Performance impact of programmer-inserted Data Prefetches for irregular access patterns with a case study of FMM VList algorithm

textData Prefetching is a well-known technique to speed up applications wherein hardware prefetchers or compilers speculatively prefetch data into caches closer to the processor to ensure it’s readily available when the processor demands it. Since incorrect speculation leads to prefetching useless data which, in turn, results in wasting memory bandwidth and polluting caches, prefetch mechanisms are usually conservative and prefetch on spotting fairly regular access patterns only. This gives the programmer with a knowledge of application, an opportunity to insert fine-grain software prefetches in the code to clinically prefetch the data that is certain to be demanded but whose access pattern is not too obvious for hardware prefetchers or compiler to detect. In this study, the author demonstrates the performance improvement obtained by such programmer-inserted prefetches with the case study of an FMM (Fast Multipole Method) VList application kernel run with several different configurations. The VList computation requires computing the Hadamard product of matrices. However, the way each node of the octree is stored in the memory, leads to indirect accessing of elements where memory accesses themselves are not sequential but the pointers pointing to those memory locations are still stored sequentially. Since compilers do not insert prefetches for indirect accesses, and to hardware, the access pattern appears random, programmer-inserted prefetching is the only solution for such a case. The author demonstrates the performance gain obtained by employing different prefetching choices in terms of what all structures in the code to prefetch and which level of cache to prefetch those to and also presents an analysis of the impact of different configuration parameters on performance gain. The author shows that there are several prefetching combinations which always bring performance gain without ever hurting the performance, and also identifies prefetching to L1 cache and prefetching all data structures in question, as the best prefetching recommendation for this application kernel. It is shown that this one combination gets the highest performance gain for most run configurations and an average performance gain of 10.14% across all run configurations.Electrical and Computer Engineerin

Basic and Applied Studies of Cell-Matrix Interactions

Extracellular matrix is a complex network of molecules that accomplishes various roles within each tissue. The mechanical properties and biochemical composition of the extracellular matrix vary considerably across tissues. In addition to providing structural support and elasticity, extracellular matrix properties influence various cellular behavior and processes like adhesion, differentiation and proliferation, among others. In these studies, I focused on elucidating the effects of changes in matrix composition and stresses on cellular architecture. In addition, the insights gained from these studies were utilized to develop a novel cell-based disease model of Malignant Bone Disease in which human mesenchymal stem cells and bone tumor cells are co-cultured on osteogenic microsphere in a rotating wall vessel to promote the growth of 3D tissue constructs. Successful execution of these studies will lead to a range of new methods for the investigation of tumor-stem cell interactions without the limitations of 2D tissue culture or in vivo approaches. Furthermore, we expect that this approach will significantly accelerate drug research and substantially improve our understanding of tumor expansion and bone repair during long term exposure to micro-gravity

Progressive Trends of Childhood Immunization in Rajasthan: A study based on the NFHS database

Any public health program's efficacy may be evaluated solely based on the available statistics. A program's ability to be tracked relies heavily on data. There are several systems in place in India for gathering data on the health of individual states and the country as a whole. The National Family Health Survey (NFHS) is one of these mechanisms. Children's vaccination status is one of the many data points collected by the National Health Interview Study (NFIS), a representative sample survey. NFHS is commonly used to evaluate and monitor the progress of any health program in the country, therefore, to sum it up: According to Rajasthan's NFHS-4 and NFHS-5 reports, there has been a significant increase in the state's coverage status. Despite the difficulties and the closure of the corona, this research will investigate the data that has demonstrated extraordinary rises and the causes that have made it possible or the huge efforts by the state government

Effective Atomic Number Dependence of Radiological Parameters of Some Organic Compounds at 122 KeV Gamma Rays

Mass attenuation coefficient is a fundamental parameter of radiation interaction, from which the other radiological parameters like half Value Layer [HVL], tenth Value Layer [TVL], total atomic and electronic cross-sections, mass energy absorption coefficient, KERMA, CT number and effective atomic number are deduced. These parameters are extensively required in a number of fields such as diagnostic radiology, gamma ray spectroscopy, fluorescence analysis and reactor shielding. In the present work, mass attenuation coefficients are determined experimentally for some organic compounds at 122 keV incident photons using narrow-beam transmission geometry to establish a relation between effective atomic number (Zeff) and other deduced parameters. The experimental data for all these parameters are compared with the values deduced from WinXcom software package and are found to agree within experimental estimated errors. This study gives some insight about the photon interaction in some organic compounds whose effective atomic numbers match with some human body fluids

Occupational COVID-19 exposure among health care workers in obstetric unit in a Central Government Hospital in India: initial experience

Background: Health care workers (HCW) are the frontline warriors who are at a high risk of acquiring the COVID-19. HCW in obstetrical department are at high-risk due to their close proximity with the patient for examination, giving treatment and in delivery. The objectives of this study were to evaluate the positivity rate of COVID-19 in the initial 3 months of pandemic in health care personnel working in obstetric unit in a tertiary care hospital.Methods: Prospective cohort study was conducted in department of obstetrics and gynecology at tertiary care hospital in Delhi from 10 April to 10 June 2020. Predesigned questionnaire was used to record data of HCWs exposed to COVID-19 patients.Results: In a period of 3 months (April-June 2020), 152 health care workers were exposed to 30 COVID-19 patients.  Out of this, 10 HCW were found to be positive on testing, showing a positivity rate of 6.58%. Positivity ratio was 6:3:1 among nurses, auxiliary workers and doctors respectively. Labor room was area of high infection as 80% of HCW were infected in the labor room .80% HCW acquired infection during patient care in hospital and 20% were infected in contact with asymptomatic COVID-19 positive HCW.Conclusions: Positivity rate in obstetric department is comparable to that of general population. Appropriate infection prevention measures like use of PPE, handwashing and maintain safe distance from the patient is the key to prevention of infection. Gloves and N95 masks have been shown to provide superior protection as compared to triple layer masks. Nursing staff and auxiliary workers should be reinforced the importance of use of PPE, hand hygiene and physical distancing

A feedback-loop extended stress fiber growth model with focal adhesion formation

Contractile cells play a prominent role in the adaptive nature of biological tissues. Contractility is mainly attributed to the growth of the tension dependent actomyosin bundles called stress fibers within the cytoskeleton. Stress fibers extend along the length of the cell and end at focal adhesions on the cell membrane. At the focal adhesion junctions on the cell membrane the integrin proteins are capable of sensing the environment, thereby making the cellular behavior dependent on the cell supporting substrate. It has been observed that the growth of stress fibers influences focal adhesions and vice-versa, resulting in a continuous cross-talk between different processes in the cell. Recent experiments have shown that cells subjected to uni-axial cyclic loading, depending on the substrate properties reorient themselves in a direction away from the loading direction, exhibiting strain avoidance. Mathematical models are important to understand the dependence of the cellular behavior on the substrate properties along with feedback mechanisms and are further used in designing in-vitro experiments. The coupling of the models for stress fibers and focal adhesions results in a non-linear bio-chemo-mechanical problem. In this contribution, we present the positive influence of the growth of focal adhesions along with a mechanosensitive feedback loop on the stress fiber growth and further reveal the characteristics of the re-orientation process due to cyclic loading. We use a non-linear Hill-type model to capture the growth of the active stress involved in the evolution law for the stress fibers and a thermodynamical approach to model the focal adhesions. A highly stable and reliable monolithic solution scheme is used to solve the governing system of coupled equations. Finally, we validate our simulation results with experimental results in regard to different loading conditions

On the monolithic and staggered solution of cell contractility and focal adhesion growth

The mechanical response of cells to stimuli tightly couples biochemical and biomechanical processes, which describe fundamental properties such as cell growth and reorientation. Cells interact continuously with their external surroundings, the extracellular matrix (ECM), by establishing a bond between cell and ECM through the formation of focal adhesions. Focal adhesions are made up of integrins, which are mechanosensitive proteins and responsible for the communication between the cell and the ECM. The governing biochemomechanical processes can be modeled by means of a continuum approach considering mechanical and thermodynamic equilibrium to describe cell contractility and focal adhesion growth. The immanent multiphysical character of cell mechanics involves important aspects such as the coupling of fields of different scales and corresponding interface conditions that are sensitive to the solution of the governing numerical problem. These aspects become even more relevant when considering a feedback loop among the multiphysical solutions fields. In this contribution, we consider solution properties and sensitivity aspects of a nonlinear mechanical continuum model for the prognosis of stress fiber growth and reorientation incorporating a mechanosensitive feedback loop. We provide the governing equations of a Hill model-based stress fiber growth, which is coupled to a thermodynamical approach modeling the focal adhesions. Furthermore, a variational formulation including the algebraic equations is derived for staggered and monolithic solution approaches and the reaction-diffusion equation that models the feedback mechanism. We test both schemes with regard to reliability, accuracy, and numerical efficiency for different model parameters and loading scenarios. We present algorithmic aspects of the considered solution schemes and reveal their robustness with regard to model refinement in space and time and finally provide an assessment of their overall solution performance for multiphysics problems in the context of cell mechanics

Systematic review and case series: flexible sigmoidoscopy identifies most cases of checkpoint inhibitor‐induced colitis

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149542/1/apt15263_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149542/2/apt15263.pd