GraphBLAST: A High-Performance Linear Algebra-based Graph Framework on the GPU

High-performance implementations of graph algorithms are challenging to implement on new parallel hardware such as GPUs because of three challenges: (1) the difficulty of coming up with graph building blocks, (2) load imbalance on parallel hardware, and (3) graph problems having low arithmetic intensity. To address some of these challenges, GraphBLAS is an innovative, on-going effort by the graph analytics community to propose building blocks based on sparse linear algebra, which will allow graph algorithms to be expressed in a performant, succinct, composable and portable manner. In this paper, we examine the performance challenges of a linear-algebra-based approach to building graph frameworks and describe new design principles for overcoming these bottlenecks. Among the new design principles is exploiting input sparsity, which allows users to write graph algorithms without specifying push and pull direction. Exploiting output sparsity allows users to tell the backend which values of the output in a single vectorized computation they do not want computed. Load-balancing is an important feature for balancing work amongst parallel workers. We describe the important load-balancing features for handling graphs with different characteristics. The design principles described in this paper have been implemented in "GraphBLAST", the first high-performance linear algebra-based graph framework on NVIDIA GPUs that is open-source. The results show that on a single GPU, GraphBLAST has on average at least an order of magnitude speedup over previous GraphBLAS implementations SuiteSparse and GBTL, comparable performance to the fastest GPU hardwired primitives and shared-memory graph frameworks Ligra and Gunrock, and better performance than any other GPU graph framework, while offering a simpler and more concise programming model.Comment: 50 pages, 14 figures, 14 table

Development Of Sybr Green I Real-Time Pcr Method For Detection And Differentiation Of Newcastle Disease Virus Pathotypes

Newcastle disease (ND) which is caused by Newcastle disease virus (NDV) is a highly contagious viral disease of domestic poultry, cage, aviary and wild birds. ND outbreaks have led to substantial losses in the poultry industry. NDV can be classified into three major pathotypes: velogenic, mesogenic and lentogenic. Velogenic strains are highly virulent and may lead to 100% mortality in infected chicken whilst mesogenic and lentogenic strains cause mild clinical or inapparent infections, respectively. Early detection and differentiation of NDV pathotypes are very important during monitoring of suspected ND cases or during disease outbreaks. In this study, SYBR Green I real- time polymerase chain reaction (PCR) was developed for detection and differentiation of NDV pathotypes. Velogenic-specific primers (NDVIF2 & NPV2N) and lentogenic-specific primers (NDVIF2 & NPL2N) were designed to detect specific sequence of velogenic strains and lentogenic/vaccine strains, respectively. After establishing the optimum condition of the real-time PCR, the assay was performed on 22 previously characterized NDV strains. All the velogenic strains were only detected by using velogenic-specific primers (NDVIF2 & NPV2N) with threshold cycle (Ct) ranged from 12.92 to 22.76 and melting temperature between 85.6°C to 86.4°C. Similarly, all the lentogenic/vaccine strains were only successfully detected when lentogenic-specific primers (NDVIF2 & NPL2N) were used. All the lentogenic/vaccine strains amplified with the lentogenic-specific primer had a Ct value ranged from 11.93 to 18.73 and Tm between 87.2°C to 87.6°C. No amplification was found when the NDV velogenic-specific primers and lentogenic-specific primers were used to amplify avian influenza virus (AIV), infectious bronchitis virus (IBV) and infectious bursal disease virus (IBDV). This revealed that both velogenic- and lentogenic-specific primers were pathotype specific and no unrelated viral RNA can be amplified. The newly developed assay had a dynamic detection limit which spans over a 5 log10 concentration range. The velogenic and lentogenic amplifications showed high PCR efficiency of 98.8% and 103%, respectively. Mean coefficient variation (CV) of reproducibility tests for velogenic amplification and lentogenic amplification was around 1% and 2%, respectively. The SYBR Green I real-time PCR was 10-fold more sensitive when compared to the conventional detection method using agarose gel electrophoresis. Turnaround time for the developed assay was approximately 2.5 hours including reverse transcription, PCR amplification and melting curve analysis. Clinical samples from the experimental infected chickens as well as the suspected field cases were collected and then tested on the developed assay. In the experimental infection with lentogenic NDV F strain, virus could be detected 3 days post infection (p.i.), followed by day 4, 5 and 10 p.i. For the SPF chickens infected with high doses of velogenic NDV strain AF2240 (105 to 103 ELD50/0.1 ml), the virus can be detected as early as day 2 p.i., followed by day 3 and 4 p.i. All the infected chickens were dead on day 4 p.i. For the chickens group infected with low doses (102 to 100.5 ELD50/0.1 ml), the virus can be detected starting on day 4 p.i., followed by day 5, 7, 10, 11 and 12 p.i. All the infected chickens were dead on day 12 p.i. The assay was able to detect the viruses as early as day 2 before the observation of clinical signs. This is an important achievement as early detection can prevent further spread of the disease. A total of 41 suspected NDV field cases were tested with the developed assay, 33 cases were NDV negative and 8 cases were positive for velogenic NDV. The results were correlated well with the virus isolation method and F cleavage site sequence analysis. All these 8 isolates possess two pairs of dibasic amino acids at the position 112 to 116 of the F cleavage site, and a phenylalanine residue at the position 117. This F cleavage site analysis revealed that all of the 8 NDV isolates belonged to velogenic group. In the attempt to improve the efficacy of the developed assay, internal amplification control (IAC) was incorporated into the developed real-time PCR assay for detection of PCR inhibitors. The potential of simultaneous detection of IAC and NDV target was investigated. The simultaneous detection was achieved based on the melting curve analysis. The co-amplified products exhibited two distinguished melting peaks at 86.36±0.13°C and 91.42±0.21°C which corresponded to NDV NP gene product and IAC KanR gene product, respectively.In conclusion, this study successfully developed a SYBR Green I real-time PCR for NDV pathotypes detection and differentiation. The virus can be detected directly from clinical samples without the need of virus propagation in chicken embryonated eggs. Owing to these advantages, the developed assay will contribute significantly in the control and prevention of the spread of the disease. ND-infected birds can be rapidly isolated from the healthy bird in the case of field outbreaks, if the causal agent is detected at the early stage of the outbreak. Consequently, spread of the disease and economical losses can be prevente

Development of Real-Time Polymerase Chain Reaction Assays for the Detection and Differentiation of Infectious Bursal Disease Virus Subtypes

Two different real-time polymerase chain reaction (PCR) detection approaches based on SYBR Green I dye and Taqman probe based assays were developed for the detection and differentiation of infectious bursal disease virus (IBDV) subtypes. Both approaches were able to detect and differentiate IBDV subtypes based on the use of subtype-specific primers or subtype-specific probes where the primers were designed based on single nucleotide polymorphism (SNP) concept. After optimization of the primer combinations and PCR parameters, very virulent-specific primer, IF & IVIR, and classical-specific primer, IF & RCLA were used in the SYBR Green I real-time RT-PCR assay. Plasmid DNA carrying the VP4 gene of the references IBDV strains: very virulent strain UPM94/273 and classical strain D78 were established and used as positive controls in the real time RT-PCR. The developed assay had a dynamic detection limit which spans over 5 log10 concentration range for very virulent and spans over 7 log10 concentration range for classical strain, respectively. The correlation coefficient for amplification of very virulent and classical strain was R2 = 0.9918 and R2 = 0.9977, respectively. No amplification was found when the subtype-specific primers were used to amplify other avian RNA viruses. The performance of the SYBR Green I based assay was tested on various IBDV isolates including 10 previously characterized IBDV and 11 commercial vaccine strains. The very virulent-specific primer only detected and amplified the very virulent IBDV with threshold cycle (CT) ranged from 14.93 to 21.52 and melting temperature (Tm) between 85.6°C to 88.0°C. The classical-specific primer was only able to amplify the classical IBDV with CT value ranged from 11.99 to 20.89 and Tm between 85.6°C to 86.8°C. The diagnostic efficacy of the developed assay was also evaluated using bursal samples obtained from experimentally infected chickens. Bursal samples collected from D78 vaccine infected chickens at day 3 and 5 p.i were positive for IBDV with average CT of 23.05+1.31, Tm of 85.8+0.17°C and average CT 21.82+1.42, Tm of 86.0+0.28°C , respectively. Bursal samples collected at day 10 p.i from this group were also found positive for IBDV with average CT of 24.42+1.20 and Tm of 85.9+0.18°C. On the other hand, only bursal samples collected at day 3 and 5 p.i were found positive for yery virulent IBDV with average CT 19.39+0.72, Tm of 86.6+0.14°C and average CT 23.55+1.39, Tm of 86.5+0.19°C, respectively. In the case of samples from dual infection with different IBDV subtypes, viral RNA was detectable only on day 3 and 5 p.i. In general, majority of the bursal samples have higher very virulent virus with an average CT value ranged from 21.24+0.68 to 22.19+0.97 compared to vaccine virus with Ct value ranged from 23.88+0.74 to 25.36+1.19. The performance of the developed SYBR Green I based assay was analyzed with other standard diagnostic methods. In the uninfected control group, no obvious microscopic lesions were found in the bursa and the lesions score was less than 1.0. However, mild bursal lesions without signs of inflammation with lesions score less than 3.0 was detected from bursal tissue obtained from chickens inoculated with vaccine strain D78. Based on the lesion score, it was clear that bursal pathology developed rapidly, with complete loss of tissue architecture by day 3 p.i. when the chickens were infected with virulent IBDV. The correlation between ELISA antibody titers and real-time CT values were inversely related, where the lower titers of antibodies associated with higher level of viral RNA as found in chickens infected with very virulent strain UPM94/273. On the other hand, vaccine strain D78 induced higher detectable antibody titers than UPM94/273, which indirectly support less virus replication with late positive amplification in real-time RT-PCR. Thus, the level of viral RNA in bursal samples obtained from D78 infected chickens was lower than UPM94/273 infected chickens. A total of 37 bursal samples from IBD suspected field cases were collected and then tested on the developed assay. The developed SYBR Green I based PCR assay was able to detect 9 samples positive for very virulent, 4 positive for classical IBDV and 12 samples positive for both very virulent and vaccine strains of IBDV. Sequence analysis of the hypervariable region of the VP2 gene of the IBDV samples revealed that the residues involved in determining the virulence of VV IBDV and CL IBDV were highly conserved. For the Taqman based duplex real-time PCR assay development, a new set of primers FWDC and RVSC were designed from the conserved region of VP4 of both very virulent and classical strains. A dual-labeled fluorescent probe each specific for very virulent IBDV (ProVV) and vaccine IBDV (ProCL) were designed The performance of the developed Taqman assay was compared with other PCR methods namely conventional RT-PCR and previously developed SYBR Green I assay. The Taqman assay was found far more superior in terms of turn around time and sensitivity. With the aid of β-actin gene, the Taqman assay was also used to determine the viral load fold changes in bursal samples that were positive for both vaccine and very virulent IBDV. Majority of these samples have higher viral load fold change in very virulent than the classical strain except for three samples MB078/04, MB001/05 and MB033/05 which showed higher fold change in classical strain than very virulent strain. In conclusion, this study has successfully developed SYBR Green I based and Taqman based one-step real-time PCR assays for rapid detection and differentiation of IBDV subtypes in particular very virulent and classical IBDV strains

Multi-level Feature Fusion-based CNN for Local Climate Zone Classification from Sentinel-2 Images: Benchmark Results on the So2Sat LCZ42 Dataset

As a unique classification scheme for urban forms and functions, the local climate zone (LCZ) system provides essential general information for any studies related to urban environments, especially on a large scale. Remote sensing data-based classification approaches are the key to large-scale mapping and monitoring of LCZs. The potential of deep learning-based approaches is not yet fully explored, even though advanced convolutional neural networks (CNNs) continue to push the frontiers for various computer vision tasks. One reason is that published studies are based on different datasets, usually at a regional scale, which makes it impossible to fairly and consistently compare the potential of different CNNs for real-world scenarios. This study is based on the big So2Sat LCZ42 benchmark dataset dedicated to LCZ classification. Using this dataset, we studied a range of CNNs of varying sizes. In addition, we proposed a CNN to classify LCZs from Sentinel-2 images, Sen2LCZ-Net. Using this base network, we propose fusing multi-level features using the extended Sen2LCZ-Net-MF. With this proposed simple network architecture and the highly competitive benchmark dataset, we obtain results that are better than those obtained by the state-of-the-art CNNs, while requiring less computation with fewer layers and parameters. Large-scale LCZ classification examples of completely unseen areas are presented, demonstrating the potential of our proposed Sen2LCZ-Net-MF as well as the So2Sat LCZ42 dataset. We also intensively investigated the influence of network depth and width and the effectiveness of the design choices made for Sen2LCZ-Net-MF. Our work will provide important baselines for future CNN-based algorithm developments for both LCZ classification and other urban land cover land use classification

World Class Sustainable Supply Chain Management: critical review and further research directions

Purpose Sustainable supply chain management (SSCM) has attracted considerable interest among academics and practitioners. The purpose of this paper is to present a critical review of the literature, to identify missing links, to argue for the use of world class SSCM (WCSSCM) through a framework, and suggest further research directions. Design/methodology/approach In the paper the authors have undertaken an extensive review of literature and classified articles using a novel classification scheme. Findings Through the extensive review and identification of research gaps, the paper identifies significant differences between definitions and methodologies in the SSCM literature; and argues for “WCSSCM.” This term is elaborated on via a theoretical framework in which 18 dimensions are classified under six constructs of SSCM. Furthermore, a list of potential research directions for WCSSCM is discussed. Research limitations/implications The research is an attempt to critically review literature, argue for WCSSCM, and develop a theoretical framework. Originality/value The paper offers a new approach to SSCM literature, arguing for WCSSCM through a framework, and providing further research directions