135 research outputs found
Data processing model for the CDF experiment
The data processing model for the CDF experiment is described. Data
processing reconstructs events from parallel data streams taken with different
combinations of physics event triggers and further splits the events into
datasets of specialized physics datasets. The design of the processing control
system faces strict requirements on bookkeeping records, which trace the status
of data files and event contents during processing and storage. The computing
architecture was updated to meet the mass data flow of the Run II data
collection, recently upgraded to a maximum rate of 40 MByte/sec. The data
processing facility consists of a large cluster of Linux computers with data
movement managed by the CDF data handling system to a multi-petaByte Enstore
tape library. The latest processing cycle has achieved a stable speed of 35
MByte/sec (3 TByte/day). It can be readily scaled by increasing CPU and
data-handling capacity as required.Comment: 12 pages, 10 figures, submitted to IEEE-TN
Data production models for the CDF experiment
The data production for the CDF experiment is conducted on a large Linux PC
farm designed to meet the needs of data collection at a maximum rate of 40
MByte/sec. We present two data production models that exploits advances in
computing and communication technology. The first production farm is a
centralized system that has achieved a stable data processing rate of
approximately 2 TByte per day. The recently upgraded farm is migrated to the
SAM (Sequential Access to data via Metadata) data handling system. The software
and hardware of the CDF production farms has been successful in providing large
computing and data throughput capacity to the experiment.Comment: 8 pages, 9 figures; presented at HPC Asia2005, Beijing, China, Nov 30
- Dec 3, 200
Cancer-associated fibroblasts promote aggressive gastric cancer phenotypes via heat shock factor 1-mediated secretion of extracellular vesicles
Hierarchical colour image segmentation by leveraging RGB channels independently
In this paper, we introduce a hierarchical colour image segmentation based on cuboid partitioning using simple statistical features of the pixel intensities in the RGB channels. Estimating the difference between any two colours is a challenging task. As most of the colour models are not perceptually uniform, investigation of an alternative strategy is highly demanding. To address this issue, for our proposed technique, we present a new concept for colour distance measure based on the inconsistency of pixel intensities of an image which is more compliant to human perception. Constructing a reliable set of superpixels from an image is fundamental for further merging. As cuboid partitioning is a superior candidate to produce superpixels, we use the agglomerative merging to yield the final segmentation results exploiting the outcome of our proposed cuboid partitioning. The proposed cuboid segmentation based algorithm significantly outperforms not only the quadtree-based segmentation but also existing state-of-the-art segmentation algorithms in terms of quality of segmentation for the benchmark datasets used in image segmentation. © 2019, Springer Nature Switzerland AG
Predicting the protein-protein interactions using primary structures with predicted protein surface
<p>Abstract</p> <p>Background</p> <p>Many biological functions involve various protein-protein interactions (PPIs). Elucidating such interactions is crucial for understanding general principles of cellular systems. Previous studies have shown the potential of predicting PPIs based on only sequence information. Compared to approaches that require other auxiliary information, these sequence-based approaches can be applied to a broader range of applications.</p> <p>Results</p> <p>This study presents a novel sequence-based method based on the assumption that protein-protein interactions are more related to amino acids at the surface than those at the core. The present method considers surface information and maintains the advantage of relying on only sequence data by including an accessible surface area (ASA) predictor recently proposed by the authors. This study also reports the experiments conducted to evaluate a) the performance of PPI prediction achieved by including the predicted surface and b) the quality of the predicted surface in comparison with the surface obtained from structures. The experimental results show that surface information helps to predict interacting protein pairs. Furthermore, the prediction performance achieved by using the surface estimated with the ASA predictor is close to that using the surface obtained from protein structures.</p> <p>Conclusion</p> <p>This work presents a sequence-based method that takes into account surface information for predicting PPIs. The proposed procedure of surface identification improves the prediction performance with an <it>F-measure </it>of 5.1%. The extracted surfaces are also valuable in other biomedical applications that require similar information.</p
Severe Exercise and Exercise Training Exert Opposite Effects on Human Neutrophil Apoptosis via Altering the Redox Status
Neutrophil spontaneous apoptosis, a process crucial for immune regulation, is mainly controlled by alterations in reactive oxygen species (ROS) and mitochondria integrity. Exercise has been proposed to be a physiological way to modulate immunity; while acute severe exercise (ASE) usually impedes immunity, chronic moderate exercise (CME) improves it. This study aimed to investigate whether and how ASE and CME oppositely regulate human neutrophil apoptosis. Thirteen sedentary young males underwent an initial ASE and were subsequently divided into exercise and control groups. The exercise group (n = 8) underwent 2 months of CME followed by 2 months of detraining. Additional ASE paradigms were performed at the end of each month. Neutrophils were isolated from blood specimens drawn at rest and immediately after each ASE for assaying neutrophil spontaneous apoptosis (annexin-V binding on the outer surface) along with redox-related parameters and mitochondria-related parameters. Our results showed that i) the initial ASE immediately increased the oxidative stress (cytosolic ROS and glutathione oxidation), and sequentially accelerated the reduction of mitochondrial membrane potential, the surface binding of annexin-V, and the generation of mitochondrial ROS; ii) CME upregulated glutathione level, retarded spontaneous apoptosis and delayed mitochondria deterioration; iii) most effects of CME were unchanged after detraining; and iv) CME blocked ASE effects and this capability remained intact even after detraining. Furthermore, the ASE effects on neutrophil spontaneous apoptosis were mimicked by adding exogenous H2O2, but not by suppressing mitochondrial membrane potential. In conclusion, while ASE induced an oxidative state and resulted in acceleration of human neutrophil apoptosis, CME delayed neutrophil apoptosis by maintaining a reduced state for long periods of time even after detraining
Measurement of the mass difference m(D-s(+))-m(D+) at CDF II
We present a measurement of the mass difference m(D-s(+))-m(D+), where both the D-s(+) and D+ are reconstructed in the phipi(+) decay channel. This measurement uses 11.6 pb(-1) of data collected by CDF II using the new displaced-track trigger. The mass difference is found to be m(D-s(+))-m(D+)=99.41+/-0.38(stat)+/-0.21(syst) MeV/c(2)
Enhanced 2,3-butanediol production from biodiesel-derived glycerol by engineering of cofactor regeneration and manipulating carbon flux in Bacillus amyloliquefaciens
Search for a Very Light CP-Odd Higgs Boson in Top Quark Decays from p(p)over-bar Collisions at root s=1.96 TeV
We present the results of a search for a very light CP-odd Higgs boson a(1)(0) originating from top quark decays t -> H(+/-)b -> W-+/-(*) a(1)(0)b, and subsequently decaying into tau(+)tau(-). Using a data sample corresponding to an integrated luminosity of 2.7 fb(-1) collected by the CDF II detector in p (p) over bar collisions at 1.96 TeV, we perform a search for events containing a lepton, three or more jets, and an additional isolated track with transverse momentum in the range 3 to 20 GeV/c. Observed events are consistent with background sources, and 95% C.L. limits are set on the branching ratio of t -> H(+/-)b for various masses of H-+/- and a(1)(0)
- …