Accelerating 3-D GPU-based Motion Tracking for Ultrasound Strain Elastography Using Sum-Tables: Analysis and Initial Results.

Now, with the availability of 3-D ultrasound data, a lot of research efforts are being devoted to developing 3-D ultrasound strain elastography (USE) systems. Because 3-D motion tracking, a core component in any 3-D USE system, is computationally intensive, a lot of efforts are under way to accelerate 3-D motion tracking. In the literature, the concept of Sum-Table has been used in a serial computing environment to reduce the burden of computing signal correlation, which is the single most computationally intensive component in 3-D motion tracking. In this study, parallel programming using graphics processing units (GPU) is used in conjunction with the concept of Sum-Table to improve the computational efficiency of 3-D motion tracking. To our knowledge, sum-tables have not been used in a GPU environment for 3-D motion tracking. Our main objective here is to investigate the feasibility of using sum-table-based normalized correlation coefficient (ST-NCC) method for the above-mentioned GPU-accelerated 3-D USE. More specifically, two different implementations of ST-NCC methods proposed by Lewis et al. and Luo-Konofagou are compared against each other. During the performance comparison, the conventional method for calculating the normalized correlation coefficient (NCC) was used as the baseline. All three methods were implemented using compute unified device architecture (CUDA; Version 9.0, Nvidia Inc., CA, USA) and tested on a professional GeForce GTX TITAN X card (Nvidia Inc., CA, USA). Using 3-D ultrasound data acquired during a tissue-mimicking phantom experiment, both displacement tracking accuracy and computational efficiency were evaluated for the above-mentioned three different methods. Based on data investigated, we found that under the GPU platform, Lou-Konofaguo method can still improve the computational efficiency (17-46%), as compared to the classic NCC method implemented into the same GPU platform. However, the Lewis method does not improve the computational efficiency in some configuration or improves the computational efficiency at a lower rate (7-23%) under the GPU parallel computing environment. Comparable displacement tracking accuracy was obtained by both methods

Projected Urbanization Impacts on Surface Climate and Energy Budgets in the Pearl River Delta of China

The climate impacts of future urbanization in the Pearl River Delta (PRD) region in China were simulated with the Dynamics of Land Systems (DLS) model and the Weather Research and Forecasting (WRF) model in this study. The land use and land cover data in 2000 and 2020 were simulated with the DLS model based on the regional development planning. Then the spatial and temporal changes of surface air temperature, ground heat flux, and regional precipitation in 2020 were quantified and analyzed through comparing simulation results by WRF. Results show that the built-up land will become the dominant land use type in the PRD in 2020. Besides, the near-surface air temperature shows an increasing trend on the whole region in both summer and winter, but with some seasonal variation. The urban temperature rise is more apparent in summer than it is in winter. In addition, there is some difference between the spatial pattern of precipitation in summer and winter in 2020; the spatial variation of precipitation is a bit greater in summer than it is in winter. Results can provide significant reference for the land use management to alleviate the climate change

Response Properties of Interneurons and Pyramidal Neurons in Macaque MSTd and VPS Areas During Self-Motion

To perceive self-motion perception, the brain needs to integrate multi-modal sensory signals such as visual, vestibular and proprioceptive cues. Self-motion perception is very complex and involves multi candidate areas. Previous studies related to self-motion perception during passive motion have revealed that some of the areas show selective response to different directions for both visual (optic flow) and vestibular stimuli, such as the dorsal subdivision of the medial superior temporal area (MSTd) and the visual posterior sylvian fissure (VPS), although MSTd is dominated by visual signals and VPS is dominated by vestibular signals. However, none of studies related to self-motion perception have distinguished the different neuron types with distinct neuronal properties in cortical microcircuitry, which limited our understanding of the local circuits for self-motion perception. In the current study, we classified the recorded MSTd and VPS neurons into putative pyramidal neurons and putative interneurons based on the extracellular action potential waveforms and spontaneous firing rates. We found that: (1) the putative interneurons exhibited obviously broader direction tuning than putative pyramidal neurons in response to their dominant (visual for MSTd; vestibular for VPS) stimulation type; (2) either in visual or vestibular condition, the putative interneurons were more responsive but with larger variability than the putative pyramidal neurons for both MSTd and VPS areas; and (3) the timing of vestibular and visual peak directional tuning was earlier in the putative interneurons than that of the putative pyramidal neurons for both MSTd and VPS areas. Based on these findings we speculated that, within the microcircuitry, several adjacent putative interneurons with broad direction tuning receive earlier strong but variable signals, which might act feedforward input to shape the direction tuning of the target putative pyramidal neuron, but each interneuron may participate in several microcircuitries, targeting different output neurons

Increased Numbers of NK Cells, NKT-Like Cells, and NK Inhibitory Receptors in Peripheral Blood of Patients with Chronic Obstructive Pulmonary Disease

T cells and B cells participate in the pathogenesis of COPD. Currently, NK cells and NKT cells have gained increasing attention. In the present study, 19 COPD patients and 12 healthy nonsmokers (HNS) were recruited, and their pulmonary function was assessed. The frequencies of CD3+ T, CD4+ T, CD8+ T, B, NK, and NKT-like cells were determined using flow cytometry. The frequencies of spontaneous and inducible IFN-γ+ or CD107a+ NK and NKT-like cells as well as activating or inhibitory receptors were also detected. The potential association of lymphocyte subsets with disease severity was further analyzed. Significantly decreased numbers of CD3+ and CD4+ T cells, and the CD4+/CD8+ ratio, but increased numbers of CD3−CD56+ NK and CD3+CD56+ NKT-like cells were observed in COPD patients compared to HNS. The frequencies of inducible IFN-γ-secreting NK and NKT-like cells were less in COPD patients. The frequencies of CD158a and CD158b on NK cells and CD158b on NKT-like cells were greater. The frequency of CD158b+ NK cells was negatively correlated with FEV1% prediction and FEV1/FVC. Our data indicate that COPD patients have immune dysfunction, and higher frequencies of inhibitory NK cells and NKT-like cells may participate in the pathogenesis of COPD

Control of apico-basal epithelial polarity by the microtubule minus-end-binding protein CAMSAP3 and spectraplakin ACF7

The microtubule cytoskeleton regulates cell polarity by spatially organizing membrane trafficking and signaling processes. In epithelial cells, microtubules form parallel arrays aligned along the apico–basal axis, and recent work has demonstrated that the members of CAMSAP/Patronin family control apical tethering of microtubule minus ends. Here, we show that in mammalian intestinal epithelial cells, the spectraplakin ACF7 (also known as MACF1) specifically binds to CAMSAP3 and is required for the apical localization of CAMSAP3-decorated microtubule minus ends. Loss of ACF7 but not of CAMSAP3 or its homolog CAMSAP2 affected the formation of polarized epithelial cysts in three-dimensional cultures. In short-term epithelial polarization assays, knockout of CAMSAP3, but not of CAMSAP2, caused microtubule re-organization into a more radial centrosomal array, redistribution of Rab11-positive (also known as Rab11A) endosomes from the apical cell surface to the pericentrosomal region and inhibition of actin brush border formation at the apical side of the cell. We conclude that ACF7 is an important regulator of apico–basal polarity in mammalian intestinal cells and that a radial centrosome-centered microtubule organization can act as an inhibitor of epithelial polarity

Epigenetic regulation of programmed cell death in hypoxia-induced pulmonary arterial hypertension

Pulmonary arterial hypertension (PAH) is a severe progressive disease that may cause early right ventricular failure and eventual cardiac failure. The pathogenesis of PAH involves endothelial dysfunction, aberrant proliferation of pulmonary artery smooth muscle cells (PASMCs), and vascular fibrosis. Hypoxia has been shown to induce elevated secretion of vascular endothelial growth factor (VEGF), leading to the development of hypoxic PAH. However, the molecular mechanisms underlying hypoxic PAH remain incompletely understood. Programmed cell death (PCD) is a natural cell death and regulated by certain genes. Emerging evidence suggests that apoptotic resistance contributes to the development of PAH. Moreover, several novel types of PCD, such as autophagy, pyroptosis, and ferroptosis, have been reported to be involved in the development of PAH. Additionally, multiple diverse epigenetic mechanisms including RNA methylation, DNA methylation, histone modification, and the non-coding RNA molecule-mediated processes have been strongly linked to the development of PAH. These epigenetic modifications affect the expression of genes, which produce important changes in cellular biological processes, including PCD. Consequently, a better understanding of the PCD processes and epigenetic modification involved in PAH will provide novel, specific therapeutic strategies for diagnosis and treatment. In this review, we aim to discuss recent advances in epigenetic mechanisms and elucidate the role of epigenetic modifications in regulating PCD in hypoxia-induced PAH

A survey on tree matching and XML retrieval

International audienceWith the increasing number of available XML documents, numerous approaches for retrieval have been proposed in the literature. They usually use the tree representation of documents and queries to process them, whether in an implicit or explicit way. Although retrieving XML documents can be considered as a tree matching problem between the query tree and the document trees, only a few approaches take advantage of the algorithms and methods proposed by the graph theory. In this paper, we aim at studying the theoretical approaches proposed in the literature for tree matching and at seeing how these approaches have been adapted to XML querying and retrieval, from both an exact and an approximate matching perspective. This study will allow us to highlight theoretical aspects of graph theory that have not been yet explored in XML retrieval

CT-guided iodine-125 seed permanent implantation for recurrent head and neck cancers

<p>Abstract</p> <p>Background</p> <p>To investigate the feasibility, and safety of ¹²⁵I seed permanent implantation for recurrent head and neck carcinoma under CT-guidance.</p> <p>Results</p> <p>A retrospective study on 14 patients with recurrent head and neck cancers undergone ¹²⁵I seed implantation with different seed activities. The post-plan showed that the actuarial D90 of ¹²⁵I seeds ranged from 90 to 218 Gy (median, 157.5 Gy). The follow-up was 3 to 60 months (median, 13 months). The median local control was 18 months (95% CI, 6.1-29.9 months), and the 1-, 2-, 3-, and 5- year local controls were 52%, 39%, 39%, and 39%, respectively. The 1-, 2-, 3-, and 5- survival rates were 65%, 39%, 39% and 39%, respectively, with a median survival time of 20 months (95% CI, 8.7-31.3 months). Of all patients, 28.6% (4/14) died of local recurrence, 7.1% (1/14) died of metastases, one patient died of hepatocirrhosis, and 8 patients are still alive to the date of data analysis.</p> <p>Conclusion</p> <p>CT-guided ¹²⁵I seed implantation is feasible and safe as a salvage or palliative treatment for patients with recurrent head and neck cancers.</p

Mesoscale phenomena and their contribution to the global response: a focus on the magnetotail transition region and magnetosphere-ionosphere coupling

An important question that is being increasingly studied across subdisciplines of Heliophysics is “how do mesoscale phenomena contribute to the global response of the system?” This review paper focuses on this question within two specific but interlinked regions in Near-Earth space: the magnetotail’s transition region to the inner magnetosphere and the ionosphere. There is a concerted effort within the Geospace Environment Modeling (GEM) community to understand the degree to which mesoscale transport in the magnetotail contributes to the global dynamics of magnetic flux transport and dipolarization, particle transport and injections contributing to the storm-time ring current development, and the substorm current wedge. Because the magnetosphere-ionosphere is a tightly coupled system, it is also important to understand how mesoscale transport in the magnetotail impacts auroral precipitation and the global ionospheric system response. Groups within the Coupling, Energetics and Dynamics of Atmospheric Regions Program (CEDAR) community have also been studying how the ionosphere-thermosphere responds to these mesoscale drivers. These specific open questions are part of a larger need to better characterize and quantify mesoscale “messengers” or “conduits” of information—magnetic flux, particle flux, current, and energy—which are key to understanding the global system. After reviewing recent progress and open questions, we suggest datasets that, if developed in the future, will help answer these questions

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio