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In this study, we analyzed the dynamic molecular epidemiology of herpangina based on pharyngeal swabs and demographic data collected from children with herpangina monitored in Tongzhou district in China from January 2021 to December 2022. A total of 1022 herpangina cases were diagnosed. Out of 225 samples collected, 56.4% (127/225) were positive for non-polio enterovirus, with seven genotypes identified: coxsackievirus A4 (CV-A4), CV-A6, CV-A10, CV-A2, CV-A16, CV-B3, and CV-A8. The predominant genotypes associated with herpangina changed during and after the COVID-19 pandemic, with the predominant genotypes being CV-A4 and CV-A6 in 2021 and CV-A10 and CV-A6 in 2022. [ABSTRACT FROM AUTHOR]

Human genetics analysis has identified many noncoding SNPs associated with diabetic traits, but whether and how these variants contribute to diabetes is largely unknown. Here, we focus on a noncoding variant, rs6048205, and report that the risk-G variant impairs the generation of PDX1+/NKX6-1+ pancreatic progenitor cells and further results in the abnormal decrease of functional β cells during pancreatic differentiation. Mechanistically, this risk-G variant greatly enhances RXRA binding and over-activates FOXA2 transcription, specifically in the pancreatic progenitor stage, which in turn represses NKX6-1 expression. Consistently, inducible FOXA2 overexpression could phenocopy the differentiation defect. More importantly, mice carrying risk-G exhibit abnormal pancreatic islet architecture and are more sensitive to streptozotocin or a high-fat diet to develop into diabetes eventually. This study not only identifies a causal noncoding variant in diabetes susceptibility but also dissects the underlying gain-of-function mechanism by recruiting stage-specific factors. How GWAS-annotated noncoding SNPs contribute to diabetes remains unclear. Here, the authors report that the noncoding SNP rs6048205 drives stage-specific defects in human pancreatic differentiation and increases diabetes susceptibility in mice. [ABSTRACT FROM AUTHOR]

On May 21, 2023, the Macao Science Satellite-1B (MSS-1B), a low-inclination, low-latitude, and high-precision scientific exploration satellite for geomagnetic fields and space environments, was successfully launched. The solar X-ray detector (SXD), one of the two major scientific payloads onboard the MSS-1B, has obtained a large amount of solar X-ray radiation data, which reveals the distribution law of the magnetic field in the low Earth orbit, as well as the coupling law of the Earth's magnetic field and the solar radiation and energy particle distributions. First, the overall design of the multi-detection-unit, broad-energy-range, small-volume, and low-power SXD was implemented to achieve the scientific objectives of the mission. Second, the technical indicators of the instrument were decomposed into various components, and the key technologies, such as collimator, processing circuit, thermal, and payload dataset designs, were reviewed. Third, the backgrounds, including electronic noise, cosmic diffuse X-ray background, and high-energy background in the Earth's radiation belts in and out of the field of view, were analyzed for the instrument. Then, the ground calibrations of the energy response, detection efficiency, and temperature-dependent peak drift of the SXD flight model were conducted. Finally, the in-orbit temperature, energy spectrum data, background, and solar flare process observation of the instrument in the in-orbit test stage are presented, verifying the instrument design, analysis, and ground calibration, providing a foundation for obtaining accurate solar X-ray radiation data, and achieving the scientific objectives of the satellite. [ABSTRACT FROM AUTHOR]

Data race is one of the most important concurrent anomalies in multi-threaded programs. Emerging constraint- based techniques are leveraged into race detection, which is able to find all the races that can be found by any other sound race detector. However, this constraint-based approach has serious limitations on helping programmers analyze and understand data races. First, it may report a large number of false positives due to the unrecognized dataflow propagation of the program. Second, it recommends a wide range of thread context switches to schedule the reported race (including the false one) whenever this race is exposed during the constraint-solving process. This ad hoc recommendation imposes too many context switches, which complicates the data race analysis. To address these two limitations in the state-of-the-art constraint-based race detection, this paper proposes DFTracker, an improved constraint-based race detector to recommend each data race with minimal thread context switches. Specifically, we reduce the false positives by analyzing and tracking the dataflow in the program. By this means, DFTracker thus reduces the unnecessary analysis of false race schedules. We further propose a novel algorithm to recommend an effective race schedule with minimal thread context switches for each data race. Our experimental results on the real applications demonstrate that 1) without removing any true data race, DFTracker effectively prunes false positives by 68% in comparison with the state-of-the-art constraint-based race detector; 2) DFTracker recommends as low as 2.6–8.3 (4.7 on average) thread context switches per data race in the real world, which is 81.6% fewer context switches per data race than the state-of-the-art constraint based race detector. Therefore, DFTracker can be used as an effective tool to understand the data race for programmers. [ABSTRACT FROM AUTHOR]

To enhance its properties, ammonium polyphosphate (APP) was subjected to modification using a synthesized phosphorus-containing silica gel, resulting in MAPP. Ammonium polyphosphate (APP) was modified by synthesized phosphorus-containing silica gel, resulting in MAPP, which was then used to form thermoplastic polyurethane composites. MAPP exhibited better thermal stability with a smaller dispersion size, lower initial decomposition temperature and better resistance to heat at high temperatures than APP. At the same time, MAPP showed more obvious advantages in improving the char yield, flame retardant performance and mechanical properties of TPU. TPU/5%MAPP showed a limiting oxygen index of 29.1% during burning tests, significantly better than TPU/5%APP (27.3%). The cone calorimeter test results also indicated that the incorporation of MAPP resulted in a significant reduction in key parameters such as peak heat release rate, total heat release, and total smoke release and an increase of the char yield of TPU composite. The TG result showed that the Tmax of the TPU/5%MAPP composite increased and the mass loss rate decreased compared with that of TPU/5%APP. Moreover, the tensile strength of the TPU/5%MAPP composite increased by 18.5% compared with the TPU/5%APP composite due to the improved dispersibility of MAPP than APP. An analysis of the fire resistance mechanism showed that the improved flame retardance in the TPU/5%MAPP composite resulted from the structural changes in the char residue. This study provides an efficient and extensible approach for the synthesis of high-performance flame retardant TPU materials. [ABSTRACT FROM AUTHOR]

Computer vision (CV) algorithms have been extensively used for a myriad of applications nowadays. As the multimedia data are generally well-formatted and regular, it is beneficial to leverage the massive parallel processing power of the underlying platform to improve the performances of CV algorithms. Single Instruction Multiple Data (SIMD) instructions, capable of conducting the same operation on multiple data items in a single instruction, are extensively employed to improve the efficiency of CV algorithms. In this paper, we evaluate the power and effectiveness of RISC-V vector extension (RV-V) on typical CV algorithms, such as Gray Scale, Mean Filter, and Edge Detection. By our examinations, we show that compared with the baseline OpenCV implementation using scalar instructions, the equivalent implementations using the RV-V (version 0.8) can reduce the instruction count of the same CV algorithm up to 24x, when processing the same input images. Whereas, the actual performances improvement measured by the cycle counts is highly related with the specific implementation of the underlying RV-V co-processor. In our evaluation, by using the vector co-processor (with eight execution lanes) of Xuantie C906, vector-version CV algorithms averagely exhibit up to 2.98x performances speedups compared with their scalar counterparts. [ABSTRACT FROM AUTHOR]

Since the first report of diketopyrrolopyrrole (DPP)-based conjugated polymers for organic thin-film transistors (OTFTs), these polymers have attracted great attention as representative semiconductors in high-performance OTFTs. Through unremitting efforts in molecular-structure regulation and device optimization, significant mobilities exceeding 10 cm2·V−1·s−1 have been achieved in OTFTs, greatly promoting the applied development of organic circuits. In this review, we summarize our progress in molecular design, synthesis and solution-processing of DPP-based conjugated polymers for OTFT devices and circuits, focusing on the roles of design strategies, synthesis methods and processing techniques. Furthermore, the remaining issues and future outlook in the field are briefly discussed. [ABSTRACT FROM AUTHOR]

Zika virus (ZIKV) is a potential threat to male reproductive health but the mechanisms underlying its influence on testes during ZIKV infection remain obscure. To address this question, we perform single-cell RNA sequencing using testes from ZIKV-infected mice. The results reveal the fragility of spermatogenic cells, especially spermatogonia, to ZIKV infection and show that the genes of the complement system are significantly upregulated mainly in infiltrated S100A4 + monocytes/macrophages. Complement activation and its contribution to testicular damage are validated by ELISA, RT‒qPCR and IFA and further verify in ZIKV-infected northern pigtailed macaques by RNA genome sequencing and IFA, suggesting that this might be the common response to ZIKV infection in primates. On this basis, we test the complement inhibitor C1INH and S100A4 inhibitors sulindac and niclosamide for their effects on testis protection. C1INH alleviates the pathological change in the testis but deteriorates ZIKV infection in general. In contrast, niclosamide effectively reduces S100A4 + monocyte/macrophage infiltration, inhibits complement activation, alleviates testicular damage, and rescues the fertility of male mice from ZIKV infection. This discovery therefore encourages male reproductive health protection during the next ZIKV epidemic. Zika virus poses a potential threat to male reproductive health but the underlying mechanisms remain obscure. To address this question, the study by Yang et al performs single-cell RNA sequencing with ZIKV-infected mice testes. The authors find that spermatogenic cells are fragile to ZIKV infection and the complement system components produced by infiltrated S100A4 + monocytes/macrophages are crucial for the injury of spermatogenic cells. [ABSTRACT FROM AUTHOR]

Optoelectronic devices consist of heterointerfaces formed between dissimilar semiconducting materials. The relative energy-level alignment between contacting semiconductors determinately affects the heterointerface charge injection and extraction dynamics. For perovskite solar cells (PSCs), the heterointerface between the top perovskite surface and a charge-transporting material is often treated for defect passivation1–4 to improve the PSC stability and performance. However, such surface treatments can also affect the heterointerface energetics1. Here we show that surface treatments may induce a negative work function shift (that is, more n-type), which activates halide migration to aggravate PSC instability. Therefore, despite the beneficial effects of surface passivation, this detrimental side effect limits the maximum stability improvement attainable for PSCs treated in this way. This trade-off between the beneficial and detrimental effects should guide further work on improving PSC stability via surface treatments.Surface treatments for the passivation of defects in perovskite solar cells have a detrimental side effect that limits the maximum stability improvement. [ABSTRACT FROM AUTHOR]

Increasing evidence suggests that genetic factors play a key role in the development of Parkinson's disease (PD). The variant rs11240572 in the PARK16 gene locus is strongly associated with PD. However, its effect on the pathogenesis of PD is yet to be clarified. The objective of the study was to explore the effect of the PARK16 rs11240572 variant on brain structure in PD patients. A total of 51 PD patients were enrolled in the study and genotyped for the rs11240572 variant. Clinical assessments and MRI scans were conducted across all participants. Voxel-based morphometry (VBM) was used to investigate gray matter volume (GMV) of the whole brain between these two groups. Correlation analysis was performed to identify the relationships between GMV and clinical features. There were 17 rs11240572-A variant carriers and 34 non-carriers, with no significant demographic differences between these two groups. Compared with non-carriers, rs11240572-A carriers showed increased GMV in the left caudate nucleus and putamen, but decreased GMV in the left superior temporal gyrus and supramarginal gyrus. In non-carriers, left basal ganglia GMV was positively correlated with UPDRS III (r = 0.365, p = 0.034) and bradykinesia (r = 0.352, p = 0.042), but negatively correlated with MMSE (r = – 0.344, p = 0.047), while in carriers negative correlation between basal ganglia GMV and MMSE was also observed (r = – 0.666, p = 0.004). Moreover, the GMV of left temporoparietal cortex was positively associated with cognitive function in both groups (carriers, r = 0.692, p = 0.002; non-carriers, r = 0.879, p < 0.001). When reducing the sample size of non-carriers to the level of the carrier sample, similar correlations were observed in both groups. Our study showed that the PARK16 rs11240572 variant affects the brain structure of patients with PD, especially in the basal ganglia and temporoparietal cortex. This indicated that this variant might play an important role in the pathogenesis of PD. [ABSTRACT FROM AUTHOR]

With the rapid growth of real-world graphs, the size of which can easily exceed the on-chip (board) storage capacity of an accelerator, processing large-scale graphs on a single Field Programmable Gate Array (FPGA) becomes difficult. The multi-FPGA acceleration is of great necessity and importance. Many cloud providers (e.g., Amazon, Microsoft, and Baidu) now expose FPGAs to users in their data centers, providing opportunities to accelerate large-scale graph processing. In this paper, we present a communication library, called FDGLib, which can easily scale out any existing single FPGA-based graph accelerator to a distributed version in a data center, with minimal hardware engineering efforts. FDGLib provides six APIs that can be easily used and integrated into any FPGA-based graph accelerator with only a few lines of code modifications. Considering the torus-based FPGA interconnection in data centers, FDGLib also improves communication efficiency using simple yet effective torus-friendly graph partition and placement schemes. We interface FDGLib into AccuGraph, a state-of-the-art graph accelerator. Our results on a 32-node Microsoft Catapult-like data center show that the distributed AccuGraph can be 2.32x and 4.77x faster than a state-of-the-art distributed FPGA-based graph accelerator ForeGraph and a distributed CPU-based graph system Gemini, with better scalability. [ABSTRACT FROM AUTHOR]

The variations among shapes, sizes, and locations of tumors are obstacles for accurate automatic segmentation. U-Net is a simplified approach for automatic segmentation. Generally, the convolutional or the dilated convolutional layers are used for brain tumor segmentation. However, existing segmentation methods of the significant dilation rates degrade the final accuracy. Moreover, tuning parameters and imbalance ratio between the different tumor classes are the issues for segmentation. The proposed model, known as Residual-Dilated Dense Atrous-Spatial Pyramid Pooling (RD2A) 3D U-Net, is found adequate to solve these issues. The RD2A is the combination of the residual connections, dilation, and dense ASPP to preserve more contextual information of small sizes of tumors at each level encoder path. The multi-scale contextual information minimizes the ambiguities among the tissues of the white matter (WM) and gray matter (GM) of the infant's brain MRI. The BRATS 2018, BRATS 2019, and iSeg-2019 datasets are used on different evaluation metrics to validate the RD2A. In the BRATS 2018 validation dataset, the proposed model achieves the average dice scores of 90.88, 84.46, and 78.18 for the whole tumor, the tumor core, and the enhancing tumor, respectively. We also evaluated on iSeg-2019 testing set, where the proposed approach achieves the average dice scores of 79.804, 77.925, and 80.569 for the cerebrospinal fluid (CSF), the gray matter (GM), and the white matter (WM), respectively. Furthermore, the presented work also obtains the mean dice scores of 90.35, 82.34, and 71.93 for the whole tumor, the tumor core, and the enhancing tumor, respectively on the BRATS 2019 validation dataset. Experimentally, it is found that the proposed approach is ideal for exploiting the full contextual information of the 3D brain MRI datasets. [ABSTRACT FROM AUTHOR]

The variations among shapes, sizes, and locations of tumors are obstacles for accurate automatic segmentation. U-Net is a simplified approach for automatic segmentation. Generally, the convolutional or the dilated convolutional layers are used for brain tumor segmentation. However, existing segmentation methods of the significant dilation rates degrade the final accuracy. Moreover, tuning parameters and imbalance ratio between the different tumor classes are the issues for segmentation. The proposed model, known as Residual-Dilated Dense Atrous-Spatial Pyramid Pooling (RD2A) 3D U-Net, is found adequate to solve these issues. The RD2A is the combination of the residual connections, dilation, and dense ASPP to preserve more contextual information of small sizes of tumors at each level encoder path. The multi-scale contextual information minimizes the ambiguities among the tissues of the white matter (WM) and gray matter (GM) of the infant's brain MRI. The BRATS 2018, BRATS 2019, and iSeg-2019 datasets are used on different evaluation metrics to validate the RD2A. In the BRATS 2018 validation dataset, the proposed model achieves the average dice scores of 90.88, 84.46, and 78.18 for the whole tumor, the tumor core, and the enhancing tumor, respectively. We also evaluated on iSeg-2019 testing set, where the proposed approach achieves the average dice scores of 79.804, 77.925, and 80.569 for the cerebrospinal fluid (CSF), the gray matter (GM), and the white matter (WM), respectively. Furthermore, the presented work also obtains the mean dice scores of 90.35, 82.34, and 71.93 for the whole tumor, the tumor core, and the enhancing tumor, respectively on the BRATS 2019 validation dataset. Experimentally, it is found that the proposed approach is ideal for exploiting the full contextual information of the 3D brain MRI datasets. [ABSTRACT FROM AUTHOR]

Genomic evolution among bacteriophages infecting Caulobacter crescentus is inevitable. However, the conservation of the proteins associated with intact phage particles has not been investigated. In this study, we compared the structural proteins associated with two genomically diverse but morphologically similar C. crescentus-infecting bacteriophages, phiCbK and CcrSC. We were able to detect more than 20 proteins that are part of the bacteriophage particle in both phages, and we were able to identify a small number of proteins that were found in only one of the two phage particles. All but one of the genes coding for these structural proteins were located in a region of the genome that had been designated a structural region, confirming the idea that the genes in these phage genomes are clustered according to their function. During the purification process, we also discovered that phiCbk has a replication complex that can be recovered from the cell lysate, and this complex allowed us to identify many of the phage proteins involved in phage genome replication. [ABSTRACT FROM AUTHOR]

General purpose graphics processing units (GPGPUs) can be used to improve computing performance considerably for regular applications. However, irregular memory access exists in many applications, and the benefits of graphics processing units (GPUs) are less substantial for irregular applications. In recent years, several studies have presented some solutions to remove static irregular memory access. However, eliminating dynamic irregular memory access with software remains a serious challenge. A pure software solution without hardware extensions or offline profiling is proposed to eliminate dynamic irregular memory access, especially for indirect memory access. Data reordering and index redirection are suggested to reduce the number of memory transactions, thereby improving the performance of GPU kernels. To improve the efficiency of data reordering, an operation to reorder data is offloaded to a GPU to reduce overhead and thus transfer data. Through concurrently executing the compute unified device architecture (CUDA) streams of data reordering and the data processing kernel, the overhead of data reordering can be reduced. After these optimizations, the volume of memory transactions can be reduced by 16.7%–50% compared with CUSPARSE-based benchmarks, and the performance of irregular kernels can be improved by 9.64%–34.9% using an NVIDIA Tesla P4 GPU. [ABSTRACT FROM AUTHOR]

An efficient strategy for synthesizing of 3-substituted bis-isoxazole ether bearing 2-chloro-3-pyridyl under microwave radiation was reported. The reactive regioselectivity was improved by changing mainly the solvent and acid-binding agent. 3-(2-Chloropyridin-3-yl)-5-(((3-substituted phenyl isoxazol-5-yl)methoxy)methyl)isoxazoles were synthesized in 31–92% yields and were characterized by FT-IR, HRMS, 1H and 13C NMR spectroscopy. The single crystal of 3-(2-chloropyridin-3-yl)-5-(((3-(p-tolyl)isoxazol-5-yl)methoxy)methyl)isoxazole was obtained, and the structure of compound has also been determined by X-ray diffraction technique. Weak intra- and intermolecular C–H∙∙∙O interactions and a C–H∙∙∙π interaction link molecules into a three-dimensional network. The results showed that the synthesized compounds belonged to triclinic system, and their regioselectivity depended on the solvent and acid-binding agent. The merits of this method include the environmentally friendly, efficient, simple operation, and higher regional selectivity. An efficient synthesis of 3-substituted bis-isoxazole ethers was developed via 1,3-dipolar cycloaddition reaction starting from 3-substituted phenyl-5-((prop-2-yn-1-yloxy))methyl)isoxazoles and (Z)-2-chloro-N-hydroxynicotinimidoyl chloride using NaHCO3 as an acid-binding agent in THF solvent-dissolved trace water under catalyst-free microwave-assisted conditions. [ABSTRACT FROM AUTHOR]

A new poly(N-allyl-tetrasubstituted imidazole) containing furan rings and benzene ring was synthesized starting from 1-allyl-4,5-di(furan-2-yl)-2-phenyl-1H-imidazole (N-allyl-tetrasubstituted imidazole, monomer) using benzoyl peroxide as an initiator coupled with the mixture of benzene and water as solvents. The influence factors on the conversion of N-allyl-tetrasubstituted imidazole (monomer) were optimized by the orthogonal experiment. The structure and property of the obtained monomer and polymers were characterized by Fourier infrared spectroscopy, high-resolution mass spectroscopy, nuclear magnetic resonance spectroscopy, X-ray diffraction, gel permeation chromatography, differential scanning calorimetry and thermogravimetric analysis. Moreover, the luminescence property of monomer and polymers from the different polymerization conditions was investigated. The results showed that the luminescence property and thermal stability of polymer were related to molecular weight and the crystallization degree of polymer, and their thermal stability was markedly better than monomer. It suggested that poly(N-allyl-tetrasubstituted imidazole) had potential application in the fields of heat-resistant material and luminescence material. [ABSTRACT FROM AUTHOR]

Automatic accurate segmentation of medical images has significant role in computer-aided diagnosis and disease treatment. The segmentation of cerebrospinal fluid (CSF), gray matter (GM), and white matter (WM) tissues plays an important role in infant brain structure for studying early brain development. However, this task is very challenging due to low contrast between GM and WM in isointense phase (approximately 6-8 months of age). In this study, we develop a hyper-densely connected convolutional neural network (CNN) for segmentation of volumetric infant brain. The proposed model provides dense connection between layers to improve the performance of flow information in the network. It also allows the multiscale contextual information by concatenating the feature maps of early, intermediate, and later layers. This architecture employs MR-T1 and T2 as input, which are processed in two separate independent paths, and then their low, intermediate, and high layer features are fused for final segmentation. An important change relative to earlier densely connected networks is the application of direct layer connections from the same and different paths. In this scenario, each modality is processed in an independent path, and dense connections occur not only between layers within the same path, but also between layers in different paths. Adopting such dense connectivity leads to benefits of deep supervision and improved gradient flow. Furthermore, by combining the feature maps of early, intermediate, and late convolutional layers, our architecture injects multiscale information into the final segmentation. This suggested approach is examined in the MICCAI Grand Challenge iSEG and obtains significant advantages over existing approaches in terms of parameter efficiency and segmentation accuracy on 6-month infant brain MRI segmentation. [ABSTRACT FROM AUTHOR]

Two new chitosan-grafting copolymers (chitosan-g-PAM-AA and C-chitosan-g-PAM-AA) as sludge conditioners (flocculation and aggregation) have been prepared by employing ceric sulfate as a free radical initiator under nitrogen atmosphere in aqueous solution. The optimum condition for synthesizing chitosan-grafting copolymer was determined by orthogonal experiments. The structure, morphology and property of the obtained graft polymers were characterized by FT-IR, XRD, SEM, TGA and contact angle. Further, the municipal activated sludge dewatering performance of the synthesized copolymers was evaluated by the filter cake moisture content. Herein, the effects of pH value and dewatering temperatures of activated sludge, loading dosage or cationic degree of C-chitosan-g-PAM-AA on the filter cake moisture content were investigated. The synthesized amphoteric flocculant C-chitosan-g-PAM-AA showed a highly effective flocculation capability for activated sludge compared with chitosan-g-PAM-AA, chitosan, polyacrylamide (PAM). Also, the lowest filter cake moisture content was up to 61.41%. [ABSTRACT FROM AUTHOR]

In many activities, we need to predict the arrival of an occluded object. This action is called prediction motion or motion extrapolation. Previous researchers have found that both eye tracking and the internal clocking model are involved in the prediction motion task. Additionally, it is reported that concurrent hand movement facilitates the eye tracking of an externally generated target in a tracking task, even if the target is occluded. The present study examined the effect of concurrent hand movement on the estimated time to contact in a prediction motion task. We found different (accurate/inaccurate) concurrent hand movements had the opposite effect on the eye tracking accuracy and estimated TTC in the prediction motion task. That is, the accurate concurrent hand tracking enhanced eye tracking accuracy and had the trend to increase the precision of estimated TTC, but the inaccurate concurrent hand tracking decreased eye tracking accuracy and disrupted estimated TTC. However, eye tracking accuracy does not determine the precision of estimated TTC. [ABSTRACT FROM AUTHOR]

Triangulated surface flattening plays an important role in the surface shape design of a complex product, such as a vehicle, a train and an air plane. We propose a new method of generating 2D flat patterns from a 3D triangulated surface by the physical shell model to assist in the design of the surface model. The proposed method can be divided into two primary steps: Local and global steps. In the local step, edge based spring stretching and hinge based bending model are constructed and only the local spring stretch element is projected onto the constraint manifold. In the global step, the results of individual projections are combined, and by solving a simplified global matrix, a compromise between all of the individual constraints is obtained, and the global effects are also considered. The result indicates that the proposed method can compute a flattenable mesh surface from complex 3D mesh surfaces successfully and efficiently. [ABSTRACT FROM AUTHOR]

In many scientific computing applications, sparse Cholesky factorization is used to solve large sparse linear equations in distributed environment. GPU computing is a new way to solve the problem. However, sparse Cholesky factorization on GPU is hardly to achieve excellent performance due to the structure irregularity of matrix and the low GPU resource utilization. A hybrid CPU-GPU implementation of sparse Cholesky factorization is proposed based on multifrontal method. A large sparse coefficient matrix is decomposed into a series of small dense matrices (frontal matrices) in the method, and then multiple GEMM (General Matrix-matrix Multiplication) operations are computed on them. GEMMs are the main operations in sparse Cholesky factorization, but they are hardly to perform better in parallel on GPU. In order to improve the performance, the scheme of multiple task queues is adopted to perform multiple GEMMs parallelized with multifrontal method; all GEMM tasks are scheduled dynamically on GPU and CPU based on computation scales for load balance and computing-time reduction. Experimental results show that the approach can outperform the implementations of cuBLAS, achieving up to 1.98× speedup on GTX460 (Fermi micro-architecture) and 3.06× speedup on K20m (Kepler micro-architecture), respectively. [ABSTRACT FROM AUTHOR]

In recent years, convolutional neural networks (CNNs) as important parts of deep neural networks (DNNs) have achieved great successes in the field of computer vision. However, Convolution always takes much computation time in the DNNs. In order to improve the efficiency of CNNs, many solutions focusing on training algorithms and parallelism strategies have been proposed. In this paper, different from traditional GPU-based algorithms, a novel algorithm based on look-up table is proposed to speed up the CNNs with small filters by applying GPU. By transforming complex matrix multiplications operations in the convolution computation to some table-based simple summation operations, the overhead of convolution computation can be considerably reduced. The process of creating a table and looking up values in the table is very appropriate for parallelization on a GPU. The experimental results show that the proposed approach can improve the speed of convolution computation by 20-30 %, compared with existing state-of-the-art works with less accuracy loss. [ABSTRACT FROM AUTHOR]

Purpose: Mesenchymal stromal cells (MSCs) hold promise in the treatment of liver disease. However, short survival time of MSCs after intrahepatic transplantation limits their value; therefore, understanding the basis of MSCs survival and rejection may increase their utility. This study was aimed at determining the role of intrahepatic natural killer (NK) cells on MSCs survival and their retention in the liver shortly after transplant.Procedures: Human MSCs were labeled with the Luc2-mKate2 dual-fusion reporter gene (MSCs-R), and the residence time and survival of MSCs-R xenografts after intrahepatic transplantation were evaluated by in vivo bioluminescence imaging (BLI). Coculture of MSCs and NK cells was performed to assess cytotoxicity. To evaluate the role of NK cells in rejection of the xenografted cells, the fates of transplanted MSCs-R were then assessed in vivo by BLI after activation of intrahepatic NK cells.Results: We observed a linear correlation between luciferase activity from live MSCs-R and cell number in vitro (R 2 = 0.9956). In vivo, we observed a gradual decline in bioluminescent signals from transplanted MSCs-R over a region corresponding to the liver in both the control group and the NK-activated group. However, the survival time and retention of intrahepatic MSCs-R decreased more rapidly in the NK-activated group of mice compared to the control group. This indicated that activated NK cells accelerate the elimination of transplanted MSCs. Also, we found that the number of hepatic NK cells and the expression of NK activation markers significantly increased after intrahepatic delivery of MSCs. This suggested that resident NK cells, in a resting state, were activated by intrahepatic transplantation of human MSCs. Taken together, the data suggests that activated hepatic NK cells mediate, in part, rejection of the MSCs xenografts. Cytotoxicity assays showed that activated NK cells may inhibit the proliferation of MSCs and, to a certain extent, induce MSCs death.Conclusion: Human MSCs could be followed dynamically in vivo by BLI, and the role of murine hepatic NK cells, especially activated NK cells, could be inferred from the loss of signals from MSCs. This finding may have practical clinical implications in MSCs transplantation in treating liver disease. [ABSTRACT FROM AUTHOR]

Finding regions of similarity between two data streams is a computational intensive and memory consuming problem, which refers as sequence alignment for biological sequences. Smith-Waterman algorithm is an optimal method of finding the local sequence alignment. It requires a large amount of computation and memory space, and is also constrained by the memory access speed of the Graphics Processing Units (GPUs) global memory when accelerating by using GPUs. Since biologists are commonly concerned with one or a few species in their research areas, SpecAlign is proposed to accelerate Smith-Waterman alignment of species-based protein sequences within the available GPU memory. It is designed to provide the best alignments of all the database sequences aligned on GPU. The new implementation improves performance by optimizing the organization of database, increasing GPU threads for every database sequence, and reducing the number of memory accesses to alleviate memory bandwidth bottleneck. Experimental results show that SpecAlign improves the performance by about 32 % on average when compared with CUDASW++2.0 and DOPA with Ssearch trace for 100 shortlisted sequences on NVIDIA GTX295. It also outperforms CUDASW++2.0 with Ssearch trace for 100 shortlisted sequences by about 52 % on NVIDIA GTX460. [ABSTRACT FROM AUTHOR]

Non-parametric classifier, Naive Bayes nearest neighbor, is designed with no training phase, and its performance outperforms many well-trained learning-based image classifiers. Unfortunately, despite its high accuracy, it suffers from great computational pressure from distance computations in space of local feature. This paper explores accelerating strategies from perspectives of both algorithm design and software development. Our approach integrates space decomposition capability of Product quantization (PQ) and parallel accelerating capability of underlying computational platform, Graphics processing unit (GPU). PQ is exploited to compress the indexed local features and prune the search space. GPU is used to ease most of computational pressure by processing the tasks in parallel. To achieve good parallel efficiency, a new sequential classification process is first designed and decomposed into independent components with high parallelism. Effective parallelization techniques are then presented to make use of computational resources. Parallel heap array is built to accelerate the process of feature quantization. Distance table lookup is built to speed up the process of feature search. Comparative experiments on UIUC-Sport dataset demonstrate that our integrated solution outperforms other implementations significantly on Core-quad Intel Core i7 950 CPU and GPU of NVIDIA Geforce GTX460. Scalability experiment on 80 million tiny images database shows that our approach still performs well when large-scale image database is explored. [ABSTRACT FROM AUTHOR]

The response to epidermal growth factor receptor (EGFR)-targeted therapy in metastatic colorectal cancer (mCRC) is variable because of intra-tumor heterogeneity at the genetic level, and consequently, it is important to develop sensitive and selective assays to predict patient responses to therapy. Low-abundance BRAF V600E mutations are associated with poor response to treatment with EGFR inhibitors. We developed a method for the detection of BRAF V600E mutations in mCRC using real-time wild-type blocking PCR (WTB-PCR), in which a chimera composed of locked nucleic acids and DNA is incorporated to amplify the mutant allele at high efficiency while simultaneously inhibiting the amplification of wild-type alleles. Mixing experiments showed that this method is exquisitely sensitive, with detection of the mutated allele at a mutant/wild-type ratio of 1:10,000. To demonstrate the applicability of this approach for mCRC patients, we assessed the V600E mutations in 50 clinical cases of mCRC by real-time WTB-PCR. The percentage of patients with V600E mutation as determined by WTB-PCR (16 %, 8/50) was higher than by traditional PCR (10 %, 5/50), suggesting an increased sensitivity for WTB-PCR. By calculating the Δ C for real-time traditional PCR, which amplifies all BRAF alleles, versus WTB-PCR, which selectively amplifies mutant BRAF, we demonstrated that among the V600E-positive mCRC patient samples, the percentage of BRAF DNA with the V600E mutation ranged from 0.05 to 52.32 %. In conclusion, WTB-PCR provides a rapid, simple, and low-cost method to detect trace amounts of mutated BRAF V600E gene. [ABSTRACT FROM AUTHOR]

The high-resolution melting curve analysis (HRMA) might be a good alternative method for rapid detection of BRAF mutations. However, the accuracy of HRMA in detection of BRAF mutations has not been systematically evaluated. We performed a systematic review and meta-analysis involving 1324 samples from 14 separate studies. The overall sensitivity of HRMA was 0.99 (95% confidence interval (CI) = 0.75-0.82), and the overall specificity was very high at 0.99 (95% CI = 0.94-0.98). The values for the pooled positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were 68.01 (95% CI = 25.33-182.64), 0.06 (95% CI = 0.03-0.11), and1263.76 (95% CI = 393.91-4064.39), respectively. The summary receiver operating characteristic curve for the same data shows an area of 1.00 and a Q* value of 0.97. The high sensitivity and specificity, simplicity, low cost, less labor or time and rapid turnaround make HRMA a good alternative method for rapid detection of BRAF mutations in the clinical practice. [ABSTRACT FROM AUTHOR]

Objectives: To describe the technique, efficacy, and safety of transvenous embolisation (TVE) of cavernous sinus arteriovenous fistulas (CSDAVFs) via the inferior petrosal sinus (IPS) with detachable coils and acrylic glue.Methods: Spontaneous unilateral CSDAVFs were confirmed by cerebral angiography in eight patients, with angiographic patency of the ipsilateral IPS in three and angiographic non-visualisation of the ipsilateral IPS in five. There were two patients with complete occlusion of the ipsilateral internal jugular vein (IJV). TVE with detachable coils and acrylic glue were performed through a femoral vein and an IPS approach.Results: TVE viaipsilateral IPS was successfully performed in all eight patients in our group. The number of detachable coils for each patient ranged from 2 to 8 (mean, 5.0). Angiography immediately after TVE showed complete occlusion of the CSCAVFs in seven patients and nearly complete occlusion in one. Complete recovery of clinical symptoms was achieved in all eight patients. No recurrence of clinical symptoms was observed at follow-up.Conclusions: Transvenous embolisation via an IPS approach is a highly efficient and safe treatment for CSDAVFs. Embolisation with a combination of coils and acrylic glue may help to achieve complete occlusion of fistulas with fewer coils. [ABSTRACT FROM AUTHOR]