bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust Estimation of the Phylogenetic Origin of Plastids Using a tRNA-Based Phyloclassifier
Authors: Lawrence Travis J. , Amrine Katherine C. H. , Swingley Wesley D. , Ardell David H. 
Published: October 2018

AbstractThe trait of oxygenic photosynthesis was acquired by the last common ancestor of Archaeplastida through endosymbiosis of the cyanobacterial progenitor of modern-day plastids. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies report contradictory evidence that plastids branch either early or late within the cyanobacterial Tree of Life. Here we describe CYANO-MLP, a general-purpose phyloclassifier of cyanobacterial genomes implemented using a Multi-Layer Perceptron. CYANO-MLP exploits consistent phylogenetic signals in bioinformatically estimated structure-function maps of tRNAs. CYANO-MLP accurately classifies cyanobacterial genomes into one of eight well-supported cyanobacterial clades in a manner that is robust to missing data, unbalanced data and variation in model specification. CYANO-MLP supports a late-branching origin of plastids: we classify 99.32% of 440 plastid genomes into one of two late-branching cyanobacterial clades with strong statistical support, and confidently assign 98.41% of plastid genomes to one late-branching clade containing unicellular starch-producing marine/freshwater diazotrophic Cyanobacteria. CYANO-MLP correctly classifies the chromatophore of Paulinella chromatophora and rejects a sister relationship between plastids and the early-branching cyanobacterium Gloeomargarita lithophora. We show that recently applied phylogenetic models and character recoding strategies fit cyanobacterial/plastid phylogenomic datasets poorly, because of heterogeneity both in substitution processes over sites and compositions over lineages.
Metatranscriptome profiling of the dynamic transcription of mRNA and sRNA of a probioticLactobacillusstrain in human gut
Authors: Wang Jicheng , Sun Zhihong , Qiao Jianmin , Chen Dong , Cheng Chao , Luo Xiaotian , Ding Jia , Zhang Jiachao , Hou Qiangchuan , Zhang Yi , Zhang Heping 
Published: October 2018

AbstractMetatranscriptomic sequencing has recently been applied to study how pathogens and probiotics affect human gastrointestinal (GI) tract microbiota, which provides new insights into their mechanisms of action. In this study, metatranscriptomic sequencing was applied to deduce thein vivoexpression patterns of an ingestedLactobacillus caseistrain, which was compared with itsin vitrogrowth transcriptomes. Extraction of the strain-specific reads revealed that transcripts from the ingestedL. caseiwere increased, while those from the residentL. paracaseistrains remained unchanged. Mapping of all metatranscriptomic reads and transcriptomic reads toL. caseigenome showed that gene expressionin vitroandin vivodiffered dramatically. About 39% (1163) mRNAs and 45% (93) sRNAs ofL. caseiwell-expressed were repressed after ingested into human gut. Expression of ABC transporter genes and amino acid metabolism genes was induced at day-14 of ingestion; and genes for sugar and SCFA metabolisms were activated at day-28 of ingestion. Moreover, expression of sRNAs specific to thein vitrolog phase was more likely to be activated in human gut. Expression of rli28c sRNA with peaked expression during thein vitrostationary phase was also activated in human gut; this sRNA repressedL. caseigrowth and lactic acid productionin vitro. These findings implicate that the ingestedL. caseimight have to successfully change its transcription patterns to survive in human gut, and the time-dependent activation patterns indicate a highly dynamic cross-talk between the probiotic and human gut including its microbe community.ImportanceProbiotic bacteria are important in food industry and as model microorganisms in understanding bacterial gene regulation. Although probiotic functions and mechanisms in human gastrointestinal tract are linked to the unique probiotic gene expression, it remains elusive how transcription of probiotic bacteria is dynamically regulated after being ingested. Previous study of probiotic gene expression in human fecal samples has been restricted due to its low abundance and the presence of of closely related species. In this study, we took the advantage of the good depth of metatranscriptomic sequencing reads and developed a strain-specific read analysis method to discriminate the transcription of the probioticLactobacillus caseiand those of its resident relatives. This approach and additional bioinformatics analysis allowed the first study of the dynamic transcriptome profiles of probioticL casei in vivo. The novel findings indicate a highly regulated repression and dynamic activation of probiotic genome in human GI tract.
Tissue-specific genes as an underutilized resource in drug discovery
Authors: Ryaboshapkina Maria , Hammar Mårten 
Published: October 2018

ABSTRACTTissue-specific genes are believed to be good drug targets due to improved safety. Here we show that this intuitive notion is not reflected in phase 1 and 2 clinical trials, despite the historic success of tissue-specific targets and their 2.3-fold overrepresentation among targets of marketed non-oncology drugs. We compare properties of tissue-specific genes and drug targets. We show that tissue-specificity of the target may also be related to efficacy of the drug. The relationship may be indirect (enrichment in Mendelian disease genes) or direct (elevated ability to spread perturbations in human protein-protein interactome for tissue-specifically produced enzymes and secreted proteins). Reduced evolutionary conservation of tissue-specific genes may represent a bottleneck for drug projects, prompting development of novel models with smaller evolutionary gap to humans. We highlight numerous open opportunities to use tissue-specific genes in drug research and hope that the current study will facilitate discovery efforts.
I knew that! Response-based Outcome Predictions and Confidence Regulate Feedback Processing and Learning
Authors: Frömer R. , Nassar M.R. , Bruckner R. , Stürmer B. , Sommer W. , Yeung N. 
Published: October 2018

AbstractInfluential theories emphasize the importance of predictions in learning: we learn from feedback to the extent that it is surprising, and thus conveys new information. Here we explore the hypothesis that surprise depends not only on comparing current events to past experience, but also on online evaluation of performance via internal monitoring. Specifically, we propose that people leverage insights from response-based performance monitoring – outcome predictions and confidence – to control learning from feedback. In line with predictions from a Bayesian inference model, we find that people who are better at calibrating their confidence to the precision of their outcome predictions learn more quickly. Further in line with our proposal, EEG signatures of feedback processing are sensitive to the accuracy of, and confidence in, post-response outcome predictions. Taken together, our results suggest that online predictions and confidence serve to calibrate neural error signals to improve the efficiency of learning.
Affectively biased competition: sustained attention is tuned to rewarding expressions and is not modulated by norepinephrine receptor gene variant
Authors: Roberts Kevin H. , Manaligod Maria G. M. , Ross Colin J. D. , Müller Daniel J. , Wieser Matthias J. , Todd Rebecca M. 
Published: October 2018

AbstractIt is well established that emotionally salient stimuli evoke greater visual cortex activation than neutral ones, and can distract attention from competing tasks. Yet less is known about underlying neurobiological processes. As a proxy of population level biased competition, EEG steady-state visual evoked potentials are sensitive to competition effects from salient stimuli. Here we wished to examine whether individual differences in norepinephrine activity play a role in emotionally-biased competition.Our previous research has found robust effects of a common variation in the ADRA2B gene, coding for alpha2B norepinephrine (NE) receptors, on emotional modulation of attention and memory. In the present study, EEG was collected while 87 carriers of the ADRA2B deletion variant and 95 non-carriers (final sample) performed a change detection task in which target gratings (gabor patches) were superimposed directly over angry, happy, and neutral faces. Participants indicated the number of phase changes (0-3) in the target. Overlapping targets and distractors were flickered at a distinct driving frequencies. Relative EEG power for faces vs. targets at the driving frequency served as an index of cortical resources allocated to each of the competing stimuli. Deletion carriers and non-carriers were randomly assigned to Discovery and Replication samples and reliability of results across samples was assessed before the groups were combined for greater power.Overall happy faces evoked higher competition than angry or neutral faces; however, we observed no hypothesized effects of ADRA2B. Increased competition from happy faces was not due to the effect of low-level visual features or individuals low in social anxiety. Our results indicate that emotionally biased competition during sustained attention, while reliably observed in young adults, is not influenced by commonly observed individual differences linked to NE receptor function. They further indicate an overall pattern of affectively-biased competition for happy faces, which we interpret in relation to previously observed boundary conditions.
ADAR2-mediated Q/R editing of GluK2 regulates kainate receptor upscaling in response to suppression of synaptic activity
Authors: Gurung Sonam , Evans Ashley J. , Wilkinson Kevin A. , Henley Jeremy M. 
Published: October 2018

AbstractKainate receptors (KARs) regulate neuronal excitability and network function. Most KARs contain the subunit GluK2 and the properties of these receptors are determined in part by ADAR2-mediated mRNA editing of GluK2 that changes a genomically encoded glutamine (Q) to arginine (R). Suppression of synaptic activity reduces ADAR2-dependent Q/R editing of GluK2 with a consequential increase in GluK2-containing KAR surface expression. However, the mechanism underlying this reduction in GluK2 editing has not been addressed. Here we show that induction of KAR upscaling results in proteasomal degradation of ADAR2, which reduces GluK2 Q/R editing. Because KARs incorporating unedited GluK2(Q) assemble and exit the ER more efficiently this leads to an upscaling of KAR surface expression. Consistent with this, we demonstrate that partial ADAR2 knockdown phenocopies and occludes KAR upscaling. Moreover, we show that although the AMPAR subunit GluA2 also undergoes ADAR2-dependent Q/R editing, this process does not mediate AMPAR upscaling. These data demonstrate that activity-dependent regulation of ADAR2 proteostasis and GluK2 Q/R editing are key determinants of KAR, but not AMPAR, trafficking and upscaling.Summary statementSynaptic suppression promotes proteasomal degradation of the mRNA-editing enzyme ADAR2. Decreased ADAR2 levels reduce Q/R editing of the kainate receptor subunit GluK2 leading to enhanced surface expression and homeostatic upscaling.
Mutually exclusive locales for N-linked glycans and disorder in glycoproteins
Authors: Singh Alvina , Kumari Indu , Pally Dharma , Goutham Shyamili , Ghosh Sujasha , Akhter Yusuf , Bhat Ramray 
Published: October 2018

AbstractSeveral post-translational modifications of proteins lie within regions of disorder, stretches of amino acid residues that exhibit a dynamic tertiary structure and resist crystallization. Such localization has been proposed to expand the binding versatility of the disordered regions, and hence, the repertoire of interacting partners for the proteins. However, investigating a dataset of 500 human N-linked glycoproteins, we observed that the sites of N-linked glycosylations, or N-glycosites, lay predominantly within the regions of predicted order rather than their unstructured counterparts. This mutual exclusivity between disordered stretches and N-glycosites could not be reconciled merely through asymmetry in distribution of asparagines, serines or threonines residues, which comprise the minimum-required signature for conjugation by N-linked glycans, but rather by a contextual enrichment of these residues next to each other within the ordered portions. In fact, N-glycosite neighborhoods and disordered stretches showed distinct sets of enriched residues suggesting their individualized roles in protein phenotype. N-glycosite neighborhood residues also showed higher phylogenetic conservation than disordered stretches within amniote orthologs of glycoproteins. However, a universal search for residue-combinations that are putatively domain-constitutive ranked the disordered regions higher than the N-glycosite neighborhoods. We propose that amino acid residue-combinations bias the permissivity for N-glycoconjugation within ordered regions, so as to balance the tradeoff between the evolution of protein stability, and function, contributed by the N-linked glycans and disordered regions respectively.
Mis-perception of motion in depth originates from an incomplete transformation of retinal signals
Authors: Scott Murdison T. , Leclercq Guillaume , Lefèvre Philippe , Blohm Gunnar 
Published: October 2018

AbstractDepth perception requires the use of an internal model of the eye-head geometry to infer distance from binocular retinal images and extraretinal 3D eye-head information, particularly ocular vergence. Similarly for motion in depth perception, gaze angle is required to correctly interpret the spatial direction of motion from retinal images; however, it is unknown whether the brain can make adequate use of extraretinal version and vergence information to correctly interpret binocular retinal motion for spatial motion in depth perception. Here, we tested this by asking participants to reproduce the perceived spatial trajectory of an isolated point stimulus moving on different horizontal-depth paths either peri-foveally or peripherally while participants’ gaze was oriented at different vergence and version angles. We found large systematic errors in the perceived motion trajectory that reflected an intermediate reference frame between a purely retinal interpretation of binocular retinal motion (ignoring vergence and version) and the spatially correct motion. A simple geometric model could capture the behavior well, revealing that participants tended to underestimate their version by as much as 17%, overestimate their vergence by as much as 22%, and underestimate the overall change in retinal disparity by as much as 64%. Since such large perceptual errors are not observed in everyday viewing, we suggest that other monocular and/or contextual cues are required for accurate real-world motion in depth perception.
Microplate Assay for Denatured Collagen using Collagen Hybridizing Peptides
Authors: Lin Allen H. , Zitnay Jared L. , Li Yang , Yu S. Michael , Weiss Jeffrey A. 
Published: October 2018

ABSTRACTThe purpose of this study was to develop a microplate assay for quantifying denatured collagen by measuring the fluorescence of carboxyfluorescein bound collagen hybridizing peptides (F-CHP). We have shown that F-CHP binds selectively with denatured collagen, and that mechanical overload of tendon fascicles causes collagen denaturation. Proteinase K was used to homogenize tissue samples after F-CHP staining, allowing fluorescence measurement using a microplate reader. We compared our new assay to our previous image analysis method and the trypsin-hydroxyproline assay, which is the only other available method to directly quantify denatured collagen. Relative quantification of denatured collagen was performed in rat tail tendon fascicles subjected to incremental tensile overload, and normal and ostoeoarthritic guinea pig cartilage. In addition, the absolute amount of denatured collagen was determined in rat tail tendon by correlating F-CHP fluorescence with percent denatured collagen as determined by the trypsin-hydroxyproline assay. Rat tail tendon fascicles stretched to low strains (<7.5%) exhibited minimal denature collagen, but values rapidly increased at medium strains (7.5-10.5%) and plateaued at high strains (≥12%). Osteoarthritic cartilage had higher F-CHP fluorescence than healthy cartilage. Both of these outcomes are consistent with previous studies. With the calibration curve, the microplate assay was able to absolutely quantify denatured collagen in mechanically damaged rat tail tendon fascicles as reliably as the trypsin-hydroxyproline assay. Further, we achieved these results more efficiently than current methods in a rapid, high-throughput manner, with multiple types of collagenous tissue while maintaining accuracy.
The effects of training population design on genomic prediction accuracy in wheat
Authors: Edwards Stefan McKinnon , Buntjer Jaap B. , Jackson Robert , Bentley Alison R. , Lage Jacob , Byrne Ed , Burt Chris , Jack Peter , Berry Simon , Flatman Edward , Poupard Bruno , Smith Stephen , Hayes Charlotte , Gaynor R. Chris , Gorjanc Gregor , Howell Phil , Ober Eric , Mackay Ian J. , Hickey John M. 
Published: October 2018

AbstractGenomic selection offers several routes for increasing genetic gain or efficiency of plant breeding programs. In various species of livestock there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeder’s equation. Accurate predictions of genomic breeding value are central to this and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable accurate predictions.To quantify the effect of some of the properties of training sets on the accuracy of genomic selection in crops we performed an extensive field-based winter wheat trial. In summary, this trial involved the construction of 44 F2:4 bi- and triparental populations, from which 2992 lines were grown on four field locations and yield was measured. For each line, genotype data were generated for 25,000 segregating single nucleotide polymorphism markers. The overall heritability of yield was estimated to 0.65, and estimates within individual families ranged between 0.10 and 0.85. Within cross genomic prediction accuracies of yield BLUEs were 0.125 – 0.127 using two different cross-validation approaches, and generally increased with training set size. Using related crosses in training and validation sets generally resulted in higher prediction accuracies than using unrelated crosses. The results of this study emphasize the importance of the training set design in relation to the genetic material to which the resulting prediction model is to be applied.
Programmed Delayed Splicing: A Mechanism for Timed Inflammatory Gene Expression
Authors: Majumdar Devdoot S. , Frankiw Luke , Burns Christian H. , Garcia-Flores Yvette , Baltimore David 
Published: October 2018

SUMMARYInflammation involves timed gene expression, suggesting that the fine-tuned onset, amplitude, and termination of expression of hundreds of genes is of critical importance to organismal homeostasis. Recent study of post-transcriptional regulation of inflammatory gene expression led to the suggestion of a regulatory role for pre-mRNA splicing. Here, using a hybrid capture approach to purify incompletely spliced, chromatin-associated pre-mRNAs, we use deep sequencing to study pre-mRNA splicing of the NF-kB transcriptome. By freezing transcription and examining subsequent splicing of complete transcripts, we find many introns splice tens to hundreds of times slower than average. In many cases, this is attributable to poor splice donor sequences that are evolutionarily conserved. When these introns were altered by ~2 base pairs to yield stronger splice donors, gene expression levels increased markedly for several genes in the context of a reporter system. We propose that such splice sites represent a regulatory mechanism that determines the timing of production of the mRNAs from certain inflammatory genes and may also limit mRNA expression from these genes. Further work will be needed to understand the roles of this regulation in the inflammatory response. The suggestion of extensive temporal regulation of pre-mRNA splicing as a regulatory process in inflammation raises the question of where else in biology there may be timed processes with a similar underlying cause.
A bibliometric analysis of event detection in social media
Authors: Chen Xieling , Wang Shan , Tang Yong , Hao Tianyong 
Published: October 2018

Purpose
The purpose of this paper is to explore the research status and development trend of the field of event detection in social media (ED in SM) through a bibliometric analysis of academic publications.

Design/methodology/approach
First, publication distributions are analyzed including the trends of publications and citations, subject distribution, predominant journals, affiliations, authors, etc. Second, an indicator of collaboration degree is used to measure scientific connective relations from different perspectives. A network analysis method is then applied to reveal scientific collaboration relations. Furthermore, based on keyword co-occurrence analysis, major research themes and their evolutions throughout time span are discovered. Finally, a network analysis method is applied to visualize the analysis results.

Findings
The area of ED in SM has received increasing attention and interest in academia with Computer Science and Engineering as two major research subjects. The USA and China contribute the most to the area development. Affiliations and authors tend to collaborate more with those within the same country. Among the 14 identified research themes, newly emerged themes such as Pharmacovigilance event detection are discovered.

Originality/value
This study is the first to comprehensively illustrate the research status of ED in SM by conducting a bibliometric analysis. Up-to-date findings are reported, which can help relevant researchers understand the research trend, seek scientific collaborators and optimize research topic choices.