A novel hypothesis-unbiased method for gene ontology enrichment based on transcriptome data

Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribute equally to the final GO classification regardless of their actual expression levels. Gene expression levels can significantly affect protein production and hence should be reflected in GO term enrichment. Genes with low expression levels can also participate in GO term enrichment through cumulative effects. In this report, we have introduced a new GO enrichment method that is suitable for multiple samples and time series experiments that uses a statistical outlier test to detect GO categories with special patterns of variation that can potentially identify candidate biological mechanisms. To demonstrate the value of our approach, we have performed two case studies. Whole transcriptome expression profiles of Salmonella enteritidis and Alzheimer's disease (AD) were analysed in order to determine GO term enrichment across the entire transcriptome instead of a subset of differentially expressed genes used in traditional GO analysis. Our result highlights the key role of inflammation related functional groups in AD pathology as granulocyte colony-stimulating factor receptor binding, neuromedin U binding, and interleukin were remarkably upregulated in AD brain when all using all of the gene expression data in the transcriptome. Mitochondrial components and the molybdopterin synthase complex were identified as potential key cellular components involved in AD pathology.Mario Fruzangohar, Esmaeil Ebrahimie, David L. Adelso

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

A Survey for Infall Motions toward Starless Cores. II. CS(2−1)CS (2-1) and N2H+(1−0)N_2H^+ (1-0) Mapping Observations

We present the results of an extensive mapping survey of 53 `starless' cores in the optically thick line of CS 2-1 and the optically thin lines of N2H+ 1-0 and C18O 1-0. The purpose of this survey was to search for signatures of extended inward motions. This study finds 10 `strong' and 9 `probable' infall candidates, based on $\delta V_{CS}$ analysis and on the spectral shapes of CS lines. From our analysis of the blue-skewed CS spectra and the $\delta V_{CS}$ parameter, we find typical infall radii of 0.06-0.14 pc. Also, using a simple two layer radiative transfer model to fit the profiles, we derive one-dimensional infall speeds, half of whose values lie in the range of 0.05-0.09 km s$^{-1}$. These values are similar to those found in L1544 by Tafalla et al., and this result confirms that infall speeds in starless cores are generally faster than expected from ambipolar diffusion in a strongly sub-critical core. In addition, the observed infall regions are too extended to be consistent with the `inside-out' collapse model applied to a very low-mass star. In the largest cores, the spatial extent of the CS spectra with infall asymmetry is larger than the extent of the $\rm N_2H^+$ core by a factor of 2-3. All these results suggest that extended inward motions are a common feature in starless cores, and that they could represent a necessary stage in the condensation of a star-forming dense core.Comment: Two tex files for manuscript and tables, and 38 figures. To appear in ApJ

Baseline and triangulation geometry in a standard plenoptic camera

In this paper, we demonstrate light field triangulation to determine depth distances and baselines in a plenoptic camera. The advancement of micro lenses and image sensors enabled plenoptic cameras to capture a scene from different viewpoints with sufficient spatial resolution. While object distances can be inferred from disparities in a stereo viewpoint pair using triangulation, this concept remains ambiguous when applied in case of plenoptic cameras. We present a geometrical light field model allowing the triangulation to be applied to a plenoptic camera in order to predict object distances or to specify baselines as desired. It is shown that distance estimates from our novel method match those of real objects placed in front of the camera. Additional benchmark tests with an optical design software further validate the model’s accuracy with deviations of less than 0:33 % for several main lens types and focus settings. A variety of applications in the automotive and robotics field can benefit from this estimation model

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

Deep Depth From Focus

Depth from focus (DFF) is one of the classical ill-posed inverse problems in computer vision. Most approaches recover the depth at each pixel based on the focal setting which exhibits maximal sharpness. Yet, it is not obvious how to reliably estimate the sharpness level, particularly in low-textured areas. In this paper, we propose `Deep Depth From Focus (DDFF)' as the first end-to-end learning approach to this problem. One of the main challenges we face is the hunger for data of deep neural networks. In order to obtain a significant amount of focal stacks with corresponding groundtruth depth, we propose to leverage a light-field camera with a co-calibrated RGB-D sensor. This allows us to digitally create focal stacks of varying sizes. Compared to existing benchmarks our dataset is 25 times larger, enabling the use of machine learning for this inverse problem. We compare our results with state-of-the-art DFF methods and we also analyze the effect of several key deep architectural components. These experiments show that our proposed method `DDFFNet' achieves state-of-the-art performance in all scenes, reducing depth error by more than 75% compared to the classical DFF methods.Comment: accepted to Asian Conference on Computer Vision (ACCV) 201

Detection of Candida species in vaginal samples in a clinical laboratory setting.

OBJECTIVE: To present the detection rates of Candida species in vaginal samples from patients visiting physicians. METHODS: The presence of C. albicans, C. glabrata, C. parapsilosis and C. tropicalis in 3978 vaginal swabs from patients in six US states was detected by PCR amplification. RESULTS: Candida DNA was detected in 33.1% of the population studied. Of the 1316 positive samples, 80.2% contained C. albicans, 14.3% contained C. glabrata, 5.9% contained C. parapsilosis and 8.0% contained C. tropicalis. Comparing samples by patients' state of residence revealed an association with the detection of C. glabrata (p = 0.029). Comparing samples by patients' age revealed a decrease in the overall detection of Candida (p < 0.001) and C. albicans (p < 0.001), concomitant with an increase in the detection of C. glabrata (p < 0.001) and C. parapsilosis (p = 0.025). CONCLUSIONS: These results provide geographic- and age-specific data on four Candida species associated with vaginitis

Infall, Outflow, Rotation, and Turbulent Motions of Dense Gas within NGC 1333 IRAS 4

Millimeter wavelength observations are presented of NGC 1333 IRAS 4, a group of highly-embedded young stellar objects in Perseus, that reveal motions of infall, outflow, rotation, and turbulence in the dense gas around its two brightest continuum objects, 4A and 4B. These data have finest angular resolution of approximately 2" (0.0034 pc) and finest velocity resolution of 0.13 km/s. Infall motions are seen from inverse P-Cygni profiles observed in H2CO 3_12-2_11 toward both objects, but also in CS 3-2 and N2H+ 1-0 toward 4A, providing the least ambiguous evidence for such motions toward low-mass protostellar objects. Outflow motions are probed by bright line wings of H2CO 3_12-2_11 and CS 3-2 observed at positions offset from 4A and 4B, likely tracing dense cavity walls. Rotational motions of dense gas are traced by a systematic variation of the N2H+ line velocities, and such variations are found around 4A but not around 4B. Turbulent motions appear reduced with scale, given N2H+ line widths around both 4A and 4B that are narrower by factors of 2 or 3 than those seen from single-dish observations. Minimum observed line widths of approximately 0.2 km/s provide a new low, upper bound to the velocity dispersion of the parent core to IRAS 4, and demonstrate that turbulence within regions of clustered star formation can be reduced significantly. A third continuum object in the region, 4B', shows no detectable line emission in any of the observed molecular species.Comment: LateX, 51 pages, 9 figures, accepted by Ap