GAIA: framework annotation of genomic sequence

As increasing amounts of genomic sequence from many organisms become available, and as DNA sequences become a primary reagent in biologic investigations, the role of annotation as a prospective guide for laboratory experiments will expand rapidly. Here we describe a process of high-throughput, reliable annotation, called framework annotation, which is designed to provide a foundation for initial biologic characterization of previously unexamined sequence. To examine this concept in practice, we have constructed Genome Annotation and Information Analysis (GAIA), a prototype software architecture that implements several elements important for framework annotation. The center of GAIA consists of an annotation database and the associated data management subsystem that forms the software bus along which other components communicate. The schema for this database defines three principal concepts: (1) Entries, consisting of sequence and associated historical data; (2) Features, comprising information of biologic interest; and (3) Experiments, describing the evidence that supports Features. The database permits tracking of annotation results over time, as well as assessment of the reliability of particular results. New framework annotation is produced by CARTA, a set of autonomous sensors that perform automatic analyses and assert results into the annotation database. These results are available via a Web-based query interface that uses graphical Java applets as well as text-based HTML pages to display data at different levels of resolution and permit interactive exploration of annotation. We present results for initial application of framework annotation to a set of test sequences, demonstrating its effectiveness in providing a starting point for biologic investigation, and discuss ways in which the current prototype can be improved. The prototype is available for public use and comment at http://www.cbil.upenn.edu/gaia.     

Oxidation of aqueous sulfide solutions by dioxygen Part II: Catalysis by soluble and immobilized cobalt(II) phthalocyanines

The oxidation of sulfide in oxygen-saturated aqueous solutions is accelerated by dissolved or silica-bonded cobalt phthalocyanines. On the basis of thermodynamical considerations it is postulated that the catalyst enhances the formation of disulfide as the initial elementary reaction step. The following reaction steps are largely unaffected by the catalyst, as indicated by a product ratio sulfate/thiosulfate=0.86, comparable to that of the uncatalyzed autoxidation. A Langmuir-Hinshelwood formalism is developed for the catalytic reaction step and is demonstrated to fit best with the kinetics. In addition, from the kinetic data free enthalpies for the adsorption of HS^? (i) at the dissolved phthalocyanine (ΔG = ?17.6 kJ/mole) and (ii) at the immobilized complex (ΔG = ?20.0 kJ/mole) are calculated.     

The past,present, and future of DARPA’s investment strategy in smart materials

The Defense Advanced Research Projects Agency (DARPA) smart materials research programs past, present, and future are reviewed in this article. Several articles have been written about the history of smart materials at DARPA;^1–4 therefore, discussions of past efforts are limited and present and future work is emphasized. More importantly, this article presents the authors’ vision of what is next in the smart materials arena, for it is their belief that the journey to truly smart materials and structures has really just begun. For more information, contact Steven Wax, DARPA, Defense Sciences Office, Arlington, Virginia; swax@Darpa.mil.     

Causal attributions and the perception of political figures.

Assessed the impact of political partisanship and audience support (ADS) on the impressions individuals form of political figures. 115 undergraduates (aged 18–43 yrs) read a speech which had supposedly been given by a member of Parliament from northern Ontario. Results indicate that perceptions of the politician were affected by both partisanship and ADS. Partisanship influenced perceptions of the politician's integrity, with the politician being perceived as having greater integrity when he gave a nonpartisan speech (inconsistent with his party's stand) than when he gave a partisan speech. ADS influenced perceptions of the politician's strength, with the politician who spoke to a hostile audience being perceived as stronger than the politician who spoke to a supportive audience. (French abstract) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

On the relationship between topography and transistor matching inan analog CMOS technology

A source of drain current mismatch of transistors in a 1.75-μm analog CMOS process is described. Matching of closely spaced transistors is degraded by capacitor topography created prior to the gate level. The effects extend over distances greater than 30 μm and are not reduced by common-centroid layout techniques. Symmetry and wafer position dependencies of the mismatch lead to an explanation of the effect. The topography is thought to interfere with the radial flow of gate level photoresist as it is spun on the wafer. Thickness variations in the photoresist result in channel length variations in the transistors following patterning. Transistor matching is improved by more than a factor of two with the use of a tri-level photoresist sequence at the gate level. Simple theoretical expressions and more exact numerical simulations support the explanation of channel length differences as the source of the measured mismatch. These calculations suggest how mismatch due to channel length, dopant concentration, or gate-oxide thickness may be differentiated with simple current-voltage measurements     

Acute effect of ursodeoxycholic acid on gallbladder volume in healthy subjects

The features of time domain and power spectrum of high frequency electrocardiogram (HF-ECG) were studied in normal Kunming mice using a microprocessor ECG system. The results were as follows (mean +/- SD): (1) P-R interval was 34.9 +/- 4.7 ms (n = 58), about one third of the cardiac cycle. (2) The duration and peak-to-peak amplitude of QRS complex were 9.2 +/- 1.2 ms and 1.456 +/- 0.480 mV (n = 74) respectively. (3) The duration and amplitude of T wave were 10.2 +/- 3.2 ms and 0.336 +/- 0.115 mV, respectively (n = 58). (4) Q-T interval was 19.4 +/- 3.2 ms (n = 58), about one fifth of the cardiac cycle. (5) The total number of notches and slurs of leads II of 73 mice were 3 and 26 respectively. (6) The relative power content of each frequency range was: 0-80 Hz: 45.48 +/- 15.32%; 80-200 Hz: 43.97 +/- 9.95%; 200-300 Hz: 8.89 +/- 7.83%; 300-1000 Hz: 1.66 +/- 2.74%; 80-1000 Hz: 54.52 +/- 15.32%.     

Analog RRS cells—An alternative approach for sampled-data low-pass filters

Running recursive sum (RRS) or moving average filters are simple building blocks that are commonly applied in digital signal processing for prefiltering and decimation purposes. This paper presents an efficient implementation of RRS filters employing switched-capacitor techniques. The resulting filter topologies are stray-capacitance insensitive. In order to improve the inherent low-frequency selectivity of these low-pass cells, two novel sharpening procedures are proposed. The zero locations of the analog RRS blocks are, analogous to their digital counterparts, determined exclusively by the applied sampling rate and the order of the filter cell. Hence, the corresponding analog circuits exhibit extremely low element sensitivities. The feasibility of the presented approach is demonstrated by means of two 24th-order silicon prototype filters implemented by a 2-m double-poly CMOS process.