The Palomar Transient Factory: System Overview, Performance and First Results

The Palomar Transient Factory (PTF) is a fully-automated, wide-field survey aimed at a systematic exploration of the optical transient sky. The transient survey is performed using a new 8.1 square degree camera installed on the 48-inch Samuel Oschin telescope at Palomar Observatory; colors and light curves for detected transients are obtained with the automated Palomar 60-inch telescope. PTF uses eighty percent of the 1.2-m and fifty percent of the 1.5-m telescope time. With an exposure of 60-s the survey reaches a depth of approximately 21.3 in g' and 20.6 in R (5 sigma, median seeing). Four major experiments are planned for the five-year project: 1) a 5-day cadence supernova search; 2) a rapid transient search with cadences between 90 seconds and 1 day; 3) a search for eclipsing binaries and transiting planets in Orion; and 4) a 3-pi sr deep H-alpha survey. PTF provides automatic, realtime transient classification and follow up, as well as a database including every source detected in each frame. This paper summarizes the PTF project, including several months of on-sky performance tests of the new survey camera, the observing plans and the data reduction strategy. We conclude by detailing the first 51 PTF optical transient detections, found in commissioning data.Comment: 12 pages, 11 figures, 3 tables, submitted to PAS

Status of the PALM-3000 high-order adaptive optics system

The PALM-3000 upgrade to the Palomar Adaptive Optics system on the 5.1 meter Hale telescope will deliver extreme adaptive optics correction in near-infrared wavelengths and diffraction-limited images in visible wavelengths. PALM-3000 will use a 3388-actuator tweeter and a 241-actuator woofer deformable mirror, a Shack-Hartmann wavefront sensor with selectable pupil sampling, and an innovative wavefront control computer based on a cluster of 17 graphics processing units to correct wavefront aberrations at scales as fine as 8.1 cm at the telescope pupil using natural guide stars. The system is currently undergoing integration and testing, with deployment at Palomar Observatory planned in early 2011. We present the detailed design of key aspects of the adaptive optics system, and the current status of the deformable mirror characterization, wavefront sensor performance, and testbed activities

Decorrelation and efficient coding by retinal ganglion cells

An influential theory of visual processing asserts that retinal center-surround receptive fields remove spatial correlations in the visual world, producing ganglion cell spike trains that are less redundant than the corresponding image pixels. For bright, high-contrast images, this decorrelation would enhance coding efficiency in optic nerve fibers of limited capacity. We tested the central prediction of the theory and found that the spike trains of retinal ganglion cells were indeed decorrelated compared with the visual input. However, most of the decorrelation was accomplished not by the receptive fields, but by nonlinear processing in the retina. We found that a steep response threshold enhanced efficient coding by noisy spike trains and that the effect of this nonlinearity was near optimal in both salamander and macaque retina. These results offer an explanation for the sparseness of retinal spike trains and highlight the importance of treating the full nonlinear character of neural codes

An expression module of WIPF1-coexpressed genes identifies patients with favorable prognosis in three tumor types

Wiskott–Aldrich syndrome (WAS) predisposes patients to leukemia and lymphoma. WAS is caused by mutations in the protein WASP which impair its interaction with the WIPF1 protein. Here, we aim to identify a module of WIPF1-coexpressed genes and to assess its use as a prognostic signature for colorectal cancer, glioma, and breast cancer patients. Two public colorectal cancer microarray data sets were used for discovery and validation of the WIPF1 co-expression module. Based on expression of the WIPF1 signature, we classified more than 400 additional tumors with microarray data from our own experiments or from publicly available data sets according to their WIPF1 signature expression. This allowed us to separate patient populations for colorectal cancers, breast cancers, and gliomas for which clinical characteristics like survival times and times to relapse were analyzed. Groups of colorectal cancer, breast cancer, and glioma patients with low expression of the WIPF1 co-expression module generally had a favorable prognosis. In addition, the majority of WIPF1 signature genes are individually correlated with disease outcome in different studies. Literature gene network analysis revealed that among WIPF1 co-expressed genes known direct transcriptional targets of c-myc, ESR1 and p53 are enriched. The mean expression profile of WIPF1 signature genes is correlated with the profile of a proliferation signature. The WIPF1 signature is the first microarray-based prognostic expression signature primarily developed for colorectal cancer that is instrumental in other tumor types: low expression of the WIPF1 module is associated with better prognosis

A feature selection method for classification within functional genomics experiments based on the proportional overlapping score

Background: Microarray technology, as well as other functional genomics experiments, allow simultaneous measurements of thousands of genes within each sample. Both the prediction accuracy and interpretability of a classifier could be enhanced by performing the classification based only on selected discriminative genes. We propose a statistical method for selecting genes based on overlapping analysis of expression data across classes. This method results in a novel measure, called proportional overlapping score (POS), of a feature's relevance to a classification task.Results: We apply POS, along-with four widely used gene selection methods, to several benchmark gene expression datasets. The experimental results of classification error rates computed using the Random Forest, k Nearest Neighbor and Support Vector Machine classifiers show that POS achieves a better performance.Conclusions: A novel gene selection method, POS, is proposed. POS analyzes the expressions overlap across classes taking into account the proportions of overlapping samples. It robustly defines a mask for each gene that allows it to minimize the effect of expression outliers. The constructed masks along-with a novel gene score are exploited to produce the selected subset of genes

One Step Nucleic Acid Amplification (OSNA) - a new method for lymph node staging in colorectal carcinomas

<p>Abstract</p> <p>Background</p> <p>Accurate histopathological evaluation of resected lymph nodes (LN) is essential for the reliable staging of colorectal carcinomas (CRC). With conventional sectioning and staining techniques usually only parts of the LN are examined which might lead to incorrect tumor staging. A molecular method called OSNA (One Step Nucleic Acid Amplification) may be suitable to determine the metastatic status of the complete LN and therefore improve staging.</p> <p>Methods</p> <p>OSNA is based on a short homogenisation step and subsequent automated amplification of cytokeratin 19 (CK19) mRNA directly from the sample lysate, with result available in 30-40 minutes. In this study 184 frozen LN from 184 patients with CRC were investigated by both OSNA and histology (Haematoxylin & Eosin staining and CK19 immunohistochemistry), with half of the LN used for each method. Samples with discordant results were further analysed by RT-PCR for CK19 and carcinoembryonic antigen (CEA).</p> <p>Results</p> <p>The concordance rate between histology and OSNA was 95.7%. Three LN were histology+/OSNA- and 5 LN histology-/OSNA+. RT-PCR supported the OSNA result in 3 discordant cases, suggesting that metastases were exclusively located in either the tissue analysed by OSNA or the tissue used for histology. If these samples were excluded the concordance was 97.2%, the sensitivity 94.9%, and the specificity 97.9%. Three patients (3%) staged as UICC I or II by routine histopathology were upstaged as LN positive by OSNA. One of these patients developed distant metastases (DMS) during follow up.</p> <p>Conclusion</p> <p>OSNA is a new and reliable method for molecular staging of lymphatic metastases in CRC and enables the examination of whole LN. It can be applied as a rapid diagnostic tool to estimate tumour involvement in LN during the staging of CRC.</p

Ganglion Cell Adaptability: Does the Coupling of Horizontal Cells Play a Role?

Background: The visual system can adjust itself to different visual environments. One of the most well known examples of this is the shift in spatial tuning that occurs in retinal ganglion cells with the change from night to day vision. This shift is thought to be produced by a change in the ganglion cell receptive field surround, mediated by a decrease in the coupling of horizontal cells. Methodology/Principal Findings: To test this hypothesis, we used a transgenic mouse line, a connexin57-deficient line, in which horizontal cell coupling was abolished. Measurements, both at the ganglion cell level and the level of behavioral performance, showed no differences between wild-type retinas and retinas with decoupled horizontal cells from connexin57-deficient mice. Conclusion/Significance: This analysis showed that the coupling and uncoupling of horizontal cells does not play a dominant role in spatial tuning and its adjustability to night and day light conditions. Instead, our data suggest that anothe

Status of the PALM-3000 high-order adaptive optics system

The PALM-3000 upgrade to the Palomar Adaptive Optics system on the 5.1 meter Hale telescope will deliver extreme adaptive optics correction in near-infrared wavelengths and diffraction-limited images in visible wavelengths. PALM-3000 will use a 3388-actuator tweeter and a 241-actuator woofer deformable mirror, a Shack-Hartmann wavefront sensor with selectable pupil sampling, and an innovative wavefront control computer based on a cluster of 17 graphics processing units to correct wavefront aberrations at scales as fine as 8.1 cm at the telescope pupil using natural guide stars. The system is currently undergoing integration and testing, with deployment at Palomar Observatory planned in early 2011. We present the detailed design of key aspects of the adaptive optics system, and the current status of the deformable mirror characterization, wavefront sensor performance, and testbed activities

Neuronal precision and the limits for acoustic signal recognition in a small neuronal network

Recognition of acoustic signals may be impeded by two factors: extrinsic noise, which degrades sounds before they arrive at the receiver’s ears, and intrinsic neuronal noise, which reveals itself in the trial-to-trial variability of the responses to identical sounds. Here we analyzed how these two noise sources affect the recognition of acoustic signals from potential mates in grasshoppers. By progressively corrupting the envelope of a female song, we determined the critical degradation level at which males failed to recognize a courtship call in behavioral experiments. Using the same stimuli, we recorded intracellularly from auditory neurons at three different processing levels, and quantified the corresponding changes in spike train patterns by a spike train metric, which assigns a distance between spike trains. Unexpectedly, for most neurons, intrinsic variability accounted for the main part of the metric distance between spike trains, even at the strongest degradation levels. At consecutive levels of processing, intrinsic variability increased, while the sensitivity to external noise decreased. We followed two approaches to determine critical degradation levels from spike train dissimilarities, and compared the results with the limits of signal recognition measured in behaving animals