Performance Modeling and Prediction for the Scalable Solution of Partial Differential Equations on Unstructured Grids

This dissertation studies the sources of poor performance in scientific computing codes based on partial differential equations (PDEs), which typically perform at a computational rate well below other scientific simulations (e.g., those with dense linear algebra or N-body kernels) on modern architectures with deep memory hierarchies. We identify that the primary factors responsible for this relatively poor performance are: insufficient available memory bandwidth, low ratio of work to data size (good algorithmic efficiency), and nonscaling cost of synchronization and gather/scatter operations (for a fixed problem size scaling). This dissertation also illustrates how to reuse the legacy scientific and engineering software within a library framework. Specifically, a three-dimensional unstructured grid incompressible Euler code from NASA has been parallelized with the Portable Extensible Toolkit for Scientific Computing (PETSc) library for distributed memory architectures. Using this newly instrumented code (called PETSc-FUN3D) as an example of a typical PDE solver, we demonstrate some strategies that are effective in tolerating the latencies arising from the hierarchical memory system and the network. Even on a single processor from each of the major contemporary architectural families, the PETSc-FUN3D code runs from 2.5 to 7.5 times faster than the legacy code on a medium-sized data set (with approximately 105 degrees of freedom). The major source of performance improvement is the increased locality in data reference patterns achieved through blocking, interlacing, and edge reordering. To explain these performance gains, we provide simple performance models based on memory bandwidth and instruction issue rates. Experimental evidence, in terms of translation lookaside buffer (TLB) and data cache miss rates, achieved memory bandwidth, and graduated floating point instructions per memory reference, is provided through accurate measurements with hardware counters. The performance models and experimental results motivate algorithmic and software practices that lead to improvements in both parallel scalability and per-node performance. We identify the bottlenecks to scalability (algorithmic as well as implementation) for a fixed-size problem when the number of processors grows to several thousands (the expected level of concurrency on terascale architectures). We also evaluate the hybrid programming model (mixed distributed/shared) from a performance standpoint

Breeding for Biofortification Traits in Rice: Means to Eradicate Hidden Hunger

Rice (Oryza sativa L.) supplies nourishment to about half of the population of the world’s inhabitants. Of them, more than 2 billion people suffer from ‘hidden hunger’ in which they are unable to meet the recommended nutrients or micronutrients from their daily dietary intake. Biofortification refers to developing micronutrient-rich diet foods using traditional breeding methods and modern biotechnology, a promising approach to nutrition enrichment as part of an integrated strategy for food systems. To improve the profile of rice grain for the biofortification-related traits, understanding the genetics of important biofortification traits is required. Moreover, these attributes are quantitative in nature and are influenced by several genes and environmental variables. In the course of past decades, several endeavours such as finding the important quantitative trait loci (QTLs) for improving the nutrient profile of rice seeds were successfully undertaken. In this review, we have presented the information regarding the QTLs identified for the biofortification traits in the rice

Directing for Higher Seed Production in Vegetables

Vegetables are essential for human health and well-being. For sustaining an excellent production of vegetable crops, the seed is a primary input. Moreover, good quality seed is an important requirement for the vegetable industry, and there is a huge demand that has been expanding, considering the fact that seed multiplication is economically pertinent for vegetable cultivars to contend commercially. But the healthy seed production is usually a sumptuous trait and tormented by agricultural tactics, genetics as well as by the environmental factors. Features like seed output of the vegetables, sizeable genetic variation, the prerequisite for advancement and acceptance of a good quality vegetable seed. Here different mechanisms for seed production in vegetable crops has been presented, also vital areas and factors influencing seed production, and eventually discourses regarding the opportunity of plant breeding to sustainably make improvements to vegetable seed production

Impact and modifications of in-hospital trauma care workflow due to COVID 19 pandemic: Lessons learnt for the future

Objective: To describe the restructuring if in-hospital systems of care at a Level -1 trauma center in India and to analyze volume and patterns of injury for future preparedness as well as to institute preventive measures for specific injuries during health emergencies like COVID-19.Methods: The data were extracted from a prospectively managed trauma registry at level-1 trauma center in India. We compared data of lockdown period with data of the same number of days from the pre-lockdown period. Patients were grouped according to age, gender, cause of injury, place of injury, injury severity, and injury outcome for comparative analysis between two periods.Results: Total emergency department (ED) footfall due to trauma decreased significantly by 73% during lockdown period. Injuries resulting due to blunt forces, increased significantly. There was a significant decrease in the percentage of patients having major injury. The road traffic injuries (RTIs) cases were less, but number of falls reported increased significantly during lockdown. Significantly less number of patients presented without receiving primary care. Majority of the patients were transported using private cars, police vehicle, and two wheelers during lockdown, however, as expected significantly less number of patients were transported by three wheelers. The comparative analysis between quantitative data points shows significant difference in median ISS and length of stay during lockdown. Conclusion: This study highlighted that the preparedness during health emergencies should not focus solely on the response to treatment of infectious disease but also on ensuring access and provision of reasonable quality of care for non-infectious illnesses, especially acute conditions like trauma

Recent progress in development of dressings used for diabetic wounds with special emphasis on scaffolds

Diabetic wound (DW) is a secondary application of uncontrolled diabetes and affects about 42.2% of diabetics. If the disease is left untreated/uncontrolled, then it may further lead to amputation of organs. In recent years, huge research has been done in the area of wound dressing to have a better maintenance of DW. These include gauze, films, foams or, hydrocolloid-based dressings as well as polysaccharide-and polymer-based dressings. In recent years, scaffolds have played major role as biomaterial for wound dressing due to its tissue regeneration properties as well as fluid absorption capacity. These are three-dimensional polymeric structures formed from polymers that help in tissue rejuvenation. These offer a large surface area to volume ratio to allow cell adhesion and exudate absorbing capacity and antibacterial properties. They also offer a better retention as well as sustained release of drugs that are directly impregnated to the scaffolds or the ones that are loaded in nanocarriers that are impregnated onto scaffolds. The present review comprehensively describes the pathogenesis of DW, various dressings that are used so far for DW, the limitation of currently used wound dressings, role of scaffolds in topical delivery of drugs, materials used for scaffold fabrication, and application of various polymer-based scaffolds for treating DW

Ground Water Pollution and Emerging Environmental Challenges of Industrial Effluent Irrigation: A Case Study of Mettupalayam Taluk, Tamilnadu

Industrial disposal of effluents on land and the subsequent pollution of groundwater and soil of surrounding farmlands – is a relatively new area of research. The environmental and socioeconomic aspects of industrial effluent irrigation have not been studied as extensively as domestic sewage based irrigation practices, at least for a developing country like India. The disposal of effluents on land has become a regular practice for some industries. Industries located in Mettupalayam Taluk, Tamil Nadu, dispose their effluents on land, and the farmers of the adjacent farmlands have complained that their shallow open wells get polluted and also the salt content of the soil has started building up slowly. This study attempts to capture the environmental and socioeconomic impacts of industrial effluent irrigation in different industrial locations at Mettupalayam Taluk, Tamil Nadu, through primary surveys and secondary information. This study found that the continuous disposal of industrial effluents on land, which has limited capacity to assimilate the pollution load, has led to groundwater pollution. The quality of groundwater in shallow open wells surrounding the industrial locations has deteriorated, and the application of polluted groundwater for irrigation has resulted in increased salt content of soils. In some locations drinking water wells (deep bore wells) also have a high concentration of salts. Since the farmers had already shifted their cropping pattern to salt-tolerant crops (like jasmine, curry leaf, tobacco, etc.) and substituted their irrigation source from shallow open wells to deep bore wells and/or river water, the impact of pollution on livelihoods was minimized. Since the local administration is supplying drinking water to households, the impact in the domestic sector has been minimized. It has also been noticed that in some locations industries are supplying drinking water to the affected households. However, if the pollution continues unabated it could pose serious problems in the future

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Silicon as a Vegetable Crops Modulator—A Review

Vegetables require an optimum supply of mineral elements like silicon (Si). Si is second to oxygen in its abundance in the earth crust, and its role is quite significant in tackling biotic and abiotic stresses of vegetables. Si application also improves several agronomic and quality traits of vegetables. Hence, Si application is recommended as a strategy for the improvement of vegetable crops production. Although the research about the role of Si in vegetable dicots still lags far behind than cereals. Recently, omics-based approaches were used to provide a deeper understanding of the role of Si in vegetable protection. Here, we have compiled the studies focusing on the role of Si for vegetables, thus, enabling all of the important information regarding the effect Si application to vegetables at one place