ISP: An optimal out-of-core image-set processing streaming architecture for parallel heterogeneous systems

Journal ArticleImage population analysis is the class of statistical methods that plays a central role in understanding the development, evolution, and disease of a population. However, these techniques often require excessive computational power and memory that are compounded with a large number of volumetric inputs. Restricted access to supercomputing power limits its influence in general research and practical applications. In this paper we introduce ISP, an Image-Set Processing streaming framework that harnesses the processing power of commodity heterogeneous CPU/GPU systems and attempts to solve this computational problem. In ISP, we introduce specially designed streaming algorithms and data structures that provide an optimal solution for out-of-core multiimage processing problems both in terms of memory usage and computational efficiency. ISP makes use of the asynchronous execution mechanism supported by parallel heterogeneous systems to efficiently hide the inherent latency of the processing pipeline of out-of-core approaches. Consequently, with computationally intensive problems, the ISP out-of-core solution can achieve the same performance as the in-core solution. We demonstrate the efficiency of the ISP framework on synthetic and real datasets

EMG activity of upper limb on spinal cord injury individuals during whole-body vibration

Whole-body vibration (WBV) has shown positive results increasing electromyographic (EMG) activity and strength in a healthy population when applied to upper and lower limbs. The aim of this study was to verify if WBV increases the EMG signal of the upper limb muscles in patients with spinal cord injury (SCI). For this study, 15 patients with SCI were selected and one single session of WBV was applied to the upper limb. Five sessions of 30 s at 30 Hz were applied and EMG of anterior deltoid and forearm muscles was measured. The results show that EMG activity had a significant increase during WBV session compared with baseline muscle activity. These results support WBV as an efficient tool to increase the upper body EMG in individuals with SCI

The 12-item WHO Disability Assessment Schedule II as an outcome measure for treatment of common mental disorders.

BACKGROUND: Common mental disorders (CMD) are among the most significant contributors to disability worldwide. Patient-reported disability outcomes should be included as a key metric in the comparative assessment of value across global mental health interventions. This study aims to evaluate the validity of a widely used, cross-cultural tool - the 12-item World Health Organization Disability Assessment Schedule II (WHODAS) - as a functional outcome measure for CMD treatment. METHODS: The study population includes 1024 participants with CMD enrolled in the MANAS trial in India. CMD was assessed using the Revised Clinical Interview Schedule (CIS-R). Disability was assessed using the 12-item WHODAS II plus a measure of disability days. This analysis presents the correlations between these disability items and CMD symptom severity at 2 months after enrollment (convergent validity) and the items' associations with CMD recovery 4 months later (external responsiveness). RESULTS: All items showed a positive correlation of disability with CMD symptom severity (p < 0.001). The WHODAS items of 'standing,' 'household responsibilities,' and 'emotional disturbance' explained the most variance in CMD symptom severity. Improvements in 'disability days,' 'emotional disturbance,' 'standing,' 'household responsibilities,' 'day-to-day work,' and 'concentrating' were significantly associated with CMD recovery over follow-up. CONCLUSIONS: Further research is recommended on a CMD-specific WHODAS subscale comprised of the six WHODAS items found to be most strongly associated with CMD severity and recovery. This shorter, CMD-specific disability subscale would critically serve as a common metric to compare intervention impact on patient-centered outcomes and, in turn, to allocate global mental health resources efficiently

Scale invariance and universality of force networks in static granular matter

Force networks form the skeleton of static granular matter. They are the key ingredient to mechanical properties, such as stability, elasticity and sound transmission, which are of utmost importance for civil engineering and industrial processing. Previous studies have focused on the global structure of external forces (the boundary condition), and on the probability distribution of individual contact forces. The disordered spatial structure of the force network, however, has remained elusive so far. Here we report evidence for scale invariance of clusters of particles that interact via relatively strong forces. We analyzed granular packings generated by molecular dynamics simulations mimicking real granular matter; despite the visual variation, force networks for various values of the confining pressure and other parameters have identical scaling exponents and scaling function, and thus determine a universality class. Remarkably, the flat ensemble of force configurations--a simple generalization of equilibrium statistical mechanics--belongs to the same universality class, while some widely studied simplified models do not.Comment: 15 pages, 4 figures; to appear in Natur

Electric impedance microflow cytometry for characterization of cell disease states

The electrical properties of biological cells have connections to their pathological states. Here we present an electric impedance microflow cytometry (EIMC) platform for the characterization of disease states of single cells. This platform entails a microfluidic device for a label-free and non-invasive cell-counting assay through electric impedance sensing. We identified a dimensionless offset parameter δ obtained as a linear combination of a normalized phase shift and a normalized magnitude shift in electric impedance to differentiate cells on the basis of their pathological states. This paper discusses a representative case study on red blood cells (RBCs) invaded by the malaria parasite Plasmodium falciparum. Invasion by P. falciparum induces physical and biochemical changes on the host cells throughout a 48-h multi-stage life cycle within the RBC. As a consequence, it also induces progressive changes in electrical properties of the host cells. We demonstrate that the EIMC system in combination with data analysis involving the new offset parameter allows differentiation of P. falciparum infected RBCs from uninfected RBCs as well as among different P. falciparum intraerythrocytic asexual stages including the ring stage. The representative results provided here also point to the potential of the proposed experimental and analysis platform as a valuable tool for non-invasive diagnostics of a wide variety of disease states and for cell separation.Singapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology)Massachusetts Institute of Technology. Center for Integrated Circuits and SystemsNational Institutes of Health (U.S.) (Grant R01 HL094270

Mutation (G275E) of the nicotinic acetylcholine receptor α6 subunit is associated with high levels of resistance to spinosyns in Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae).

PublishedJournal ArticleThe tomato leafminer, Tuta absoluta, now a major pest of tomato crops worldwide, is primarily controlled using chemical insecticides. Recently, high levels of resistance to the insecticide spinosad have been described in T. absoluta populations in Brazil. Selection of a resistant field-collected strain led to very high levels of resistance to spinosad and cross-resistance to spinetoram, but not to other insecticides that target the nicotinic acetylcholine receptor (nAChR). In this study the mechanisms underlying resistance to spinosad were investigated using toxicological, biochemical and molecular approaches. Inhibition of metabolic enzymes using synergists and biochemical assessment of detoxification enzyme activity provided little evidence of metabolic resistance in the selected strain. Cloning and sequencing of the nAChR α6 subunit from T. absoluta, the spinosad target-site, from susceptible and spinosad-resistant strains were done to investigate the role of a target-site mechanism in resistance. A single nucleotide change was identified in exon 9 of the α6 subunit of the resistant strain, resulting in the replacement of the glycine (G) residue at position 275 observed in susceptible T. absoluta strains with a glutamic acid (E). A high-throughput DNA-based diagnostic assay was developed and used to assess the prevalence of the G275E mutation in 17 field populations collected from different geographical regions of Brazil. The resistant allele was found at low frequency, and in the heterozygous form, in seven of these populations but at much higher frequency and in the homozygous form in a population collected in the Iraquara municipality. The frequency of the mutation was significantly correlated with the mortality of these populations in discriminating dose bioassays. In summary our results provide evidence that the G275E mutation is an important mechanism of resistance to spinosyns in T. absoluta, and may be used as a marker for resistance monitoring in field populations.Thanks to CAPES for the scholarship granted to the first author and to Conselho Nacional de Desenvolvimento Científico e Tecnológico — CNPq for the financial support to the project (Universal 484240/2011-0, H.A.A.S.). The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union Seventh Framework Programme FP7/2007-2013/ under REA grant agreement PIRSES-GA-2012 – 318246. This work was in part funded by a fellowship grant (BB/G023352/1) from the Biotechnology and Biological Sciences Research Council of the UK to Dr. Chris Bass and a PhD studentship award from the BBSRC which funded Madeleine Berger

Efficient Probabilistic and Geometric Anatomical Mapping Using Particle Mesh Approximation on GPUs

Deformable image registration in the presence of considerable contrast differences and large size and shape changes presents significant research challenges. First, it requires a robust registration framework that does not depend on intensity measurements and can handle large nonlinear shape variations. Second, it involves the expensive computation of nonlinear deformations with high degrees of freedom. Often it takes a significant amount of computation time and thus becomes infeasible for practical purposes. In this paper, we present a solution based on two key ideas: a new registration method that generates a mapping between anatomies represented as a multicompartment model of class posterior images and geometries and an implementation of the algorithm using particle mesh approximation on Graphical Processing Units (GPUs) to fulfill the computational requirements. We show results on the registrations of neonatal to 2-year old infant MRIs. Quantitative validation demonstrates that our proposed method generates registrations that better maintain the consistency of anatomical structures over time and provides transformations that better preserve structures undergoing large deformations than transformations obtained by standard intensity-only registration. We also achieve the speedup of three orders of magnitudes compared to a CPU reference implementation, making it possible to use the technique in time-critical applications

Integrated optical fiber force myography sensor as pervasive predictor of hand postures

Force myography (FMG) is an appealing alternative to traditional electromyography in biomedical applications, mainly due to its simpler signal pattern and immunity to electrical interference. Most FMG sensors, however, send data to a computer for further processing, which reduces the user mobility and, thus, the chances for practical application. In this sense, this work proposes to remodel a typical optical fiber FMG sensor with smaller portable components. Moreover, all data acquisition and processing routines were migrated to a Raspberry Pi 3 Model B microprocessor, ensuring the comfort of use and portability. The sensor was successfully demonstrated for 2 input channels and 9 postures classification with an average precision and accuracy of ~99.5% and ~99.8%, respectively, using a feedforward artificial neural network of 2 hidden layers and a competitive output layer11CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPNão tem0012017/25666-

Effects of diabetes on microcirculation and leukostasis in retinal and non-ocular tissues : implications for diabetic retinopathy

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Changes in retinal microcirculation are associated with the development of diabetic retinopathy (DR). However, it is unclear whether such changes also develop in capillary beds of other non-retinal tissues. Here, we investigated microcirculatory changes involving velocity of rolling neutrophils, adherence of neutrophils, and leukostasis during development of retinal vascular lesions in diabetes in other non-retinal tissues. Intravital microscopy was performed on post-capillary venules of cremaster muscle and ear lobe of mice with severe or moderate diabetes and compared to those of non-diabetic mice. Additionally, number and velocity of rolling leukocytes, number of adherent leukocytes, and areas of leukostasis were quantified, and retinal capillary networks were examined for acellular capillaries (AC) and pericyte loss (PL), two prominent vascular lesions characteristic of DR. The number of adherent neutrophils and areas of leukostasis in the cremaster and ear lobe post-capillary venules of diabetic mice was increased compared to those of non-diabetic mice. Similarly, a significant increase in the number of rolling neutrophils and decrease in their rolling velocities compared to those of non-diabetic control mice were observed and severity of diabetes exacerbated these changes. Understanding diabetes-induced microcirculatory changes in cremaster and ear lobe may provide insight into retinal vascular lesion development in DR.info:eu-repo/semantics/publishedVersio