Ongoing verification of a multiphysics community code: FLASH

When developing a complex, multi‐authored code, daily testing on multiple platforms and under a variety of conditions is essential. It is therefore necessary to have a regression test suite that is easily administered and configured, as well as a way to easily view and interpret the test suite results. We describe the methodology for verification of FLASH, a highly capable multiphysics scientific application code with a wide user base. The methodology uses a combination of unit and regression tests and an in‐house testing software that is optimized for operation under limited resources. Although our practical implementations do not always comply with theoretical regression‐testing research, our methodology provides a comprehensive verification of a large scientific code under resource constraints.Copyright © 2013 John Wiley & Sons, Ltd.     

Evaluating and improving the effectiveness and efficiency of design process communication

Project information management research enables the efficient exchange of information, but does not effectively communicate process. Design process management research effectively communicates processes, but with methods too inefficient to be adopted in practice. The lack of methods for effective and efficient design process communication manifests as a struggle for Architecture, Engineering, and Construction industry professionals to: (1) collaborate within projects, (2) share processes between projects, and (3) understand processes across projects to strategically invest in improvement. These struggles motivate the paper’s first contribution: a research method for evaluating a design management methodology’s ability to effectively and efficiently communicate design processes. As a second contribution, this paper validates the Design Process Communication Methodology (DPCM). DPCM specifies elements and methods for exchanging and organizing digital information to support knowledge-intensive design processes. Cloud computing enables the operationalization of DPCM as a tool that enables interaction with a project’s information. Results from this operationalization demonstrate that designers employing DPCM accurately capture processes with little effort. When collaborating, improved process clarity and information consistency result in less rework, and positive iteration enables increased consideration of multi-disciplinary design trends. Designers share processes between project teams with fewer process mistakes. DPCM enables the understanding of processes providing more insights into the relationships between design integration and project performance; and more opportunities for strategic investment in improved processes.     

Semantic constraints on word learning: proper names and adjectives

4 experiments examined 3- and 4-year-olds' interpretations of novel words applied to familial objects in the sentence frame, "This Y is X," where X is a novel word, and Y is a familiar basic-level count noun (e.g., "dog," "cup"). These novel words are ambiguous and could be interpreted either as proper names (e.g., "Fred") or as adjectives/mass nouns (e.g., "red"/"lead"). The experiments addressed 2 questions. First, do children appreciate that the words can be construed either as proper names referring to individuals or as adjectives/mass nouns referring to salient properties/material kinds? The results showed that children could easily make either interpretation. Second, what factors affect children's tendency to make either a proper name or an adjective/mass noun interpretation? In the experiments, children learned the novel words for a range of animals and artifacts. Most children who learned the words for typical pets (e.g., a bird) made proper name interpretations, as did the majority of those who learned the words for certain non-pet animals (e.g., a caterpillar) described as possessed by someone, but only about half of those who learned the words for such non-pet animals not so described. Very few children who learned the words for either simple (e.g., a shoe) or complex (e.g., a boat) artifacts made proper name interpretations. The results provide clear evidence of the role of semantic information in constraining children's interpretation of a novel word, and they help to refine an understanding of what counts as a nameable individual for preschoolers.     

Autoradiographic assessment of blood flow heterogeneity in the hamster heart

OBJECTIVE: Provide regional flow measurement in the hearts of small mammals using a new, higher-resolution technique based on the deposition of a molecular marker. METHODS: We determined the instantaneous extraction and retention of the "molecular microsphere" radiolabeled desmethylimipramine in retrogradely perfused hamster hearts. In a separate series of experiments, autoradiography was used to measure regional myocardial deposition densities in hamster hearts of about 0.5 g with spatial area resolution of 16 x 16 microns. RESULTS: Radiolabeled desmethylimipramine is almost 100% extracted during a single transcapillary passage and is retained in the tissue for many minutes. Autoradiographic images demonstrated a spatial flow heterogeneity with standard deviations of 31 +/- 4% of the mean flow (N = 5) in 16 x 16 x 20-micronm3 voxels. This is equivalent to the projections made using fractal relationships from cruder observations obtained with microspheres in the hearts of baboons, sheep, and rabbits. CONCLUSIONS: Autoradiography using a molecular deposition marker provides quantitative information on myocardial flow heterogeneities with resolution at the size of cardiac myocytes. Because the regions resolved are smaller than the volume of regions supplied by single arterioles, the results must slightly exaggerate the true heterogeneity of regional flows.     

Evidence that human cardiac allograft acceptance is associated with a decrease in donor-reactive helper T lymphocytes

We have reported that acute cardiac allograft rejection is associated with increased numbers of donor-reactive helper T lymphocytes (HTL) in the peripheral blood of patients. Further, increased frequencies of circulating donor-reactive HTL may predict allograft rejection episodes diagnosed by endomyocardial biopsy. The present study evaluates the relationship between donor-reactive HTL and allograft "acceptance" in cardiac transplant recipients bearing long-term allografts (> 1 year). Patients were categorized as either long-term acceptors or persistent rejecters based on the number of rejection episodes and the ability to withdraw steroid therapy. Limiting dilution analysis for IL-2-producing HTL was utilized, with cadaver donor splenocytes as a source of donor alloantigens. Donor-reactive HTL frequencies were determined from peripheral blood samples obtained before transplant, and at 1 month and 1 year after transplant. Individuals who accommodated their allografts and were withdrawn from steroid therapy had reduced numbers of donor-reactive HTL at 1 year after transplant as compared with earlier time points. Further, PBMC obtained from these individuals at 1 year after transplant responded weakly to donor alloantigens in a mixed lymphocyte response (MLR). This relationship between donor-reactive HTL and allograft accommodation was exemplified in a cardiac/liver transplant patient who was diagnosed with progressive multifocal leukoencephalopathy and removed from all immunosuppression. No subsequent rejection episodes were diagnosed. Donor-reactive HTL were not detectable and this individual failed to mount an MLR to donor alloantigens. However, a vigorous donor-reactive response was observed when MLR cultures were supplemented with exogenous IL-2. Therefore, nonresponsiveness to the allograft appeared to be due to a deficit in IL-2 production. In contrast, patients who experienced persistent rejection episodes and required continued steroid therapy maintained large numbers of donor-reactive HTL at 1 year after transplant. PBMC from these individuals responded vigorously to donor alloantigens in an MLR. Hence, monitoring donor-reactive HTL may identify individuals who have accommodated their graft and may tolerate a reduction in immunosuppression.     

Enzyme structure with two catalytic sites for double-sieve selection of substrate

High-fidelity transfers of genetic information in the central dogma can be achieved by a reaction called editing. The crystal structure of an enzyme with editing activity in translation is presented here at 2.5 angstroms resolution. The enzyme, isoleucyl-transfer RNA synthetase, activates not only the cognate substrate L-isoleucine but also the minimally distinct L-valine in the first, aminoacylation step. Then, in a second, "editing" step, the synthetase itself rapidly hydrolyzes only the valylated products. For this two-step substrate selection, a "double-sieve" mechanism has already been proposed. The present crystal structures of the synthetase in complexes with L-isoleucine and L-valine demonstrate that the first sieve is on the aminoacylation domain containing the Rossmann fold, whereas the second, editing sieve exists on a globular beta-barrel domain that protrudes from the aminoacylation domain.     

Evaluating medication response in ADHD: cognitive, behavioral, and single-subject methodology

We introduce a novel application for linkage analysis: using bone marrow donor-recipient sib pairs to search for genes influential in graft-versus-host disease (GVHD), a major cause of morbidity and mortality following allogeneic bone marrow transplantation. In particular, we show that transplant sib pairs in which the recipient developed severe GVHD can be used to map genes in the same way as traditional discordant (affected/unaffected) sib pairs (DSPs). For a plausible GVHD model, we demonstrate that the transplant/discordant sib pair analog of the "possible triangle test" [Holmans (1993) Am J Hum Genet 52:362-374] has similar power to that of the simpler "restricted test" proposed by Risch [(1990b) Am J Hum Genet 46:229-241; (1992) Am J Hum Genet 51:673-675]. Moreover, we show that the restricted test has superior power in much of the DSP possible triangle and significantly inferior power in only a small region. Thus, we conclude that the restricted test is preferable for localizing genes with transplant/discordant sib pairs. Finally, we examine the effects of heterogeneity on the power to detect GVHD loci and demonstrate the gain in efficiency by dividing the sample into genetically more homogeneous subgroups.