bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local network-level integration mediates effects of transcranial Alternating Current Stimulation
Authors: Fuscà Marco , Ruhnau Philipp , Neuling Toralf , Weisz Nathan 
Published: November 2017

AbstractTranscranial alternating current stimulation (tACS) has been proposed as a tool to draw causal inferences on the role of oscillatory activity in cognitive functioning and has the potential to induce long-term changes in cerebral networks. However, the mechanisms of action of tACS are not yet clear, though previous modeling works have suggested that variability may be mediated by local and network-level brain states. We used magnetoencephalography (MEG) to record brain activity from 17 healthy participants as they kept their eyes open (EO) or closed (EC) while being stimulated either with sham, weak, or strong alpha-tACS using a montage commonly assumed to target occipital areas. We reconstructed the activity of sources in all stimulation conditions by means of beamforming. The analysis of resting-state data revealed an interaction of the external stimulation with the endogenous alpha power difference between EO and EC in the posterior cingulate. This region is remote from occipital cortex, which showed strongest EC vs. EO alpha modulation, thus suggesting state-dependency long-range effects of tACS. In a follow-up analysis of this online-tACS effect, we find evidence that this dependency effect could be mediated by functional network changes: connection strength from the precuneus, a region adjusting for a measure of network integration in the two states (EC vs. EO during no-tACS), was significantly correlated with the state-dependency effect in the posterior cingulate (during tACS). No analogous correlation could be found for alpha power modulations in occipital cortex. Altogether, this is the first strong evidence to illustrate how functional network architectures can shape tACS effects.
Basal forebrain GABAergic innervation of olfactory bulb periglomerular interneurons
Authors: Sanz Diez Alvaro , Najac Marion , De Saint Jan Didier 
Published: November 2017

AbstractOlfactory bulb circuits are dominated by multiple inhibitory pathways that finely tune the activity of mitral and tufted cells, the principal neurons, and regulate odor discrimination. Granule cells mediate interglomerular lateral inhibition between mitral and tufted cells lateral dendrites whereas diverse subtypes of periglomerular (PG) cells mediate intraglomerular lateral inhibition between their apical dendrites. Deep short axon cells form broad intrabulbar inhibitory circuits that regulate both populations of interneurons. Little is known about the extrabulbar GABAergic circuits that control the activity of these various interneurons. We examined this question using patch-clamp recordings and optogenetics in olfactory bulb slices from transgenic mice. We show that axonal projections emanating from diverse basal forebrain GABAergic neurons densely project in all layers of the olfactory bulb. These long-range GABAergic projections provide a prominent synaptic input on granule and short axon cells in deep layers as well as on selective subtypes of PG cells. Specifically, three different subclasses of type 2 PG cells receive robust and target-specific basal forebrain inputs but have little local interactions with other PG cells. In contrast, type 1 PG cells are not innervated by basal forebrain fibers but do interact with other PG cells. Thus, attention-regulated basal forebrain inputs regulate inhibition in all layers of the olfactory bulb with a previously overlooked synaptic complexity that further defines interneuron subclasses.Key points summaryBasal forebrain long-range projections to the olfactory bulb are important for olfactory sensitivity and odor discrimination.Using optogenetics, we confirm that basal forebrain afferents mediate IPSCs on granule and deep short axon cells. We also show that they selectively innervate specific subtypes of periglomerular (PG) cells.Three different subtypes of type 2 PG cells receive GABAergic IPSCs from the basal forebrain but not from other PG cells.Type 1 PG cells, in contrast, do not receive inputs from the basal forebrain but do receive inhibition from other PG cells.These results bring new light on the complexity and specificity of glomerular inhibitory circuits, as well as on their modulation by the basal forebrain.
Do priority effects outweigh environmental filtering in a guild of dominant freshwater macroinvertebrates?
Authors: Little Chelsea J. , Altermatt Florian 
Published: November 2017

AbstractAbiotic conditions have long been considered essential in structuring freshwater macroinvertebrate communities. Ecological drift, dispersal, and biotic interactions also structure communities, and although these mechanisms are more difficult to detect, they may be of equal importance in natural communities. Here, we conducted repeated surveys of locally-dominant amphipod species across ten naturally replicated stream catchments. We then used a hierarchical joint species distribution model to assess the influence of different drivers on species co-occurrences. The species had unique environmental requirements, but a distinct spatial structure in their distributions was unrelated to habitat. Species co-occurred much less frequently than predicted by their niches, which was surprising because laboratory and field evidence suggests they are capable of coexisting in equal densities. We suggest that niche preemption may limit their distribution and that a blocking effect determines which species colonizes and dominates a given stream catchment, thus resolving a long-standing conundrum in freshwater ecology.
Visual working memory is independent of the cortical spacing between memoranda
Authors: Harrison William J. , Bays Paul M. 
Published: November 2017

AbstractThe sensory recruitment hypothesis states that visual short term memory is maintained in the same visual cortical areas that initially encode a stimulus’ features. Although it is well established that the distance between features in visual cortex determines their visibility, a limitation known as crowding, it is unknown whether short term memory is similarly constrained by the cortical spacing of memory items. Here we investigated whether the cortical spacing between sequentially presented memoranda affects the fidelity of memory in humans (of both sexes). In a first experiment, we varied cortical spacing by taking advantage of the log-scaling of visual cortex with eccentricity, sequentially presenting memoranda in peripheral vision along either the radial or tangential visual axis with respect to the fovea. In a second experiment, we sequentially presented memoranda either within or beyond the critical spacing of visual crowding, a distance within which visual features cannot be perceptually distinguished due to their nearby cortical representations. In both experiments and across multiple measures, we found strong evidence that the ability to maintain visual features in memory is unaffected by cortical spacing. These results indicate that the neural architecture underpinning working memory has properties inconsistent with the known behaviour of sensory neurons in visual cortex. Instead, the dissociation between perceptual and memory representations supports a role of higher cortical areas, such as posterior parietal or prefrontal regions, or may involve an as yet unspecified mechanism in visual cortex in which stimulus features are bound to their temporal order.Significance StatementAlthough much is known about the resolution with which we can remember visual objects, the cortical representation of items held in short term memory remains contentious. A popular hypothesis suggests that memory of visual features is maintained via the recruitment of the same neural architecture in sensory cortex that encodes stimuli. We investigated this claim by manipulating the spacing in visual cortex between sequentially presented memoranda such that some items shared cortical representations more than others, while preventing perceptual interference between stimuli. We found clear evidence that short term memory is independent of the intra-cortical spacing of memoranda, revealing a dissociation between perceptual and memory representations. Our data indicate that working memory relies on different neural mechanisms from sensory perception.
Russian doll genes and complex chromosome rearrangements inOxytricha trifallax
Authors: Braun Jasper , Nabergall Lukas , Neme Rafik , Landweber Laura F. , Saito Masahico , Jonoska Nataša 
Published: November 2017

ABSTRACTCiliates have two different types of nuclei per cell, with one acting as a somatic, transcriptionally active nucleus (macronucleus; abbr. MAC) and another serving as a germline nucleus (micronucleus; abbr. MIC). Furthermore,Oxytricha trifallaxundergoes extensive genome rearrangements during sexual conjugation and post-zygotic development of daughter cells. These rearrangements are necessary because the precursor MIC loci are often both fragmented and scrambled, with respect to the corresponding MAC loci. Such genome architectures are remarkably tolerant of encrypted MIC loci, because RNA-guided processes during MAC development reorganize the gene fragments in the correct order to resemble the parental MAC sequence. Here, we describe the germline organization of several nested and highly scrambled genes inOxytricha trifallax. These include cases with multiple layers of nesting, plus highly interleaved or tangled precursor loci that appear to deviate from previously described patterns. We present mathematical methods to measure the degree of nesting between precursor MIC loci, and revisit a method for a mathematical description of scrambling. After applying these methods to the chromosome rearrangement maps ofO. trifallaxwe describe cases of nested arrangements with up to five layers of embedded genes, as well as the most scrambled loci inO. trifallax.
Breaking the spell of nestedness
Authors: Payrató Borrás Clàudia , Hernández Laura , Moreno Yamir 
Published: November 2017

AbstractMutualistic interactions, which are beneficial for both interacting species, are recurrently present in ecosystems. Observations of natural systems showed that, if we draw mutualistic relationships as binary links between species, the resulting bipartite network of interactions displays a widespread particular ordering called nestedness [1]. On the other hand, theoretical works have shown that a nested structure has a positive impact on a number of relevant features ranging from species coexistence [2], to a higher structural stability of communities and biodiversity [3,4]. However, how nestedness emerges and what are its determinants, are still open challenges that have led to multiple debates to date [5–7]. Here, we show, by applying a theoretical approach to the analysis of 167 real mutualistic networks, that nestedness is not an irreducible feature, but a consequence of the degree sequences of both guilds of the mutualistic network. Remarkably, we find that an outstanding majority of the analyzed networks does not show statistical significant nestedness. These findings point to the need of revising previous claims about the role of nestedness and might contribute to expand our understanding of how evolution shapes mutualistic interactions and communities by placing the focus on the local properties rather than on global quantities.
The application of zeta diversity as a continuous measure of compositional change in ecology
Authors: Mcgeoch Melodie A. , Latombe Guillaume , Andrew Nigel R. , Nakagawa Shinichi , Nipperess David A. , Roige Mariona , Marzinelli Ezequiel M. , Campbell Alexandra H. , Vergés Adriana , Thomas Torsten , Steinberg Peter D. , Selwood Katherine E. , Hui Cang 
Published: November 2017

AbstractZeta diversity provides the average number of shared species acrossnsites (or shared operational taxonomic units (OTUs) acrossncases). It quantifies the variation in species composition of multiple assemblages in space and time to capture the contribution of the full suite of narrow, intermediate and wide-ranging species to biotic heterogeneity. Zeta diversity was proposed for measuring compositional turnover in plant and animal assemblages, but is equally relevant for application to any biological system that can be characterised by a row by column incidence matrix. Here we illustrate the application of zeta diversity to explore compositional change in empirical data, and how observed patterns may be interpreted. We use 10 datasets from a broad range of scales and levels of biological organisation – from DNA molecules to microbes, plants and birds – including one of the original data sets used by R.H. Whittaker in the 1960’s to express compositional change and distance decay using beta diversity. The applications show (i) how different sampling schemes used during the calculation of zeta diversity may be appropriate for different data types and ecological questions, (ii) how higher orders of zeta may in some cases better detect shifts, transitions or periodicity, and importantly (iii) the relative roles of rare versus common species in driving patterns of compositional change. By exploring the application of zeta diversity across this broad range of contexts, our goal is to demonstrate its value as a tool for understanding continuous biodiversity turnover and as a metric for filling the empirical gap that exists on spatial or temporal change in compositional diversity.
The cost of enforcing a marine protected area to achieve ecological targets for the recovery of fish biomass
Authors: Brown Christopher J , Parker Brett , Ahmadia Gabby N , Ardiwijaya Rizya , Purwanto  , Game Edward T 
Published: November 2017

AbstractProtected areas are the primary management tool for conserving ecosystems, yet their intended outcomes may often be compromised by poaching. Consequently, many protected areas are ineffective ‘paper parks’ that contribute little towards conserving ecosystems. Poaching can be prevented through enforcement and engaging with community members so they support protected areas. It is not clear how much needs to be spent on enforcement and engagement to ensure they are frequent enough to be effective at conserving biodiversity. We develop models of enforcement against illegal fishing in marine protected areas. We apply the models to data on fishing rates and fish biomass from a marine protected area in Raja Ampat, Indonesia and explore how frequent enforcement patrols need to be to achieve targets for coral reef fish biomass. Achieving pristine levels of reef fish biomass required almost year-round enforcement of the protected area. Surveillance of the protected area may also be enhanced if local fishers who support the reserve report on poaching. The opportunity for local fishing boats to participate in surveillance was too small for it to have much benefit for total reef fish biomass, which increases slowly. However, specific functional groups of fish have much higher population growth rates and their biomass was predicted to increase markedly with community surveillance. We conclude that budgets for park management must balance the cost of conducting frequent patrols against supporting alternative activities, like education to build community support. Optimized budgets will be much more likely to achieve ecological targets for recovering fish biomasses and will contribute to fiscal sustainability of protected areas.
Condensin’s ATPase Machinery Drives and Dampens Mitotic Chromosome Condensation
Authors: Elbatsh Ahmed M.O. , Raaijmakers Jonne A. , van der Weide Robin H. , Kuit de Bos Jelmi , Teunissen Hans , Bravo Sol , Medema René H. , de Wit Elzo , Haering Christian H. , Rowland Benjamin D. 
Published: November 2017

ABSTRACTChromosome condensation by condensin is essential for faithful chromosome segregation. Metazoans have two complexes, named condensin I and II. Both are thought to act by creating looped structures in DNA, but how they do so is unknown. Condensin’s SMC subunits together form a composite ATPase with two pseudo-symmetric ATPase sites. We reveal that these sites have opposite functions in the condensation process. One site drives condensation, while the other site rather has a dampening function. Mutation of this dampener site hyperactivates both condensin I and II complexes. We find that hyperactive condensin I efficiently shortens chromosomes in the total absence of condensin II. The two complexes form loops with different lengths, and specifically condensin II is key to the decatenation of sister chromatids and the formation of a straight chromosomal axis.
Improving the calling of non-invasive prenatal testing on 13-/18-/21-trisomy by support vector machine discrimination
Authors: Yang Jianfeng , Ding Xiaofan , Zhu Weidong 
Published: November 2017

AbstractWith the advance of next-generation sequencing technologies, non-invasive prenatal testing (NIPT) has been developed and employed in fetal aneuploidy screening on 13-/18-/21-trisomies through detecting cell-free fetal DNA (cffDNA) in maternal blood. Although Z test is widely used in NIPT nowadays, there is still necessity to improve its accuracy for removing a) false negatives and false positives, and b) the ratio of unclassified data, so as to reduce the potential harm to patients caused by these inaccuracies as well as the induced cost of retests.Employing multiple Z tests with machine-learning algorithm could provide a better prediction on NIPT data. Combining the multiple Z values with indexes of clinical signs and quality control, features were collected from the known samples and scaled for model training in support vector machine (SVM) discrimination. The trained model was applied to predict the unknown samples, which showed significant improvement. In 4752 qualified NIPT data, our method reached 100% accuracies on all three chromosomes, including 151 data that were grouped as unclassified by one-Z-value based method. Moreover, four false positives and four false negatives were corrected by using this machine-learning model.To our knowledge, this is the first study to employ support vector machine in NIPT data analysis. It is expected to replace the current one-Z-value based NIPT analysis in clinical use.
DiscoSnp-RAD: de novo detection of small variants for population genomics
Authors: Gauthier Jèrèmy , Mouden Charlotte , Suchan Tomasz , Alvarez Nadir , Arrigo Nils , Riou Chloé , Lemaitre Claire , Peterlongo Pierre 
Published: November 2017

AbstractWe present an original method to de novo call variants for Restriction site associated DNA Sequencing (RAD-Seq). RAD-Seq is a technique characterized by the sequencing of specific loci along the genome, that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, as STACKS or IPyRAD, are based on all-versus-all read comparisons, which require consequent time and computing resources. Based on the variant caller DiscoSnp, initially designed for shotgun sequencing, DiscoSnp-RAD avoids this pitfall as variants are detected by exploring the De Bruijn Graph built from all the read datasets. We tested the implementation on RAD data from 259 specimens of Chiastocheta flies, morphologically assigned to 7 species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within species structuration and the existence of two populations linked to their geographic distributions. Furthermore, our results show that DiscoSnp-RAD is at least one order of magnitude faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD data, and stands out from other tools due to his completely different principle, making it significantly faster, in particular on large datasets.LicenseGNU Affero general public licenseAvailabilityhttps://github.com/GATB/DiscoSnpContactjeremy.gauthier@inria.fr
GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens
Authors: Zhou Zhemin , Alikhan Nabil-Fareed , Sergeant Martin J. , Luhmann Nina , Vaz Cátia , Francisco Alexandre P. , Carriço João André , Achtman Mark 
Published: November 2017

AbstractCurrent methods struggle to reconstruct and visualise the genomic relationships of ≥100,000 bacterial genomes.GrapeTree facilitates the analyses of allelic profiles from 10,000’s of core genomes within a web browser window.GrapeTree implements a novel minimum spanning tree algorithm to reconstruct genetic relationships despite missing data together with a static “GrapeTree Layout” algorithm to render interactive visualisations of large trees.GrapeTree is a stand-along package for investigating Newick trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among >160,000 genomes from bacterial pathogens.The GrapeTree package was released under the GPL v3.0 Licence.
A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection
Authors: Singhania Akul , Verma Raman , Graham Christine M. , Lee Jo , Trang Tran , Richardson Matthew , Lecine Patrick , Leissner Philippe , Berry Matthew P.R. , Wilkinson Robert J. , Kaiser Karine , Rodrigue Marc , Woltmann Gerrit , Haldar Pranabashis , O’Garra Anne 
Published: November 2017

AbstractWhole blood transcriptional signatures distinguishing active tuberculosis patients from asymptomatic latently infected individuals exist. Consensus has not been achieved regarding the optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases. Here we show a blood transcriptional signature of active tuberculosis using RNA-Seq, confirming microarray results, that discriminates active tuberculosis from latently infected and healthy individuals, validating this signature in an independent cohort. Using an advanced modular approach, we utilise information from the entire transcriptome, which includes over-abundance of type I interferon-inducible genes and under-abundance ofIFNGandTBX21, to develop a signature that discriminates active tuberculosis patients from latently infected individuals, or those with acute viral and bacterial infections. We suggest methods targeting gene selection across multiple discriminant modules can improve development of diagnostic biomarkers with improved performance. Finally, utilising the modular approach we demonstrate dynamic heterogeneity in a longitudinal study of recent tuberculosis contacts.
Asubstratefor modular, extensible data-visualization
Authors: Matelsky Jordan K , Downs Joseph , Cowley Hannah , Wester Brock , Gray-Roncal William 
Published: November 2017

AbstractAs the scope of scientific questions increase and datasets grow larger, the visualization of relevant information correspondingly becomes more difficult and complex. Sharing visualizations amongst collaborators and with the public can be especially onerous, as it is challenging to reconcile software dependencies, data formats, and specific user needs in an easily accessible package. We presentsubstrate, a data-visualization framework designed to simplify communication and code reuse across diverse research teams. Our platform provides a simple, powerful, browser-based interface for scientists to rapidly build effective three-dimensional scenes and visualizations. We aim to reduce the gap of existing systems, which commonly prescribe a limited set of high-level components, that are rarely optimized for arbitrarily large data visualization or for custom data types. To further engage the broader scientific community and enable seamless integration with existing scientific workflows, we also presentpytri, a Python library that bridges the use ofsubstratewith the ubiquitous scientific computing platform,Jupyter. Our intention is to reduce the activation energy required to transition between exploratory data analysis, data visualization, and publication-quality interactive scenes.