Extinction Curves, Distances, and Clumpiness of Diffuse Interstellar Dust Clouds

We present CCD photometry in UBVRI of several thousand Galactic field stars in four large (>1 degree^2) regions centered on diffuse interstellar dust clouds, commonly referred to as ``cirrus'' clouds (with optical depth A_V less than unity). Our goal in studying these stars is to investigate the properties of the cirrus clouds. A comparison of the observed stellar surface density between on-cloud and off-cloud regions as a function of apparent magnitude in each of the five bands effectively yields a measure of the extinction through each cloud. For two of the cirrus clouds, this method is used to derive UBVRI star counts-based extinction curves, and U-band counts are used to place constraints on the cloud distance. The color distribution of stars and their location in (U-B, B-V) and (B-V, V-I) color-color space are analyzed in order to determine the amount of selective extinction (reddening) caused by the cirrus. The color excesses, A_lambda-A_V, derived from stellar color histogram offsets for the four clouds, are better fit by a reddening law that rises steeply towards short wavelengths [R_V==A_V/E(B-V)<=2] than by the standard law (R_V=3.1). This may be indicative of a higher-than-average abundance of small dust grains relative to larger grains in diffuse cirrus clouds. The shape of the counts-based effective extinction curve and a comparison of different estimates of the dust optical depth (extinction optical depth derived from background star counts/colors; emission optical depth derived from far infrared measurements), are used to measure the degree of clumpiness in clouds. The set of techniques explored in this paper can be readily adapted to the Sloan Digital Sky Survey data set in order to carry out a systematic, large-scale study of cirrus clouds.Comment: 22 pages, 13 figures (postscript, gif, jpg). Accepted for publication in the Astronomical Journal, scheduled for the May 1999 issue. Full resolution postscript versions of all figures are available at http://www.ucolick.org/~arpad

Optical Spectroscopy of Galactic Cirrus Clouds: Extended Red Emission in the Diffuse Interstellar Medium

We present initial results from the first optical spectroscopic survey of high latitude Galactic cirrus clouds. The observed shape of the cirrus spectrum does not agree with that of scattered ambient Galactic starlight. This mismatch can be explained by the presence of Extended Red Emission (ERE) in the diffuse interstellar medium, as found in many other astronomical objects, probably caused by photoluminescence of hydrocarbons. The integrated ERE intensity, I_ERE \approx 1.2 x 10^{-5} erg s^{-1} cm^{-2} sr^{-1}, is roughly a third of the scattered light intensity, consistent with recent color measurements of diffuse Galactic light. The peak of the cirrus ERE (lambda_{0} \sim 6000 AA) is shifted towards short (bluer) wavelengths compared to the ERE in sources excited by intense ultraviolet radiation, such as HII regions (lambda_{0} sim 8000 AA); such a trend is seen in laboratory experiments on hydrogenated amorphous carbon films.Comment: 7 pages, 2 figures. Accepted for publication in ApJ Letter

SandflyMap: leveraging spatial data on sand fly vector distribution for disease risk assessments

We feature SandflyMap (www.sandflymap.org), a new map service within VectorMap (www.vectormap.org) that allows free public online access to global sand fly, tick and mosquito collection records and habitat suitability models. Given the short home range of sand flies, combining remote sensing and collection point data give a powerful insight into the environmental determinants of sand fly distribution. SandflyMap is aimed at medical entomologists, vector disease control workers, public health officials and health planners. Data are checked for geographical and taxonomic errors, and are comprised of vouchered specimen information, and both published and unpublished observation data. SandflyMap uses Microsoft Silverlight and ESRI’s ArcGIS Server 10 software platform to present disease vector data and relevant remote sensing layers in an online geographical information system format. Users can view the locations of past vector collections and the results of models that predict the geographic extent of individual species. Collection records are searchable and downloadable, and Excel collection forms with drop down lists, and Excel charts to country, are available for data contributors to map and quality control their data. SandflyMap makes accessible, and adds value to, the results of past sand fly collecting efforts. We detail the workflow for entering occurrence data from the literature to SandflyMap, using an example for sand flies from South America. We discuss the utility of SandflyMap as a focal point to increase collaboration and to explore the nexus between geography and vector-borne disease transmission

Synthesis, Characterization, and Spectroscopy of Model Molybdopterin Complexes

The preparation and characterization of new model complexes for the molybdenum cofactor are reported. The new models are distinctive for the inclusion of pterin-substituted dithiolene chelates and have the formulation Tp*MoX(pterin-R-dithiolene) (Tp* = tris(3,5,-dimethylpyrazolyl)borate), X= O, S, R= aryl or –C(OH)(CH3)2). Syntheses of Mo(4+) and (5+) complexes of two pterin-dithiolene derivatives as both oxo and sulfido compounds, and improved syntheses for pterinyl alkynes and [Et4N][Tp*MoIV(S)S4] reagents are described. Characterization methods include electrospray ionization mass spectrometry, electrochemistry, infrared spectroscopy, electron paramagnetic resonance and magnetic circular dichroism. Cyclic voltammetry reveals that the Mo(5+/4+) reduction potential is intermediate between that for dithiolene with electron-withdrawing substituents and simple dithiolate chelates. Electron paramagnetic resonance and magnetic circular dichroism of Mo(5+) complexes where X = O, R = aryl indicates that the molybdenum environment in the new models is electronically similar to that in Tp*MoO(benzenedithiolate)

Simultaneous computed tomography-guided biopsy and radiofrequency ablation of solitary pulmonary malignancy in high-risk patients

Background: In recent years experience has been accumulated in percutaneous radiofrequency ablation (RFA) of lung malignancies in nonsurgical patients. Objectives: In this study, we retrospectively evaluated a simultaneous diagnostic and therapeutic approach including CT-guided biopsy followed immediately by RFA of solitary malignant pulmonary lesions. Methods: CT-guided transthoracic core needle biopsy of solitary pulmonary lesions suspicious for malignancy was performed and histology was proven based on immediate frozen sections. RFA probes were placed into the pulmonary tumors under CT guidance and the ablation was performed subsequently. The procedure-related morbidity was analyzed. Follow-up included a CT scan and pulmonary function parameters. Results: A total of 33 CT-guided biopsies and subsequent RFA within a single procedure were performed. Morbidity of CT-guided biopsy included pulmonary hemorrhage (24%) and a mild pneumothorax (12%) without need for further interventions. The RFA procedure was not aggravated by the previous biopsy. The rate of pneumothorax requiring chest tube following RFA was 21%. Local tumor control was achieved in 77% with a median follow-up of 12 months. The morbidity of the CT-guided biopsy had no statistical impact on the local recurrence rate. Conclusions: The simultaneous diagnostic and therapeutic approach including CT-guided biopsy followed immediately by RFA of solitary malignant pulmonary lesions is a safe procedure. The potential of this combined approach is to avoid unnecessary therapies and to perform adequate therapies based on histology. Taking the local control rate into account, this approach should only be performed in those patients who are unable to undergo or who refuse surgery. Copyright (C) 2012 S. Karger AG, Base

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards

Harmonization of cancer variant representation, efficient communication, and free distribution of clinical variant-associated knowledge are central problems that arise with increased usage of clinical next-generation sequencing. The Clinical Genome Resource (ClinGen) Somatic Working Group (WG) developed a minimal variant level data (MVLD) representation of cancer variants, and has an ongoing collaboration with Clinical Interpretations of Variants in Cancer (CIViC), an open-source platform supporting crowdsourced and expert-moderated cancer variant curation. Harmonization between MVLD and CIViC variant formats was assessed by formal field-by-field analysis. Adjustments to the CIViC format were made to harmonize with MVLD and support ClinGen Somatic WG curation activities, including four new features in CIViC: (1) introduction of an assertions feature for clinical variant assessment following the Association of Molecular Pathologists (AMP) guidelines, (2) group-level curation tracking for organizations, enabling member transparency, and curation effort summaries, (3) introduction of ClinGen Allele Registry IDs to CIViC, and (4) mapping of CIViC assertions into ClinVar submission with automated submissions. A generalizable workflow utilizing MVLD and new CIViC features is outlined for use by ClinGen Somatic WG task teams for curation and submission to ClinVar, and provides a model for promoting harmonization of cancer variant representation and efficient distribution of this information

CIViCpy: A Python software evelopment and analysis toolkit for the CIViC knowledgebase

PURPOSE: Precision oncology depends on the matching of tumor variants to relevant knowledge describing the clinical significance of those variants. We recently developed the Clinical Interpretations for Variants in Cancer (CIViC; civicdb.org) crowd-sourced, expert-moderated, and open-access knowledgebase. CIViC provides a structured framework for evaluating genomic variants of various types (eg, fusions, single-nucleotide variants) for their therapeutic, prognostic, predisposing, diagnostic, or functional utility. CIViC has a documented application programming interface for accessing CIViC records: assertions, evidence, variants, and genes. Third-party tools that analyze or access the contents of this knowledgebase programmatically must leverage this application programming interface, often reimplementing redundant functionality in the pursuit of common analysis tasks that are beyond the scope of the CIViC Web application. METHODS: To address this limitation, we developed CIViCpy (civicpy.org), a software development kit for extracting and analyzing the contents of the CIViC knowledgebase. CIViCpy enables users to query CIViC content as dynamic objects in Python. We assess the viability of CIViCpy as a tool for advancing individualized patient care by using it to systematically match CIViC evidence to observed variants in patient cancer samples. RESULTS: We used CIViCpy to evaluate variants from 59,437 sequenced tumors of the American Association for Cancer Research Project GENIE data set. We demonstrate that CIViCpy enables annotation of \u3e 1,200 variants per second, resulting in precise variant matches to CIViC level A (professional guideline) or B (clinical trial) evidence for 38.6% of tumors. CONCLUSION: The clinical interpretation of genomic variants in cancers requires high-throughput tools for interoperability and analysis of variant interpretation knowledge. These needs are met by CIViCpy, a software development kit for downstream applications and rapid analysis. CIViCpy is fully documented, open-source, and available free online