bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Dual And Triple RSVP Paradigm For P300 Speller
Authors: Mohammad Mijani Amir , Bagher Shamsollahi Mohammad , Sheikh Hassani Mohsen 
Published: October 2018

AbstractObjectiveA speller system enables disabled people, specifically those with spinal cord injuries, to visually select and spell characters. A problem of primary speller systems is that they are gaze shift dependent. To overcome this problem, a single RSVP paradigm was introduced in which characters are displayed one by one at the center of a screen. In this paper, two new protocols named Dual and Triple RSVP paradigms are introduced and their results are compared against the single paradigm.MethodsIn the Dual and Triple paradigms, two and three characters are displayed at the center of the screen simultaneously, therefore holding the advantage of displaying the target character twice and three times respectively, compared to the one-time appearance in the single paradigm. Subsequently, by reducing the number of repetitions in the Dual and Triple paradigms, it is expected that ITR decreases. To compare the results of these three paradigms, three subjects participated in experiments using all three paradigms.ResultsThe offline results demonstrate an average character detection accuracy of 97% for the single and double protocols, and 80% for the Triple paradigm. In addition, average ITR is calculated to be 5.45, 7.62 and 7.90 bit/min for the single, Dual and Triple paradigms respectively. Results demonstrate an equally good character detection accuracy for the single and Dual paradigms, and a significant increase in ITR in the Dual paradigm compared to the single. The Triple RSVP paradigm demonstrates an almost equal ITR to that of the Dual paradigm, while decreasing character detection accuracy significantly.ConclusionsResults demonstrate that the Dual RSVP paradigm can be recognized as the most suitable approach, by providing the best balance between ITR and character detection accuracy.SignificanceThis research demonstrates the improved performance of a newly proposed speller system (the Dual RSVP paradigm). By replacing existing methods with this new approach, the performance of speller matrices will be enhanced, and in addition the gaze dependency issue that caused limitations for users suffering from unimpaired oculomotor control will be overcome.
Development of a novel signature of long noncoding RNAs as a prognostic biomarker for esophageal cancer
Authors: Miao Yan , Sui Jing , Zhang Ying , Yin Lihong 
Published: October 2018

ABSTRACTObjectivesThis study aims to develop a lncRNA signature based on RNA-Seq data to predict overall survival in esophageal cancer patients.MethodsThe lncRNA expression profiles and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database on August 30, 2017. Differentially expressed lncRNAs were screened out between tumor tissues and adjacent normal tissues. The univariate and multivariate Cox regression models were used to develop a prognostic signature for all esophageal cancer patients. The receiver operating curve (ROC) was used to test the sensitivity and specificity of lncRNA signature. Survivals were compared via log-rank test. GO and KEGG enrichment analyses were used to explore the potential functions of prognostic lncRNAs.ResultsWe identified two lncRNAs (RPL34-AS1 and GK3P) were significantly associated with the overall survival of the total 150 esophageal cancer patients. A novel two-lncRNA signature was constructed by Cox regression models. Signature low-risk cases showed better overall survival (median 625.560 days vs. 478.000 days, p = 0.002) than high-risk cases. Further analysis suggested that this two-lncRNA signature was independent of clinical characteristics. GO functional and KEGG pathway enrichment analyses revealed potential functional roles of the two prognostic lncRNAs in tumorigenesis.ConclusionsOur findings suggest that the two-lncRNA signature may be a useful prognostic biomarker for predicting overall survival in esophageal cancer patients.
Density dependent enhancement effect ofWolbachiaand the host RNAi response to a densovirus inAedescells
Authors: Parry Rhys , Bishop Cameron , Hayr Lachlan de , Asgari Sassan 
Published: October 2018

AbstractThe endosymbiotic bacteriumWolbachia pipientishas been shown to restrict a range of RNA viruses inDrosophila melanogasterand transinfected dengue mosquito,Aedes aegypti. Here, we show thatWolbachiainfection enhances replication of Aedes albopictus densovirus (AalDNV-1), a single stranded DNA virus, inAedescell lines in a density-dependent manner. Analysis of previously produced small RNAs of Aag2 cells showed thatWolbachia-infected cells produced greater proportions of viral derived short interfering RNAs as compared to uninfected cells. Additionally, we found production of viral derived PIWI-like RNAs (vpiRNA) produced in response to AalDNV-1 infection. Nuclear fractions of Aag2 cells produced a primary vpiRNA signature U1bias whereas the typical “ping-pong” signature (U1- A10) was evident in the cytoplasmic fraction. This is the first report of the density-dependent enhancement of DNA viruses byWolbachia. Further, we report the generation of vpiRNAs in a DNA virus-host interaction for the first time.
Role of RIG-I-like receptors in innate immune sensing of Coxsackievirus B3 and encephalomyocarditis virus in murine macrophages and fibroblasts
Authors: Francisco Esther , Suthar Mehul , Gale Michael , Rosenfeld Amy B. , Racaniello Vincent R. 
Published: October 2018

AbstractViral infections are sensed by pattern recognition receptors that trigger an innate immune response through the expression of interferons (IFNs) and other cytokines. Most RNA viruses are sensed by the RIG-I like receptors (RLR)s. The contributions of these receptors to sensing viruses of thePicornaviridaefamily were investigated. Encephalomyocarditis virus (EMCV) and Coxsackievirus B3 (CVB3), picornaviruses of theCardiovirusandEnterovirusgenera, are detected by both MDA5 and RIG-I in bone marrow derived macrophages. In macrophages from wild type mice, type I IFN is produced early after infection; IFNβ synthesis is reduced in the absence of each sensor, while IFNα production is reduced in the absence of MDA5. EMCV and CVB3 do not replicate in murine macrophages, and their detection is different in murine embryonic fibroblasts (MEFs), in which the viruses replicate to high titers. In MEFs RIG-I was essential for the expression of type I IFNs but contributes to increased yields of CVB3, while MDA5 inhibited CVB3 replication but in an IFN independent manner. These observations demonstrate that innate sensing of similar viruses by RLRs depends upon the cell type.ImportanceEnteroviruses such as Coxsackieviruses are the most common human respiratory pathogens. The host’s innate immune response, in particular that modulated by the production of type I and III interferons, is thought to restrict picornavirus infection. Two cytoplasmic proteins, MDA5 and RIG-I, are critical for initiating the early innate immune response against these viruses. Mutations within MDA5 encoding gene have been associated with the development of severe enterovirus associated respiratory illnesses in healthy children. To further understand how the innate immune response dependent upon MDA5 and Rig-I is initiated during picornavirus infection, macrophages from mice lacking MDA5 or RIG-I were infected with Coxsackievirus B3 (CVB3) and a related animal virus. RIG-I is essential for type I IFN production during CVB3 infection; when MDA5 is present, viral titers are reduced by an IFN-independent pathway. These observations demonstrate that innate sensing of viruses by MDA5 and RIG-I depends upon the cell type.
Immunoinformatics Prediction of Epitope Based Peptide Vaccine AgainstMadurella mycetomatis Translationally Controlled Tumor Protein
Authors: Bolis Samira Munir , Omer Walaa Abdullah , Abdelhamed Mohamed Anwar , Shambal Masajed Abdelmagid , Adam Esameldeen Ahmed , Abass Mohammed Abaker , Abdalla Wiaam Abdelwahab , Is-haq Suzan Hashim , Abdalla Aisha Abubakralsiddig , Zeinalabedeen Abeer Algaali , Ahmed Omar Hashim , Hassan Mohamed A 
Published: October 2018

AbstractBackgroundMadurella. mycetomatisis most common causative agent of mycetoma in Sudan and worldwide. No vaccines are available till now so design of effective vaccine is essential as protection tool. Peptide vaccine can overcome the common side effects of the conventional vaccines. The aim of this study was to design peptide based vaccine forM.Mycetomatis Translationally Controlled Tumor Protein (TCTP)using immunoinformatics tools.Materials and methodsTCTPsequences were retrieved from NCBI and then processed using BioEdit program to determine conserved regions and different immunoinformatics tools from IEDB. Population coverage analysis was performed for the most promising epitopes. Homology modelling was performed to show their structural positions inTCTP.Protein analysis was done using Expasy (ProtParamsotware).Results and conclusionFour epitopes passed the Bepipred, Emini, Kolaskar and Tongaonkar tools. 111 epitopes were predicted to interact with MHCI alleles with IC50 < 500 nM, three of them were most promising. 274 predicted epitopes were interacted with MHCII alleles with IC50 < 100 nM, four of them were most promising. The epitope (YMKSVKKAL) was the most promising one concerning its binding with MHCI alleles, while (FRLQSTSFD) was the most promising for MHC II. The epitope (YLKAYMKSV) is shared betweenMHC I and II. For the population coverage ofM. Mycetomatis TCTPvaccine Sudan (90.39%) had the highest percentage for MHC I. This is the first computational vaccinology study conducted in mycetoma caused byM. MycetomatisusingTCTP.
Reactive SINDy: Discovering governing reactions from concentration data
Authors: Hoffmann Moritz , Fröhner Christoph , Noé Frank 
Published: October 2018

AbstractThe inner workings of a biological cell or a chemical reaction can be rationalized by the network of reactions, whose structure reveals the most important functional mechanisms. For complex systems, these reaction networks are not known a priori and cannot be efficiently computed with ab initio methods, therefore an important approach goal is to estimate effective reaction networks from observations, such as time series of the main species. Reaction networks estimated with standard machine learning techniques such as least-squares regression may fit the observations, but will typically contain spurious reactions. Here we extend the sparse identification of nonlinear dynamics (SINDy) method to vector-valued ansatz functions, each describing a particular reaction process. The resulting sparse tensor regression method “reactive SINDy” is able to estimate a parsimonious reaction network. We illustrate that a gene regulation network can be correctly estimated from observed time series.
Word stress representations are language-specific: evidence from event-related brain potentials
Authors: Honbolygó Ferenc , Kóbor Andrea , German Borbála , Csépe Valéria 
Published: October 2018

AbstractUnderstanding speech at the basic levels entails the simultaneous and independent processing of phonemic and prosodic features. While it is well-established that phoneme perception relies on language-specific long-term traces, it is unclear if the processing of prosodic features similarly involves language-specific representations. In the present study, we investigated the processing of a specific prosodic feature, word stress, using the method of event-related brain potentials (ERPs) employing a cross-linguistic approach. Hungarian participants heard disyllabic pseudowords stressed either on the first (legal stress) or on the second (illegal stress) syllable, pronounced either by a Hungarian or a German speaker. Results obtained using a data-driven ERP analysis methodology showed that all pseudowords in the deviant position elicited an Early Differentiating Negativity (EDN) and a Mismatch Negativity (MMN) component, except for the Hungarian pseudowords stressed on the first syllable. This suggests that Hungarian listeners did not process the native legal stress pattern as deviant, but the same stress pattern with a non-native accent was processed as deviant. This implies that the processing of word stress was based on language-specific long-term memory traces.
High Temporal Sub-millisecond Time Resolution Stimulation Increases Performances of Retina Prosthetic Vision
Authors: Kime S. , Simon-Shane C. , Sabatier Q. , Galluppi F. , Benosman R. 
Published: October 2018

AbstractVision loss has an enormous impact on affected individuals, and increasing social and economics costs for the whole of society. Important approaches have been introduced, aimed at restoring visual functionality in the case of vision degradation and loss. Currently the most promising technology is represented by retinal implants, with companies producing devices approved for commercialization. The first clinical studies encouragingly reported perception elicited by both devices. Some patients retrieve autonomy, but only a few could reach satisfactory perception levels, allowing more complex tasks such as reading. Fundamental limitations however still exist in both spatial and temporal resolution, and these limitations call for improvements of the technology and of the stimulation strategies used therein. This study focuses on the importance of temporal resolution for retinal stimulation, and how it can be used to improve restored perception for implanted patients. We show a quantification of the improvement of discrimination performance when stimulating with high frame rates compared to conventional 30-60Hz frame rates. Such effect is evaluated using data collected from implanted patients, and deriving from it a realistic phosphene model. This study allowed to accurately replicate the perceptual effects of the studied technologies, and to evaluate the hypotheses regarding performance improvements using higher temporal resolutions for stimulation strategies in visual restoration devices.
Variational Infinite Heterogeneous Mixture Model for Semi-supervised Clustering of Heart Enhancers
Authors: Mehdi Tahmid F. , Singh Gurdeep , Mitchell Jennifer A. , Moses Alan M. 
Published: October 2018

AbstractMotivationPMammalian genomes can contain thousands of enhancers but only a subset are actively driving gene expression in a given cellular context. Integrated genomic datasets can be harnessed to predict active enhancers. One challenge in integration of large genomic datasets is the increasing heterogeneity: continuous, binary and discrete features may all be relevant. Coupled with the typically small numbers of training examples, semi-supervised approaches for heterogeneous data are needed; however, current enhancer prediction methods are not designed to handle heterogeneous data in the semi-supervised paradigm.ResultsWe implemented a Dirichlet Process Heterogeneous Mixture model that infers Gaussian, Bernoulli and Poisson distributions over features. We derived a novel variational inference algorithm to handle semi-supervised learning tasks where certain observations are forced to cluster together. We applied this model to enhancer candidates in mouse heart tissues based on heterogeneous features. We constrained a small number of known active enhancers to appear in the same cluster, and 47 additional regions clustered with them. Many of these are located near heart-specific genes. The model also predicted 1176 active promoters, suggesting that it can discover new enhancers and promoters.AvailabilityWe created the ‘dphmix’ Python package:https://pypi.org/project/dphmix/Contactalan.moses@utoronto.ca
A Framework for Intelligence and Cortical Function Based on Grid Cells in the Neocortex
Authors: Hawkins Jeff , Lewis Marcus , Klukas Mirko , Purdy Scott , Ahmad Subutai 
Published: October 2018

AbstractHow the neocortex works is a mystery. In this paper we propose a novel framework for understanding its function. Grid cells are neurons in the entorhinal cortex that represent the location of an animal in its environment. Recent evidence suggests that grid cell-like neurons may also be present in the neocortex. We propose that grid cells exist throughout the neocortex, in every region and in every cortical column. They define a location-based framework for how the neocortex functions. Whereas grid cells in the entorhinal cortex represent the location of one thing, the body relative to its environment, we propose that cortical grid cells simultaneously represent the location of many things. Cortical columns in somatosensory cortex track the location of tactile features relative to the object being touched and cortical columns in visual cortex track the location of visual features relative to the object being viewed. We propose that mechanisms in the entorhinal cortex and hippocampus that evolved for learning the structure of environments are now used by the neocortex to learn the structure of objects. Having a representation of location in each cortical column suggests mechanisms for how the neocortex represents object compositionality and object behaviors. It leads to the hypothesis that every part of the neocortex learns complete models of objects and that there are many models of each object distributed throughout the neocortex. The similarity of circuitry observed in all cortical regions is strong evidence that even high-level cognitive tasks are learned and represented in a location-based framework.
The geometry of habitat fragmentation: effects of distribution patterns on short-term species persistence
Authors: May Felix , Rosenbaum Benjamin , Schurr Frank M. , Chase Jonathan M. 
Published: October 2018

AbstractLand-use changes cause habitat loss and fragmentation and are thus important drivers of anthropogenic biodiversity change. However, there is an ongoing debate about how fragmentationper seaffects biodiversity in a given amount of habitat. We illustrate why it is important to distinguish two different aspects of fragmentation to resolve this debate: (i) geometric fragmentation effects, which exclusively arise from the spatial distributions of species and habitat fragments, and (ii) demographic fragmentation effects due to reduced fragment size, increased isolation, or edge effects. While most empirical studies are primarily interested in quantifying demographic fragmentation effects, geometric effects are typically invoked only as post-hoc explanations of biodiversity responses to fragmentationper se. Here, we present an approach to quantify geometric fragmentation effects on species persistence probability. We illustrate this approach using spatial simulations where we systematically varied the initial abundances and distribution patterns (i.e. random, aggregated, and regular) of species as well as habitat amount and fragmentationper se.As expected, we found no geometric fragmentation effects when species were randomly distributed. However, when species were aggregated, we found positive effects of fragmentationper seon persistence probability for a large range of scenarios. For regular species distributions, we found weakly negative geometric effects. These findings are independent of the ecological mechanisms which generate non-random species distributions. Our study helps to reconcile seemingly contradictory results of previous fragmentation studies. Since intraspecific aggregation is a ubiquitous pattern in nature, our findings imply widespread positive geometric fragmentation effects. This expectation is supported by many studies that find positive effects of fragmentationper seon species occurrences and diversity after controlling for habitat amount. We outline how to disentangle geometric and demographic effects of fragmentation, which is critical for predicting the response of biodiversity to landscape change.
Sulfated RaxX, which represents an unclassified group of ribosomally synthesized post-translationally modified peptides, binds a host immune receptor
Authors: Luu Dee Dee , Joe Anna , Chen Yan , Parys Katarzyna , Bahar Ofir , Pruitt Rory , Chen Leanne Jade G. , Petzold Christopher J. , Long Kelsey , Adamchak Clifford , Stewart Valley , Belkhadir Youssef , Ronald Pamela C. 
Published: October 2018

ABSTRACTThe rice immune receptor XA21 is activated by the sulfated microbial peptide RaxX (required foractivation ofXA21-mediated immunityX) produced byXanthomonas oryzaepv.oryzae(Xoo). Mutational studies and targeted proteomics revealed that RaxX is processed and secreted by the protease/transporter RaxB, whose function can be partially fulfilled by a noncognatepeptidase-containing transporterB(PctB). RaxX is cleaved at a Gly-Gly motif, yielding a mature peptide that retains the necessary elements for RaxX function as an immunogen and host peptide hormone mimic. These results indicate that RaxX is a founding member of a previously unclassified and understudied group of tyrosine sulfated RiPPs (ribosomally synthesized,post-translationally modifiedpeptides). We further demonstrate that sulfated RaxX directly binds XA21 with high affinity. This work reveals a complete, previously uncharacterized biological process: bacterial RiPP biosynthesis, secretion, binding to a eukaryotic receptor and triggering of a robust host immune response.
Tropical arboreal ants form dominance hierarchies over nesting resources in agroecosystems
Authors: Yibarek Senay , Philpott Stacy M. 
Published: October 2018

AbstractInterspecific dominance hierarchies have been widely reported across animal systems. While some dominant individuals (winners) get to monopolize resources, during dyadic interactions, they can increase their relative fitness as compared to subdominant individuals (losers). In some ant species, dominance hierarchies have been used to explain species coexistence and community structure. However, it remains unclear whether or in what contexts dominance hierarchies occur in tropical ant communities. Furthermore, it can be challenging to infer and quantify reliable dominance hierarchies from observed interactions. This study seeks to examine whether arboreal twig-nesting ants competing for nesting resources in a Mexican coffee agricultural ecosystem are arranged in a dominance hierarchy. Using network analysis, we quantified interactions between ten species by measuring the uncertainty and steepness in the dominance hierarchy. We also assessed the orderliness of the hierarchy by considering species interactions at the network level. Based on the Elo-ranking method, we found that the twig-nesting ant species Myrmelachista mexicana ranked highest in the ranking, while Pseudomyrmex ejectus was ranked as the lowest in the hierarchy. We quantified the uncertainty in the dominance hierarchy and found that the hierarchy was intermediate in its steepness, suggesting that the probability of higher ranked individuals winning contests against lower ranked individuals was fairly high. Motif analysis and significant excess of triads further revealed that the species networks were largely transitive. This study highlights that some tropical arboreal ant communities self-organize into dominance hierarchies.