bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymptotic Analysis of Frictional Contact Problem for Piezoelectric Shallow Shell
Authors: Mezabia M E , Ghezal A , Chacha D A 
Published: July 2019

Summary
The objective of this work is to study the asymptotic justification of a new two-dimensional model for the equilibrium state of a piezoelectric linear shallow shell in frictional contact with a rigid foundation. More precisely, we consider the Signorini problem with Tresca friction of a piezoelectric linear shallow shell in contact with a rigid foundation. Then, we establish the convergence of the mechanical displacement and the electric potential as the thickness of the shallow shell goes to zero.
A rapid diagnostic multiplex PCR approach for xenomonitoring of human and animal schistosomiasis in a ‘One Health’ context
Authors: Schols Ruben , Carolus Hans , Hammoud Cyril , Mulero Stephen , Mudavanhu Aspire , Huyse Tine 
Published: July 2019

Abstract
Studying the epidemiology of schistosomiasis—the most prevalent gastropod-borne human disease and an economic burden for the livestock industry—relies on adequate monitoring tools. Here we describe a molecular assay for detecting human and animal African schistosome species in their planorbid gastropod host (xenomonitoring) using a two-step approach. First, schistosome infections are detected and discriminated from other trematode infections using a multiplex polymerase chain reaction (PCR) that includes a trematode-specific marker (in 18S rDNA), a Schistosoma genus-specific marker (in internal transcribed spacer 2 [ITS2]) and a general gastropod marker (in 18S rDNA) as an internal control. Upon Schistosoma sp. detection, a second multiplex PCR is performed to discriminate among Schistosoma haematobium, Schistosoma mansoni, Schistosoma mattheei and Schistosoma bovis/Schistosoma curassoni/Schistosoma guineensis using markers of differential lengths in the cytochrome c oxidase subunit 1 (COX1) gene. The specificity of these assays was validated with adult worms, naturally infected gastropods and human urine and stool samples. Sensitivity was tested on experimentally infected snail specimens that were sacrificed 10 and 40 days post-infection in order to mimic a natural prepatent and mature infection, respectively. The assay provides a diagnostic tool to support the xenomonitoring of planorbid gastropods for trematode infections in a One Health context, with a focus on the transmission monitoring of schistosomiasis.
A discussion on technologies for improving the operational speed of high-speed railway networks
Authors: Lu Chun-fang 
Published: July 2019

Abstract:
China’s high-speed railway network has already achieved speeds of 350 km/h; however, this could be further increased to 400 km/h. After considering the development status and technical level of the high-speed railway system in China, this study indicates that there are four key technologies involved in improving its operational speed: the track, the electrical moving unit, the control system and the traction power supply. Through an experimental analysis, an evaluation index for the high-speed railway is then constructed based on four aspects: safety, comfort, intelligence and environmental protection. Using this system, the rationality of the high-speed railway speed-improvement plan can be scientifically evaluated. The results are of practical significance to the Chinese railway administration, as they can be used to formulate specific plans to increase rail speeds, and therefore promote the rapid development of the high-speed railway network in China.
Research transparency promotion by surgical journals publishing randomised controlled trials: a survey
Authors: Lombard N. , Gasmi A. , Sulpice L. , Boudjema K. , Naudet F. , Bergeat D. 
Published: July 2019

AbstractObjectiveTo describe the surgical journal position statement on data-sharing policies (primary objective) and to describe the other features of their research transparency promotion.MethodsOnly “SURGICAL” journals with an impact factor superior to 2 (Web of Science) were eligible for the study. They were not included if there were no explicit instructions for clinical trial publication in the instructions for authors and if there were no RCT published between January 2016 and January 2019. The primary outcome was the existence of a data-sharing policy in the instructions for authors. Details on research transparency promotion were also collected, namely the existence of a “prospective registration of clinical trials requirement” policy; a “COIs” disclosure requirement and a specific reference to reporting guidelines such as CONSORT for RCT.ResultsAmong the 87 surgical journals eligible, 82 (94%) were included in the analysis: 67 (77%) had explicit instructions for RCT and of the remaining, 15 (17.2%) had published at least one RCT between 2016-2019. The median impact factor was 2.98 [IQR=2.48-3.77] and in 2016 and 2017, the journals published a median of 11.5 RCT [IQR=5-20.75]. Data-sharing statement instructions (primary outcome) were ICMJE-compliant in four cases (4.88%), weaker in 45.12% (n=37) and inexistent in 50% (n=41) of the journals. As for data-sharing statements, no association was found between journal characteristics and the existence of data-sharing policies (ICMJE-compliant or weaker). A “prospective registration of clinical trials requirement” was associated with ICMJE allusion or affiliation and higher impact factors. Journals with specific RCT instructions in their OIA and journals referenced on the ICMJE website more frequently mandated the use of CONSORT guidelines.ConclusionResearch transparency promotion is still limited in surgical journals. Uniformization of journal requirements vis-à-vis ICMJE guidelines could be a first step forward for research transparency promotion in surgery.
ChromSCape : a Shiny/R application for interactive analysis of single-cell chromatin profiles
Authors: Prompsy Pacôme , Kirchmeier Pia , Vallot Céline 
Published: July 2019

AbstractAssessing chromatin profiles at single-cell resolution is now feasible thanks to recently published experimental methods such as single cell chromatin immunoprecipitation followed by sequencing (scChIP-seq) (Grosselin et al., 2019; Rotem et al., 2015) and single-cell assay for transposase-accessibility chromatin (scATAC-seq) (Buenrostro et al., 2015; Chen et al., 2018; Cusanovich et al., 2015; Lareau et al., 2019). With these methods, we can detect the heterogeneity of epigenomic profiles within complex biological samples. Yet, existing tools used to analyze bulk epigenomic experiments are not fit for the low coverage and sparsity of single-cell epigenomic datasets. Here, we present ChromSCape: a user-friendly Shiny/R application that processes single-cell epigenomic data to help the biological interpretation of epigenomic landscapes within cell populations. The user can identify different sub-populations within heterogeneous samples, find differentially enriched regions between subpopulations and identify associated genes and pathways. ChromSCape accepts multiple samples to allow comparisons of cell populations between and within samples. ChromSCape source code is written in Shiny/R, works as a stand-alone application and is freely downloadable athttps://github.com/vallotlab/ChromSCape. Here, using ChromSCape on multiple H3K27me3 scChIP-seq datasets, we deconvolve chromatin landscapes within the tumor microenvironment, identifying distinct H3K27me3 landscapes associated to cell identity and tumor subtype.Contactpacome.prompsy@curie.fr;celine.vallot@curie.fr
Performance of Complex Visual Tasks using Simulated Prosthetic Vision via Augmented-Reality Glasses
Authors: Ho Elton , Boffa Jack , Palanker Daniel 
Published: July 2019

AbstractPurposePhotovoltaic subretinal prosthesis is designed for restoration of central vision in patients with age-related macular degeneration (AMD). We investigated the utility of prosthetic central vision for complex visual tasks using augmented-reality (AR) glasses simulating reduced acuity, contrast and visual field.MethodsAR glasses with blocked central 20° of visual field included an integrated video camera and software which adjusts the image quality according to three user-defined parameters: resolution, corresponding to the equivalent pixel size of an implant, field of view, corresponding to the implant size, and number of contrast levels. The real-time processed video was streamed on a screen in front of the right eye. Nineteen healthy participants were recruited to complete visual tasks including vision charts, sentence reading, and face recognition.ResultsWith vision charts, letter acuity exceeded the pixel-sampling limit by 0.2 logMAR. Reading speed decreased with increasing pixel size and with reduced field of view (7-12°). In the face recognition task (4-way forced choice, 5° angular size) participants identified faces at >75% accuracy, even with 100 μm pixels and only 2 grey levels. With 60 μm pixels and 8 grey levels, the accuracy exceeded 97%.ConclusionsSubjects with simulated prosthetic vision performed slightly better than the sampling limit on the letter acuity tasks, and were highly accurate at recognizing faces, even with 100 μm/pixel resolution. These results indicate feasibility of the reading and face recognition using prosthetic central vision even with 100 μm pixels, and performance improves further with smaller pixels.
Sex Differences in Predictors of Seizure in Contrast-Enhancing Gliomas at Clinical Presentation: A Network Approach
Authors: Johnston Sandra K , Khurana Aditya , Whitmire Paula , Ranjbar Sara , Sharma Akanksha , Hawkins-Daarud Andrea , Rubin Joshua B , Porter Alyx B , Canoll Peter D , Egan Kathleen , Hu Leland S , Mrugala Maciej M , Kumthekar Priya , Swanson Kristin R 
Published: July 2019

ABSTRACTBackgroundBrain tumor related epilepsy (BTE) is a major co-morbidity related to the management of patients with brain cancer. Despite published practice guidelines recommending against anti-epileptic drug (AED) utilization in patients with gliomas, there is heterogeneity in prescription practices of AEDs in these patients. In an attempt to impact BTE management, we statistically analyzed clinically relevant attributes (sex, age, tumor size, tumor growth kinetics, and tumor location) pertaining to seizure at presentation and used them to build a computational machine learning model to predict the probability of a seizure (at presentation).MethodsFrom our clinical data repository, we identified 223 patients (females, n=86; males, n=137) with pathologically-determined glioma and known seizure status at clinical presentation. Non-parametric and Fisher’s Exact tests were used to identify statistical differences in clinical characteristics. We utilized a random forest machine learning method for generating our predictive models by entire cohort and separated by male and female.FindingsPatients were divided into those that presented with seizure (SP, n=96, 43%; F, n= 28; M, n= 68) and those that presented without seizure (nSP, n=127, 57%, F n=58, M n=69). Females presented with seizures significantly less often than males (x2=6·28, p=0·01). SP patients had significantly smaller T1Gd radius compared to nSP (SP 11·30mm, nSP 18.66mm, p<0·0001). Tumor size and patient age were significant negative predictors for SP; patients with larger tumors, older age and less tumor diffusivity (p/D) were at lower risk for SP.InterpretationDespite heterogeneity across our patient cohort, there is strong evidence of a role for patient sex, tumor size, tumor invasion, and patient age in predicting the incidence of seizures at diagnosis. Future studies, with prospectively detailed data collection, may provide clearer insights into the incidence of seizures through a patient’s treatment course.
Diffusive Flux Analysis of Tumor Vascular Permeability for 3-Helix-Micelles in Comparison to Other Nanoparticles
Authors: Lim Marc , Dharmaraj Vishnu , Gong Boying , Xu Ting 
Published: July 2019

AbstractUnderstanding the complex interplay of factors affecting nanoparticle accumulation in solid tumors is a challenge that must be surmounted to develop effective cancer nanomedicine. The tumor microenvironment is unique in comparison to healthy tissue, possessing elevated interstitial pressure that limits convective transport, hence leaving diffusive processes to predominate especially in the tumor’s necrotic core. Certain tumor types such as glioblastoma multiforme and pancreatic tumor are known to be poorly permeable, making them less accessible for nanoparticle drug delivery. Evidence indicates that small and long-circulating nanoparticles are ideal for taking advantage of the enhanced permeability and retention effect, even in such intractable tumor models. Three-helix-micelle (3HM) self-assembled nanoparticles possess these characteristics, and previous studies have shown that 3HM can achieve more favorable tumor accumulation and penetration than liposomes in several tumor models. The reason for its superior performance had yet to be determined, and thus we sought to examine its passive transport into tumors. In this paper we present a simple mathematical model based on diffusive flux to describe particle accumulation in tumors with respect to particle plasma pharmacokinetics. Fitting the diffusive flux equation to in vivo particle tumor concentration yields the particle effective permeability value, which for 3HM is 2.31 ± 0.18 x 10−8 cm/s in U87MG glioblastoma and 4.25 ± 0.91 x 10−8 cm/s in HT29 colon cancer murine models. Applying this diffusive flux model to other nanoparticles reported in literature enables the effect of plasma half-life to be decoupled from particle permeability in influencing tumor accumulation, reinforced trends reported in the field regarding the impact of particle size, and provided a semi-quantitative means of comparing various tumor models. This work is also the first demonstration, to the best our knowledge, of extracting particle permeability values from bulk biodistribution data obtained via positron emission tomography, as opposed to laborious tumor optical window intravital microscopy experiments. As such the analysis provided here presents a simple and accessible tool to further enhance nanomedicine development.Abstract FigureGraphical abstract
Description of Klebsiella indica sp. nov., isolated from the surface of tomato
Authors: Gujarati Sukriti , Chaudhari Diptaraj , Khairnar Mitesh , Shouche Yogesh , Rahi Praveen 
Published: July 2019

AbstractA novel bacterial strain designated TOUT106T was isolated from the surface of a tomato collected from the local vegetable market in Pune, India. The cells were rod shaped, Gram-stain-negative, encapsulated and non-motile. The strain TOUT106T grows as mucoid and translucent colonies on blood agar medium and the best growth was observed at 28°C and at pH 7.0, and could tolerate up to 2% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain TOUT106T was placed under Salmonella clade, with close similarity to Salmonella enterica subsp. arizonae strain NCTC 8297T (98.42%). Genome-based phylogenetic analysis revealed that the strain forms a distinct branch within the Klebsiella clade and K. michiganensis DSM25444T and K. oxytoca NBRC105695T were the closest neighbor. The genomic DNA G+C content of strain TOUT106T was 53.53 mol%. The average nucleotide identity of TOUT106T was less 86.4% with closely related members of the family Enterobacteriaceae. The major fatty acids of strain TOUT106T were C16:0, C17:0 cyclo, C14:0 3OH/C16:1 iso, C14:0, C19:0cyclow8c, C18:1 w6c/C18:1 w7c, C12:0 and C16:1 w7c/C16:1 w6c. The strain TOUT106T showed differences in physiological, phenotypic and protein profiles by MALDI-TOF MS to its closest relatives. Based on the phenotypic including chemotaxonomic properties and phylogenetic analysis the strain TOUT106T could be distinguished from the recognized species of the genus Klebsiella, was suggested to represent a novel species of this genus, for which the name Klebsiella indica sp. nov. is proposed. The type strain is TOUT106T (=MCC 2901T).
A method for the unbiased quantification of reassortment in segmented viruses
Authors: Hockman Megan R. , Phipps Kara , Lowen Anice C. 
Published: July 2019

AbstractThe diversification of segmented viruses via reassortment is important to understand due to the contributions of reassortment to viral evolution and emergence. Methods for the quantification of reassortment have been described, but are often cumbersome and best suited for the analysis of reassortment between highly divergent parental strains. While it is useful to understand the potential of divergent parents to reassort, outcomes of such heterologous reassortment are driven by differential selection acting on the progeny and are typically strain specific. To quantify reassortment, a system free of differential selection is needed. We have generated such a system for influenza A virus and for mammalian orthoreovirus by constructing well-matched parental viruses carrying small genetic tags. The method utilizes high-resolution melt technology for the identification of reassortant viruses. Ease of sample preparation and data analysis enables streamlined genotyping of a large number of virus clones. The method described here thereby allows quantification of the efficiency of unbiased reassortment and can be applied to diverse segmented viruses.HighlightsGenetic tagging of viruses can be achieved without altering fitnessHigh-resolution melt can detect single nucleotide differences in virusesUnbiased reassortment of influenza A virus and mammalian orthoreovirus can be quantified
Dopamine modulates dynamic decision-making during foraging
Authors: Le Heron Campbell , Kolling Nils , Plant Olivia , Kienast Annika , Janska Rebecca , Ang Yuen-Siang , Fallon Sean , Husain Masud , Apps Matthew A J 
Published: July 2019

ABSTRACTThe mesolimbic dopaminergic system exerts a crucial influence on incentive processing. However, the contribution of dopamine in dynamic, ecological situations where reward rates vary, and decisions evolve over time, remains unclear. In such circumstances, current (foreground) reward accrual needs to be compared continuously with potential rewards that could be obtained by travelling elsewhere (background reward rate), in order to determine the opportunity cost of staying versus leaving. We hypothesised that dopamine specifically modulates the influence of background – but not foreground – reward information when making a dynamic comparison of these variables for optimal behaviour. On a novel foraging task based on an ecological account of animal behaviour (marginal value theorem), human participants were required to decide when to leave locations in situations where foreground rewards depleted at different rates, either in rich or poor environments with high or low background rates. In line with theoretical accounts, people’s decisions to move from current locations were independently modulated by both foreground and background reward rates. Pharmacological manipulation of dopamine D2 receptor activity using the agonist cabergoline significantly affected decisions to move on, specifically modulating the effect of background but not foreground rewards rates. In particular, when on cabergoline, people left patches in poor environments much earlier. These results demonstrate a role of dopamine in signalling the opportunity cost of rewards, not value per se. Using this ecologically derived framework we uncover a specific mechanism by which D2 dopamine receptor activity modulates decision-making when foreground and background reward rates are dynamically compared.Significance statementMany decisions, across economic, political and social spheres, involve choices to “leave”. Such decisions depend on a continuous comparison of a current location’s value, with that of other locations you could move on to. However, how the brain makes such decisions is poorly understood. Here, we developed a computerized task, based around theories of how animals make decisions to move on when foraging for food. Healthy human participants had to decide when to leave collecting financial rewards in a location, and travel to collect rewards elsewhere. Using a pharmacological manipulation, we show that the activity of dopamine in the brain modulates decisions to move on, with people valuing other locations differently depending on their dopaminergic state.
Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing
Authors: Arpat Alaaddin Bulak , Liechti Angélica , Matos Mara De , Dreos René , Janich Peggy , Gatfield David 
Published: July 2019

AbstractTranslation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of non-uniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ∼10% of translating ribosomes in the disome state. A distinct class of pause sites, independent of translation rate, is indicative of deterministic pausing signals. Pause site association with specific amino acids, peptide motifs and nascent polypeptide structure, is suggestive of programmed pausing as a widespread mechanism associated with protein folding. Evolutionary conservation at disome sites indicates functional relevance of translational pausing. Collectively, our disome profiling approach allows unique insights into gene regulation occurring at the step of translation elongation.
CBP80/20-dependent translation initiation factor (CTIF) inhibits HIV-1 Gag synthesis by targeting the function of the viral protein Rev
Authors: García-de-Gracia Francisco , Toro-Ascuy Daniela , Riquelme-Barrios Sebastián , Pereira-Montecinos Camila , Rojas-Araya Bárbara , Gaete-Argel Aracelly , Acevedo Mónica L. , Chnaiderman Jonás , Valiente-Echeverría Fernando , Soto-Rifo Ricardo 
Published: July 2019

ABSTRACTTranslation initiation of the human immunodeficiency virus type-1 (HIV-1) unspliced mRNA has been shown to occur through cap-dependent and IRES-driven mechanisms. Previous studies suggested that the nuclear cap-binding complex (CBC) rather than eIF4E drives cap-dependent translation of the unspliced mRNA and we have recently reported that the CBC subunit CBP80 supports the function of the viral protein Rev during nuclear export and translation of this viral transcript. Ribosome recruitment during CBC-dependent translation of cellular mRNAs relies on the activity CBP80/20 translation initiation factor (CTIF), which bridges CBP80 and the 40S ribosomal subunit through interactions with eIF3g. Here, we report that CTIF restricts HIV-1 replication by interfering with Gag synthesis from the unspliced mRNA. Our results indicate that CTIF associates with Rev through its N-terminal domain and is recruited onto the unspliced mRNA ribonucleoprotein complex in order to block translation. We also demonstrate that CTIF induces the cytoplasmic accumulation of Rev impeding the association of the viral protein with CBP80. We finally show that CTIF restricts HIV-2 but not MLV Gag synthesis indicating an inhibitory mechanism conserved in Rev-expressing human lentiviruses.