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排序方式: 共有408条查询结果,搜索用时 10 毫秒
1.
Berthold Lausen Torsten Hothorn Frank Bretz Martin Schumacher 《Biometrical journal. Biometrische Zeitschrift》2004,46(3):364-374
The identification and assessment of prognostic factors is one of the major tasks in clinical research. The assessment of one single prognostic factor can be done by recently established methods for using optimal cutpoints. Here, we suggest a method to consider an optimal selected prognostic factor from a set of prognostic factors of interest. This can be viewed as a variable selection method and is the underlying decision problem at each node of various tree building algorithms. We propose to use maximally selected statistics where the selection is defined over the set of prognostic factors and over all cutpoints in each prognostic factor. We demonstrate that it is feasible to compute the approximate null distribution. We illustrate the new variable selection test with data of the German Breast Cancer Study Group and of a small study on patients with diffuse large B‐cell lymphoma. Using the null distribution for a p‐value adjusted regression trees algorithm, we adjust for the number of variables analysed at each node as well. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) 相似文献
2.
N. A. Tchurikov 《Genetica》1992,87(2):113-117
Based on both the occurrence of families of DNA sequences complementary in the same direction in different genomes and the physical possibility of DNA forming a parallel double helix, we postulate an unusual enzymatic synthesis of parallel DNA on a DNA template from its 5-end. We discuss the assumed evolutionary aspects of this problem and suggest ways to check the hypothesis. 相似文献
3.
随着分子生物信息数据量高速增长,生物信息学面临着大规模、高通量、密集型计算的巨大挑战。为有效利用计算机资源,缩短高通量生物信息计算程序执行时间,我们基于Globus Toolkit网格中间件,实现了一个支持高通量生物数据计算的网格系统(Biological Data Computing Grid,简称BDCGrid)。BDCGrid计算网格系统模型可以有效整合中小型生物信息学实验室计算机资源,大大缩短高通量生物信息计算程序执行时间,为相关研究人员利用现有计算机资源处理大规模、高通量生物信息计算任务提供一种新的途径。 相似文献
4.
Baomin Xu Jin GaoChunyan Li 《Biochemical and biophysical research communications》2012,426(3):395-398
Fragment assembly is one of the most important problems of sequence assembly. Algorithms for DNA fragment assembly using de Bruijn graph have been widely used. These algorithms require a large amount of memory and running time to build the de Bruijn graph. Another drawback of the conventional de Bruijn approach is the loss of information. To overcome these shortcomings, this paper proposes a parallel strategy to construct de Bruijin graph. Its main characteristic is to avoid the division of de Bruijin graph. A novel fragment assembly algorithm based on our parallel strategy is implemented in the MapReduce framework. The experimental results show that the parallel strategy can effectively improve the computational efficiency and remove the memory limitations of the assembly algorithm based on Euler superpath. This paper provides a useful attempt to the assembly of large-scale genome sequence using Cloud Computing. 相似文献
5.
MOSIX is a cluster management system that supports preemptive process migration. This paper presents the MOSIX Direct File System Access (DFSA), a provision that can improve the performance of cluster file systems by allowing a migrated process to directly access files in its current location. This capability, when combined with an appropriate file system, could substantially increase the I/O performance and reduce the network congestion by migrating an I/O intensive process to a file server rather than the traditional way of bringing the file's data to the process. DFSA is suitable for clusters that manage a pool of shared disks among multiple machines. With DFSA, it is possible to migrate parallel processes from a client node to file servers for parallel access to different files. Any consistent file system can be adjusted to work with DFSA. To test its performance, we developed the MOSIX File-System (MFS) which allows consistent parallel operations on different files. The paper describes DFSA and presents the performance of MFS with and without DFSA. 相似文献
6.
Zhi-Hui Su Osamu Tominaga Takeshi Ohama Eiji Kajiwara Ryoshuke Ishikawa Tokindo S. Okada Keiko Nakamura Syozo Osawa 《Journal of molecular evolution》1996,43(6):662-671
Molecular phylogenetic analyses using mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequences representing all 15 species and the majority of subspecies or races of theOhomopterus ground beetles from all over the Japanese archipelago have uncovered a remarkable evolutionary history. Clustering of the species in the molecular phylogenetic tree is linked to their geographic distribution and does not correlate with morphological characters. Taxonomically the same species or the members belonging to the same species-group fall out in more than two different places on the ND5 tree. Evidence has been presented against a possible participation of ancestral polymorphism and random lineage sorting or of hybrid individuals for the observed distribution of mitochondrial DNA haplotypes. The most plausible explanation of our results is that parallel evolution took place in different lineages. Most notably,O. dehaanii, O. yaconinus, andO. japonicus in a lineage reveal almost identical morphology with those of the same species (or subspecies) but belonging to the phylogenetically remote lineages.The nucleotide sequence data reported in this paper will appear in the DDBJ, EMBL, and GenBank nucleotide sequence databases with accession numbers D50711-DD-50733 and D87131-D87186. 相似文献
7.
Von H. Zwölfer J. Herbst 《Journal of Zoological Systematics and Evolutionary Research》1988,26(5):320-340
Preadaptation, host shifts and parallel cladogenesis in the evolution of phytophagous insects In this contribution we investigate the possibilities to apply concepts developed for the evolution of animal parasites to insect-plant systems. We compare host parasite systems in animals with plant-herbivore systems and list similarities and differences. The terms preadaptation, predisposition, expansion and contraction of host ranges, and parallel cladogenesis are discussed. We enumerate general preadaptations for the evolution of herbivory in insects and preadaptations for shifts between herbivory and entomophagy. Examples are given for expansions of host ranges based on phytochemical or structural characters of host plants. Cases of parallel cladogenesis in herbivoreparasitoid systems and plant-herbivore systems are compiled from the literature. An analysis of the insect fauna of the “thistles” (Cynaroideae) in the Palearctic and Nearctic demonstrates the importance of the evolutionary history of the plant taxa and of the existence of preadapted pools of herbivores for the evolution of guilds of specialized herbivores. The members of the Curculionid taxon Cleoninae provide examples for multiple colonizations and radiations of herbivores on the Cynaroideae. The taxonomic and biological relationships of the weevil genera Rhinocyllus, Bangasternus and Larinus which exploit the flower heads of Cynaroideae, can be interpreted as result of a basic parallel cladogenesis between herbivore and host. A gelelectrophoretic analysis of Larinus spp. supports this hypothesis. 相似文献
8.
《基因组蛋白质组与生物信息学报(英文版)》2020,18(2):104-119
To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000. 相似文献
9.
Maximum Likelihood (ML) method has an excellent performance for Direction-Of-Arrival (DOA) estimation, but a multidimensional nonlinear solution search is required which complicates the computation and prevents the method from practical use. To reduce the high computational burden of ML method and make it more suitable to engineering applications, we apply the Artificial Bee Colony (ABC) algorithm to maximize the likelihood function for DOA estimation. As a recently proposed bio-inspired computing algorithm, ABC algorithm is originally used to optimize multivariable functions by imitating the behavior of bee colony finding excellent nectar sources in the nature environment. It offers an excellent alternative to the conventional methods in ML-DOA estimation. The performance of ABC-based ML and other popular meta-heuristic-based ML methods for DOA estimation are compared for various scenarios of convergence, Signal-to-Noise Ratio (SNR), and number of iterations. The computation loads of ABC-based ML and the conventional ML methods for DOA estimation are also investigated. Simulation results demonstrate that the proposed ABC based method is more efficient in computation and statistical performance than other ML-based DOA estimation methods. 相似文献
10.
While aggregating the throughput of existing disks on cluster nodes is a cost-effective approach to alleviate the I/O bottleneck
in cluster computing, this approach suffers from potential performance degradations due to contentions for shared resources
on the same node between storage data processing and user task computation. This paper proposes to judiciously utilize the
storage redundancy in the form of mirroring existed in a RAID-10 style file system to alleviate this performance degradation.
More specifically, a heuristic scheduling algorithm is developed, motivated from the observations of a simple cluster configuration,
to spatially schedule write operations on the nodes with less load among each mirroring pair. The duplication of modified
data to the mirroring nodes is performed asynchronously in the background. The read performance is improved by two techniques:
doubling the degree of parallelism and hot-spot skipping. A synthetic benchmark is used to evaluate these algorithms in a
real cluster environment and the proposed algorithms are shown to be very effective in performance enhancement.
Yifeng Zhu received his B.Sc. degree in Electrical Engineering in 1998 from Huazhong University of Science and Technology, Wuhan, China;
the M.S. and Ph.D. degree in Computer Science from University of Nebraska – Lincoln in 2002 and 2005 respectively. He is an
assistant professor in the Electrical and Computer Engineering department at University of Maine. His main research interests
are cluster computing, grid computing, computer architecture and systems, and parallel I/O storage systems. Dr. Zhu is a Member
of ACM, IEEE, the IEEE Computer Society, and the Francis Crowe Society.
Hong Jiang received the B.Sc. degree in Computer Engineering in 1982 from Huazhong University of Science and Technology, Wuhan, China;
the M.A.Sc. degree in Computer Engineering in 1987 from the University of Toronto, Toronto, Canada; and the PhD degree in
Computer Science in 1991 from the Texas A&M University, College Station, Texas, USA. Since August 1991 he has been at the
University of Nebraska-Lincoln, Lincoln, Nebraska, USA, where he is Professor and Vice Chair in the Department of Computer
Science and Engineering. His present research interests are computer architecture, parallel/distributed computing, cluster
and Grid computing, computer storage systems and parallel I/O, performance evaluation, real-time systems, middleware, and
distributed systems for distance education. He has over 100 publications in major journals and international Conferences in
these areas and his research has been supported by NSF, DOD and the State of Nebraska. Dr. Jiang is a Member of ACM, the IEEE
Computer Society, and the ACM SIGARCH.
Xiao Qin received the BS and MS degrees in computer science from Huazhong University of Science and Technology in 1992 and 1999, respectively.
He received the PhD degree in computer science from the University of Nebraska-Lincoln in 2004. Currently, he is an assistant
professor in the department of computer science at the New Mexico Institute of Mining and Technology. He had served as a subject
area editor of IEEE Distributed System Online (2000–2001). His research interests are in parallel and distributed systems, storage systems, real-time computing, performance
evaluation, and fault-tolerance. He is a member of the IEEE.
Dan Feng received the Ph.D degree from Huazhong University of Science and Technology, Wuhan, China, in 1997. She is currently a professor
of School of Computer, Huazhong University of Science and Technology, Wuhan, China. She is the principal scientist of the
the National Grand Fundamental Research 973 Program of China “Research on the organization and key technologies of the Storage
System on the next generation Internet.” Her research interests include computer architecture, storage system, parallel I/O,
massive storage and performance evaluation.
David Swanson received a Ph.D. in physical (computational) chemistry at the University of Nebraska-Lincoln (UNL) in 1995, after which he
worked as an NSF-NATO postdoctoral fellow at the Technical University of Wroclaw, Poland, in 1996, and subsequently as a National
Research Council Research Associate at the Naval Research Laboratory in Washington, DC, from 1997–1998. In 1999 he returned
to UNL where he directs the Research Computing Facility and currently serves as an Assistant Research Professor in the Department
of Computer Science and Engineering. The Office of Naval Research, the National Science Foundation, and the State of Nebraska
have supported his research in areas such as large-scale scientific simulation and distributed systems. 相似文献