Implementing an open source knowledge base

The concept of knowledge bases originated in artificial intelligence as one side of expert systems-namely, the fundamental body of knowledge available to a domain. KBs are particularly appropriate in knowledge-intensive activities like software development. They offer context-based access to complex information, including informal documents and multimedia, as well as a centralized means of storing and preserving digital assets. KBs can help software engineers with many tasks-from project management and design rationale to version control, defect tracking, code reuse, and staff training and development. We recently implemented an open source KB to support the Consortium for Studying Open Source in Public Administrations. COSPA originated in a EU initiative to study the use of open source software to reduce public administrative software and system support costs. The KB project aimed to build a multilingual knowledge base for comparing and pooling knowledge and experience.     

Screening natural products for inhibitors of quinone reductase-2 using ultrafiltration LC-MS

Inhibitors of quinone reductase-2 (NQO2; QR-2) can have antimalarial activity and antitumor activities or can function as chemoprevention agents by preventing the metabolic activation of toxic quinones such as menadione. To expedite the search for new natural product inhibitors of QR-2, we developed a screening assay based on ultrafiltration liquid chromatography-mass spectrometry that is compatible with complex samples such as bacterial or botanical extracts. Human QR-2 was prepared recombinantly, and the known QR-2 inhibitor, resveratrol, was used as a positive control and as a competitive ligand to eliminate false positives. Ultrafiltration LC-MS screening of extracts of marine sediment bacteria resulted in the discovery of tetrangulol methyl ether as an inhibitor of QR-2. When applied to the screening of hop extracts from the botanical, Humulus lupulus L., xanthohumol and xanthohumol D were identified as ligands of QR-2. Inhibition of QR-2 by these ligands was confirmed using a functional enzyme assay. Furthermore, binding of xanthohumol and xanthohumol D to the active site of QR-2 was confirmed using X-ray crystallography. Ultrafiltration LC-MS was shown to be a useful assay for the discovery of inhibitors of QR-2 in complex matrixes such as extracts of bacteria and botanicals.     

Discrimination of auditory distance cues by black-capped chickadees (Poecile atricapillus) and zebra finches (Taeniopygia guttata).

The authors examined auditory distance perception using a go/no-go operant discrimination task in the laboratory. They taught male black-capped chickadees (Poecile atricapillus) and male zebra finches (Taeniopygia guttata) to discriminate degraded (far) from undegraded (near) versions of male chickadee songs and female zebra finch calls, showing for the 1st time that males can discriminate distance cues in heterospecific vocalizations and in female calls. Chickadees learned faster than zebra finches, and both species learned to discriminate chickadee songs faster than zebra finch calls. Chickadees more than zebra finches attended to amplitude in tests pitting it against other distance cues, demonstrating that amplitude is a potentially useful cue for estimating distance from vocalizations. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Statistical classification of black-capped (Poecile atricapillus) and mountain chickadee (Poecile gambeli) call notes.

Both black-capped (Poecile atricapillus) and mountain chickadees (Poecile gambeli) produce a chick-a-dee call that consists of several distinct note types. In some regions, these 2 species live sympatrically, and it has been shown that 1 species will respond weakly to songs of the other. This suggests that chickadee song, and potentially other of their vocalizations, contains species-specific information. We tested the possibility that call notes were acoustically sufficient for species identification. Black-capped and mountain non-D notes were summarized as a set of 9 features and then analyzed by linear discriminant analysis. Linear discriminant analysis was able to use these notes to identify species with 100% accuracy. We repeated this approach, but with black-capped and mountain D notes that were summarized as a set of 4 features. Linear discriminant analysis was able to use these notes to identify species with 94% accuracy. This demonstrates that any of the note types in these chickadee calls possesses sufficient information for species classification. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Timing and classifying brief acoustic stimuli by songbirds and humans.

The durations of animals' brief vocalizations provide conspecifics with important recognition cues. In the present experiments, zebra finches and humans (trained musicians) were rewarded for responding after S+ (standard) auditory signals from 56 to 663 ms; and not for responding, after shorter or longer S– (comparison) durations from 10 to 3684 ms. With either a single standard (Experiment 1) or multiple standards (Experiment 2), both zebra finches and humans timed brief signals to about the same level of accuracy. The results were in qualitative agreement with predictions from scalar timing theory and its connectionist implementation in both experiments. The connectionist model provides a good quantitative account of temporal gradients with a single standard (Experiment 1) but not with multiple standards (Experiment 2). (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Frequency–range discriminations: Special and general abilities in zebra finches (Taeniopygia guttata) and humans (Homo sapiens).

The acoustic frequency ranges in birdsongs and human speech can provide important pitch cues for recognition. Zebra finches and humans were trained to sort contiguous frequencies into 3 or 8 ranges, based on associations between the ranges and reward. The 3-range task was conducted separately in 3 spectral regions. Zebra finches discriminated 3 ranges in the medium and high spectral regions faster than in the low region and discriminated 8 ranges with precision. Humans discriminated 3 ranges in all 3 spectral regions to the same modest standard and acquired only a crude discrimination of the lowest and highest of 8 ranges. The results indicate that songbirds have a special sensitivity to the pitches in conspecific songs and, relative to humans, have a remarkable general ability to sort pitches into ranges. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Frequency-range discriminations and absolute pitch in black-capped chickadees (Poecile atricapillus), mountain chickadees (Poecile gambeli), and zebra finches (Taeniopygia guttata).

The acoustic frequency ranges in birdsongs provide important absolute pitch cues for the recognition of conspecifics. Black-capped chickadees (Poecile atricapillus), mountain chickadees (Poecile gambeli), and zebra finches (Taeniopygia guttata) were trained to sort tones contiguous in frequency into 8 ranges on the basis of associations between response to the tones in each range and reward. All 3 species acquired accurate frequency-range discriminations, but zebra finches acquired the discrimination in fewer trials and to a higher standard than black-capped or mountain chickadees, which did not differ appreciably in the discrimination. Chickadees' relatively poorer accuracy was traced to poorer discrimination of tones in the higher frequency ranges. During transfer tests, the discrimination generalized to novel tones when the training tones were included, but not when they were omitted. (PsycINFO Database Record (c) 2010 APA, all rights reserved)