High Performance Algorithms for Counting Collisions and Pairwise Interactions

The problem of counting collisions or interactions is common in areas as computer graphics and scientific simulations. Since it is a major bottleneck in applications of these areas, a lot of research has been carried out on such subject, mainly focused on techniques that allow calculations to be performed within pruned sets of objects. This paper focuses on how interaction calculation (such as collisions) within these sets can be done more efficiently than existing approaches. Two algorithms are proposed: a sequential algorithm that has linear complexity at the cost of high memory usage; and a parallel algorithm, mathematically proved to be correct, that manages to use GPU resources more efficiently than existing approaches. The proposed and existing algorithms were implemented, and experiments show a speedup of 21.7 for the sequential algorithm (on small problem size), and 1.12 for the parallel proposal (large problem size). By improving interaction calculation, this work contributes to research areas that promote interconnection in the modern world, such as computer graphics and robotics.Comment: Accepted in ICCS 2019 and published in Springer's LNCS series. Supplementary content at https://mjsaldanha.com/articles/1-hpc-ssp

Time-Resolved Imaging Reveals Heterogeneous Landscapes of Nanomolar Ca(2+) in Neurons and Astroglia

Maintaining low intracellular calcium is essential to the functioning of brain cells, yet the phenomenology and mechanisms involved remain an enigma. We have advanced a two-photon excitation time-resolved imaging technique, which exploits high sensitivity of the OGB-1 fluorescence lifetime to nanomolar Ca(2+) concentration ([Ca(2+)]) and enables a high data acquisition rate in situ. The [Ca(2+)] readout is not affected by dye concentration, light scattering, photobleaching, micro-viscosity, temperature, or the main known concomitants of cellular activity. In quiescent tissue, standard whole-cell configuration has little effect on resting [Ca(2+)] inside neuronal dendrites or inside astroglia dye-filled via gap junctions. Mapping basal [Ca(2+)] in neurons and astrocytes with submicron resolution unveils heterogeneous concentration landscapes that depend on age and preceding activity. The rich information content represented by such landscapes in acute slices and in vivo promises to unveil the hitherto unexplored, potentially fundamental aspects of brain cell physiology. VIDEO ABSTRACT

Bone Marrow Stem Cell Treatment for Ischemic Heart Disease in Patients with No Option of Revascularization: A Systematic Review and Meta-Analysis

PMCID: PMC3686792This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Multiplexed calcium imaging of single-synapse activity and astroglial responses in the intact brain

All-optical registration of neuronal and astrocytic activities within the intact mammalian brain has improved significantly with recent advances in optical sensors and biophotonics. However, relating single-synapse release events and local astroglial responses to sensory stimuli in an intact animal has not hitherto been feasible. Here, we present a multiplexed multiphoton excitation imaging approach for assessing the relationship between presynaptic Ca2+ entry at thalamocortical axonal boutons and perisynaptic astrocytic Ca2+ elevations, induced by whisker stimulation in the barrel cortex of C57BL/6 mice. We find that, unexpectedly, Ca2+ elevations in the perisynaptic astrocytic regions consistently precede local presynaptic Ca2+ signals during spontaneous brain activity associated with anaesthesia. The methods described here can be adapted to a variety of optical sensors and are compatible with experimental designs that might necessitate repeated sampling of single synapses over a longitudinal behavioural paradigm

Micro-CT Imaging Reveals Mekk3 Heterozygosity Prevents Cerebral Cavernous Malformations in Ccm2-Deficient Mice.

Mutations in CCM1 (aka KRIT1), CCM2, or CCM3 (aka PDCD10) gene cause cerebral cavernous malformation in humans. Mouse models of CCM disease have been established by deleting Ccm genes in postnatal animals. These mouse models provide invaluable tools to investigate molecular mechanism and therapeutic approaches for CCM disease. However, the full value of these animal models is limited by the lack of an accurate and quantitative method to assess lesion burden and progression. In the present study we have established a refined and detailed contrast enhanced X-ray micro-CT method to measure CCM lesion burden in mouse brains. As this study utilized a voxel dimension of 9.5μm (leading to a minimum feature size of approximately 25μm), it is therefore sufficient to measure CCM lesion volume and number globally and accurately, and provide high-resolution 3-D mapping of CCM lesions in mouse brains. Using this method, we found loss of Ccm1 or Ccm2 in neonatal endothelium confers CCM lesions in the mouse hindbrain with similar total volume and number. This quantitative approach also demonstrated a rescue of CCM lesions with simultaneous deletion of one allele of Mekk3. This method would enhance the value of the established mouse models to study the molecular basis and potential therapies for CCM and other cerebrovascular diseases

Tectonic affinity of the west Qinling terrane (central China): North China or Yangtze?

[33] Neogene (̃14 Ma) basaltic magmatism has occurred in west Qinling, at the northeastern corner of the Tibetan Plateau. Furthermore, U-Pb ages and Hf isotopic data of xenocrystic zircons indicate that the unexposed Neoarchean (2.7-2.5 Ga) basement beneath the Phanerozoic outcrops in west Qinling has affinities with the southern margin of the north China block. The basement has a complex evolution, including the addition of juvenile mantle material at ̃2.7- 2.4 Ga and 1.1-0.8 Ga and reworking at ̃1.8 Ga and possibly at 1.4 Ga. Phanerozoic thermal events at 320-300 Ma, 230 Ma, and 160 Ma also have affected the basement. We interpret the west Qinling orogenic terrane as originally separated from the north China block, joined to the northern Yangtze block during the Meso-Neoproterozoic, and finally involved in the northward subduction and collision of the Yangtze block in the Paleozoic and early Mesozoic and subsequent lithospheric extension in the Jurassic. © 2010 by the American Geophysical Union.published_or_final_versio

Dynamic predicting by landmarking as an alternative for multi-state modeling: an application to acute lymphoid leukemia data

This paper considers the problem of obtaining a dynamic prediction for 5-year failure free survival after bone marrow transplantation in ALL patients using data from the EBMT, the European Group for Blood and Marrow Transplantation. The paper compares the new landmark methodology as developed by the first author and the established multi-state modeling as described in a recent Tutorial in Biostatistics in Statistics in Medicine by the second author and colleagues. As expected the two approaches give similar results. The landmark methodology does not need complex modeling and leads to easy prediction rules. On the other hand, it does not give the insight in the biological processes as obtained for the multi-state model

Respiratory modulation of oscillometric cuff pressure pulses and Korotkoff sounds during clinical blood pressure measurement in healthy adults

BACKGROUND: Accurate blood pressure (BP) measurement depends on the reliability of oscillometric cuff pressure pulses (OscP) and Korotkoff sounds (KorS) for automated oscillometric and manual techniques. It has been widely accepted that respiration is one of the main factors affecting BP measurement. However, little is known about how respiration affects the signals from which BP measurement is obtained. The aim was to quantify the modulation effect of respiration on oscillometric pulses and KorS during clinical BP measurement. METHODS: Systolic and diastolic BPs were measured manually from 40 healthy subjects (from 23 to 65 years old) under normal and regular deep breathing. The following signals were digitally recorded during linear cuff deflation: chest motion from a magnetometer to obtain reference respiration, cuff pressure from an electronic pressure sensor to derive OscP, and KorS from a digital stethoscope. The effects of respiration on both OscP and KorS were determined from changes in their amplitude associated with respiration between systole and diastole. These changes were normalized to the mean signal amplitude of OscP and KorS to derive the respiratory modulation depth. Reference respiration frequency, and the frequencies derived from the amplitude modulation of OscP and KorS were also calculated and compared. RESULTS: Respiratory modulation depth was 14 and 40 % for OscP and KorS respectively under normal breathing condition, with significant increases (both p  0.05) during deep breathing, and for the oscillometric signal during normal breathing (p > 0.05). CONCLUSIONS: Our study confirmed and quantified the respiratory modulation effect on the oscillometric pulses and KorS during clinical BP measurement, with increased modulation depth under regular deeper breathing