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  • 99
    New England Biolabs phi 29 dna polymerase
    Phi 29 Dna Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi 29 dna polymerase/product/New England Biolabs
    Average 99 stars, based on 32 article reviews
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    phi 29 dna polymerase - by Bioz Stars, 2020-09
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    99
    ATCC bacillus subtilis phage phi 3t
    Bacillus Subtilis Phage Phi 3t, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 117 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bacillus subtilis phage phi 3t/product/ATCC
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    91
    Intel intel xeon phi
    Two levels of parallelism in the docking kernel. ( A ) At the coarse-grained level, individual replicas are assigned to different CUDA thread blocks on <t>GPU</t> streaming multiprocessors (SMs) and different threads on <t>CPU/Xeon</t> Phi cores. ( B ) At the fine-gained level, data points for each replica are organized as Structure of Arrays containing Cartesian coordinates x , y , z , and parameters p associated with atoms, such as type, charge, and etc. Parameters for neighboring atoms are placed closely in memory to ensure the best execution efficiency. ( C ) Data points at the fine-gained level are accessed in parallel by CUDA threads on GPU and SIMD lanes on CPU and Xeon Phi.
    Intel Xeon Phi, supplied by Intel, used in various techniques. Bioz Stars score: 91/100, based on 190 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/intel xeon phi/product/Intel
    Average 91 stars, based on 190 article reviews
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    intel xeon phi - by Bioz Stars, 2020-09
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    89
    ULVAC phi 5000 versaprobe
    Two levels of parallelism in the docking kernel. ( A ) At the coarse-grained level, individual replicas are assigned to different CUDA thread blocks on <t>GPU</t> streaming multiprocessors (SMs) and different threads on <t>CPU/Xeon</t> Phi cores. ( B ) At the fine-gained level, data points for each replica are organized as Structure of Arrays containing Cartesian coordinates x , y , z , and parameters p associated with atoms, such as type, charge, and etc. Parameters for neighboring atoms are placed closely in memory to ensure the best execution efficiency. ( C ) Data points at the fine-gained level are accessed in parallel by CUDA threads on GPU and SIMD lanes on CPU and Xeon Phi.
    Phi 5000 Versaprobe, supplied by ULVAC, used in various techniques. Bioz Stars score: 89/100, based on 187 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi 5000 versaprobe/product/ULVAC
    Average 89 stars, based on 187 article reviews
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    phi 5000 versaprobe - by Bioz Stars, 2020-09
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    94
    ATCC s aureus 8325 4
    Effects of SteLL on cell size of  S. aureus  8325-4. ( A ) Exponentially growing cells; ( B ) Cells treated with 0.78 µg/mL ciprofloxacin for 3 h; ( C ) Cells treated with 2 × MIC SteLL (4 µg/mL) for 3 h; ( D ) Cells treated with 8 × MIC (16 µg/mL) SteLL for 3 h.
    S Aureus 8325 4, supplied by ATCC, used in various techniques. Bioz Stars score: 94/100, based on 337 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/s aureus 8325 4/product/ATCC
    Average 94 stars, based on 337 article reviews
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    s aureus 8325 4 - by Bioz Stars, 2020-09
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    91
    Alpha-Omega phi beta kappa
    Effects of SteLL on cell size of  S. aureus  8325-4. ( A ) Exponentially growing cells; ( B ) Cells treated with 0.78 µg/mL ciprofloxacin for 3 h; ( C ) Cells treated with 2 × MIC SteLL (4 µg/mL) for 3 h; ( D ) Cells treated with 8 × MIC (16 µg/mL) SteLL for 3 h.
    Phi Beta Kappa, supplied by Alpha-Omega, used in various techniques. Bioz Stars score: 91/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi beta kappa/product/Alpha-Omega
    Average 91 stars, based on 14 article reviews
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    phi beta kappa - by Bioz Stars, 2020-09
    91/100 stars
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    88
    ULVAC phi quantera sxm
    Effects of SteLL on cell size of  S. aureus  8325-4. ( A ) Exponentially growing cells; ( B ) Cells treated with 0.78 µg/mL ciprofloxacin for 3 h; ( C ) Cells treated with 2 × MIC SteLL (4 µg/mL) for 3 h; ( D ) Cells treated with 8 × MIC (16 µg/mL) SteLL for 3 h.
    Phi Quantera Sxm, supplied by ULVAC, used in various techniques. Bioz Stars score: 88/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi quantera sxm/product/ULVAC
    Average 88 stars, based on 37 article reviews
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    phi quantera sxm - by Bioz Stars, 2020-09
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    89
    Intel intel phi co processors
    Effects of SteLL on cell size of  S. aureus  8325-4. ( A ) Exponentially growing cells; ( B ) Cells treated with 0.78 µg/mL ciprofloxacin for 3 h; ( C ) Cells treated with 2 × MIC SteLL (4 µg/mL) for 3 h; ( D ) Cells treated with 8 × MIC (16 µg/mL) SteLL for 3 h.
    Intel Phi Co Processors, supplied by Intel, used in various techniques. Bioz Stars score: 89/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/intel phi co processors/product/Intel
    Average 89 stars, based on 14 article reviews
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    intel phi co processors - by Bioz Stars, 2020-09
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    88
    Thermo Fisher phi 29 dna polymerase
    Percentages of reads classified to the genus level using Kraken2 (taxonomic classification tool) from beef samples with in-house databases of mammals, archaea, bacteria, fungi, human, protozoa, and viruses. Light blue represents the proportion of “ Bos ” corresponding to beef reads. Yellow represents the presence of “ Escherichia ” in the sample. The reads that could not be classified to the genus level for mammals, archaea, bacteria, fungi, human, protozoa, or viruses are represented in gray. ( A ) Blank meat samples; Bk-0h—non-enriched blank; BK-24h—non-spiked meat sample enriched for 24 h, 1–3 biological replicates. ( B ) Extraction kits; workflow A—Nucleospin Food, workflow B—DNeasy Blood Tissue and workflow C—Zymo HostZERO. ( C ) Enrichment times; workflow A—24 h culture enrichment, workflow D—16 h culture enrichment, workflow E—16 h culture enrichment, extraction followed by DNA amplification using <t>phi</t> 29 DNA polymerase; all extracted with Nucleospin Food kit. ( D ) Biological and technical replicates of workflow A. Small differences in the detected species shown in panels A, C, and D can be explained by the heterogeneity of the samples and biological variation, as different replicates of the experiment were used.
    Phi 29 Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi 29 dna polymerase/product/Thermo Fisher
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    phi 29 dna polymerase - by Bioz Stars, 2020-09
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    88
    ULVAC phi quantera sxm spectrometer
    Percentages of reads classified to the genus level using Kraken2 (taxonomic classification tool) from beef samples with in-house databases of mammals, archaea, bacteria, fungi, human, protozoa, and viruses. Light blue represents the proportion of “ Bos ” corresponding to beef reads. Yellow represents the presence of “ Escherichia ” in the sample. The reads that could not be classified to the genus level for mammals, archaea, bacteria, fungi, human, protozoa, or viruses are represented in gray. ( A ) Blank meat samples; Bk-0h—non-enriched blank; BK-24h—non-spiked meat sample enriched for 24 h, 1–3 biological replicates. ( B ) Extraction kits; workflow A—Nucleospin Food, workflow B—DNeasy Blood Tissue and workflow C—Zymo HostZERO. ( C ) Enrichment times; workflow A—24 h culture enrichment, workflow D—16 h culture enrichment, workflow E—16 h culture enrichment, extraction followed by DNA amplification using <t>phi</t> 29 DNA polymerase; all extracted with Nucleospin Food kit. ( D ) Biological and technical replicates of workflow A. Small differences in the detected species shown in panels A, C, and D can be explained by the heterogeneity of the samples and biological variation, as different replicates of the experiment were used.
    Phi Quantera Sxm Spectrometer, supplied by ULVAC, used in various techniques. Bioz Stars score: 88/100, based on 69 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi quantera sxm spectrometer/product/ULVAC
    Average 88 stars, based on 69 article reviews
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    phi quantera sxm spectrometer - by Bioz Stars, 2020-09
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    90
    Intel intel phi se10p
    Acceleration attained in the <t>SE10P</t> Intel Phi as compared to 1-CPU core for input data with varying tissue coverage.
    Intel Phi Se10p, supplied by Intel, used in various techniques. Bioz Stars score: 90/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/intel phi se10p/product/Intel
    Average 90 stars, based on 6 article reviews
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    intel phi se10p - by Bioz Stars, 2020-09
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    90
    Med Services Europe GmbH phi med europe s l
    Acceleration attained in the <t>SE10P</t> Intel Phi as compared to 1-CPU core for input data with varying tissue coverage.
    Phi Med Europe S L, supplied by Med Services Europe GmbH, used in various techniques. Bioz Stars score: 90/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi med europe s l/product/Med Services Europe GmbH
    Average 90 stars, based on 6 article reviews
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    phi med europe s l - by Bioz Stars, 2020-09
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    88
    ULVAC phi quantera ii
    Acceleration attained in the <t>SE10P</t> Intel Phi as compared to 1-CPU core for input data with varying tissue coverage.
    Phi Quantera Ii, supplied by ULVAC, used in various techniques. Bioz Stars score: 88/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi quantera ii/product/ULVAC
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    91
    Phi Therapeutics hiv infection phi
    Frequency of γδ T cells is negatively correlated with CD8 T cell activation in primary <t>HIV</t> infection <t>(PHI).</t> (A) Relationship between the frequency of γδ T cells and the proportion of CD38 + γδ T cells in viremic patients [PHI and untreated chronic HIV infection (UT-CHI)]. (B,C) Correlation analysis between the frequency of γδ T cells and the proportion of CD38 + HLA-DR + CD8 T cells in PHI and UT-CHI. (D,E) Correlation between the frequencies of CD38 + γδ T cells and CD38 + CD8 T cells in PHI or UT-CHI. Spearman rank correlation coefficients ( r ) and corresponding p values are indicated in each panel; p -values are indicated as significant when
    Hiv Infection Phi, supplied by Phi Therapeutics, used in various techniques. Bioz Stars score: 91/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiv infection phi/product/Phi Therapeutics
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    90
    ULVAC phi 5000 versaprobetm
    Frequency of γδ T cells is negatively correlated with CD8 T cell activation in primary <t>HIV</t> infection <t>(PHI).</t> (A) Relationship between the frequency of γδ T cells and the proportion of CD38 + γδ T cells in viremic patients [PHI and untreated chronic HIV infection (UT-CHI)]. (B,C) Correlation analysis between the frequency of γδ T cells and the proportion of CD38 + HLA-DR + CD8 T cells in PHI and UT-CHI. (D,E) Correlation between the frequencies of CD38 + γδ T cells and CD38 + CD8 T cells in PHI or UT-CHI. Spearman rank correlation coefficients ( r ) and corresponding p values are indicated in each panel; p -values are indicated as significant when
    Phi 5000 Versaprobetm, supplied by ULVAC, used in various techniques. Bioz Stars score: 90/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi 5000 versaprobetm/product/ULVAC
    Average 90 stars, based on 24 article reviews
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    phi 5000 versaprobetm - by Bioz Stars, 2020-09
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    91
    ULVAC phi quantera microprobe
    Frequency of γδ T cells is negatively correlated with CD8 T cell activation in primary <t>HIV</t> infection <t>(PHI).</t> (A) Relationship between the frequency of γδ T cells and the proportion of CD38 + γδ T cells in viremic patients [PHI and untreated chronic HIV infection (UT-CHI)]. (B,C) Correlation analysis between the frequency of γδ T cells and the proportion of CD38 + HLA-DR + CD8 T cells in PHI and UT-CHI. (D,E) Correlation between the frequencies of CD38 + γδ T cells and CD38 + CD8 T cells in PHI or UT-CHI. Spearman rank correlation coefficients ( r ) and corresponding p values are indicated in each panel; p -values are indicated as significant when
    Phi Quantera Microprobe, supplied by ULVAC, used in various techniques. Bioz Stars score: 91/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi quantera microprobe/product/ULVAC
    Average 91 stars, based on 22 article reviews
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    phi quantera microprobe - by Bioz Stars, 2020-09
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    96
    ATCC bacteriophage φx174
    A typical SPR reflectance angle minimum-time response used for the detection of bacteriophage (b. phage) <t>φX174</t> and other somatic coliphages present in the wastewater samples. Arrows indicate the different steps from the cycle that were described in Materials and Methods: (i) incubation of the host strain E. coli WG5, (ii) PBS washing, and (iii) addition of the sample bacteriophage in one chamber (and negative control in the other chamber).
    Bacteriophage φx174, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Two levels of parallelism in the docking kernel. ( A ) At the coarse-grained level, individual replicas are assigned to different CUDA thread blocks on GPU streaming multiprocessors (SMs) and different threads on CPU/Xeon Phi cores. ( B ) At the fine-gained level, data points for each replica are organized as Structure of Arrays containing Cartesian coordinates x , y , z , and parameters p associated with atoms, such as type, charge, and etc. Parameters for neighboring atoms are placed closely in memory to ensure the best execution efficiency. ( C ) Data points at the fine-gained level are accessed in parallel by CUDA threads on GPU and SIMD lanes on CPU and Xeon Phi.

    Journal: PLoS ONE

    Article Title: GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

    doi: 10.1371/journal.pone.0158898

    Figure Lengend Snippet: Two levels of parallelism in the docking kernel. ( A ) At the coarse-grained level, individual replicas are assigned to different CUDA thread blocks on GPU streaming multiprocessors (SMs) and different threads on CPU/Xeon Phi cores. ( B ) At the fine-gained level, data points for each replica are organized as Structure of Arrays containing Cartesian coordinates x , y , z , and parameters p associated with atoms, such as type, charge, and etc. Parameters for neighboring atoms are placed closely in memory to ensure the best execution efficiency. ( C ) Data points at the fine-gained level are accessed in parallel by CUDA threads on GPU and SIMD lanes on CPU and Xeon Phi.

    Article Snippet: Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU).

    Techniques:

    Distribution of speedups of parallel GeauxDock over the serial CPU version. Benchmarking calculations are conducted for the dataset of 204 CCDC/Astex compounds using ( A - C , red) modified input data providing an ample coarse-grained parallelism and ( D - F , green) unmodified input data. Three kernel implementations are tested for ( A , D ) multi-core CPU, ( B , E ) Xeon Phi, and ( C , F ) GPU.

    Journal: PLoS ONE

    Article Title: GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

    doi: 10.1371/journal.pone.0158898

    Figure Lengend Snippet: Distribution of speedups of parallel GeauxDock over the serial CPU version. Benchmarking calculations are conducted for the dataset of 204 CCDC/Astex compounds using ( A - C , red) modified input data providing an ample coarse-grained parallelism and ( D - F , green) unmodified input data. Three kernel implementations are tested for ( A , D ) multi-core CPU, ( B , E ) Xeon Phi, and ( C , F ) GPU.

    Article Snippet: Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU).

    Techniques: Modification

    Correlation between the estimated and real docking time. Simulation time is estimated from static data size using a general linear regression model for ( A ) multi-core CPU, ( B ) Xeon Phi, and ( C ) GPU.

    Journal: PLoS ONE

    Article Title: GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

    doi: 10.1371/journal.pone.0158898

    Figure Lengend Snippet: Correlation between the estimated and real docking time. Simulation time is estimated from static data size using a general linear regression model for ( A ) multi-core CPU, ( B ) Xeon Phi, and ( C ) GPU.

    Article Snippet: Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU).

    Techniques:

    Time breakdowns for docking kernels running on different platforms. Kernel implementations for ( A , D , G ) multi-core CPU, ( B , E , H ) Xeon Phi, and ( C , F , I ) GPU are tested. Three major operations compute the following interaction matrices: protein ColumnVector × ligand RowVector ( PRT , green), KDE ColumnVector × ligand RowVector ( KDE , red), and MCS Matrix × ligand ColumnVector ( MCS , blue). Purple areas correspond to the remaining operations. KDE (Kernel Density Estimation) and MCS (Maximum Common Substructure) points are used to calculate evolution-based components of the docking force field, whereas the PRT matrix is used to calculate the majority of physics-based potentials. Results collected for the dataset of 204 CCDC/Astex compounds are sorted on the x -axis with respect to increasing time of computing ( A , B , C ) PRT , ( D , E , F ) KDE , and ( G , H , I ) MCS matrices.

    Journal: PLoS ONE

    Article Title: GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

    doi: 10.1371/journal.pone.0158898

    Figure Lengend Snippet: Time breakdowns for docking kernels running on different platforms. Kernel implementations for ( A , D , G ) multi-core CPU, ( B , E , H ) Xeon Phi, and ( C , F , I ) GPU are tested. Three major operations compute the following interaction matrices: protein ColumnVector × ligand RowVector ( PRT , green), KDE ColumnVector × ligand RowVector ( KDE , red), and MCS Matrix × ligand ColumnVector ( MCS , blue). Purple areas correspond to the remaining operations. KDE (Kernel Density Estimation) and MCS (Maximum Common Substructure) points are used to calculate evolution-based components of the docking force field, whereas the PRT matrix is used to calculate the majority of physics-based potentials. Results collected for the dataset of 204 CCDC/Astex compounds are sorted on the x -axis with respect to increasing time of computing ( A , B , C ) PRT , ( D , E , F ) KDE , and ( G , H , I ) MCS matrices.

    Article Snippet: Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU).

    Techniques:

    Correlation between computing time and static data size. Blue points are collected from original GeauxDock, whereas red points correspond to a modified docking code, where dynamic branches are turned off forcing the execution of all instructions. Three major operations compute ( A - C ) protein ColumnVector × ligand RowVector ( PRT ), ( D - F ) KDE ColumnVector × ligand RowVector ( KDE ), and ( G - I ) MCS Matrix × ligand ColumnVector ( MCS ) matrices. Three kernel implementations are tested for ( A , D , G ) multi-core CPU, ( B , E , H ) Xeon Phi, and ( C , F , I ) GPU.

    Journal: PLoS ONE

    Article Title: GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

    doi: 10.1371/journal.pone.0158898

    Figure Lengend Snippet: Correlation between computing time and static data size. Blue points are collected from original GeauxDock, whereas red points correspond to a modified docking code, where dynamic branches are turned off forcing the execution of all instructions. Three major operations compute ( A - C ) protein ColumnVector × ligand RowVector ( PRT ), ( D - F ) KDE ColumnVector × ligand RowVector ( KDE ), and ( G - I ) MCS Matrix × ligand ColumnVector ( MCS ) matrices. Three kernel implementations are tested for ( A , D , G ) multi-core CPU, ( B , E , H ) Xeon Phi, and ( C , F , I ) GPU.

    Article Snippet: Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU).

    Techniques: Modification

    Implementation of GeauxDock. ( A ) The code repository is divided into three modules, a common front-end module for the CPU host and two back-end modules, one for GPU and one for CPU and Xeon Phi. ( B ) Compiling the source codes produces a series of architecture-specific object files. ( C ) Linking object files creates three binary versions for GPU, CPU and Xeon Phi.

    Journal: PLoS ONE

    Article Title: GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

    doi: 10.1371/journal.pone.0158898

    Figure Lengend Snippet: Implementation of GeauxDock. ( A ) The code repository is divided into three modules, a common front-end module for the CPU host and two back-end modules, one for GPU and one for CPU and Xeon Phi. ( B ) Compiling the source codes produces a series of architecture-specific object files. ( C ) Linking object files creates three binary versions for GPU, CPU and Xeon Phi.

    Article Snippet: Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU).

    Techniques:

    Performance scaling of docking kernels with different numbers of system replicas. Benchmarking calculations are performed using ( A ) multi-core CPU, ( B ) Xeon Phi, and ( C ) GPU. The width of horizontal lines is 20 replicas for a dual 10-core CPU, 240 for a 60-core Xeon Phi with 4-way multi-threading, and 14 for a 14-multiprocessor GPU.

    Journal: PLoS ONE

    Article Title: GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

    doi: 10.1371/journal.pone.0158898

    Figure Lengend Snippet: Performance scaling of docking kernels with different numbers of system replicas. Benchmarking calculations are performed using ( A ) multi-core CPU, ( B ) Xeon Phi, and ( C ) GPU. The width of horizontal lines is 20 replicas for a dual 10-core CPU, 240 for a 60-core Xeon Phi with 4-way multi-threading, and 14 for a 14-multiprocessor GPU.

    Article Snippet: Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU).

    Techniques:

    The specialized GPU workstation used in this study, consisting of one Intel Xeon 5650 CPU and 6 NVIDIA M2090 GPUs.

    Journal: Medical Physics

    Article Title: ARCHERRT – A GPU-based and photon-electron coupled Monte Carlo dose computing engine for radiation therapy: Software development and application to helical tomotherapy

    doi: 10.1118/1.4884229

    Figure Lengend Snippet: The specialized GPU workstation used in this study, consisting of one Intel Xeon 5650 CPU and 6 NVIDIA M2090 GPUs.

    Article Snippet: In fact, several challenges can be readily identified in the current research: (1) Considerable software development is needed to truly optimize algorithms in new hardware/software environments. (2) There is little or no effort to understand the underlying challenges presented. (3) Comparison against traditional CPU-based methods lacks fairness, leading to false performance rating for GPUs. (4) Clinical benefits have not been systematically evaluated. (5) There is an uncertainty about the GPUs future as a parallel computing technology because Intel Xeon Phi coprocessors were adopted in the world's #1 supercomputer (the Tianhe-2) in 2013 and NVIDIA on longer dominates the market place.

    Techniques:

    MIC code snippet. The first pragma directive marks the start of a MIC code section. Keywords in and out indicate the data to be transferred to and from the Xeon Phi. The OpenMP clause omp parallel for launches all available threads in parallel, which execute the code in the body of the loop and score the SNP pairs.

    Journal: BMC Bioinformatics

    Article Title: Heterogeneous computing architecture for fast detection of SNP-SNP interactions

    doi: 10.1186/1471-2105-15-216

    Figure Lengend Snippet: MIC code snippet. The first pragma directive marks the start of a MIC code section. Keywords in and out indicate the data to be transferred to and from the Xeon Phi. The OpenMP clause omp parallel for launches all available threads in parallel, which execute the code in the body of the loop and score the SNP pairs.

    Article Snippet: Xeon Phi and MIC Intel designed the Xeon Phi family of coprocessors around the new MIC architecture [ ] to compete with GPUs specialized in general-purpose computing.

    Techniques:

    Effects of SteLL on cell size of  S. aureus  8325-4. ( A ) Exponentially growing cells; ( B ) Cells treated with 0.78 µg/mL ciprofloxacin for 3 h; ( C ) Cells treated with 2 × MIC SteLL (4 µg/mL) for 3 h; ( D ) Cells treated with 8 × MIC (16 µg/mL) SteLL for 3 h.

    Journal: Scientific Reports

    Article Title: Schinus terebinthifolia leaf lectin (SteLL) has anti-infective action and modulates the response of Staphylococcus aureus-infected macrophages

    doi: 10.1038/s41598-019-54616-x

    Figure Lengend Snippet: Effects of SteLL on cell size of S. aureus 8325-4. ( A ) Exponentially growing cells; ( B ) Cells treated with 0.78 µg/mL ciprofloxacin for 3 h; ( C ) Cells treated with 2 × MIC SteLL (4 µg/mL) for 3 h; ( D ) Cells treated with 8 × MIC (16 µg/mL) SteLL for 3 h.

    Article Snippet: The MIC values for these two drugs towards S. aureus 8325-4 were 0.78 µg/mL and 25 µg/mL, respectively.

    Techniques:

    Effects of SteLL on survival ( A ) and bacteria load in hemolymph ( B ) of  G. mellonella  larvae infected with  S. aureus . In all experiments the larvae were infected with a  S. aureus  8325-4 suspension (10 μL of 1.0 × 10 5  CFU/mL) and treated with SteLL at 0.2 mg/kg. (*) Indicates significant differences in relation to control cells (p 

    Journal: Scientific Reports

    Article Title: Schinus terebinthifolia leaf lectin (SteLL) has anti-infective action and modulates the response of Staphylococcus aureus-infected macrophages

    doi: 10.1038/s41598-019-54616-x

    Figure Lengend Snippet: Effects of SteLL on survival ( A ) and bacteria load in hemolymph ( B ) of G. mellonella larvae infected with S. aureus . In all experiments the larvae were infected with a S. aureus 8325-4 suspension (10 μL of 1.0 × 10 5 CFU/mL) and treated with SteLL at 0.2 mg/kg. (*) Indicates significant differences in relation to control cells (p 

    Article Snippet: The MIC values for these two drugs towards S. aureus 8325-4 were 0.78 µg/mL and 25 µg/mL, respectively.

    Techniques: Infection

    Effects of SteLL on  recA  expression of  S. aureus . The expression of  recA  were performed using a derivative  S. aureus  8325-4 strain carrying a  recA::lacZ  fusion. β-galactosidase activity was measured using ONPG. (*) Indicates significant differences in relation to control cells (p 

    Journal: Scientific Reports

    Article Title: Schinus terebinthifolia leaf lectin (SteLL) has anti-infective action and modulates the response of Staphylococcus aureus-infected macrophages

    doi: 10.1038/s41598-019-54616-x

    Figure Lengend Snippet: Effects of SteLL on recA expression of S. aureus . The expression of recA were performed using a derivative S. aureus 8325-4 strain carrying a recA::lacZ fusion. β-galactosidase activity was measured using ONPG. (*) Indicates significant differences in relation to control cells (p 

    Article Snippet: The MIC values for these two drugs towards S. aureus 8325-4 were 0.78 µg/mL and 25 µg/mL, respectively.

    Techniques: Expressing, Activity Assay

    Effects of SteLL and selected antimicrobials on DNA content of  S. aureus  8325-4. ( A ) Exponentially growing cells; ( B ) Cells treated with 0.78 µg/mL ciprofloxacin for 3 h; ( C ) Cells treated with 12.5 µg/mL chloramphenicol for 3 h; ( D ) Cells treated with 2 × MIC SteLL (4 µg/mL) for 3 h; ( E ) Cells treated with 8 × MIC (16 µg/mL) SteLL for 3 h.

    Journal: Scientific Reports

    Article Title: Schinus terebinthifolia leaf lectin (SteLL) has anti-infective action and modulates the response of Staphylococcus aureus-infected macrophages

    doi: 10.1038/s41598-019-54616-x

    Figure Lengend Snippet: Effects of SteLL and selected antimicrobials on DNA content of S. aureus 8325-4. ( A ) Exponentially growing cells; ( B ) Cells treated with 0.78 µg/mL ciprofloxacin for 3 h; ( C ) Cells treated with 12.5 µg/mL chloramphenicol for 3 h; ( D ) Cells treated with 2 × MIC SteLL (4 µg/mL) for 3 h; ( E ) Cells treated with 8 × MIC (16 µg/mL) SteLL for 3 h.

    Article Snippet: The MIC values for these two drugs towards S. aureus 8325-4 were 0.78 µg/mL and 25 µg/mL, respectively.

    Techniques:

    Percentages of reads classified to the genus level using Kraken2 (taxonomic classification tool) from beef samples with in-house databases of mammals, archaea, bacteria, fungi, human, protozoa, and viruses. Light blue represents the proportion of “ Bos ” corresponding to beef reads. Yellow represents the presence of “ Escherichia ” in the sample. The reads that could not be classified to the genus level for mammals, archaea, bacteria, fungi, human, protozoa, or viruses are represented in gray. ( A ) Blank meat samples; Bk-0h—non-enriched blank; BK-24h—non-spiked meat sample enriched for 24 h, 1–3 biological replicates. ( B ) Extraction kits; workflow A—Nucleospin Food, workflow B—DNeasy Blood Tissue and workflow C—Zymo HostZERO. ( C ) Enrichment times; workflow A—24 h culture enrichment, workflow D—16 h culture enrichment, workflow E—16 h culture enrichment, extraction followed by DNA amplification using phi 29 DNA polymerase; all extracted with Nucleospin Food kit. ( D ) Biological and technical replicates of workflow A. Small differences in the detected species shown in panels A, C, and D can be explained by the heterogeneity of the samples and biological variation, as different replicates of the experiment were used.

    Journal: Microorganisms

    Article Title: A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine

    doi: 10.3390/microorganisms8081191

    Figure Lengend Snippet: Percentages of reads classified to the genus level using Kraken2 (taxonomic classification tool) from beef samples with in-house databases of mammals, archaea, bacteria, fungi, human, protozoa, and viruses. Light blue represents the proportion of “ Bos ” corresponding to beef reads. Yellow represents the presence of “ Escherichia ” in the sample. The reads that could not be classified to the genus level for mammals, archaea, bacteria, fungi, human, protozoa, or viruses are represented in gray. ( A ) Blank meat samples; Bk-0h—non-enriched blank; BK-24h—non-spiked meat sample enriched for 24 h, 1–3 biological replicates. ( B ) Extraction kits; workflow A—Nucleospin Food, workflow B—DNeasy Blood Tissue and workflow C—Zymo HostZERO. ( C ) Enrichment times; workflow A—24 h culture enrichment, workflow D—16 h culture enrichment, workflow E—16 h culture enrichment, extraction followed by DNA amplification using phi 29 DNA polymerase; all extracted with Nucleospin Food kit. ( D ) Biological and technical replicates of workflow A. Small differences in the detected species shown in panels A, C, and D can be explained by the heterogeneity of the samples and biological variation, as different replicates of the experiment were used.

    Article Snippet: One DNA extract of the beef sample enriched for 16 h and extracted with the Nucleospin Food kit was amplified using phi 29 DNA polymerase (ThermoFisher scientific, Waltham, MA, USA) according to the manufacturer’s instructions (method E, ).

    Techniques: Amplification

    Acceleration attained in the SE10P Intel Phi as compared to 1-CPU core for input data with varying tissue coverage.

    Journal: Proceedings / Symposium on Computer Architecture and High Performance Computing. Symposium on Computer Architecture and High Performance Computing

    Article Title: Efficient irregular wavefront propagation algorithms on Intel® Xeon Phi™

    doi: 10.1109/SBAC-PAD.2015.13

    Figure Lengend Snippet: Acceleration attained in the SE10P Intel Phi as compared to 1-CPU core for input data with varying tissue coverage.

    Article Snippet: The experiments were carried out using the Intel Phi SE10P and Morphological Reconstruction with FIFO queue only, because its performance is similar to that of Imfill as data sizes are varied.

    Techniques:

    Frequency of γδ T cells is negatively correlated with CD8 T cell activation in primary HIV infection (PHI). (A) Relationship between the frequency of γδ T cells and the proportion of CD38 + γδ T cells in viremic patients [PHI and untreated chronic HIV infection (UT-CHI)]. (B,C) Correlation analysis between the frequency of γδ T cells and the proportion of CD38 + HLA-DR + CD8 T cells in PHI and UT-CHI. (D,E) Correlation between the frequencies of CD38 + γδ T cells and CD38 + CD8 T cells in PHI or UT-CHI. Spearman rank correlation coefficients ( r ) and corresponding p values are indicated in each panel; p -values are indicated as significant when

    Journal: Frontiers in Immunology

    Article Title: Potential Role of Vδ2+ γδ T Cells in Regulation of Immune Activation in Primary HIV Infection

    doi: 10.3389/fimmu.2017.01189

    Figure Lengend Snippet: Frequency of γδ T cells is negatively correlated with CD8 T cell activation in primary HIV infection (PHI). (A) Relationship between the frequency of γδ T cells and the proportion of CD38 + γδ T cells in viremic patients [PHI and untreated chronic HIV infection (UT-CHI)]. (B,C) Correlation analysis between the frequency of γδ T cells and the proportion of CD38 + HLA-DR + CD8 T cells in PHI and UT-CHI. (D,E) Correlation between the frequencies of CD38 + γδ T cells and CD38 + CD8 T cells in PHI or UT-CHI. Spearman rank correlation coefficients ( r ) and corresponding p values are indicated in each panel; p -values are indicated as significant when

    Article Snippet: In the primary HIV infection (PHI), there is prolific viral replication, high levels of immune activation, and induction of HIV-specific CD4 and CD8 T-cell cytotoxic responses ( – ).

    Techniques: Activation Assay, Infection

    Distribution of γδ T cells and its subsets in peripheral blood. Peripheral blood mononuclear cells were stained ex vivo for γδ T cells, as well as its subsets (Vδ2 − and Vδ2 + ), and compared between healthy donors (HD), and patients with primary HIV infection (PHI), as well as chronic HIV infection (CHI)—untreated (UT) and treated with ART (ART). (A) Frequency of γδ T cells among T cells. (B) Graphical representation of frequencies of Vδ2 − and Vδ2 + cells within γδ T cells. (C) Comparison of the ratio of Vδ2 − /Vδ2 + cells among γδ T cells. Comparison of absolute numbers of (D) γδ T cells, (E) Vδ2 − cells, and (F) Vδ2 + cells between PHI, untreated chronic HIV infection (UT-CHI), and ART-CHI. (G) Correlation between absolute count of γδ T cells and log 10 Vδ2 − /Vδ2 + ratio among γδ T cells in all HIV-infected patients. Data are displayed as median and IQR. Mann–Whitney and Spearman rank correlation tests were performed. Spearman rank correlation coefficient ( r ) is indicated in the panel. p -Values are indicated as significant when

    Journal: Frontiers in Immunology

    Article Title: Potential Role of Vδ2+ γδ T Cells in Regulation of Immune Activation in Primary HIV Infection

    doi: 10.3389/fimmu.2017.01189

    Figure Lengend Snippet: Distribution of γδ T cells and its subsets in peripheral blood. Peripheral blood mononuclear cells were stained ex vivo for γδ T cells, as well as its subsets (Vδ2 − and Vδ2 + ), and compared between healthy donors (HD), and patients with primary HIV infection (PHI), as well as chronic HIV infection (CHI)—untreated (UT) and treated with ART (ART). (A) Frequency of γδ T cells among T cells. (B) Graphical representation of frequencies of Vδ2 − and Vδ2 + cells within γδ T cells. (C) Comparison of the ratio of Vδ2 − /Vδ2 + cells among γδ T cells. Comparison of absolute numbers of (D) γδ T cells, (E) Vδ2 − cells, and (F) Vδ2 + cells between PHI, untreated chronic HIV infection (UT-CHI), and ART-CHI. (G) Correlation between absolute count of γδ T cells and log 10 Vδ2 − /Vδ2 + ratio among γδ T cells in all HIV-infected patients. Data are displayed as median and IQR. Mann–Whitney and Spearman rank correlation tests were performed. Spearman rank correlation coefficient ( r ) is indicated in the panel. p -Values are indicated as significant when

    Article Snippet: In the primary HIV infection (PHI), there is prolific viral replication, high levels of immune activation, and induction of HIV-specific CD4 and CD8 T-cell cytotoxic responses ( – ).

    Techniques: Staining, Ex Vivo, Infection, MANN-WHITNEY

    Vδ2 + γδ T cells exhibit anti-inflammatory cytokine profile in primary HIV infection (PHI). (A) Correlation analyses in viremic patients (A) between absolute numbers of Vδ2 − γδ T cells and the proportion of CD45RA + CD27 − (T EMRA ) Vδ2 − γδ T cells, and (B) between Vδ2 + γδ T cells and the proportion of CD45RA + CD27 − (T EMRA ) Vδ2 + γδ T cells. (C) Relationship between the frequency of Ki-67 + Vδ2 + γδ T cells and the proportion of CD38 + Vδ2 + γδ T cells in PHI patients. (D) Representative FACS staining of IFN-γ production by Vδ2 + and Vδ2 − γδ T cells from a UT-CHI patient with or without CD3/CD28 stimulation for 24 h. Comparison of frequencies of IFN-γ + Vδ2 + γδ T cells between healthy donors (HD), and patients with primary HIV infection (PHI) as well as chronic HIV infection (CHI)—untreated (UT) and treated with ART (ART). (E) Representative FACS staining of TGF-β production by Vδ2 + γδ T cells from a PHI patient with or without 4 days of isopentenyl pyrophosphate (IPP) stimulation. Comparison of frequencies of TGF-β + Vδ2 + γδ T cells between HD, PHI, UT-CHI, and ART-CHI. (F) Comparison of the ratio of frequencies of TGF-β + /IFN-γ + Vδ2 + γδ T cells between HD, PHI, UT-CHI, and ART-CHI. Data are displayed as median and IQR. Mann–Whitney and Spearman rank correlation tests were performed. Spearman rank correlation coefficients ( r ) are indicated in the panels. p -Values are indicated as significant when

    Journal: Frontiers in Immunology

    Article Title: Potential Role of Vδ2+ γδ T Cells in Regulation of Immune Activation in Primary HIV Infection

    doi: 10.3389/fimmu.2017.01189

    Figure Lengend Snippet: Vδ2 + γδ T cells exhibit anti-inflammatory cytokine profile in primary HIV infection (PHI). (A) Correlation analyses in viremic patients (A) between absolute numbers of Vδ2 − γδ T cells and the proportion of CD45RA + CD27 − (T EMRA ) Vδ2 − γδ T cells, and (B) between Vδ2 + γδ T cells and the proportion of CD45RA + CD27 − (T EMRA ) Vδ2 + γδ T cells. (C) Relationship between the frequency of Ki-67 + Vδ2 + γδ T cells and the proportion of CD38 + Vδ2 + γδ T cells in PHI patients. (D) Representative FACS staining of IFN-γ production by Vδ2 + and Vδ2 − γδ T cells from a UT-CHI patient with or without CD3/CD28 stimulation for 24 h. Comparison of frequencies of IFN-γ + Vδ2 + γδ T cells between healthy donors (HD), and patients with primary HIV infection (PHI) as well as chronic HIV infection (CHI)—untreated (UT) and treated with ART (ART). (E) Representative FACS staining of TGF-β production by Vδ2 + γδ T cells from a PHI patient with or without 4 days of isopentenyl pyrophosphate (IPP) stimulation. Comparison of frequencies of TGF-β + Vδ2 + γδ T cells between HD, PHI, UT-CHI, and ART-CHI. (F) Comparison of the ratio of frequencies of TGF-β + /IFN-γ + Vδ2 + γδ T cells between HD, PHI, UT-CHI, and ART-CHI. Data are displayed as median and IQR. Mann–Whitney and Spearman rank correlation tests were performed. Spearman rank correlation coefficients ( r ) are indicated in the panels. p -Values are indicated as significant when

    Article Snippet: In the primary HIV infection (PHI), there is prolific viral replication, high levels of immune activation, and induction of HIV-specific CD4 and CD8 T-cell cytotoxic responses ( – ).

    Techniques: Infection, FACS, Staining, MANN-WHITNEY

    A typical SPR reflectance angle minimum-time response used for the detection of bacteriophage (b. phage) φX174 and other somatic coliphages present in the wastewater samples. Arrows indicate the different steps from the cycle that were described in Materials and Methods: (i) incubation of the host strain E. coli WG5, (ii) PBS washing, and (iii) addition of the sample bacteriophage in one chamber (and negative control in the other chamber).

    Journal: Applied and Environmental Microbiology

    Article Title: Surface Plasmon Resonance Assay for Real-Time Monitoring of Somatic Coliphages in Wastewaters

    doi: 10.1128/AEM.02806-07

    Figure Lengend Snippet: A typical SPR reflectance angle minimum-time response used for the detection of bacteriophage (b. phage) φX174 and other somatic coliphages present in the wastewater samples. Arrows indicate the different steps from the cycle that were described in Materials and Methods: (i) incubation of the host strain E. coli WG5, (ii) PBS washing, and (iii) addition of the sample bacteriophage in one chamber (and negative control in the other chamber).

    Article Snippet: Bacteriophage φX174 (ATCC 13706-B1) was used as a reference bacteriophage for somatic coliphages.

    Techniques: SPR Assay, Incubation, Negative Control

    Variation of the reflectance angle minimum in response time detection with different concentrations of bacteriophages. (a) Detection of various concentrations of bacteriophage φX174 as measured by the SPR minimum angle change with time. Threshold time for 10 8 PFU/ml φX174 is marked on the plot for illustration. (b) Mean values of SPR minimum angle with time for detection of somatic coliphages in wastewater samples. Error bars show standard errors for triplicate repeats.

    Journal: Applied and Environmental Microbiology

    Article Title: Surface Plasmon Resonance Assay for Real-Time Monitoring of Somatic Coliphages in Wastewaters

    doi: 10.1128/AEM.02806-07

    Figure Lengend Snippet: Variation of the reflectance angle minimum in response time detection with different concentrations of bacteriophages. (a) Detection of various concentrations of bacteriophage φX174 as measured by the SPR minimum angle change with time. Threshold time for 10 8 PFU/ml φX174 is marked on the plot for illustration. (b) Mean values of SPR minimum angle with time for detection of somatic coliphages in wastewater samples. Error bars show standard errors for triplicate repeats.

    Article Snippet: Bacteriophage φX174 (ATCC 13706-B1) was used as a reference bacteriophage for somatic coliphages.

    Techniques: SPR Assay