The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

Identification of GBV-D, a Novel GB-like Flavivirus from Old World Frugivorous Bats (Pteropus giganteus) in Bangladesh

Bats are reservoirs for a wide range of zoonotic agents including lyssa-, henipah-, SARS-like corona-, Marburg-, Ebola-, and astroviruses. In an effort to survey for the presence of other infectious agents, known and unknown, we screened sera from 16 Pteropus giganteus bats from Faridpur, Bangladesh, using high-throughput pyrosequencing. Sequence analyses indicated the presence of a previously undescribed virus that has approximately 50% identity at the amino acid level to GB virus A and C (GBV-A and -C). Viral nucleic acid was present in 5 of 98 sera (5%) from a single colony of free-ranging bats. Infection was not associated with evidence of hepatitis or hepatic dysfunction. Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades

Fiscal Year 2010

During FY 2010, work under the Spectroscopy-Based Process Monitoring task included ordering and receiving four fluid flow meters and four flow visible-near infrared spectrometer cells to be instrumented within the centrifugal contactor system at Pacific Northwest National Laboratory (PNNL). Initial demonstrations of real-time spectroscopic measurements on cold-stream simulants were conducted using plutonium (Pu)/uranium (U) (PUREX) solvent extraction process conditions. The specific test case examined the extraction of neodymium nitrate (Nd(NO3)3) from an aqueous nitric acid (HNO3) feed into a tri-n-butyl phosphate (TBP)/ n-dodecane solvent. Demonstration testing of this system included diverting a sample from the aqueous feed meanwhile monitoring the process in every phase using the on-line spectroscopic process monitoring system. The purpose of this demonstration was to test whether spectroscopic monitoring is capable of determining the mass balance of metal nitrate species involved in a cross-current solvent extraction scheme while also diverting a sample from the system. The diversion scenario involved diverting a portion of the feed from a counter-current extraction system while a continuous extraction experiment was underway. A successful test would demonstrate the ability of the process monitoring system to detect and quantify the diversion of material from the system during a real-time continuous solvent extraction experiment. The system was designed to mimic a PUREX-type extraction process with a bank of four centrifugal contactors. The aqueous feed contained Nd(NO3)3 in HNO3, and the organic phase was composed of TBP/n-dodecane. The amount of sample observed to be diverted by on-line spectroscopic process monitoring was measured to be 3 mmol (3 x 10-3 mol) Nd3+. This value was in excellent agreement with the 2.9 mmol Nd3+ value based on the known mass of sample taken (i.e., diverted) directly from the system feed solution

Phylogenetic relationship of GBV-D to other GBV and hepaciviruses.

<p>GBV-D amino acid sequences for A: NS5B, B: NS3, and C: the polyprotein (PPT) were analyzed in comparison to representative sequences of GBV-A, -B, -C and hepatitis C viruses. GenBank accession numbers for the respective sequences are indicated. Entebbe bat virus was used as an outgroup; distance in substitutions per site is indicated by scale bars; percent bootstrap support for values greater than 85% is indicated at respective nodes.</p

Percent sequence similarity between GBV-D (bat-68), -A, -C, and hepaciviruses.

<p>*Sequence similarity at nt level in upper right, and at aa level in lower left portion of the table.</p

Genomic organization of GBV-D, a novel flavivirus identified in the sera of frugivorous bats in Bangladesh.

<p>Arrows, glycosylation sites; solid diamond, active center sites H₉₂₁, E₁₀₁₁, and C₁₀₃₂ in the autocatalytic NS2/NS3 endoprotease domain; triangle, catalytic triad H₁₁₂₃, D₁₁₄₇, S₁₂₀₄ of NS3 serine protease; rectangle, NS3 helicase and DEAD-like helicase motifs; open diamond, zinc finger motif; and NS5 polymarase motifs A (T₂₇₄₄VDAICFDSCIT), B (R₂₈₀₂ASGVLTTSSSNCISSFLKVSAAC), C (F₂₈₃₅LIHGDDVMII), D (L₂₈₇₆DTAQSCSA),and E (H₂₉₀₀YFLSTDFR) motifs.</p