The UCSC Kestrel parallel processor

The architectural landscape of high-performance computing stretches from superscalar uniprocessor to explicitly parallel systems, to dedicated hardware implementations of algorithms. Single-purpose hardware can achieve the highest performance and uniprocessors can be the most programmable. Between these extremes, programmable and reconfigurable architectures provide a wide range of choice in flexibility, programmability, computational density, and performance. The UCSC Kestrel parallel processor strives to attain single-purpose performance while maintaining user programmability. Kestrel is a single-instruction stream, multiple-data stream (SIMD) parallel processor with a 512-element linear array of 8-bit processing elements. The system design focuses on efficient high-throughput DNA and protein sequence analysis, but its programmability enables high performance on computational chemistry, image processing, machine learning, and other applications. The Kestrel system has had unexpected longevity in its utility due to a careful design and analysis process. Experience with the system leads to the conclusion that programmable SIMD architectures can excel in both programmability and performance. This work presents the architecture, implementation, applications, and observations of the Kestrel project at the University of California at Santa Cruz.     

Generation(s) of phonological codes in reading: A reply to Guttentag.

Addresses R. E. Guttentag's (see record 1982-11297-001) 2 questions about the review by L. X. McCusker et al (see record 1981-11846-001) of the phonological recoding literature. Following Guttentag's suggestion, the possibility of phonological mediation without the use of grapheme–phoneme correspondence rules is considered. It is recognized as a logically possible supplement to phonological recoding, but no empirical support was found. Guttentag's discussion of how dependence on phonological recoding might change with increased age and reading skill is also addressed. (12 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The psychological four-color mapping problem.

Mathematicians have proven that four colors are sufficient to color 2-D maps so that no neighboring regions share the same color. Here we consider the psychological 4-color problem: Identifying which 4 colors should be used to make a map easy to use. We build a model of visual search for this design task and demonstrate how to apply it to the task of identifying the optimal colors for a map. We parameterized the model with a set of 7 colors using a visual search experiment in which human participants found a target region on a small map. We then used the model to predict search times for new maps and identified the color assignments that minimize or maximize average search time. The differences between these maps were predicted to be substantial. The model was then tested with a larger set of 31 colors on a map of English counties under conditions in which participants might memorize some aspects of the map. Empirical tests of the model showed that an optimally best colored version of this map is searched 15% faster than the correspondingly worst colored map. Thus, the color assignment seems to affect search times in a way predicted by the model, and this effect persists even when participants might use other sources of knowledge about target location. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Phonological recoding and reading.

Examines contradictory research that attempted to determine whether the process of lexical access in silent reading is mediated by an internal phonological representation or only by visual representations. More recent evidence is discussed that suggests that factors such as difficulty of material, frequency of occurrence of items, Ss' fluency, and task demands—which are seldom manipulated in typical studies of word recognition—play important roles in determining the type of mediation used. It is noted that interest has shifted to a family of dual access models in which both phonological mediation and visual mediation are ordinarily used in parallel. Thus, data point to a dual access model in which high-frequency words enjoy high-speed access via a visually based representation, whereas low-frequency words are accessed using a slower, phonological recoding process. (113 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Is ABH nonsecretor status a risk factor for obstructive lung disease?

In a multidisciplinary study of risk factors for chronic obstructive pulmonary disease (COPD), a significantly more impairment of forced expiration was observed in ABH nonsecretors than in ABH secretors among 1017 white adults. (ABH refers to the "A" and "B" antigens of the ABO blood group system and "H", the heterogenetic substance which is found in persons of all ABO types including type "O".) Nonsecretors had significantly lower mean values of forced expiratory volume in one second as a percentage of forced vital capacity (FEV1/FVC%) and a significantly larger proportion of them had aberrant values, defined as FEV1/FVC% less than 68. These differences remained when mean values or rates of aberrancy were adjusted for other factors reported to alter risk of airway obstruction. In view of the known COPD-peptic ulcer and nonsecretor-duodenal ulcer associations, these findings suggest that the ability to secrete ABH antigens into secretions of the respiratory and gastrointestinal tract may have a protective effect on epithelialized organs in general, or on the lung and portions of the gut specifically.     

Trace nutrient deficiency in Daphnia magna cultured in standard medium for toxicity testing. Effects of the optimization of culture conditions on life history parameters of D. magna

The suitability of various synthetic media for the culture of Daphnia magna was tested. Daphnids cultured in a standard medium for toxicity testing proposed by ISO showed low reproduction, reduced growth, high numbers of undeveloped parthenogenetic eggs and high mortality of neonates and adults. As a feature, animals cultured in the ISO medium lost parts of their second antennae. It could be shown that this was caused by selenium deficiency. The addition of selenium to the ISO medium clearly improved the quality of this medium. However, results of several tests were more variable than when a medium with a complex trace element composition (medium M4) was used. Medium M4 has allowed continuous culture of daphnids for three years up to now without any signs of reduced viability or reproduction. A mean reproduction rate of about 140 progeny/parent daphnid was calculated from 19 non simultaneous experiments. Neither a fourfold increase nor a reduction to one tenth of the trace element concentration of M4 had any effect on reproduction, growth or survival of daphnids. It was shown in this study that ion-exchanger cartridges can leach detrimental substances into the matrix water. Therefore, only ultrapure matrix waters should be used for the preparation of culture media.