bluuebunny/crossref_metadata_2025_split huggingface dataset:
The wind and the magnetospheric accretion onto the T Tauri star S Coronae Australis at sub-au resolution
Authors:   GRAVITY Collaboration, Garcia Lopez R. , Perraut K. , Caratti o Garatti A. , Lazareff B. , Sanchez-Bermudez J. , Benisty M. , Dougados C. , Labadie L. , Brandner W. , Garcia P. J. V. , Henning Th. , Ray T. P. , Abuter R. , Amorim A. , Anugu N. , Berger J. P. , Bonnet H. , Buron A. , Caselli P. , Clénet Y. , Coudé du Foresto V. , de Wit W. , Deen C. , Delplancke-Ströbele F. , Dexter J. , Eckart A. , Eisenhauer F. , Garcia Dabo C. E. , Gendron E. , Genzel R. , Gillessen S. , Haubois X. , Haug M. , Haussmann F. , Hippler S. , Hubert Z. , Hummel C. A. , Horrobin M. , Jocou L. , Kellner S. , Kervella P. , Kulas M. , Kolb J. , Lacour S. , Le Bouquin J.-B. , Léna P. , Lippa M. , Mérand A. , Müller E. , Ott T. , Panduro J. , Paumard T. , Perrin G. , Pfuhl O. , Ramirez A. , Rau C. , Rohloff R.-R. , Rousset G. , Scheithauer S. , Schöller M. , Straubmeier C. , Sturm E. , Thi W. F. , van Dishoeck E. , Vincent F. , Waisberg I. , Wank I. , Wieprecht E. , Wiest M. , Wiezorrek E. , Woillez J. , Yazici S. , Zins G. 
Published: September 2017

Aims. To investigate the inner regions of protoplanetary discs, we performed near-infrared interferometric observations of the classical T Tauri binary system S CrA.
Methods. We present the first VLTI-GRAVITY high spectral resolution (R ~ 4000) observations of a classical T Tauri binary, S CrA (composed of S CrA N and S CrA S and separated by ~1.̋4), combining the four 8m telescopes in dual-field mode.
Results. Our observations in the near-infrared K-band continuum reveal a disc around each binary component, with similar half-flux radii of about 0.1 au at d ~ 130 pc, inclinations (i = 28 ± 3° and i = 22 ± 6°), and position angles (PA = 0°± 6° and PA = –2°± 12°), suggesting that they formed from the fragmentation of a common disc. The S CrA N spectrum shows bright He i and Brγ line emission exhibiting inverse P Cygni profiles, typically associated with infalling gas. The continuum-compensated Brγ line visibilities of S CrA N show the presence of a compact Brγ emitting region whose radius is about ~0.06 au, which is twice as big as the truncation radius. This component is mostly tracing a wind. Moreover, a slight radius change between the blue- and red-shifted Brγ line components is marginally detected.
Conclusions. The presence of an inverse P Cygni profile in the He i and Brγ lines, along with the tentative detection of a slightly larger size of the blue-shifted Brγ line component, hint at the simultaneous presence of a wind and magnetospheric accretion in S CrA N.
An Upper Bound for the Volumes of Complements of Periodic Geodesics
Authors: Bergeron Maxime , Pinsky Tali , Silberman Lior 
Published: September 2017

AbstractA periodic geodesic on a surface has a natural lift to the unit tangent bundle; when the complement of this lift is hyperbolic, its volume typically grows as the geodesic gets longer. We give an upper bound for this volume which is linear in the geometric length of the geodesic.
Bézout-Type Inequality in Convex Geometry
Authors: Xiao Jian 
Published: September 2017

AbstractInspired by a result of Soprunov and Zvavitch, we present a Bézout type inequality for mixed volumes, which holds true for any convex bodies and improves the previous result. The key ingredient is the reverse Khovanskii–Teissier inequality for convex bodies, which was obtained in our previous work and inspired by its correspondence in complex geometry.
Implantation of Depth Electrodes in Children Using VarioGuide® Frameless Navigation System: Technical Note
Authors: Budke Marcelo , Avecillas-Chasin Josue M , Villarejo Francisco 
Published: September 2017

Abstract

BACKGROUND
Electrode placement in epilepsy surgery seeks to locate the sites of ictal onset and early propagation. An invasive diagnostic procedure, stereoelectroencephalography (SEEG) is usually implemented with frame-based methods that can be especially problematic in young children.

OBJECTIVE
To evaluate the feasibility and accuracy of a new technique for frameless SEEG in children using the VarioGuide® system (Brainlab AG, München, Germany).

METHODS
A frameless stereotactic navigation system was used to implant depth electrodes with percutaneous drilling and bolt insertion in pediatric patients with medically refractory epilepsy. Data on general demographic information of electrode implantation, duration, number, and complications were retrospectively collected. To determine the placement accuracy of the VarioGuide® frameless system, the mean Euclidean distances were calculated by comparing the preoperatively planned trajectories with the final electrode position observed on postoperative computed tomography scans.

RESULTS
From May 2011 to December 2015, 15 patients (8 males, 7 females; mean age: 8 yr, range: 3-16 yr) underwent SEEG depth electrode implantation of a total of 111 electrodes. The mean error measured by the Euclidean distance from the center of the entry point to the intended entry point was 3.64 ± 1.78 mm (range: 0.58-7.59 mm) and the tip of the electrode to the intended target was 2.96 ± 1.49 mm (range: 0.58-7.82 mm). There were no significant complications.

CONCLUSION
Depth electrodes can be placed safely and accurately in children using the VarioGuide® frameless stereotactic navigation system.
Polygenic selection underlies evolution of human brain structure and behavioral traits
Authors: Beiter Evan R. , Khramtsova Ekaterina A. , Van Der Merwe Celia , Chimusa Emile R. , Simonti Corinne , Stein Jason , Thompson Paul , Fisher Simon E. , Stein Dan J. , Capra John A. , Knowles James A. , Stranger Barbara E. , Davis Lea K. 
Published: September 2017

AbstractSeemingly paradoxical characteristics of psychiatric disorders, including moderate to high prevalence, reduced fecundity, and high heritability have motivated explanations for the persistence of common risk alleles for severe psychiatric phenotypes throughout human evolution. Proposed mechanisms include balancing selection, drift, and weak polygenic adaptation acting either directly, or indirectly through selection on correlated traits. While many mechanisms have been proposed, few have been empirically tested. Leveraging publicly available data of unprecedented sample size, we studied twenty-five traits (i.e., ten neuropsychiatric disorders, three personality traits, total intracranial volume, seven subcortical brain structure volume traits, and four complex traits without neuropsychiatric associations) for evidence of several different signatures of selection over a range of evolutionary time scales. Consistent with the largely polygenic architecture of neuropsychiatric traits, we found no enrichment of trait-associated single-nucleotide polymorphisms (SNPs) in regions of the genome that underwent classical selective sweeps (i.e., events which would have driven selected alleles to near fixation). However, we discovered that SNPs associated with some, but not all, behaviors and brain structure volumes are enriched in genomic regions under selection since divergence from Neanderthals ~600,000 years ago, and show further evidence for signatures of ancient and recent polygenic adaptation. Individual subcortical brain structure volumes demonstrate genome-wide evidence in support of a mosaic theory of brain evolution while total intracranial volume and height appear to share evolutionary constraints consistent with concerted evolution. We further characterized the biological processes potentially targeted by selection, through expression Quantitative Trait Locus (eQTL) and Gene Ontology (GO) enrichment analyses and found evidence for the role of regulatory functions among selected SNPs in immune and brain tissues. Taken together, our results suggest that alleles associated with neuropsychiatric, behavioral, and brain volume phenotypes have experienced both ancient and recent polygenic adaptation in human evolution, acting through neurodevelopmental and immune-mediated pathways.
Analysis of the immunological biomarker profile during acute Zika virus infection reveals the overexpression of CXCL10, a chemokine already linked to neuronal damage
Authors: Naveca Felipe Gomes , Pontes Gemilson Soares , Chang Aileen Yu-hen , da Silva George Allan Villarouco , do Nascimento Valdinete Alves , da Silva Monteiro Dana Cristina , da Silva Marineide Souza , Abdalla Lígia Fernandes , Santos João Hugo Abdalla , de Almeida Tatiana Amaral Pires , del Carmen Contreras Mejía Matilde , de Mesquita Tirza Gabrielle Ramos , de Souza Encarnação Helia Valeria , de Souza Gomes Matheus , Amaral Laurence Rodrigues , Campi-Azevedo Ana Carolina , Coelho-dos-Reis Jordana Graziela , do Vale Antonelli Lis Ribeiro , Teixeira-Carvalho Andréa , Martins-Filho Olindo Assis , Ramasawmy Rajendranath 
Published: September 2017

AbstractInfection with Zika virus (ZIKV) manifests in a broad spectrum of disease ranging from mild illness to severe neurological complications. To define immunologic correlates of ZIKV infection, we characterized the levels of circulating cytokines, chemokines and growth factors in 54 infected patients of both genders, at five different time-points after symptoms onset using microbeads multiplex immunoassay; statistical analysis and data mining compared to 100 age-matched controls. ZIKV-infected patients present a striking systemic inflammatory response with high levels of pro-inflammatory mediators. Despite the strong inflammatory pattern, IL-1Ra and IL-4 are also induced during acute infection. Interestingly, the inflammatory cytokines, IL-1β, IL-13, IL-17, TNF-α, IFN-γ; chemokines, CXCL8, CCL2, CCL5; and the growth factor G-CSF display a bimodal distribution accompanying viremia. While this is the first manuscript to document bimodal distributions of viremia in ZIKV infection, bimodal viremia has been documented in other viral infections with primary viremia peaks during mild systemic disease and a secondary viremia with distribution of the virus to organs and tissues. Moreover, biomarker network analysis demonstrated distinct dynamics in consonance with the bimodal viremia profiles at different time-points during ZIKV infection. Such robust cytokine and chemokine response has been associated with blood-brain barrier permeability and neuroinvasiveness in other flaviviral infections. High-dimensional data analysis further established CXCL10, a chemokine involved in fetal neuron apoptosis and Guillain-Barré syndrome, as the most promising biomarker of acute ZIKV infection for a potential clinical application.Author SummaryInfection with Zika virus manifests in a broad spectrum of disease ranging from mild illness to severe neurological complications. This study characterized the levels of circulating cytokines, chemokines and growth factors in Zika-infected patients showing an inflammatory immune response. Specifically, this study identified a chemokine, CXCL10, known to be involved in fetal neuron apoptosis and Guillain-Barré syndrome, as the most promising biomarker to characterize acute Zika virus infection.
A novel data-driven model for real-time influenza forecasting
Authors: Venna Siva R. , Tavanaei Amirhossein , Gottumukkala Raju N. , Raghavan Vijay V. , Maida Anthony , Nichols Stephen 
Published: September 2017

AbstractWe provide data-driven machine learning methods that are capable of making real-time influenza forecasts that integrate the impacts of climatic factors and geographical proximity to achieve better forecasting performance. The key contributions of our approach are both applying deep learning methods and incorporation of environmental and spatio-temporal factors to improve the performance of the influenza forecasting models. We evaluate the method on Influenza Like Illness (ILI) counts and climatic data, both publicly available data sets. Our proposed method outperforms existing known influenza forecasting methods in terms of their Mean Absolute Percentage Error and Root Mean Square Error. The key advantages of the proposed data-driven methods are as following: (1) The deep-learning model was able to effectively capture the temporal dynamics of flu spread in different geographical regions, (2) The extensions to the deep-learning model capture the influence of external variables that include the geographical proximity and climatic variables such as humidity, temperature, precipitation and sun exposure in future stages, (3) The model consistently performs well for both the city scale and the regional scale on the Google Flu Trends (GFT) and Center for Disease Control (CDC) flu counts. The results offer a promising direction in terms of both data-driven forecasting methods and capturing the influence of spatio-temporal and environmental factors for influenza forecasting methods.
Genomic and transcriptomic signals of thermal tolerance in heat-tolerant corals (Platygyra daedalea) of the Arabian/Persian Gulf
Authors: Kirk Nathan L. , Howells Emily J. , Abrego David , Burt John A. , Meyer Eli 
Published: September 2017

AbstractScleractinian corals occur in tropical regions near their upper thermal limits, and are severely threatened by rising ocean temperatures. Ocean warming leads to loss of symbiotic algae (Symbiodinium), reduced fitness for the coral host, and degradation of the reef. However, several recent studies have shown that natural populations of corals harbor genetic variation in thermal tolerance that may support adaptive responses to warming. Here we’ve extended these approaches to study heat tolerance of corals in the Persian/Arabian Gulf, where heat-tolerant local populations have adapted to warm summer temperatures (>36°C). To evaluate whether selection has depleted genetic variation in thermal tolerance, estimate the potential for future adaptive responses, and understand the functional basis for these corals’ unusual heat tolerance, we measured thermal tolerance using controlled crosses in the Gulf coralPlatygyra daedalea. We found that heat tolerance is highly heritable in this population (0.487-0.748), suggesting substantial potential for adaptive responses to selection for thermal tolerance. To identify genetic markers associated with this variation, we conducted genomewide SNP genotyping in parental corals and tested for relationships between paternal genotype and thermal tolerance of the offspring. We found that multilocus SNP genotypes explained a large fraction of variation in thermal tolerance in these crosses (69%). To investigate the functional basis of these differences in thermal tolerance, we profiled transcriptional responses in tolerant and susceptible families, revealing substantial sire effects on transcriptional responses to thermal stress. We also studied sequence variation in these expressed sequences, identifying alleles and functional groups associated with thermal tolerance. Our findings demonstrate that corals in these populations harbor extensive genetic variation in thermal tolerance, and these heat-tolerant phenotypes differ in both gene sequences and transcriptional stress responses from their susceptible counterparts.
Inferring parameters for a lattice-free model of cell migration and proliferation using experimental data
Authors: Browning Alexander P. , McCue Scott W. , Binny Rachelle N. , Plank Michael J. , Shah Esha T. , Simpson Matthew J. 
Published: September 2017

AbstractCollective cell spreading takes place in spatially continuous environments, yet it is often modelled using discrete lattice-based approaches. Here, we use data from a series of cell proliferation assays, with a prostate cancer cell line, to calibrate a spatially continuous individual based model (IBM) of collective cell migration and proliferation. The IBM explicitly accounts for crowding effects by modifying the rate of movement, direction of movement, and the rate of proliferation by accounting for pair-wise interactions. Taking a Bayesian approach we estimate the free parameters in the IBM using rejection sampling on three separate, independent experimental data sets. Since the posterior distributions for each experiment are similar, we perform simulations with parameters sampled from a new posterior distribution generated by combining the three data sets. To explore the predictive power of the calibrated IBM, we forecast the evolution of a fourth experimental data set. Overall, we show how to calibrate a lattice-free IBM to experimental data, and our work highlights the importance of interactions between individuals. Despite great care taken to distribute cells as uniformly as possible experimentally, we find evidence of significant spatial clustering over short distances, suggesting that standard mean-field models could be inappropriate.
Increased axonal bouton stability during learning in the mouse model of MECP2 duplication syndrome
Authors: Ash Ryan T. , Fahey Paul G. , Park Jiyoung , Zoghbi Huda Y. , Smirnakis Stelios M. 
Published: September 2017

ABSTRACTMECP2-duplication syndrome is an X-linked form of syndromic autism caused by genomic duplication of the region encoding Methyl-CpG-binding protein 2. Mice overexpressingMECP2demonstrate altered patterns of learning and memory, including enhanced motor learning. Previous work associated this enhanced motor learning to abnormally increased stability of dendritic spine clusters formed in the apical tuft of corticospinal, area M1, neurons during rotarod training. In the current study, we measure the structural plasticity of axonal boutons in Layer 5 (L5) pyramidal neuron projections to layer 1 of area M1 during motor learning. In wild-type mice we find that during rotarod training, bouton formation rate changes minimally, if at all, while bouton elimination rate doubles. Notably, the observed upregulation in bouton elimination with learning is absent inMECP2-duplication mice. This result provides further evidence of imbalance between structural stability and plasticity in this form of syndromic autism. Furthermore, the observation that axonal bouton elimination doubles with motor learning in wild-type animals contrasts with the increase of dendritic spine consolidation observed in corticospinal neurons at the same layer. This dissociation suggests that different area M1 microcircuits may manifest different patterns of structural synaptic plasticity during motor learning.SIGNIFICANCE STATEMENTAbnormal balance between synaptic stability and plasticity is a feature of several autism spectrum disorders, often corroborated by in vivo studies of dendritic spine turnover. Here we provide the first evidence that abnormally increased stability of axonal boutons, the presynaptic component of excitatory synapses, occurs during motor learning in the MECP2 duplication syndrome mouse model of autism. In contrast, in normal controls, axonal bouton elimination in L5 pyramidal neuron projections to layer 1 of area M1 doubles with motor learning. The fact that axonal projection boutons get eliminated, while corticospinal dendritic spines get consolidated with motor learning in layer 1 of area M1, suggests that structural plasticity manifestations differ across different M1 microcircuits.
Statistical power of gene-set enrichment analysis is a function of gene set correlation structure
Authors: Swanson David M. 
Published: September 2017

AbstractMotivation:We describe why statistical power for both self-contained and competitive gene-set tests is a function of the correlation structure of co-expressed genes, and why this characteristic is undesirable for gene-set analyses. Variable statistical power as a function of gene correlation structure has not been observed or studied previously. The observation is important in part because gene-set testing methodology is well-developed, yet this fundamental feature of many of its tests is unknown and has the potential to reinterpret past gene-set test results and guide future implementations, including those using sequence data. Type 1 error inflation is also amenable for study in our statistical framework; while it has been well-studied and described previously for both self-contained and competitive tests, it has less often been done in an analytical framework. Our observations apply to four commonly-used gene-set testing approaches for microarrays, including CAMERA, ROAST, SAFE, and GAGE, and a recently proposed one for RNAseq, MAST.Results:We characterize situations in which power is especially small relative to effect sizes of genes in a set for both competitive and self-contained gene-set tests. We propose three alternative tests, one of which replicates the properties of permutation-based self-contained tests, but avoids the need for even recently proposed, rotation-based approximations to permutations. The two other proposed tests have the unique property that statistical power is not a function of co-expression correlation in the gene-set and therefore is the preferred methodology. We compare our proposed tests to leading gene-set tests and apply them to an already-published study of smoking exposure on pregnant women.Contact:dms866@mail.harvard.eduSupplementary Material:Online supplementary material includes additional simulation results supporting the relationship between the “mixed” and “directional” gene-set tests of ROAST and closed-form implementations of them.
A singleVibrionales16S rRNA oligotype dominates the intestinal microbiome in two geographically separated Atlantic cod populations
Authors: Riiser Even Sannes , Haverkamp Thomas H.A. , Borgan Ørnulf , Jakobsen Kjetill S. , Jentoft Sissel , Star Bastiaan 
Published: September 2017

AbstractBackgroundHost-microbe interactions are particularly intriguing in Atlantic cod (Gadus morhua), as it lacks the MHC II complex involved in presentation of extracellular pathogens. Nonetheless, little is known about the diversity of its microbiome in natural populations. Here, we use 16S rRNA high-throughput sequencing to investigate the microbial community composition in gut content and mucosa of 22 adult individuals from two coastal populations in Norway, located 470 km apart.ResultsWe identify a core microbiome of 23 OTUs (97% sequence similarity) in all individuals that comprises 93% of the total number of reads. The most abundant orders are classified asVibrionales, Fusobacteriales, ClostridialesandBacteroidales. While mucosal samples show significantly lower diversity than gut content samples, no differences in OTU community composition are observed between the two populations. The differential abundance of oligotypes within two common OTUs does reveal limited spatial segregation. Remarkably, the most abundant OTU consists of a single oligotype (orderVibrionales, genusPhotobacterium) that represents nearly 50% of the reads in both locations.ConclusionsOur results show that the intestinal bacterial community of two geographically separated coastal populations of Atlantic cod is dominated by a limited number of highly abundant 16S rRNA oligotypes shared by all specimens examined. The ubiquity of these oligotypes suggests that the northern coastal Atlantic cod gut microbiome is colonized by a limited number of species with excellent dispersal capabilities that are well suited to thrive in their host environment.