A framework for characterizing overlap of communication and computation in parallel applications

Effective overlap of computation and communication is a well understood technique for latency hiding and can yield significant performance gains for applications on high-end computers. In this paper, we propose an instrumentation framework for message-passing systems to characterize the degree of overlap of communication with computation in the execution of parallel applications. The inability to obtain precise time-stamps for pertinent communication events is a significant problem, and is addressed by generation of minimum and maximum bounds on achieved overlap. The overlap measures can aid application developers and system designers in investigating scalability issues. The approach has been used to instrument two MPI implementations as well as the ARMCI system. The implementation resides entirely within the communication library and thus integrates well with existing approaches that operate outside the library. The utility of the framework is demonstrated by analyzing communication-computation overlap for micro-benchmarks and the NAS benchmarks, and the insights obtained are used to modify the NAS SP benchmark, resulting in improved overlap.

Genetic polymorphism of Baylisascaris procyonis in host infrapopulations and component populations in the Central USA

Baylisascaris procyonis is a nematode of significant concern to public and domestic animal health as well as wildlife management. The population genetics of B. procyonis is poorly understood. To gain insights into patterns of genetic diversity within (infrapopulation level) and among (component population level) raccoon (Procyon lotor) hosts, and specifically to assess the relative importance of indirect and direct transmission of the parasite for explaining observed population structure, we collected 69 B. procyonis from 17 wild raccoons inhabiting five counties in Missouri and Arkansas, USA. Informative regions of mitochondrial (CO1, CO2) and nuclear (28S, ITS2) genes were amplified and the distribution and genetic variability of these genes were assessed within and across raccoons. Concatenation of the CO1 and CO2 mtDNA sequences resulted in 5 unique haplotypes, with haplotype diversity 0.456?±?0.068. The most common haplotype occurred in 94% of raccoons and 72.5% of B. procyonis. Sequences for 28S rDNA revealed four unique nuclear genotypes, the most common found in 100% of raccoons and 82.6% of B. procyonis. ITS2 genotypes were assessed using fragment analysis, and there was a 1:1 correspondence between 28S and ITS-2 genotypes. Infrapopulation variation in haplotypes and genotypes was high and virtually all hosts infected with multiple sequenced nematodes also harbored multiple haplotypes and genotypes. There was a positive relationship between the size of the analyzed infrapopulation (i.e., the number of nematodes analyzed) and the number of haplotypes identified in an individual. Collectively this work emphasizes the importance of indirect transmission in the lifecycle to this parasite.     

Comparative histomorphology of the Mauthner cells in some freshwater teleosts.

The histomorphological observations are made on the Mauthner cells in eight species of teleosts belonging to six different families. The cells are better developed in Channa punctatus, Heteropneustes fossilis, Labeo rohita, Danio, malabaricus and Puntius ticto. They are symmetrically situated in Nandus nandus and are found to be absent in Mastocembalus armatus. Their position, shape and size vary in different species. The axon cap is well developed in Channa punctatus, Heteropneustes fossilis and carps. The cell body sends lateral and ventral dendrites besides several small dendrites. The lateral dendrite emerges through the axon cap, turns dorsolateral and becomes myelinated to form Mauthner axon. The Mauthner axon extends in the spinal region upto the caudal peduncle and forms synapses with the spinal motoneurons of the front column. There are numerous synapses and end bulbs from the vestibular fibres and VIIIth nerve distributed on the perikaryan of the Mauthner cell body. It is suggested that the Mauthner cells are comparatively well developed in those species in which the tail fin is better utilized for swimming.     

Noise Induces Hypothyroidism and Gonadal Dysfunction Via Stimulation of Pineal–Adrenal Axis in Chicks

Noise is a world-wide problem that causes nervous, endocrine and cardiovascular disorders, and eventually health hazards in humans and animals. Objective of the current work is to investigate endocrine interaction in noise stress, which subsequently affects other endocrine functions including gonads in a poultry bird like chicks. Gravimetric, ultrastructural and hormonal status of the endocrine organs were examined to ascertain the effects of noise stress. Acute noise at 60 dB had no effect, but at 80 and 100 dB each for 3 h, increased pineal and serum serotonin, and adrenal and serum corticosterone, epinephrine and norepinephrine concentrations, without any change in thyroid or gonadal hormones. Chronic noise exposure at 60, 80 and 100 dB each for 6 h, daily for 7 days, drastically disturbed normal behavior, and quantum of food consumption and water intake. Chronic exposure also significantly decreased body weight including thyroid, ovary and testis weight, and increased adrenal weight. Noise stress caused ultrastructural changes leading to stimulations of pinealocytes (with abundance of rough endoplasmic reticulum and mitochondria), adrenocortical cells (enlarged nuclei and abundance of smooth endoplasmic reticulum) and adrenomedullary cells (enlarged nuclei with presence of chromaffin granules) were observed in noise stress. Additionally, pineal and serum serotonin, N-acetyl serotonin and melatonin, and adrenal and serum corticosterone, epinephrine and norepinephrine levels were significantly elevated following chronic noise exposure. Contrarily, thyroid activity was suppressed with atrophied thyroid follicles followed by declined levels of serum T₃ and T₄ with elevation of TSH level. Simultaneously, serum 17β-estradiol (E₂) and testosterone (T) concentrations were also significantly declined in all the doses of chronic noise. These changes were dose dependent of noise exposure. The findings suggest that (a) adrenal and pineal glands respond primarily to noise and secondarily act on other endocrine organs including gonads in chicks, (b) adrenal directly and/or indirectly causes thyroid and gonadal dysfunctions via pineal following noise exposure in chicks.     

Scattering based hyperspectral imaging of plasmonic nanoplate clusters towards biomedical applications

A new optical scattering contrast‐agent based on polymer‐nanoparticle encapsulated silver nanoplates (PESNs) is presented. Silver nanoplates were chosen due to the flexibility of tuning their plasmon frequencies. The polymer coating preserves their physical and optical properties and confers other advantages such as controlled contrast agent delivery. Finite difference time domain (FDTD) simulations model the interaction of light with the nanoplates in different orientations in the cluster. Hyperspectral dark field microscopy (HYDFM) observes the scattering spectra of the PESNs. An unsupervised sequential maximum angle convex cone (SMACC) image analysis resolves spectral endmembers corresponding to different stacking orientations of the nanoplates. The orientation‐dependent endmembers qualitatively agree with the FDTD results. For contrast enhancement, the uptake and spatial distribution of PESNs are demonstrated by an HYDFM study of single melanoma cells to result in an enhanced contrast of up to 400%. A supervised spatial mapping of the endmembers obtained by the unsupervised SMACC algorithm reveals spatial distributions of PESNs with various clustering orientations of encapsulated nanoplates. Our study demonstrates tunability in plasmonics properties in clustered metal nanoparticles and its utility for the development of scatter‐based imaging contrast agents for a broad range of applications, including studies of single cells and other biomedical systems.

     

Optimal Constrained Stationary Intervention in Gene Regulatory Networks

A key objective of gene network modeling is to develop intervention strategies to alter regulatory dynamics in such a way as to reduce the likelihood of undesirable phenotypes. Optimal stationary intervention policies have been developed for gene regulation in the framework of probabilistic Boolean networks in a number of settings. To mitigate the possibility of detrimental side effects, for instance, in the treatment of cancer, it may be desirable to limit the expected number of treatments beneath some bound. This paper formulates a general constraint approach for optimal therapeutic intervention by suitably adapting the reward function and then applies this formulation to bound the expected number of treatments. A mutated mammalian cell cycle is considered as a case study.     

Algal Biomass as Potential Biosorbent for Reduction of Organic Load in Gray Water and Subsequent Reuse: Effect on Seed Germination and Enzyme Activity

Biosorptive treatment using algal biomass of Rhizoclonium riparium was proposed for higher-loading gray water for its effective utilization. A batch sorption study was conducted using composite wastewater having a wide range of initial chemical oxygen demand (COD) values (2400–44,800 mg/L). The study showed an optimum dose of 5 g/L of biosorbent resulted in 96% reduction of COD for wastewater with an initial COD of 10,500 mg/L. The equilibrium isotherm data at different temperatures were fitted to linear and nonlinear isotherms. Biosorption kinetics was studied by various kinetic models. Chemical composition and surface morphology of the biosorbent were characterized by infrared, x-ray diffraction, and scanning electron microscopy techniques before and after biosorption. Applicability of the biosorbent-treated wastewater in agricultural uses was explored by studying the effect of untreated and treated wastewater on the germination of two seeds, i.e., Vigna radiata and Lens esculenta, and subsequently the activity of peroxidase (POD) enzymes were studied to understand the toxicity in plants. The study revealed that compared with seeds treated with different dilutions of untreated wastewater, germination (%) was significantly higher for biosorbent-treated wastewater, with a reduced level of POD activity, indicating positive response of the seeds towards the biosorptive treatment.