Molecular Line Profile Fitting with Analytic Radiative Transfer Models

We present a study of analytic models of starless cores whose line profiles have ``infall asymmetry,'' or blue-skewed shapes indicative of contracting motions. We compare the ability of two types of analytical radiative transfer models to reproduce the line profiles and infall speeds of centrally condensed starless cores whose infall speeds are spatially constant and range between 0 and 0.2 km s-1. The model line profiles of HCO+ (J=1-0) and HCO+ (J=3-2) are produced by a self-consistent Monte Carlo radiative transfer code. The analytic models assume that the excitation temperature in the front of the cloud is either constant (``two-layer'' model) or increases inward as a linear function of optical depth (``hill'' model). Each analytic model is matched to the line profile by rapid least-squares fitting. The blue-asymmetric line profiles with two peaks, or with a blue shifted peak and a red shifted shoulder, can be well fit by the ``HILL5'' model (a five parameter version of the hill model), with an RMS error of 0.02 km s-1. A peak signal to noise ratio of at least 30 in the molecular line observations is required for performing these analytic radiative transfer fits to the line profiles.Comment: 48 pages, 20 figures, accepted for publication in Ap

Millimeter and Submillimeter Survey of the R Corona Australis Region

Using a combination of data from the Antarctic Submillimeter Telescope and Remote Observatory (AST/RO), the Arizona Radio Observatory Kitt Peak 12m telescope and the Arizona Radio Observatory 10m Heinrich Hertz Telescope, we have studied the most active part of the R CrA molecular cloud in multiple transitions of Carbon Monoxide, HCO$^+$ and 870\micron continuum emission. Since R CrA is nearby (130 pc), we are able to obtain physical spatial resolution as high as 0.01pc over an area of 0.16 pc$^2$, with velocity resolution finer than 1 km/s. Mass estimates of the protostar driving the mm-wave emission derived from HCO$^+$, dust continuum emission and kinematic techniques point to a young, deeply embedded protostar of $\sim$0.5-0.75 M$_\odot$, with a gaseous envelope of similar mass. A molecular outflow is driven by this source that also contains at least 0.8 M$_\odot$ of molecular gas with $\sim$0.5 L$_\odot$ of mechanical luminosity. HCO$^+$ lines show the kinematic signature of infall motions as well as bulk rotation. The source is most likely a Class 0 protostellar object not yet visible at near-IR wavelengths. With the combination of spatial and spectral resolution in our data set, we are able to disentangle the effects of infall, rotation and outflow towards this young object.Comment: 29 pages, 9 figures. Accepted for publication in the Astrophysical Journa

Provably scale-covariant networks from oriented quasi quadrature measures in cascade

This article presents a continuous model for hierarchical networks based on a combination of mathematically derived models of receptive fields and biologically inspired computations. Based on a functional model of complex cells in terms of an oriented quasi quadrature combination of first- and second-order directional Gaussian derivatives, we couple such primitive computations in cascade over combinatorial expansions over image orientations. Scale-space properties of the computational primitives are analysed and it is shown that the resulting representation allows for provable scale and rotation covariance. A prototype application to texture analysis is developed and it is demonstrated that a simplified mean-reduced representation of the resulting QuasiQuadNet leads to promising experimental results on three texture datasets.Comment: 12 pages, 3 figures, 1 tabl

Microgeometry capture using an elastomeric sensor

We describe a system for capturing microscopic surface geometry. The system extends the retrographic sensor [Johnson and Adelson 2009] to the microscopic domain, demonstrating spatial resolution as small as 2 microns. In contrast to existing microgeometry capture techniques, the system is not affected by the optical characteristics of the surface being measured---it captures the same geometry whether the object is matte, glossy, or transparent. In addition, the hardware design allows for a variety of form factors, including a hand-held device that can be used to capture high-resolution surface geometry in the field. We achieve these results with a combination of improved sensor materials, illumination design, and reconstruction algorithm, as compared to the original sensor of Johnson and Adelson [2009].National Science Foundation (U.S.) (Grant 0739255)National Institutes of Health (U.S.) (Contract 1-R01-EY019292-01

Local biases drive, but do not determine, the perception of illusory trajectories

When a dot moves horizontally across a set of tilted lines of alternating orientations, the dot appears to be moving up and down along its trajectory. This perceptual phenomenon, known as the slalom illusion, reveals a mismatch between the veridical motion signals and the subjective percept of the motion trajectory, which has not been comprehensively explained. In the present study, we investigated the empirical boundaries of the slalom illusion using psychophysical methods. The phenomenon was found to occur both under conditions of smooth pursuit eye movements and constant fixation, and to be consistently amplified by intermittently occluding the dot trajectory. When the motion direction of the dot was not constant, however, the stimulus display did not elicit the expected illusory percept. These findings confirm that a local bias towards perpendicularity at the intersection points between the dot trajectory and the tilted lines cause the illusion, but also highlight that higher-level cortical processes are involved in interpreting and amplifying the biased local motion signals into a global illusion of trajectory perception

Local biases drive, but do not determine, the perception of illusory trajectories

When a dot moves horizontally across a set of tilted lines of alternating orientations, the dot appears to be moving up and down along its trajectory. This perceptual phenomenon, known as the slalom illusion, reveals a mismatch between the veridical motion signals and the subjective percept of the motion trajectory, which has not been comprehensively explained. In the present study, we investigated the empirical boundaries of the slalom illusion using psychophysical methods. The phenomenon was found to occur both under conditions of smooth pursuit eye movements and constant fixation, and to be consistently amplified by intermittently occluding the dot trajectory. When the motion direction of the dot was not constant, however, the stimulus display did not elicit the expected illusory percept. These findings confirm that a local bias towards perpendicularity at the intersection points between the dot trajectory and the tilted lines cause the illusion, but also highlight that higher-level cortical processes are involved in interpreting and amplifying the biased local motion signals into a global illusion of trajectory perception

In depth analysis of the Sox4 gene locus that consists of sense and natural antisense transcripts

Available online 17 February 2016SRY (Sex Determining Region Y)-Box 4 or Sox4 is an important regulator of the pan-neuronal gene expression during post-mitotic cell differentiation within the mammalian brain. Sox4 gene locus has been previously characterized with multiple sense and overlapping natural antisense transcripts [1], [2]. Here we provide accompanying data on various analyses performed and described in Ling et al. [2]. The data include a detail description of various features found at Sox4 gene locus, additional experimental data derived from RNA-Fluorescence in situ Hybridization (RNA-FISH), Western blotting, strand-specific reverse-transcription quantitative polymerase chain reaction (RT-qPCR), gain-of-function and in situ hybridization (ISH) experiments. All the additional data provided here support the existence of an endogenous small interfering- or PIWI interacting-like small RNA known as Sox4_sir3, which origin was found within the overlapping region consisting of a sense and a natural antisense transcript known as Sox4ot1.King-Hwa Ling, Peter J. Brautigan, Sarah Moore, Rachel Fraser, Melody Pui-Yee Leong, Jia-Wen Leong, Shahidee Zainal Abidin, Han-Chung Lee, Pike-See Cheah, Joy M. Raison, Milena Babic, Young Kyung Lee, Tasman Daish, Deidre M. Mattiske, Jeffrey R. Mann, David L. Adelson, Paul Q. Thomas, Christopher N. Hahn, Hamish S.Scot

The detection of temporally defined objects does not require focused attention.

Perceptual grouping is crucial to distinguish objects from their background. Recent studies have shown that observers can detect an object that does not have any unique qualities other than unique temporal properties. A crucial question is whether focused attention is needed for this type of grouping. In two visual search experiments, we show that searching for an object defined by temporal grouping can occur in parallel. These findings suggest that focused attention is not needed for temporal grouping to occur. It is proposed that temporal grouping may occur because the neurons representing the changing object elements adopt firing frequencies that cause the visual system to bind these elements together without the need for focused attention. © 2008 The Experimental Psychology Society

IND-Enabling Studies for a Clinical Trial to Genetically Program a Persistent Cancer-Targeted Immune System

PURPOSE: To improve persistence of adoptively transferred T-cell receptor (TCR)-engineered T cells and durable clinical responses, we designed a clinical trial to transplant genetically-modified hematopoietic stem cells (HSCs) together with adoptive cell transfer of T cells both engineered to express an NY-ESO-1 TCR. Here, we report the preclinical studies performed to enable an investigational new drug (IND) application. EXPERIMENTAL DESIGN: HSCs transduced with a lentiviral vector expressing NY-ESO-1 TCR and the PET reporter/suicide gene HSV1-sr39TK and T cells transduced with a retroviral vector expressing NY-ESO-1 TCR were coadministered to myelodepleted HLA-A2/Kb mice within a formal Good Laboratory Practice (GLP)-compliant study to demonstrate safety, persistence, and HSC differentiation into all blood lineages. Non-GLP experiments included assessment of transgene immunogenicity and in vitro viral insertion safety studies. Furthermore, Good Manufacturing Practice (GMP)-compliant cell production qualification runs were performed to establish the manufacturing protocols for clinical use. RESULTS: TCR genetically modified and ex vivo-cultured HSCs differentiated into all blood subsets in vivo after HSC transplantation, and coadministration of TCR-transduced T cells did not result in increased toxicity. The expression of NY-ESO-1 TCR and sr39TK transgenes did not have a detrimental effect on gene-modified HSC's differentiation to all blood cell lineages. There was no evidence of genotoxicity induced by the lentiviral vector. GMP batches of clinical-grade transgenic cells produced during qualification runs had adequate stability and functionality. CONCLUSIONS: Coadministration of HSCs and T cells expressing an NY-ESO-1 TCR is safe in preclinical models. The results presented in this article led to the FDA approval of IND 17471