bluuebunny/crossref_metadata_2025_split huggingface dataset:
From image formation to image representation: the human visual system preserves the hierarchy of 2-dimensional pattern regularity
Authors: Kohler Peter J. , Norcia Anthony M. 
Published: November 2017

SummarySymmetries are present at many scales in images of natural scenes, due to a complex interplay of physical forces that govern pattern formation in nature. The importance of symmetry for visual perception has been known at least since the gestalt movement of the early 20thcentury. Since then, symmetry has been shown to contribute to the perception of shapes[1, 2] scenes[3] and surface properties[4], as well as the social process of mate selection[5]. In the two spatial dimensions relevant for images, the four fundamental symmetries, reflection, rotation, translation and glide reflection, can be combined in 17 distinct ways, the “wallpaper” groups[6–8]. The 17 wallpaper obey a hierarchy of complexity, determined by mathematical group theory, where simpler groups are subgroups of more complex ones[9]. Here we use Steady-State Visual Evoked Potentials (SSVEPs) to measure responses to the complete set of wallpaper groups, and present a complete description of the neural basis of symmetry. We find that activity in human visual cortex is remarkably consistent with the hierarchical relationships between the wallpaper groups. Specifically, the amplitudes of symmetry-specific responses in individual participants (n=25) preserve these relationships at an above-chance level in 88.3% (53 out of 60) of cases. Visual cortex thus encodes all the fundamental symmetries using a representational structure that closely approximates the subgroup relationships from group theory. Given that most participants had no knowledge of group theory, the ordered structure of visual responses to wallpaper groups is likely learned implicitly from regularities in the visual environment.
Effects of increased N and P availability on biomass allocation and root carbohydrate reserves differ between N-fixing and non-N-fixing savanna tree seedlings
Authors: Varma Varan , Catherin Arockia M , Sankaran Mahesh 
Published: November 2017

AbstractIn mixed tree-grass ecosystems, tree recruitment is limited by demographic bottlenecks to seedling establishment arising from inter- and intra-life form competition, and disturbances such as fire. Enhanced nutrient availability resulting from anthropogenic nitrogen (N) and phosphorus (P) deposition can alter the nature of these bottlenecks by changing seedling growth and biomass allocation patterns, and lead to longer-term shifts in tree community composition if different plant functional groups respond differently to increased nutrient availability. However, the extent to which tree functional types characteristic of savannas differ in their responses to increased N and P availability remains unclear. We quantified differences in above- and belowground biomass, and root carbohydrate contents – parameters known to influence the ability of plants to compete, as well as survive and recover from fires – in seedlings of multiple N-fixing and non-N-fixing tree species characteristic of Indian savanna and dry-forest ecosystems to experimental N and P additions. N-fixers in our study were co-limited by N and P availability, while non-N-fixers were N limited. Although both functional groups increased biomass production following fertilisation, non-N-fixers were more responsive and showed greater relative increases in biomass with fertilisation than N-fixers. N-fixers had greater baseline investment in belowground resources and root carbohydrate stocks, and while fertilisation reduced root:shoot ratios in both functional groups, root carbohydrate content only reduced with fertilisation in non-N-fixers. Our results indicate that, even within a given system, plants belonging to different functional groups can be limited by, and respond differentially to, different nutrients, suggesting that long-term consequences of nutrient deposition are likely to vary across savannas contingent on the relative amounts of N and P being deposited in sites.
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye
Authors: Sohn Jang-il , Nam Kyoungwoo , Hong Hyosun , Kim Jun-Mo , Lim Dajeong , Lee Kyung-Tai , Do Yoon Jung , Cho Chang Yeon , Kim Namshin , Chae Han-Ha , Nam Jin-Wu 
Published: November 2017

AbstractYeonsan Ogye (YO), an indigenous Korean chicken breed (gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short-reads (232.2X) and low-depth PacBio long-reads (11.5X). Although the contig and scaffold N50s (defined as the shortest contig or scaffold length at 50% of the entire assembly) of the initial de novo assembly were 53.6Kbp and 10.7Mbp, respectively, additional and pseudo-reference-assisted assemblies extended the assembly to 504.8Kbp for contig N50 (pseudo-contig) and 21.2Mbp for scaffold N50, which included 551 structural variations including the Fibromelanosis (FM) locus duplication, compared to galGal4 and 5. The completeness (97.6%) of the draft genome (Ogye_1) was evaluated with single copy orthologous genes using BUSCO, and found to be comparable to the current chicken reference genome (galGal5; 97.4%), which was assembled with a long read-only method, and superior to other avian genomes (92~93%), assembled with short read-only and hybrid methods. To comprehensively reconstruct transcriptome maps, RNA sequencing (RNA-seq) and representation bisulfite sequencing (RRBS) data were analyzed from twenty different tissues, including black tissues. The maps included 15,766 protein-coding and 6,900 long non-coding RNA genes, many of which were expressed in the tissue-specific manner, closely related with the DNA methylation pattern in the promoter regions.
Alpha/beta power compresses time in sub-second temporal judgments
Authors: van Viegen Tara , Charest Ian , Jensen Ole , Mazaheri Ali 
Published: November 2017

ABSTRACTWhile the perception of time plays a crucial role in our day-to-day functioning, the underlying neural mechanism of time processing on short time scales (~1s) remains to be elucidated. Recently, the power of beta oscillations (~20 Hz) has been suggested to play an important role in temporal processing. However, the paradigms supporting this view have often had confounds of working memory, as well as motor preparation. In the current EEG study, we set out to investigate if power of oscillatory activity would be involved in time perception without an explicit working memory component or confound of a motor response. Participants indicated through a button press whether the time between a tone and a visual stimulus was 1 or 1.5s.Critically, we focused on the differences in oscillatory activity in the alpha (~10 Hz) and beta (~20 Hz) ranges preceding correct versus incorrect temporal judgments. Behaviourally, we found participants made more errors on the long (1.5s) than on the short (1s) interval. In addition, we found that participants were fastest to correctly respond to a long interval. The onset of the tone induced a suppression of alpha and beta activity over occipital and parietal electrodes. In the long estimation intervals, this suppression was greater for correct than incorrect estimations. Interestingly, alpha and beta suppression allowed us to predict whether participants would judge the long interval correctly. For the short interval trials we did not find a significant difference in alpha or beta band activity for the correct and incorrect judgments. Taken together, our behavioural and EEG results suggest a multifaceted role of alpha and beta activity in the temporal estimation of sub- and supra-second intervals, where power increases seem to lead to temporal compression. Higher alpha and beta power resulted in shorter temporal judgments for sub-second intervals.HighlightsTemporal judgments without motor confounds were studied with EEG.Alpha/beta activity differences for correct and incorrect temporal judgments.Sub-second intervals were judged as short when alpha/beta power was higher.
Dorsomedial prefrontal cortex activity during learning discriminates response to Cognitive Behavioural Therapy in depression
Authors: Queirazza Filippo , Fouragnan Elsa , Steele J. Douglas , Cavanagh Jonathan , Philiastides Marios G. 
Published: November 2017

ABSTRACTBACKGROUNDCognitive behavioural therapy (CBT) is an effective evidence based treatment for depression. At present there is no reliable predictor of CBT in depression. Although the key to successful CBT in depression lies in altering maladaptive information processing, no previous imaging study has probed predictors of CBT response using pre-treatment neural encoding of information processing. METHODS: Using functional magnetic resonance imaging we scanned 37 unmedicated depressed subjects before and after completing computerised CBT (cCBT). We model the trial-by-trial appraisal of feedback information during a probabilistic learning task by means of a dynamic learning rate. To discriminate response to cCBT we capitalise on the pre-treatment blood oxygen level dependent (BOLD) activity encoding the dynamic learning rate as a function of feedback congruence and valence. Additionally, we probe between-group differences in the learning style encoded in the model’s parameters.RESULTSWe show BOLD activity in the dorsomedial prefrontal cortex (dmPFC) to be encoding the dynamic learning rate. Crucially, responders exhibit greater BOLD activity in the dmPFC during incongruent negative trials but lower BOLD activity during congruent negative trials than non-responders. Additionally, on between-group comparisons of model’s parameter estimates we show responders take relatively greater account of previous feedback history and make comparatively smaller adjustments to the learning rate as a result of outcome surprisingness.CONCLUSIONSOur findings provide novel and important insights into the cognitive mechanisms underpinning response to cCBT and lend support to the feasibility and validity of neurocomputational approaches to treatment prediction research in psychiatry.
Mapping the phenotypic repertoire of the cytoplasmic 2-Cys peroxiredoxin – thioredoxin system. 1. Understanding commonalities and differences among cell types
Authors: Selvaggio Gianluca , Coelho Pedro M. B. M. , Salvador Armindo 
Published: November 2017

AbstractThe system (PTTRS) formed by typical 2-Cys peroxiredoxins (Prx), thioredoxin (Trx), Trx reductase (TrxR), and sulfiredoxin (Srx) is central in antioxidant protection and redox signaling in the cytoplasm of eukaryotic cells. Understanding how the PTTRS integrates these functions requires tracing phenotypes to molecular properties, which is non-trivial. Here we analyze this problem based on a model that captures the PTTRS’ conserved features. We have mapped the conditions that generate each distinct response to H2O2 supply rates (νsup), and estimated the parameters for thirteen human cell types and for Saccharomyces cerevisiae. The resulting composition-to-phenotype map yielded the following experimentally testable predictions. The PTTRS permits many distinct responses including ultra-sensitivity and hysteresis. However, nearly all tumor cell lines showed a similar response characterized by limited Trx-S- depletion and a substantial but self-limited gradual accumulation of hyperoxidized Prx at high νsup. This similarity ensues from strong correlations between the TrxR, Srx and Prx activities over cell lines, which contribute to maintain the Prx-SS reduction capacity in slight excess over the maximal steady state Prx-SS production. In turn, in erythrocytes, hepatocytes and HepG2 cells high νsup depletes Trx-S- and oxidizes Prx mainly to Prx-SS. In all nucleated human cells the Prx-SS reduction capacity defined a threshold separating two different regimes. At sub-threshold νsup cytoplasmic H2O2 is determined by Prx, nM-range and spatially localized, whereas at supra-threshold νsup it is determined by much less active alternative sinks and μM-range throughout the cytoplasm. The yeast shows a distinct response where the Prx Tsa1 accumulates in sulfenate form at high νsup. This is mainly due to an exceptional stability of Tsa1’s sulfenate.The implications of these findings for thiol redox regulation and cell physiology are discussed. All estimates were thoroughly documented and provided, together with analytical approximations for system properties, as a resource for quantitative redox biology.AbbreviationsASK1, apoptosis signal-regulating kinase 1; Cat, catalase; GSH, glutathione; GPx1, glutathione peroxidase 1; Grx, glutaredoxin; KEAP1, Kelch-like ECH-associated protein 1; NRF2, nuclear factor erythroid 2-related factor 2; Prx, typical 2-Cys peroxiredoxin; PTTRS, peroxiredoxin / thioredoxin / thioredoxin reductase system; Srx, sulfiredoxin; Trx, thioredoxin; TrxR, thioredoxin reductase.
Prevalence of loss-of-function alleles does not correlate with lifetime fecundity and other life-history traits in metazoans
Authors: Bezmenova Aleksandra V. , Bazykin Georgii A. , Kondrashov Alexey S. 
Published: November 2017

AbstractNatural selection is possible only because all species produce more offspring than what is needed to maintain the population. Still, the lifetime number of offspring varies widely across species. One can expect natural selection to be stronger in high-fecundity species. We analyzed the prevalence of loss-of-function alleles in 32 metazoan species and have found that, in contrast to this expectation, the strength of negative selection does not correlate with lifetime fecundity, as well as with other life-history traits. Perhaps, higher random mortality in high-fecundity species negates the effect of increased opportunity for selection.
Is chaos making a difference? Synchronization transitions in chaotic and nonchaotic neuronal networks
Authors: Xu Kesheng , Maidana Jean Paul , Castro Samy , Orio Patricio 
Published: November 2017

AbstractChaotic dynamics of neural oscillations has been shown at the single neuron and network levels, both in experimental data and numerical simulations. Theoretical studies over the last twenty years have demonstrated an underlying role of chaos in neural systems. Nevertheless, whether chaotic neural oscillators make a significant contribution to relevant network behavior and whether the dynamical richness of neural networks are sensitive to the dynamics of isolated neurons, still remain open questions. We investigated transition dynamics of a medium-sized heterogeneous neural network of neurons connected by electrical coupling in a small world topology. We make use of an oscillatory neuron model (HB+Ih) that exhibits either chaotic or non-chaotic behavior at different combinations of conductance parameters. Measuring order parameter as a measure of synchrony, we find that the heterogeneity of firing rate and types of firing patterns make a greater contribution than chaos to the steepness of synchronization transition curve. We also show that chaotic dynamics of the isolated neurons do not always make a visible difference in process of network synchronization transitions. Moreover, the macroscopic chaos is observed regardless of the dynamics nature of the neurons. However, performing a Functional Connectivity Dynamics analysis, we show that chaotic nodes can promote what is known as the multi-stable behavior, where the network dynamically switches between a number of different semi-synchronized, metastable states.
C-terminal truncation of Pik3r1 in mice models human lipodystrophic insulin resistance uncoupled from dyslipidemia
Authors: Kwok Albert , Zvetkova Ilona , Virtue Sam , Huang-Doran Isabel , Tomlinson Patsy , Bulger David A. , Hart Daniel , Knox Rachel , Franks Stephen , Voshol Peter , Vidal-Puig Antonio , Sferruzzi-Perri Amanda N. , Jensen Jørgen , O’Rahilly Stephen , Semple Robert K 
Published: November 2017

SummaryHeterodimeric class IA phosphatidylinositol-3-kinases (PI3K) transduce signals from many receptor tyrosine kinases including the insulin receptor. PI3K recruitment to phosphotyrosines is mediated byPik3r1gene products including the most intensely studied PI3K regulatory subunit, p85α, which also binds and regulates the PIP3 phosphatasePten,and the lipogenic transcription factorXbp1.Mutations in humanPIK3R1cause SHORT syndrome, featuring lipodystrophy and severe insulin resistance which, uniquely, are uncoupled from fatty liver and dyslipidemia. We describe a novel mouse model of SHORT syndrome made by knock in of thePik3r1Y657X mutation. Homozygous embryos die at E11.5, while heterozygous mice exhibit pre-and postnatal growth impairment with diminished placental vascularity. Adipose tissue accretion on high fat feeding was reduced, however adipocyte size was unchanged and preadipocyte differentiationex vivounimpaired. Despite severe insulin resistance, heterozygous mice were hypolipidemic, and plasma adiponectin, liver weight, cholesterol, glycogen and triglyceride content were unchanged. Mild downregulation of lipogenicSrebp1, Srebp2andChrebptranscriptional activity but no suppression ofXbp1target genes was seen after fasting. These findings give new insights into the developmental role ofPik3r1,and establish a model of lipodystrophic insulin resistance dissociated from dyslipidemia as seen in SHORT syndrome.
DHSpred: support-vector-machine-based human DNase I hypersensitive sites prediction using the optimal features selected by random forest
Authors: Manavalan Balachandran , Shin Tae Hwan , Lee Gwang 
Published: November 2017

AbstractDNase I hypersensitive sites (DHSs) are genomic regions that provide important information regarding the presence of transcriptional regulatory elements and the state of chromatin. Therefore, identifying DHSs in uncharacterized DNA sequences is crucial for understanding their biological functions and mechanisms. Although many experimental methods have been proposed to identify DHSs, they have proven to be expensive for genome-wide application. Therefore, it is necessary to develop computational methods for DHS prediction. In this study, we proposed a support vector machine (SVM)-based method for predicting DHSs, called DHSpred (DNase I Hypersensitive Site predictor in human DNA sequences), which was trained with 174 optimal features. The optimal combination of features was identified from a large set that included nucleotide composition and di- and trinucleotide physicochemical properties, using a random forest algorithm. DHSpred achieved a Matthews correlation coefficient and accuracy of 0.660 and 0.871, respectively, which were 3% higher than those of control SVM predictors trained with non-optimized features, indicating the efficiency of the feature selection method. Furthermore, the performance of DHSpred was superior to that of state-of-the-art predictors. An online prediction server has been developed to assist the scientific community, and is freely available at:http://www.thegleelab.org/DHSpred.html.
MEGAN-LR: New algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs
Authors: Huson Daniel H. , Albrecht Benjamin , Bagci Caner , Bessarab Irina , Gorska Anna , Jolic Dino , Williams Rohan B.H. 
Published: November 2017

AbstractBackgroundThere are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing and there is a need to adapt short read tools to long read datasets.MethodsWe describe a new LCA-based algorithm for taxonomic binning, and an interval-tree based algorithm for functional binning, that are explicitly designed for long reads and assembled contigs. We provide a new interactive tool for investigating the alignment of long reads against reference sequences. For taxonomic and functional binning, we propose to use LAST to compare long reads against the NCBI-nr protein reference database so as to obtain frame-shift aware alignments, and then to process the results using our new methods.ResultsAll presented methods are implemented in the open source edition of MEGAN and we refer to this new extension as MEGAN-LR (MEGAN long read). We evaluate the LAST+MEGAN-LR approach in a simulation study, and on a number of mock community datasets consisting of Nanopore reads, PacBio reads and assembled PacBio reads. We also illustrate the practical application on a Nanopore dataset that we sequenced from an anammox bio-rector community.
Altered levels ofhsromegalncRNAs further enhance Ras signaling during ectopically activated Ras induced R7 differentiation inDrosophila
Authors: Ray Mukulika , Singh Gunjan , Lakhotia Subhash C. 
Published: November 2017

AbstractWe exploited the high Ras activity induced differentiation of supernumerary R7 cells inDrosophilaeyes to examine ifhsrωlncRNAs influence active Ras signaling. Surprisingly, either down- or up-regulation ofhsrωlncRNAs insev-GAL4>RasV12expressing eye discs resulted in complete pupal lethality and substantially greater increase in R7 photoreceptor number at the expense of cone cells. Enhanced nuclear p-MAPK and presence ofsev-GAL4driven RasV12bound RafRBDFLAG in cells not expressing thesev-GAL4driver indicated non-cell autonomous spread of Ras signaling whenhsrωlevels were co-altered. RNA-sequencing revealed that down-and up-regulation ofhsrωtranscripts insev-GAL4>RasV12expressing eye discs elevated transcripts of positive or negative modulators, respectively, of Ras signaling so that either condition enhances it. Alteredhsrωtranscript levels insev-GAL4>RasV12expressing discs also affected sn/sno/sca RNAs and some other RNA processing transcript levels. Post-transcriptional changes due to the disrupted intra-cellular dynamicity of omega speckle associated hnRNPs and other RNA-binding proteins that follow down- or up-regulation ofhsrωlncRNAs appear to be responsible for the further elevated Ras signaling. Cell autonomous and non-autonomous enhancement of Ras signaling by lncRNAs likehsrωhas implications for cell signaling during high Ras activity commonly associated with some cancers.HighlightsOur findings highlight roles ofhsrωlncRNAs in conditionally modulating the important Ras signaling pathway and provide evidence for cell non-autonomous Ras signaling inDrosophilaeye discs.