180,928 research outputs found
KIT mutation analysis in mast cell neoplasms: recommendations of the European competence network on mastocytosis
No full textAlthough acquired mutations in KIT are commonly detected in various categories of mastocytosis, the methodologies applied to detect and quantify the mutant type and allele burden in cells and various tissues are poorly defined. We here propose a consensus on methodologies used to detect KIT mutations in patients with mastocytosis at diagnosis and during follow up with sufficient precision and sensitivity in daily practice. In addition, we provide recommendations for sampling and storage of diagnostic material as well as a robust diagnostic algorithm. Using highly-sensitive assays, KIT D816V can be detected in peripheral blood leukocytes from most patients with systemic mastocytosis (SM) which is a major step forward in screening and SM diagnosis. In addition, the KIT D816V allele burden can be followed quantitatively during the natural course or during therapy. Our recommendations should greatly facilitate diagnostic and follow up investigations in SM in daily practice as well as in clinical trials. In addition, the new tools and algorithms proposed should lead to a more effective screen, early diagnosis of SM, and help to avoid unnecessary referral
denghuilu/deepmd-kit: optimized version of deepmd-kit for CPC
No full textIn order to reproduce the results of the paper "86 PFLOPS Deep Potential Molecular Dynamics simulation of 100 million atoms with ab initio accuracy", please follow the next steps: The following modules must be loaded for the compilation and running of the optimized deepmd-kit code.
cuda/10.1.168 gcc/4.8.5 spectrum-mpi/10.3.1.2-20200121 ibm-wml-ce/1.6.2-2
Install the DeePMD-kit's C++ interface
Download all the dependent packages according to the DOI of the artifacts. Check the download packages:
ls
cub-v2.0.0.zip cutlass-v2.0.1.zip deepmd-kit-v2.2.0.zip lammps-v2.0.0.zip
Then unzip all the packages, and rename them as cub, cutlass, deepmd-kit, and lammps accordingly.
ls
cub cutlass deepmd-kit lammps
For convenience, you may want to record the location of source to a variable, saying deepmd_source_dir by
cd deepmd-kit
deepmd_source_dir=`pwd`
Now, copy the submodules cub and cutlass into the deepmd-kit
cd ../cub
cp -r * deepmd_source_dir/source/op/cuda/cutlass
Now go to the source code directory of DeePMD-kit and make a build place.
cd tensorflow_root -DCMAKE_INSTALL_PREFIX=deepmd_root/lib
libdeepmd.so libdeepmd_op.so libdeepmd_op_cuda.so
Install LAMMPS's DeePMD-kit module
DeePMD-kit provide module for running MD simulation with LAMMPS. Now make the DeePMD-kit module for LAMMPS.
cd lammps. Now go into the LAMMPS code, and copy the DeePMD-kit module like this
cd deepmd_source_dir/source/build/USER-DEEPMD ./
Now build LAMMPS
make yes-kspace
make yes-user-deepmd
make mpi -j4
The option -j4 means using 4 processes in parallel. You may want to use a different number according to your hardware. If everything works fine, you will end up with an executable lmp_mpi.
Reproduce the results
For example, Go to the deepmd_source_dir/test/1_water: Change the system size by change the following line in the file 'water.in': replicate 64 32 32 then change the number of nodes (GPUs/CPUs) and run it.
The following is an example job script:
#!/bin/bash
# Begin LSF Directives
#BSUB -P projectname
#BSUB -W 0:10
#BSUB -nnodes 80
#BSUB -J deepmd
#BSUB -o deepmd.%J
#BSUB -e deepmd.%J
#BSUB -alloc_flags gpudefault
cd LS_SUBCWD
echo lammps/src/lmp_mpi < water.in
Please remember not to include GPU in the resource set when running the CPU version of code
denghuilu/deepmd-kit: baseline version of deepmd-kit for sc20 conference
No full textIn order to reproduce the results of pap183, please follow the next steps:
The following modules must be loaded for the compilation and running of the optimized/baseline deepmd-kit code.
gcc/4.8.5
spectrum-mpi/10.3.1.2-20200121
ibm-wml-ce/1.6.2-2
Install the DeePMD-kit's C++ interface
Download all the dependent packages according to the DOI of the artifacts. Check the download packages:
ls
deepmd-kit-v1.4.0.zip lammps-v2.0.0.zip
Then unzip all the packages, and rename them as deepmd-kit and lammps accordingly.
ls
deepmd-kit lammps
For convenience, you may want to record the location of source to a variable, saying deepmd_source_dir by
cd deepmd-kit
deepmd_source_dir=`pwd`
Now go to the source code directory of DeePMD-kit and make a build place.
cd tensorflow_root -DCMAKE_INSTALL_PREFIX=deepmd_root/lib
libdeepmd.so libdeepmd_op.so
Install LAMMPS's DeePMD-kit module
DeePMD-kit provide module for running MD simulation with LAMMPS. Now make the DeePMD-kit module for LAMMPS.
cd lammps. Now go into the LAMMPS code and copy the DeePMD-kit module like this
cd deepmd_source_dir/source/build/USER-DEEPMD ./
Now build LAMMPS
make yes-kspace
make yes-user-deepmd
make mpi -j4
The option -j4 means using 4 processes in parallel. You may want to use a different number according to your hardware.
If everything works fine, you will end up with an executable lmp_mpi.
Reproduce the results
For example, Go to the deepmd_source_dir/test/1_water:
Change the system size by change the following line in the file 'water.in':
replicate 64 32 32
then change the number of nodes (GPUs/CPUs) and run it.
The following is an example job script:
#!/bin/bash
# Begin LSF Directives
#BSUB -P projectname
#BSUB -W 0:10
#BSUB -nnodes 80
#BSUB -J deepmd
#BSUB -o deepmd.%J
#BSUB -e deepmd.%J
#BSUB -alloc_flags gpudefault
cd LS_SUBCWD
echo lammps/src/lmp_mpi < water.in
Please remember not to include GPU in the resource set when running the CPU version of cod
G-quadruplexes: Kinetic stability and effects on the c-KIT promoter
No full textIn addition to the famous Watson & Crick model for B-form duplex DNA, guanine-rich DNA sequences can self-assemble under certain conditions to form a four-stranded structure known as a G-quadruplex. G-quadruplexes are composed of stacks of Gquartets, in which four guanines are arranged in a square planar array, interacting via eight hydrogen bonds. Monovalent cations especially K+ and Na+ but not Li+ stabilize this structure by binding with the central carbonyl O6 atoms. Bioinformatic databases have revealed potential quadruplex-forming sequences throughout the genome and tandem repeats of guanines are found to accumulate upstream of the transcription initiation site of several proto-oncogenes. The promoter region of the c-kit proto-oncogene contains two potential quadruplex forming sequences. The first part of this work focuses on understanding how the c-kit promoter is regulated by potential G-quadruplex forming structures. We have incorporated 165 base pairs of the c-kit promoter region into a luciferase reporter vector and have constructed several mutant variants of this sequence. Determining the level of luciferase expression of these constructed vectors in HeLa and HCT 116 cells have allowed us to elucidate the effect of quadruplex formation on gene expression. Our results reveal that a decrease in gene expression level is observed from the constructed vectors that carry a very stable quadruplex-forming sequence. In genomic DNA, these putative quadruplex-forming G-rich sequences are normally base paired with their complementary C-rich strands to generate duplex DNA. Structural transitions of B-form DNA (duplex) to non-B-form DNA (quadruplex) require local melting, which is facilitated by negative superhelical tension. We have examined in vitro the effect of DNA supercoiling on the reaction of the c-kit promoter (and some variants of the natural sequences) with three chemical probes KMnO4, DEPC, and DMS. The results demonstrated that negative superhelicity did not significantly affect the formation of G-quadruplex. For the first time, we have used two-dimensional agarose gel electrophoresis to probe topology-dependent structural transitions in the c-kit promoter and some of its modified versions. Our results showed that the constructed vectors that carried the very stable quadruplex-forming sequence undergo unusual structural transition. Finally, we have used a gel based assay to understand the dynamic equilibrium between quadruplex and duplex DNA under defined conditions. The results show that at elevated temperatures, the formation of duplex DNA with these G-rich sequences is kinetically reversible and we have measured the rate at which the duplex strand exchanges with single-stranded DNA. The formation of both quadruplex and duplex DNA are cation and concentration-dependent
Breves notas para um só lado do dínamo: O kit de sobrevivência do descobridor português no mundo anticolonial, de Patrícia Lino / Brief Notes Towards Only One Side of the Dynamum: Patricia Lino’s O kit de sobrevivência do descobridor português no mundo anticolonial
No full textLINO, Patrícia. O kit de sobrevivência do descobridor português no mundo anticolonial. Lisboa: Douda Correria, 2020
Automated detection of slum area change in Hyderabad, India using multitemporal satellite imagery
No full textThis paper presents an approach to automated identification of slum area change patterns in Hyderabad, India, using multi-year and multi-sensor very high resolution satellite imagery. It relies upon a lacunarity-based slum detection algorithm, combined with Canny- and LSD-based imagery pre-processing routines. This method outputs plausible and spatially explicit slum locations for the whole urban agglomeration of Hyderabad in years 2003 and 2010. The results indicate a considerable growth of area occupied by slums between these years and allow identification of trends in slum development in this urban agglomeration
Variations on the Author
No full text“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
O kit ordenha.
No full textEsta publicação apresenta as orientações necessárias para o uso correto do kit ordenha
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Targeted knockdown of canine KIT (stem cell factor receptor) using small interfering RNA
No full text- …
