PluginPlay: Enabling exascale scientific software one module at a time

For many computational chemistry packages, being able to efficiently and effectively scale across an exascale cluster is a heroic feat. Collective experience from the Department of Energy's Exascale Computing Project suggests that achieving exascale performance requires far more planning, design, and optimization than scaling to petascale. In many cases, entire rewrites of software are necessary to address fundamental algorithmic bottlenecks. This in turn requires a tremendous amount of resources and development time, resources that cannot reasonably be afforded by every computational science project. It thus becomes imperative that computational science transition to a more sustainable paradigm. Key to such a paradigm is modular software. While the importance of modular software is widely recognized, what is perhaps not so widely appreciated is the effort still required to leverage modular software in a sustainable manner. The present manuscript introduces PluginPlay, https://github.com/NWChemEx-Project/PluginPlay, an inversion-of-control framework designed to facilitate developing, maintaining, and sustaining modular scientific software packages. This manuscript focuses on the design aspects of PluginPlay and how they specifically influence the performance of the resulting package. Although, PluginPlay serves as the framework for the NWChemEx package, PluginPlay is not tied to NWChemEx or even computational chemistry. We thus anticipate PluginPlay to prove to be a generally useful tool for a number of computational science packages looking to transition to the exascale.

Performance and onsite regeneration of natural zeolite for ammonium removal in a field-scale non-sewered sanitation system

Natural zeolite clinoptilolite was used as the primary ammonium removal method from the permeate of an anaerobic membrane bioreactor (AnMBR) treating high-strength blackwater generated from a community toilet facility. This zeolite-based nutrient capture system (NCS) was a sub-component of a non-sewered sanitation system (NSSS) called the NEWgenerator and was field tested for 1.5 years at an informal settlement in South Africa. The NCS was operated for three consecutive loading cycles, each lasting 291, 110, and 52 days, respectively. Both blackwater (from toilets) and blackwater with yellow water (from toilets and urinals) were treated during the field trial. Over the three cycles, the NCS was able to remove 80 ± 28%, 64 ± 23%, and 94 ± 11%, respectively, of the influent ammonium. The addition of yellow water caused the rapid exhaustion of zeolite and the observed decrease of ammonium removal during Cycle 2. After Cycles 1 and 2, onsite regeneration was performed to recover the sorption capacity of the spent zeolite. The regenerant was comprised of NaCl under alkaline conditions and was operated as a recycle-batch to reduce the generation of regenerant waste. Modifications to the second regeneration process, including an increase in regenerant contact time from 15 to 30 h, improved the zeolite regeneration efficiency from 76 ± 0.7% to 96 ± 1.0%. The mass of recoverable ammonium in the regenerant was 2.63 kg NH4-N and 3.15 kg NH4-N after Regeneration 1 and 2, respectively. However, the mass of ammonium in the regenerant accounted for only 52.8% and 54.4% of the estimated NH4-N originally sorbed onto the zeolite beds after Cycles 1 and 2, respectively. The use of zeolite clinoptilolite is a feasible method for ammonium removal by NSSS that observe variable nitrogen loading rates, but further research is still needed to recover the nitrogen from the regenerant waste.

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

Oxidant effects on epithelial Na,K-ATPase gene expression and promoter function

The lung epithelium resorbs alveolar fluid through combined action of sodium channels and the sodium pump, Na,K-ATPase. The lung often is exposed to hyperoxia in disease states and hyperoxia generates a mixture of reactive oxygen species. In vivo and in vitro exposure of rat lung and alveolar type II cells, respectively, increases gene expression of both alpha-1 and beta-1 subunits of the sodium pump. In contrast to the primary type II cells, several type II cell lines did not increase sodium pump gene expression with hyperoxia, but the renal tubular epithelial MDCK cell line did. Using promoter-receptor constructs transfected into MDCK cells, hyperoxia did not markedly increase transcription of the alpha-1 subunit but doubled transcription of the beta-1 subunit gene. Using 5'-deletion constructs, the region required for the beta-1 increase was localized to a 40-base pair region from -44/-84. The hyperoxic responsiveness of this region was confirmed using constructs with one or two copies of this region placed in minimal promoter-luciferase reporters. This 5' promoter region contains a consensus binding sequence for SP-1, a basal transcription factor but not for binding of other known transcription factors. Thus, hyperoxia induces Na,K-ATPase beta-1 promoter transcription, likely acting through a novel mechanism.

Anti-beta-receptor antibodies in familial cardiomyopathy: correlation with HLA-DR and HLA-DQ gene polymorphisms

The presence of beta-receptor autoantibodies and their relationship to restriction fragment length polymorphisms of the human leukocyte antigen (HLA) class II genes were studied in 42 affected and unaffected members of a family with a heritable disorder of the conduction system and cardiac muscle. Antibodies were detected in 34% of all members (59% of affected and 22% of unaffected; p < 0.01). Significant differences between affected and unaffected individuals and between anti-beta-receptor antibody positive and negative individuals were noted in the prevalence of polymorphisms obtained with Taq I for the HLA-DR beta and HLA-DQ alpha genes. In affected individuals, there was a strong positive correlation between these polymorphisms and the presence of anti-beta-receptor antibodies. These results suggest that autoimmune mechanisms under the control of the class II genes play an important role in the pathogenesis of familial cardiomyopathy.

Proliferative activity of normal and neoplastic urothelium and its relation to epidermal growth factor and transferrin receptors

AIMS

To investigate the proliferative activity (given by the Ki67 index) of the normal, atypical, and neoplastic urothelium and its relation to the cellular reactivity for the epidermal growth factor (EGFr) and transferrin (Tfr) receptors.

METHODS

The Ki67 index and the level of EGFr and Tfr reactivity were determined on frozen sections from 82 patients with urothelial cancer. Relevant clinical material was reviewed to establish correlations with the degree of atypia and invasion.

RESULTS

Morphologically normal urothelium, whether derived from controls or patients with cancer, exhibited a low Ki67 index (less than 0.1%) and weak receptor reactivity. In transitional cell carcinomas (TCCs) the Ki67 index was increased: it ranged between 0.7% and 10% in non-invasive and exceeded 10% in 88% of the invasive TCCs. Strong positive reactions for EGFr were seen only in invasive TCCs, but in 47% of invasive TCCs the EGFr was not "overexpressed" and did not match the Ki67 index. A better correlation was found between the Ki67 index and the Tfr which was positive in 26% of the non-invasive and in 71% of the invasive tumours. All three variables were increased in severe atypia but varied considerably in lesser degrees of atypia.

CONCLUSIONS

Despite the absence of a close correlation, accelerated growth and enhanced receptor expression were characteristic of invasive cancers. These results suggest that the growth rate in TCCs is not causally related to overexpression of growth factor receptors but that the latter is an abnormality which may accompany the malignant phenotype.

Proliferative activity of urothelial neoplasms: comparison of BrdU incorporation, Ki67 expression, and nucleolar organiser regions

AIMS

To evaluate the proliferative activity of urothelial neoplasms, compare it with that of the normal urinary tract epithelium, and determine its relation to morphological grade and presence of invasion.

METHODS

Multiple biopsy specimens from 53 individuals--eight normal controls, five patients with severe urothelial atypia, and 40 with transitional cell carcinomas (TCCs)--were studied using in vitro bromodeoxyuridine (BrdU) incorporation, Ki67 antigen expression, and quantitation of the nucleolar organiser regions (NORs).

RESULTS

The percentage of nuclei labelled by BrdU (BrdU index) correlated well with the percentage of nuclei expressing the Ki67 antigen (Ki67 index). These proliferation indices were very low (less than 0.1% in 60% of samples) in the urothelium of normal controls and the morphologically unremarkable epithelium of patients with TCCs. Non-invasive TCCs had increased proliferation (BrdU index 6.32 (SD 0.8)%, Ki67 index 5.04 (0.6)% but lagged behind the invasive tumours (BrdU 20.9 (3.2)%, Ki67 18.6 (2.8)%). The average NOR count was 1.57 (0.03) in morphological normal epithelium, which increased progressively with grade in non-invasive TCCs, but varied greatly in invasive tumours and did not correlate with the proliferation indices. The spectrum of values for both proliferation indices and NORs was particularly wide in grade 2 TCCs. Severe atypias without exophytic growth had an increase in BrdU and Ki67 indices comparable with that found in grade 3-4 invasive TCCs; these also had the highest NORs per nucleus.

CONCLUSIONS

The growth potential of urothelial neoplasms is an important indicator of their aggressive course. In particular, growth indices over 10% are strongly associated with the presence of invasion. Papillary grade 2 TCCs show heterogeneity in their growth characteristics which may relate to their diverse clinical course. The mitotic count underestimates the growth potential of papillary TCCs and the addition of proliferation indices such as BrdU incorporation or the Ki67 index may enhance the prognostic accuracy of conventional morphological grading.

T-cell receptor gene polymorphisms in familial cardiomyopathy: correlation with anti-beta-receptor autoantibodies

Cardiac autoantibodies have been detected in a significant proportion of patients with dilated cardiomyopathy, but their relation to the pathogenesis of the disease remains unknown. This issue was examined in 41 members of an Ohio family with a heritable disorder of the cardiac conduction system and the myocardium. In 41.5% of all members studied, serum anti-beta-receptor antibodies were identified by a combination of techniques: ligand binding inhibition assay, enzyme-linked immunoassay of a beta 1-receptor peptide, and adenylate cyclase inhibition. The prevalence of autoantibodies was significantly higher (p < 0.01) in the affected (64.7%) than in the unaffected (25.0%) members. A 10.0 kb restriction fragment length polymorphism of the C beta region of the T-cell receptor gene was also overrepresented in affected males (60% versus 30% unaffected males, p < 0.01). In males, the presence of anti-beta-receptor antibodies was linked to the 10.0 kb C beta polymorphism. In affected males, a BlgII C alpha 2.14 kb polymorphism was also more frequent (62% versus 32% in unaffected, p < 0.01) and was linked to the presence of anti-beta-receptor antibodies. The distribution of haplotypes defined by V beta 8, C alpha, and C beta probes was significantly different between affected and unaffected (p < 0.04) and between antibody-positive and antibody-negative individuals. Since the major function of the T-cell receptor is the recognition of processed autoantigens, these results provide additional support for the role of autoimmunity in dilated cardiomyopathy.