi , Kumari Kiran , Bakshi Asif , Varshney Neha , Thimmappa Bhagya C. , Guin Krishnendu , Narlikar Leelavati , Padinhateeri Ranjith , Siddharthan Rahul , Sanyal Kaustuv 
Published: November 2018

AbstractSpatiotemporal regulation in DNA replication maintains kinetochore stability. The epigenetically regulated centromeres (CENs) in the budding yeastCandida albicanshave unique DNA sequences, replicate early and are clustered throughout the cell cycle. In this study, the genome-wide occupancy of replication initiation protein Orc4 reveals its abundance at all CENs inC. albicans. Orc4 associates with four different DNA motifs, one of which coincides with tRNA genes. Hi-C combined with genome-wide replication timing analyses identify enriched interactions among early or late replicating Orc4-bound regions. A simulated polymer model of chromosomes reveals that early replicating and strongly enriched Orc4-bound sites localize towards the kinetochores. Orc4 is constitutively localized to CENs, and both Orc4 and Mcm2 stabilize CENPA. CENPA chaperone Scm3 localizes at the kinetochore during anaphase, coinciding with the loading time of CENPA. We propose that this spatiotemporal nuclear localization of Orc4, with Mcm2 and Scm3, recruits CENPA and stabilizes centromeric chromatin.