Ratcave: A 3D graphics python package for cognitive psychology experiments

We present here a free, open source Python 3D graphics library called Ratcave that extends existing Python psychology stimulus software by allowing scientists to load, display, and transform 3D stimuli created in 3D modeling software. This library makes 3D programming intuitive to new users by providing 3D graphics engine concepts (Mesh, Scene, Light, and Camera classes) that can be manipulated using an interface similar to existing 2D stimulus libraries. In addition, the use of modern OpenGL constructs by Ratcave helps scientists create fast, hardware-accelerated dynamic stimuli using the same intuitive high-level, lightweight interface. Because Ratcave supplements, rather than replaces, existing Python stimulus libraries, scientists can continue to use their preferred libraries by simply adding Ratcave graphics to their existing experiments. We hope this tool will be useful both as a stimulus library and as an example of how tightly-focused libraries can add quality to the existing scientific open-source software ecosystem. Cognitive psychology and neuroscience experiments use software that presents stimuli to a subject, detects subject responses, and logs events for future analysis, all with high temporal accuracy. An ever-expanding list of other features included in this software are compatibility with third-party hardware devices (e.g. button boxes, amplifiers, eye tracking systems), support for custom experimental designs, and online analysis for adaptive stimulus sequences; these tools are available both as self-enclosed software solutions (e.g. Neurobs Presentation, BCI2000, SuperLab, E-Prime) and open-source libraries (e.g. Psychtoolbox by Brainard, 1997; PsychoPy by Peirce, 2007; VisionEgg by Straw, 2008; Expyriment by Krause & Lindemann, 2013; for a review of psychophysics libraries, see Kötter, 2009). However, these popular libraries are missing 3D graphics support, needed for a wide range visual psychophysics experiments, such as 3D mental rotation or object recognition, virtual reality in spatial navigation research, to name a few. While 3D graphics libraries do exist in Python (e.g. Panda3D, PyOgre, Vizard) and other languages (e.g. Unity3D, Unreal Engine), the stimuli, logging, and hardware support of all of these libraries are designed to work with the windows and event loops they supply, making it difficult to integrate 3D graphics functionality into different psychophysics libraries without (sometimes-extensive) modification (e.g. to mix PsychoPy’s DotStim and Expyriment’s video support). In practice, this means that each software suite is relatively self-contained; researchers who require 3D stimuli, for example, have to, thereby, resort to use or develop different experiment control software when employing 3D visual stimuli (essentially, building interface to 3D game engines), losing out on the rich features that exist in the psychophysics software ecosystem developed for the 2D graphics. Extension libraries help reduce these feature-tradeoff decisions; for example, OpenSesame, a Python-powered GUI (Mathôt & Theeuwes, 2012), uses PsychoPy, Expyriment, and PyGame as “backends” to its experiment-building graphical interface, thereby supporting all researchers who rely on those libraries. A similar extension approach could be used for 3D stimuli--not to compete with the existing 3D frameworks on a feature-by-feature basis, but to simply add simple-to-use 3D stimulus presentation and manipulation support to the feature list of existing 2D stimulus libraries in Python. In this paper, we present an open-source, cross-platform Python library called Ratcave that adds 3D stimulus support to all OpenGL-based 2D Python stimulus libraries, including VisionEgg, Psychopy, Pyglet, and PyGame. We review the core features of Ratcave (https://github.com/ratcave/ratcave) and highlight key connections of its interface to underlying graphics programming strategies (a thorough manual, complete with API guide and tutorials for first-time users can be found at https://ratcave.readthedocs.org). This library, which derives its name from our high-speed RatcaveVR experimental setup (Del Grosso, Graboski, Chen, Hernández, & Sirota, 2017), is designed to increase accessibility of 3D graphics programming to the existing ecosystem of psychology software for Python

The City Meditations

This portrait develops a new understanding of how and why cities function and their importance to humanity. Past attempts at understanding cities have focused on their economic roles or cultural centers but have overlooked their great ability to engage conversation and spark new ideas. Drawing upon ideas and theories of architectural layout such as Jane Jacobs\u27 Death and Life of Great American Cities, city planning (Lewis Mumford\u27s What is a City? and Samuel Delany\u27s Times Square Red, Times Square Blue), and social landscape (Jürgen Habermas), this project will develop a theory that considers how the city functions as a communicator. To further illustrate and illuminate the fine points of the proposed theory, this portrait will draw on portrayals of cities in literature, specifically Salman Rushdie\u27s Midnight\u27s Children, selected poems from Federico Garcia Lorca and Frank O\u27Hara, and Phaswane Mpe\u27s Welcome to Our Hillbrow. The exploration will highlight the important role cities have established for themselves, as more than centers of business and scenes for artists, stockpiling resources and cultural touchstones, but as the heart of discourse and the catalyst of invention

Design of virtual reality systems for animal behavior research

Virtual reality (VR) experimental behavior setups enable cognitive neuroscientists to study the integration of visual depth cues and self-motion cues into a single percept of three-dimensional space. Rodents can navigate a virtual environment by running on a spherical treadmill, but simulating locomotion in this way can both bias and suppress the frequency of their behaviors as well as introduce vestibulomotor and vestibulovisual sensory conflict during locomotion. Updating the virtual environment via the subject's own freely-moving head movements solves both the naturalistic behavior bias and vestibular conflict issues. In this thesis, I review elements of self-motion and 3D scene perception that contribute to a sense of immersion in virtual environments and suggest a freely-moving CAVE system as a VR solution for low-artifact neuroscience experiments. The manuscripts describing the 3D graphics Python package and the virtual reality setup are included. In this freely-moving CAVE VR setup, freely-moving rats demonstrate immersion in virtual environments by displaying height aversion to virtual cliffs, exploration preference of virtual objects, and spontaneously modify their locomotion trajectories near virtual walls. These experiments help bridge the classic behavior and virtual reality literature by showing that rats display similar behaviors to virtual environment features without training

Virtual Reality system for freely-moving rodents

Spatial navigation, active sensing, and most cognitive functions rely on a tight link between motor output and sensory input. Virtual reality (VR) systems simulate the sensorimotor loop, allowing flexible manipulation of enriched sensory input. Conventional rodent VR systems provide 3D visual cues linked to restrained locomotion on a treadmill, leading to a mismatch between visual and most other sensory inputs, sensory-motor conflicts, as well as restricted naturalistic behavior. To rectify these limitations, we developed a VR system (ratCAVE) that provides realistic and low-latency visual feedback directly to head movements of completely unrestrained rodents. Immersed in this VR system, rats displayed naturalistic behavior by spontaneously interacting with and hugging virtual walls, exploring virtual objects, and avoiding virtual cliffs. We further illustrate the effect of ratCAVE-VR manipulation on hippocampal place fields. The newly-developed methodology enables a wide range of experiments involving flexible manipulation of visual feedback in freely-moving behaving animals

Detection of a Cool, Accretion-Shock-Generated X-Ray Plasma in EX Lupi During the 2008 Optical Eruption

EX Lupi is the prototype for a class of young, pre-main-sequence stars which are observed to undergo irregular, presumably accretion-generated, optical outbursts that result in a several magnitude rise of the optical flux. EX Lupi was observed to optically erupt in 2008 January, triggering Chandra ACIS Target of Opportunity observations shortly thereafter. We find very strong evidence that most of the X-ray emission in the first few months after the optical outburst is generated by accretion of circumstellar material onto the stellar photosphere. Specifically, we find a strong correlation between the decreasing optical and X-ray fluxes following the peak of the outburst in the optical, which suggests that these observed declines in both the optical and X-ray fluxes are the result of declining accretion rate. In addition, in our models of the X-ray spectrum, we find strong evidence for an approx 0.4 keV plasma component, as expected for accretion shocks on low-mass, pre-main-sequence stars. From 2008 March through October, this cool plasma component appeared to fade as EX Lupi returned to its quiescent level in the optical, consistent with a decrease in the overall emission measure of accretion-shock-generated plasma. The overall small increase of the X-ray flux during the optical outburst of EX Lupi is similar to what was observed in previous X-ray observations of the 2005 optical outburst of the EX Lupi-type star V1118 Ori but contrasts with the large increase of the X-ray flux from the erupting young star V1647 Ori during its 2003 and 2008 optical outbursts

RNA polymerase II phosphorylated on CTD serine 5 interacts with the spliceosome during co-transcriptional splicing

© 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).The highly intronic nature of protein coding genes in mammals necessitates a co-transcriptional splicing mechanism as revealed by mNET-seq analysis. Immunoprecipitation of MNase-digested chromatin with antibodies against RNA polymerase II (Pol II) shows that active spliceosomes (both snRNA and proteins) are complexed to Pol II S5P CTD during elongation and co-transcriptional splicing. Notably, elongating Pol II-spliceosome complexes form strong interactions with nascent transcripts, resulting in footprints of approximately 60 nucleotides. Also, splicing intermediates formed by cleavage at the 5' splice site are associated with nearly all spliced exons. These spliceosome-bound intermediates are frequently ligated to upstream exons, implying a sequential, constitutive, and U12-dependent splicing process. Finally, lack of detectable spliced products connected to the Pol II active site in human HeLa or murine lymphoid cells suggests that splicing does not occur immediately following 3' splice site synthesis. Our results imply that most mammalian splicing requires exon definition for completion.This work was supported by funding to N.J.P. (Wellcome Trust Investigator Award [107928/Z/15/Z] and ERC Advanced [339270] grants) and to M.C.-F. (Fundação Ciência e Tecnologia, Portugal; grant PTDC/BEX-BCM/5899/2014).info:eu-repo/semantics/publishedVersio

Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing

© Copyright © 2015 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)Transcription is a highly dynamic process. Consequently, we have developed native elongating transcript sequencing technology for mammalian chromatin (mNET-seq), which generates single-nucleotide resolution, nascent transcription profiles. Nascent RNA was detected in the active site of RNA polymerase II (Pol II) along with associated RNA processing intermediates. In particular, we detected 5'splice site cleavage by the spliceosome, showing that cleaved upstream exon transcripts are associated with Pol II CTD phosphorylated on the serine 5 position (S5P), which is accumulated over downstream exons. Also, depletion of termination factors substantially reduces Pol II pausing at gene ends, leading to termination defects. Notably, termination factors play an additional promoter role by restricting non-productive RNA synthesis in a Pol II CTD S2P-specific manner. Our results suggest that CTD phosphorylation patterns established for yeast transcription are significantly different in mammals. Taken together, mNET-seq provides dynamic and detailed snapshots of the complex events underlying transcription in mammals.This work was supported by funding to N.J.P. (Wellcome Trust Programme [091805/Z/10/Z] and ERC Advanced [339270] Grants) and to M.C.-F. (Fundação Ciência e Tecnologia, Portugal).info:eu-repo/semantics/publishedVersio

Nut consumption on all-cause, cardiovascular, and cancer mortality risk: a systematic review and meta-analysis of epidemiologic studies

Background: Recent pooled analyses supported a beneficial impact of nut consumption on health, but to our knowledge, whether nuts are associated with overall decreased mortality has not been previously reviewed. Objectives: We aimed to systematically review prospective studies that explored the effects of nut consumption on all-cause, cardiovascular disease (CVD), and cancer mortality and quantify the size effect through a meta-analysis. We also reviewed confounding factors associated with nut consumption to assess potential clustering with other covariates. Design: We searched PubMed and EMBASE for studies published up to June 2014. Study characteristics, HRs, and 95% CIs were generated on the basis of quantitative analyses. A dose-response analysis was performed when data were available. Results: Seven studies for all-cause mortality, 6 studies for CVD mortality, and 2 studies for cancer mortality were included in the meta-analysis with a total of 354,933 participants, 44,636 cumulative incident deaths, and 3,746,534 cumulative person-years. Nut consumption was associated with some baseline characteristics such as lower body mass index and smoking status as well as increased intakes of fruit, vegetables, and alcohol. One-serving of nuts per week and per day resulted in 4% (RR: 0.96; 95% CI: 0.93, 0.98) and 27% (RR: 0.73; 95% CI: 0.60, 0.88) decreased risk of all-cause mortality, respectively, and decreased risk of CVD mortality [RR: 0.93 (95% CI: 0.88, 0.99) and 0.61 (95% CI: 0.42, 0.91), respectively]. Effects were primarily driven by decreased coronary artery disease deaths rather than stroke deaths. Nut consumption was also associated with decreased risk of cancer deaths when highest compared with lowest categories of intake were compared (RR: 0.86; 95% CI: 0.75, 0.98), but no dose-effect was shown. Conclusion: Nut consumption is associated with lower risk of allcause, CVD, and cancer mortality, but the presence of confounding factors should be taken into account when considering such findings

The Spitzer Survey of Interstellar Clouds in the Gould Belt. III. A Multi-Wavelength View of Corona Australis

We present Spitzer Space Telescope IRAC and MIPS observations of a 0.85 deg^2 field including the Corona Australis (CrA) star-forming region. At a distance of 130 pc, CrA is one of the closest regions known to be actively forming stars, particularly within its embedded association, the Coronet. Using the Spitzer data, we identify 51 young stellar objects (YSOs) in CrA which include sources in the well-studied Coronet cluster as well as distributed throughout the molecular cloud. Twelve of the YSOs discussed are new candidates, one of which is located in the Coronet. Known YSOs retrieved from the literature are also added to the list, and a total of 116 candidate YSOs in CrA are compiled. Based on these YSO candidates, the star formation rate is computed to be 12 M_o Myr^-1, similar to that of the Lupus clouds. A clustering analysis was also performed, finding that the main cluster core, consisting of 68 members, is elongated (having an aspect ratio of 2.36), with a circular radius of 0.59 pc and mean surface density of 150 pc^-2. In addition, we analyze outflows and jets in CrA by means of new CO and H_2 data. We present 1.3 mm interferometric continuum observations made with the Submillimeter Array (SMA) covering R CrA, IRS 5, IRS 7, and IRAS 18595-3712 (IRAS 32). We also present multi-epoch H_2 maps and detect jets and outflows, study their proper motions, and identify exciting sources. The Spitzer and ISAAC/VLT observations of IRAS 32 show a bipolar precessing jet, which drives a CO (2-1) outflow detected in the SMA observations. There is also clear evidence for a parsec-scale precessing outflow, E-W oriented, and originating in the SMA 2 region, likely driven by SMA 2 or IRS 7A.Comment: Accepted for publication in ApJS. 112 pages, 42 figures (quality reduced), 13 tables. Full resolution version can be found at http://www.cfa.harvard.edu/~dpeterson/CrA/CrA_highres.pd

Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated