A visual Analytics System for Optimizing Communications in Massively Parallel Applications

Current and future supercomputers have tens of thousands of compute nodes interconnected with high-dimensional networks and complex network topologies for improved performance. Application developers are required to write scalable parallel programs in order to achieve high throughput on these machines. Application performance is largely determined by efficient inter-process communication. A common way to analyze and optimize performance is through profiling parallel codes to identify communication bottlenecks. However, understanding gigabytes of profile data is not a trivial task. In this paper, we present a visual analytics system for identifying the scalability bottlenecks and improving the communication efficiency of massively parallel applications. Visualization methods used in this system are designed to comprehend large-scale and varied communication patterns on thousands of nodes in complex networks such as the 5D torus and the dragonfly. We also present efficient rerouting and remapping algorithms that can be coupled with our interactive visual analytics design for performance optimization. We demonstrate the utility of our system with several case studies using three benchmark applications on two leading supercomputers. The mapping suggestion from our system led to 38% improvement in hop-bytes for MiniAMR application on 4,096 MPI processes.This research has been sponsored in part by the U.S. National Science Foundation through grant IIS-1320229, and the U.S. Department of Energy through grants DE-SC0012610 and DE-SC0014917. This research has been funded in part and used resources of the Argonne Leadership Computing Facility at Argonne National Lab- oratory, which is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-06CH11357. This work was supported in part by the DOE Office of Science, ASCR, under award numbers 57L38, 57L32, 57L11, 57K50, and 508050

Manipulating nutrient composition of microalgal growth media to improve biomass yield and lipid content of Micractinium pusillum

Biodiesel production from microalgae depends on the algal biomass and lipid content. Both biomass production and lipid accumulation are limited by several factors in which nutrients play a key role. We investigated the influences of micronutrients on biomass, and lipid content of Micractinium pusillum GU732425 cultivated in bold basal media (BBM). The average dry biomass of microalgal strain in control medium reached 0.34 ± 0.01 g /L, while doubling (2X) the levels of Mn and Cu concentration increased the dry biomass to 0.38 ± 0.01 and 0.37 ± 0.02 g /L, respectively. M. pusillum cultivated in control medium had a biomass of 0.82 ± 0.05 g/L and a lipid productivity of 0.33 ± 0.02 g/L after 17 day cultivation. The alga cultivated in BBM with 4X Mn or 4X Cu produced more biomass (1.25 ± 0.01 or 1.28 ± 0.04 g dw/L) and lipid productivity (0.45±0.04 or 0.47±0.05 g/L), respectively. M. pusillum cultivated in different growth media had fatty acid compositions mainly comprising linoleic (49-54%), palmitic (24-29%), linolenic (16-22%), and oleic acids (2-5%). These results can be used to maximize the production of microalgal biomass and lipids in optimally designed  photobioreactors.Key words: Micractinium pusillum, biomass, lipid production, media composition, fatty acids, trace metals

Prolonged residence of an albumin–IL-4 fusion protein in secondary lymphoid organs ameliorates experimental autoimmune encephalomyelitis

Interleukin-4 (IL-4) suppresses the development of multiple sclerosis in a murine model of experimental autoimmune encephalomyelitis (EAE). Here, we show that, in mice with EAE, the accumulation and persistence in the lymph nodes and spleen of a systemically administered serum albumin (SA)–IL-4 fusion protein leads to higher efficacy in preventing disease development than the administration of wild-type IL-4 or of the clinically approved drug fingolimod. We also show that the SA–IL-4 fusion protein prevents immune-cell infiltration in the spinal cord, decreases integrin expression in antigen-specific CD4+ T cells, increases the number of granulocyte-like myeloid-derived suppressor cells (and their expression of programmed-death-ligand-1) in spinal cord-draining lymph nodes and decreases the number of T helper 17 cells, a pathogenic cell population in EAE. In mice with chronic EAE, SA–IL-4 inhibits immune-cell infiltration into the spinal cord and completely abrogates immune responses to myelin antigen in the spleen. The SA–IL-4 fusion protein may be prophylactically and therapeutically advantageous in the treatment of multiple sclerosis

Influence of curing on pore properties and strength of alkali activated mortars

The paper investigates the effect of wet/dry, wet and dry curing on the pore properties and strength of an alkali activated cementitious (AACM) mortar. The pore characteristics were determined from the cumulative and differential pore volume curves obtained by mercury intrusion porosimetry. AACM mortars possess a bimodal pore size distribution while the control PC mortar is unimodal. AACM mortars have a lower porosity, higher capillary pore volume, lower gel pore volume and lower critical and threshold pore diameters than the PC mortar which indicate greater durability potential of AACMs. Wet/dry curing is optimum for AACM mortars while wet curing is optimum for the PC mortar. Shrinkage and retarding admixtures improve the strength and pore structure of the AACMs

The Effects of Gas on Morphological Transformation in Mergers: Implications for Bulge and Disk Demographics

Transformation of disks into spheroids via mergers is a well-accepted element of galaxy formation models. However, recent simulations have shown that bulge formation is suppressed in increasingly gas-rich mergers. We investigate the global implications of these results in a cosmological framework, using independent approaches: empirical halo-occupation models (where galaxies are populated in halos according to observations) and semi-analytic models. In both, ignoring the effects of gas in mergers leads to the over-production of spheroids: low and intermediate-mass galaxies are predicted to be bulge-dominated (B/T~0.5 at <10^10 M_sun), with almost no bulgeless systems), even if they have avoided major mergers. Including the different physical behavior of gas in mergers immediately leads to a dramatic change: bulge formation is suppressed in low-mass galaxies, observed to be gas-rich (giving B/T~0.1 at <10^10 M_sun, with a number of bulgeless galaxies in good agreement with observations). Simulations and analytic models which neglect the similarity-breaking behavior of gas have difficulty reproducing the strong observed morphology-mass relation. However, the observed dependence of gas fractions on mass, combined with suppression of bulge formation in gas-rich mergers, naturally leads to the observed trends. Discrepancies between observations and models that ignore the role of gas increase with redshift; in models that treat gas properly, galaxies are predicted to be less bulge-dominated at high redshifts, in agreement with the observations. We discuss implications for the global bulge mass density and future observational tests.Comment: 14 pages, 11 figures, accepted to MNRAS (matched published version). A routine to return the galaxy merger rates discussed here is available at http://www.cfa.harvard.edu/~phopkins/Site/mergercalc.htm

Guidance on noncorticosteroid systemic immunomodulatory therapy in noninfectious uveitis: fundamentals of care for uveitis (focus) initiative

Topic: An international, expert-led consensus initiative to develop systematic, evidence-based recommendations for the treatment of noninfectious uveitis in the era of biologics. Clinical Relevance: The availability of biologic agents for the treatment of human eye disease has altered practice patterns for the management of noninfectious uveitis. Current guidelines are insufficient to assure optimal use of noncorticosteroid systemic immunomodulatory agents. Methods: An international expert steering committee comprising 9 uveitis specialists (including both ophthalmologists and rheumatologists) identified clinical questions and, together with 6 bibliographic fellows trained in uveitis, conducted a Preferred Reporting Items for Systematic Reviews and Meta-Analyses protocol systematic reviewof the literature (English language studies from January 1996 through June 2016; Medline [OVID], the Central Cochrane library, EMBASE,CINAHL,SCOPUS,BIOSIS, andWeb of Science). Publications included randomized controlled trials, prospective and retrospective studies with sufficient follow-up, case series with 15 cases or more, peer-reviewed articles, and hand-searched conference abstracts from key conferences. The proposed statements were circulated among 130 international uveitis experts for review.Atotal of 44 globally representativegroupmembersmet in late 2016 to refine these guidelines using a modified Delphi technique and assigned Oxford levels of evidence. Results: In total, 10 questions were addressed resulting in 21 evidence-based guidance statements covering the following topics: when to start noncorticosteroid immunomodulatory therapy, including both biologic and nonbiologic agents; what data to collect before treatment; when to modify or withdraw treatment; how to select agents based on individual efficacy and safety profiles; and evidence in specific uveitic conditions. Shared decision-making, communication among providers and safety monitoring also were addressed as part of the recommendations. Pharmacoeconomic considerations were not addressed. Conclusions: Consensus guidelines were developed based on published literature, expert opinion, and practical experience to bridge the gap between clinical needs and medical evidence to support the treatment of patients with noninfectious uveitis with noncorticosteroid immunomodulatory agents

Enhanced lymph node trafficking of engineered IL‐10 suppresses rheumatoid arthritis in murine models

Objective Rheumatoid arthritis (RA) is a major autoimmune disease that causes synovitis and joint damage. Although clinical trials using interleukin‐10 (IL‐10), an anti‐inflammatory cytokine, have been performed as a potential treatment of RA, its therapeutic effects have been limited, potentially due to insufficient residence in lymphoid organs, where antigen recognition primarily occurs. Here, we engineered IL‐10 as a fusion with serum albumin (SA). Methods SA‐fused IL‐10 was recombinantly expressed. After intravenous injection to mice, retention of SA‐IL‐10 at lymph node (LN), immune cell compositions at paws, and therapeutic effect on arthritis model mice were assessed. Results SA fusion to IL‐10 led to enhanced LN accumulation compared with unmodified IL‐10. Intravenous SA‐IL‐10 treatment restored immune cell composition in the paws to a normal status, elevated the frequency of suppressive M2 macrophages, reduced IL‐17A amount in the paw‐draining LN, and protected joint morphology. Intravenous SA‐IL‐10 treatment showed similar efficacy as treatment with an anti‐TNF‐α antibody. SA‐IL‐10 was equally effective when administered intravenously, locally or subcutaneously, which benefits clinical translation of this molecule. Conclusion SA fusion to IL‐10 is a simple but effective engineering strategy for RA therapy and holds clinical translational potential