NetPyNE, a tool for data-driven multiscale modeling of brain circuits

Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena

Allergic asthma is distinguished by sensitivity of allergen-specific CD4+ T cells and airway structural cells to type 2 inflammation

Despite systemic sensitization, not all allergic individuals develop asthma symptoms upon airborne allergen exposure. Determination of the factors that lead to the asthma phenotype in allergic individuals could guide treatment and identify novel therapeutic targets. In this study, we utilized segmental allergen challenge (SAC) of allergic asthmatics (AA) and allergic non-asthmatic controls (AC) to determine if there are differences in the airway immune response or airway structural cells that could drive the development of asthma. Both groups developed prominent allergic airway inflammation in response to allergen. However, asthmatic subjects had markedly higher levels of innate type 2 receptors on allergen-specific CD4+ T cells recruited into the airway. There were also increased levels of type 2 cytokines, increased total mucin and increased MUC5AC in response to allergen in the airways of AA subjects. Furthermore, type 2 cytokine levels correlated with the mucin response in AA but not AC subjects, suggesting differences in the airway epithelial response to inflammation. Finally, AA subjects had increased airway smooth muscle mass at baseline measured in vivo using novel orientation-registered optical coherence tomography (OR-OCT). Our data demonstrate that the development of allergic asthma is dependent on the responsiveness of allergen-specific CD4+ T cells to innate type 2 mediators as well as increased sensitivity of airway epithelial cells and smooth muscle to type 2 inflammation

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

A catastrophic meltwater flood event and the formation of the Hudson Shelf Valley

This paper is not subject to U.S. copyright. The definitive version was published in Palaeogeography, Palaeoclimatology, Palaeoecology 246 (2007): 120-136, doi:10.1016/j.palaeo.2006.10.030.The Hudson Shelf Valley (HSV) is the largest physiographic feature on the U.S. mid-Atlantic continental shelf. The 150-km long valley is the submerged extension of the ancestral Hudson River Valley that connects to the Hudson Canyon. Unlike other incised valleys on the mid-Atlantic shelf, it has not been infilled with sediment during the Holocene. Analyses of multibeam bathymetry, acoustic backscatter intensity, and high-resolution seismic reflection profiles reveal morphologic and stratigraphic evidence for a catastrophic meltwater flood event that formed the modern HSV. The valley and its distal deposits record a discrete flood event that carved 15-m high banks, formed a 120-km2 field of 3- to 6-m high bedforms, and deposited a subaqueous delta on the outer shelf. The HSV is inferred to have been carved initially by precipitation and meltwater runoff during the advance of the Laurentide Ice Sheet, and later by the drainage of early proglacial lakes through stable spillways. A flood resulting from the failure of the terminal moraine dam at the Narrows between Staten Island and Long Island, New York, allowed glacial lakes in the Hudson and Ontario basins to drain across the continental shelf. Water level changes in the Hudson River basin associated with the catastrophic drainage of glacial lakes Iroquois, Vermont, and Albany around 11,450 14C year BP (~ 13,350 cal BP) may have precipitated dam failure at the Narrows. This 3200 km3 discharge of freshwater entered the North Atlantic proximal to the Gulf Stream and may have affected thermohaline circulation at the onset of the Intra-Allerød Cold Period. Based on bedform characteristics and fluvial morphology in the HSV, the maximum freshwater flux during the flood event is estimated to be ~ 0.46 Sv for a duration of ~ 80 days.Support for N. Driscoll was provided by the Office of Naval Research and the National Science Foundatio

Risk of chronic traumatic encephalopathy in rugby union is associated with length of playing career

No abstract available

CMS physics technical design report : Addendum on high density QCD with heavy ions

Peer reviewe

The psychological science accelerator’s COVID-19 rapid-response dataset

In response to the COVID-19 pandemic, the Psychological Science Accelerator coordinated three large-scale psychological studies to examine the effects of loss-gain framing, cognitive reappraisals, and autonomy framing manipulations on behavioral intentions and affective measures. The data collected (April to October 2020) included specific measures for each experimental study, a general questionnaire examining health prevention behaviors and COVID-19 experience, geographical and cultural context characterization, and demographic information for each participant. Each participant started the study with the same general questions and then was randomized to complete either one longer experiment or two shorter experiments. Data were provided by 73,223 participants with varying completion rates. Participants completed the survey from 111 geopolitical regions in 44 unique languages/dialects. The anonymized dataset described here is provided in both raw and processed formats to facilitate re-use and further analyses. The dataset offers secondary analytic opportunities to explore coping, framing, and self-determination across a diverse, global sample obtained at the onset of the COVID-19 pandemic, which can be merged with other time-sampled or geographic data