bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context-based facilitation in visual word recognition: Evidence for visual and lexical but not pre-lexical contributions
Authors: Eisenhauer Susanne , Fiebach Christian J. , Gagl Benjamin 
Published: September 2018

AbstractWord familiarity and predictive context facilitate visual word processing, leading to faster recognition times and reduced neuronal responses. Previously, models with and without top-down connections, including lexical-semantic, pre-lexical (e.g., orthographic/ phonological), and visual processing levels were successful in accounting for these facilitation effects. Here we systematically assessed context-based facilitation with a repetition priming task and explicitly dissociated pre-lexical and lexical processing levels using a pseudoword familiarization procedure. Experiment 1 investigated the temporal dynamics of neuronal facilitation effects with magnetoencephalography (MEG; N=38 human participants) while Experiment 2 assessed behavioral facilitation effects (N=24 human participants). Across all stimulus conditions, MEG demonstrated context-based facilitation across multiple time windows starting at 100 ms, in occipital brain areas. This finding indicates context based-facilitation at an early visual processing level. In both experiments, we furthermore found an interaction of context and lexical familiarity, such that stimuli with associated meaning showed the strongest context-dependent facilitation in brain activation and behavior. Using MEG, this facilitation effect could be localized to the left anterior temporal lobe at around 400 ms, indicating within-level (i.e., exclusively lexical-semantic) facilitation but no top-down effects on earlier processing stages. Increased pre-lexical familiarity (in pseudowords familiarized utilizing training) did not enhance or reduce context effects significantly. We conclude that context based-facilitation is achieved within visual and lexical processing levels. Finally, by testing alternative hypotheses derived from mechanistic accounts of repetition suppression, we suggest that the facilitatory context effects found here are implemented using a predictive coding mechanism.Significance StatementThe goal of reading is to derive meaning from script. This highly automatized process benefits from facilitation depending on word familiarity and text context. Facilitation might occur exclusively within each level of word processing (i.e., visual, pre-lexical, and/or lexical-semantic) but could alternatively also propagate in a top-down manner from higher to lower levels. To test the relevance of these two alternative accounts at each processing level, we combined a pseudoword learning approach controlling for letter string familiarity with repetition priming. We found enhanced context-based facilitation at the lexical-semantic but not pre-lexical processing stage, and no evidence of top-down facilitation from lexical-semantic to earlier word recognition processes. We also identified predictive coding as the most likely mechanism underlying within-level context-based facilitation.
Hypothesis: A plastically-produced phenotype predicts host specialization and can precede subsequent mutations in bacteriophage
Authors: Maxwell Colin S. 
Published: September 2018

AbstractThe role of phenotypic plasticity in the evolution of new traits is controversial due to a lack of direct evidence. Phage host-range becomes plastic in the presence of restriction-modification (R-M) systems in their hosts. I modeled the evolution of phage host-range in the presence of R-M systems. The model makes two main predictions. First, that offspring of the first phage to gain a new methylation pattern by infecting a new host make up a disproportionate fraction of the subsequent specialist population, indicating that the plastically-produced phenotype is highly predictive of evolutionary outcome. Second, that the first phage gain this pattern is not always genetically distinct from other phages in the population. Taken together, these results suggest that plasticity could play a causal role on par with mutation during the evolution of phage host range. This uniquely tractable system could enable the first direct test of ‘plasticity first’ evolution.
Cortico-basal-ganglia communication: Temporally structured activity for selective motor control
Authors: Fischer Petra , Lipski Witold , Neumann Wolf-Julian , Turner Robert Sterling , Fries Pascal , Brown Peter , Richardson Robert Mark 
Published: September 2018

AbstractDespite the hard-wired structural connectivity of neural pathways, neural circuits allow context-dependent reactions to sensory cues by triggering the desired movement. Cortico-basal-ganglia circuits seem particularly important for flexible motor control as this is impaired in Parkinson’s disease (PD). We analysed subthalamic nucleus (STN) spike and cortical ECoG activity from PD patients performing a visually-cued hand grip task. Fast reaction times were preceded by enhanced STN spike-to-cortical gamma phase coupling irrespective of firing rate changes, suggesting a role of gamma coupling in motor preparation. STN spike timing was offset by half a cycle when comparing ipsilateral with contralateral movements. Additionally, cortical high-frequency activity increased more steeply within each gamma cycle at the sites that showed the strongest coupling with STN spikes. Cortico-basal-ganglia gamma coupling may thus help shape neural activity to facilitate selective motor control. The observation that this effect occurs independent of changes in mean firing rate has far-reaching implications.HighlightsFast RTs were preceded by enhanced STN spike-to-cortical gamma phase couplingSTN spike probability was significantly modulated relative to the gamma cycleDuring ipsilateral movement, spikes were more likely at the opposite part of the cycleSTN output may thus help shape cortical gamma for selective motor control
AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX
Authors: Shieh Kevin R. , Kratschmer Christina , Maier Keith E. , Greally John M. , Levy Matthew , Golden Aaron 
Published: September 2018

ABSTRACTSummary:High-Throughput Sequencing can enhance the analysis of aptamer libraries generated by the Systematic Evolution of Ligands by EXponential enrichment (HTS-SELEX). Robust analysis of the resulting sequenced rounds is best implemented by determining a ranked consensus of reads following the processing by multiple aptamer detection algorithms. Whilst several such approaches have been developed to this end, their installation and implementation is problematic. We developed AptCompare, a cross-platform program that combines six of the most widely used analytical approaches for the identification of RNA aptamer motifs and uses a simple weighted ranking to order the candidate aptamers, all driven within the same GUI- enabled environment. We demonstrate AptCompare’s performance by identifying the top-ranked candidate aptamers from a previously published selection experiment in our laboratory, with follow-up bench assays demonstrating good correspondence between the sequences’ rankings and their binding affinities.Availability and Implementation:The source code and pre-built virtual machine images are freely available at https://bitbucket.org/shiehk/aptcompare.
Using eDNA methodologies to identify the presence/absence of S. thermophilus in yogurt products
Authors: Bejdo Vladimir , Gao Claire 
Published: September 2018

AbstractThe advent of low-cost nuclear acid extraction allows for the creation of low-cost assays which can specifically be used to determine the presence or absence of bacteria in a variety of environments. Commercially sold dietary yogurt claims to contain bacteria forming a microbiome which has been previously linked to improved health outcomes in incidence rates of type 2 diabetes in vulnerable populations. The predicted outcome was that a main bacterial culture used in yogurt production (S. thermophilus) would be present and would be detectable using eDNA methodologies since it is fundamental to the making of yogurt. We gathered DNA from yogurt using yogurt dilutions and filter paper; we then extracted the DNA and also sequenced and used PCR to amplify the DNA. We sequenced PCR products to verify their identity through processing with publicly available BLAST tools which reference already accessioned bacterial genomes. Yogurt from four different commercially available brands (in the U.S.) was tested; not all yogurts tested positive for the bacteria, with higher concentrations of the bacteria in imported Greek-style yogurts, lower concentrations in domestically produced Greek-style yogurts, and no bacterial DNA detected in domestically produced ‘regular’ yogurt products. This research suggests that not all yogurts are equal, putting into question the whole-sale claims made on dietary yogurt’s probiotic preventative health effects and calling for a more detailed analysis to determine firm causal links between the microbiota of yogurts and preventative health effects.
A cortical route for face-like pattern processing in human newborns
Authors: Buiatti Marco , Giorgio Elisa Di , Piazza Manuela , Polloni Carlo , Menna Giuseppe , Taddei Fabrizio , Baldo Ermanno , Vallortigara Giorgio 
Published: September 2018

AbstractHumans are endowed with an exceptional ability for detecting faces, a competence that in adults is supported by a set of face-specific cortical patches. Human newborns already shortly after birth preferentially orient to faces even when they are presented in the form of highly schematic geometrical patterns, over perceptually equivalent non-face-like stimuli. The neural substrates underlying this early preference are still largely unexplored. Is the adult face-specific cortical circuit already active at birth, or does its specialization develop slowly as a function of experience and/or maturation? We measured EEG responses in 1-4 days old awake, attentive human newborns to schematic face-like patterns and non-face-like control stimuli, visually presented with a slow oscillatory “peekaboo” dynamics (0.8 Hz) in a frequency-tagging design. Despite the limited duration of newborns’ attention, reliable frequency-tagged responses could be estimated for each stimulus from the peak of the EEG power spectrum at the stimulation frequency. Upright face-like stimuli elicited a significantly stronger frequency-tagged response than inverted face-like controls in a large set of electrodes. Source reconstruction of the underlying cortical activity revealed the recruitment of a partially right-lateralized network comprising lateral occipito-temporal and medial parietal areas largely overlapping with the adult face-processing circuit. This result suggests that the cortical route specialized in face processing is already functional at birth.Significance statementNewborns show a remarkable ability to detect faces even minutes after birth, an ecologically fundamental skill that is instrumental for interacting with their conspecifics. What are the neural bases of this expertise? Using EEG and a slow oscillatory visual stimulation, we identified a reliable response specific to face-like patterns in newborns, which underlying cortical sources largely overlap with the adult face-specific cortical circuit. This suggests that the development of face perception in infants might rely on an early cortical route specialized in face processing already shortly after birth.
artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis
Authors: Javorka Peter , Raxwal Vivek , Najvarek Jan , Riha Karel 
Published: September 2018

AbstractMapping-by-sequencing is a rapid method for identifying both natural as well as induced variations in the genome. However, it requires extensive bioinformatics expertise along with the computational infrastructure to analyze the sequencing data and these requirements have limited its widespread adoption. In the current study, we develop an easy to use tool, artMAP, to discover ethyl methanesulfonate (EMS) induced mutations in the Arabidopsis genome. The artMAP pipeline consists of well-established tools including TrimGalore, BWA, BEDTools, SAMtools, and SnpEff which were integrated in a Docker container. artMAP provides a graphical user interface and can be run on a regular laptop and desktop, thereby limiting the bioinformatics expertise required. artMAP can process input sequencing files generated from single or paired-end sequencing. The results of the analysis are presented in interactive graphs which display the annotation details of each mutation. Due to its ease of use, artMAP made the identification of EMS-induced mutations in Arabidopsis possible with only a few mouse click. The source code of artMAP is available on Github (https://github.com/RihaLab/artMAP).
Effects of alternative blood sources on Wolbachia infected Aedes aegypti females within and across generations
Authors: Paris Véronique , Cottingham Ellen , Ross Perran A. , Axford Jason K. , Hoffmann Ary A. 
Published: September 2018

ABSTRACTWolbachia bacteria have been identified as a tool for reducing the transmission of arboviruses transmitted by Aedes aegypti. Research groups around the world are now mass rearing Wolbachia infected Ae. aegypti for deliberate release. We investigated the fitness impact of a crucial element of mass rearing: the blood meal required by female Ae. aegypti to lay eggs. Although Ae. aegypti almost exclusively feed on human blood, it is often difficult to use human blood in disease-endemic settings. When females were fed on sheep or pig blood rather than human blood, egg hatch rates decreased in all three lines tested (uninfected, or infected by wMel, or wAlbB Wolbachia). This finding was particularly pronounced when fed on sheep blood, although fecundity was not affected. Some of these effects persisted after an additional generation on human blood. Attempts to keep populations on sheep and pig blood sources only partly succeeded, suggesting that strong adaptation is required to develop a stably infected line on an alternative blood source. There was a decrease in Wolbachia density when Wolbachia Ae. aegypti were fed on non-human blood sources, although density was higher again in lines kept for multiple generations on the alternate sources. These findings suggest that sheep and pig blood will entail a cost when used as alternative blood sources which needs to be taken into account when considering mass release.
Origin and recent expansion of an endogenous gammaretroviral lineage in canids
Authors: Halo Julia V. , Pendleton Amanda L. , Jarosz Abigail S. , Gifford Robert J. , Day Malika L. , Kidd Jeffrey M. 
Published: September 2018

AbstractMammalian genomes contain a fossilized record of ancient retroviral infections in the form of endogenous retroviruses (ERVs). We used whole genome sequence data to assess the origin and evolution of the recently active ERV-Fc gammaretroviral lineage based on the record of past infections retained in the genome of the domestic dog,Canis lupus familiaris.We identified 165 loci, including 58 insertions absent from the dog reference assembly, and characterized element polymorphism across 332 canids from nine species. Insertions were found throughout the dog genome including within and near gene models. Analysis of 19 proviral sequences identified shared disruptive mutations indicating defective proviruses were spread via complementation. The patterns of ERV polymorphism and sequence variation indicate multiple circulating viruses infected canid ancestors within the last 20 million to within 1.6 million years with a recent bust of germline invasion in the lineage leading to wolves and dogs.
R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations
Authors: Broman Karl W. , Gatti Daniel M. , Simecek Petr , Furlotte Nicholas A. , Prins Pjotr , Sen Śaunak , Yandell Brian S. , Churchill Gary A. 
Published: September 2018

AbstractR/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely-used R/qtl software package to include multi-parent populations derived from more than two founder strains, such as the Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. R/qtl2 is designed to handle modern high-density genotyping data and high-dimensional molecular phenotypes including gene expression and proteomics. R/qtl2 includes the ability to perform genome scans using a linear mixed model to account for population structure, and also includes features to impute SNPs based on founder strain genomes and to carry out association mapping. The R/qtl2 software provides all of the basic features needed for QTL mapping, including graphical displays and summary reports, and it can be extended through the creation of add-on packages. R/qtl2 comes with a test framework and is free and open source software written in the R and C++ programming languages.
Cul4-Ddb1 ubiquitin ligases facilitate DNA replication-coupled sister chromatid cohesion through regulation of cohesin acetyltransferase Esco2
Authors: Sun Haitao , Zhang Jiaxin , Zhang Jingjing , Li Zhen , Cao Qinhong , Lou Huiqiang 
Published: September 2018

AbstractCohesin acetyltransferases Esco1 and Esco2 play a vital role in establishing sister chromatid cohesion. How Esco1 and Esco2 are controlled to achieve this in a DNA replication-coupled manner remains unclear in higher eukaryotes. Here we show that Cul4-RING ligases (CRL4s) play a critical role in sister chromatid cohesion in human cells. Depletion of Cul4A, Cul4B or Ddb1 subunits substantially reduces normal cohesion efficiency. We also show that Mms22L, a vertebrate ortholog of yeast Mms22, is one of Ddb1 and Cul4-associated factors (DCAFs) involved in cohesion. Several lines of evidence suggest a selective interaction of CRL4s with Esco2, but not Esco1. Depletion of either CRL4s or Esco2 causes a defect in Smc3 acetylation which can be rescued by HDAC8 inhibition. More importantly, both CRL4s and PCNA act as mediators for efficiently stabilizing Esco2 on chromatin and catalyzing Smc3 acetylation. Taken together, we propose an evolutionarily conserved mechanism in which CRL4s and PCNA regulate Esco2-dependent establishment of sister chromatid cohesion.Author summaryWe identified human Mms22L as a substrate specific adaptor of Cul4-Ddb1 E3 ubiquitin ligase. Downregulation of Cul4A, Cul4B or Ddb1 subunit causes reduction of acetylated Smc3, via interaction with Esco2 acetyltransferase, and then impairs sister chromatid cohesion in 293T cells. We found functional complementation between Cul4-Ddb1-Mms22L E3 ligase and Esco2 in Smc3 acetylation and sister chromatid cohesion. Interestingly, both Cul4-Ddb1 E3 ubiquitin ligase and PCNA contribute to Esco2 mediated Smc3 acetylation. To summarise, we demonstrated an evolutionarily conserved mechanism in which Cul4-Ddb1 E3 ubiquitin ligases and PCNA regulate Esco2-dependent establishment of sister chromatid cohesion.
Diagnostic Whole Exome Sequencing in Patients with Short Stature
Authors: Zhu Huijuan , Yang Ziying , Sun Jun , Li Wei , Yang Hongbo , Wang Linjie , Gong Fengying , Chen Shi , Lu Lin , Miao Hui , Yuan Xianxian , Liang Hanting , Li Ran , Huang Hui , Peng Zhiyu , Asan  , Pan Hui 
Published: September 2018

AbstractShort stature is among the most common reasons for children being referred to the pediatric endocrinology clinics. The cause of short stature is broad, in which genetic factors play a substantial role, especially in primary growth disorders. However, identifying the molecular causes for short stature remains as a challenge because of the high heterogeneity of the phenotypes. Here, whole exome sequencing (WES) was used to identify the genetic causes of short stature with unknown etiology for 20 patients aged from 1 to 16 years old. The genetic causes of short stature were identified in 9 of the 20 patients, corresponding to a molecular diagnostic rate of 45%. Notably, in 2 of the 9 patients identified with genetic causes, the diagnosed diseases based on WES are different from the original clinical diagnosis. Our results highlight the clinical utility of WES in the diagnosis of rare, high heterogeneity disorders.
Regulation of Histone Deacetylase 3 by Metal Cations and 10-Hydroxy-2E-DecenoicAcid: Possible Molecular Epigenetic Mechanisms of Queen-Worker Bee Differentiation
Authors: Polsinelli Gregory A. , Yu Hongwei D. 
Published: September 2018

AbstractHistone deacetylases (HDACs) catalyze the hydrolysis of ε-acetyl-lysine residues of histones. Removal of acetyl groups results in condensation of chromatin structure and repression of gene expression. Human class I, II, and IV HDACs are said to be zinc-dependent in that they require divalent zinc ions to catalyze the deacetylase reaction. HDACs are considered potential targets for the treatment of cancer due to their role in regulating transcription. They are also thought to play important roles in the development of organisms such as honey bees. The fatty acid, 10-hydroxy-2E-decenoic acid (10-HDA), which can account for up to 5% of royal jelly composition has been reported as an HDAC inhibitor. The crystal structure of the HDAC3:SMRT complex possesses two monovalent cations (MVCs) labeled as potassium with one MVC binding site near the active site Zn(II) and the second MVC binding site ≥20 Å from the active site Zn(II). We report here the inhibitory effects of excess Zn(II) on the catalytic activity of histone deacetylase 3 (HDAC3) bound to the deacetylase activating domain of nuclear receptor corepressor 2 (NCOR2). We also report the effects of varying concentrations of potassium ions where [K+] up to 10 mM increase HDAC3 activity with a maximum kcat/KM of approximately 80,000 M-1s-1 while [K+] above 10 mM inhibit HDAC3 activity. The inhibition constant (Ki) of 10-HDA was determined to be 5.32 mM. The regulatory effects of zinc, potassium, and 10-HDA concentration on HDAC3 activity suggest a strong correlation between these chemical species and epigenetic control over Apis mellifera caste differentiation among other control mechanisms.
Characterization of the early response ofArabidopsis thalianatoDickeya dadantiiinfection using expression profiling
Authors: Gijsegem Frédérique Van , Bitton Frédérique , Laborie Anne-Laure , Kraepiel Yvan , Pédron Jacques 
Published: September 2018

AbstractTo draw a global view of plant responses to interactions with the phytopathogenic enterobacteraleDickeya dadantii, a causal agent of soft rot diseases on many plant species, we analysed the earlyArabidopsisresponses toD. dadantiiinfection. We performed a genome-wide analysis of theArabidopsis thalianatranscriptome duringD. dadantiiinfection and conducted a genetic study of identified responses.A limited set of genes related to plant defence or interactions with the environment were induced at an early stage of infection, with an over-representation of genes involved in both the metabolism of indole glucosinolates (IGs) and the jasmonate (JA) defence pathway. Bacterial type I and type II secretion systems are required to trigger the induction of IG and JA-related genes while the type III secretion system appears to partially inhibit these defence pathways. UsingArabidopsismutants impaired in JA biosynthesis or perception, we showed that induction of some IG metabolism genes was COI1-dependent but, surprisingly, JA-independent. Moreover, characterisation ofD. dadantiidisease progression inArabidopsismutants impaired in JA or IG pathways showed that JA triggers an efficient plant defence response that does not involve IGs.The induction of the IG pathway by bacterial pathogens has been reported several timesin vitro. This study shows for the first time, that this induction does indeed occurin planta, but also that this line of defence is ineffective againstD. dadantiiinfection, in contrast to its role to counteract herbivorous or fungal pathogen attacks.