| 1. |
- Shi, Leming, et al.
(författare)
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The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
- 2010
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Ingår i: Nature Biotechnology. - 1087-0156. ; 28:8, s. 827-838
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Tidskriftsartikel (refereegranskat)abstract
- Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total, >30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis.
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| 2. |
- Chasman, Daniel I., et al.
(författare)
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Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function
- 2012
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Ingår i: Human Molecular Genetics. - 0964-6906. ; 21:24, s. 5329-5343
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Tidskriftsartikel (refereegranskat)abstract
- In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P 5.6 10(9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 10(4)2.2 10(7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.
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| 3. |
- Huang, Daming, et al.
(författare)
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A Modified Charge-Pumping Method for the Characterization of Interface-Trap Generation in MOSFETs
- 2009
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Ingår i: IEEE Transactions on Electron Devices. - 0018-9383. ; 56:2, s. 267-274
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Tidskriftsartikel (refereegranskat)abstract
- A novel recovery-free interface-trap measurement method is presented in detail. This method is the modification of the conventional charge pumping (CP) by extending the pulse low level to the stress-bias and minimizing the pulse high-level duty cycle to suppress the recovery effect. The method is applied to study the negative-bias temperature instability in p-MOSFETs. As compared with the conventional CP, a much larger interface-trap generation under stress is observed by the new method. A power law time dependence (similar to t(n)) of interface-trap generation is observed. The index n. is less than that derived from conventional CP and increases with temperature, demonstrating a dispersive process involved in the trap generation dynamics.
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| 4. |
- Hudson, Thomas J., et al.
(författare)
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International network of cancer genome projects
- 2010
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Ingår i: Nature. - Nature Publishing Group. - 0028-0836. ; 464:7291, s. 993-998
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Tidskriftsartikel (refereegranskat)abstract
- The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
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| 5. |
- Khan, Salman Naeem, et al.
(författare)
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Optimal design for a flat-top AWG demultiplexer by using a fast calculation method based on a Gaussian beam approximation
- 2006
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Ingår i: Optics Communications. - 0030-4018. ; 262:2, s. 175-179
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Tidskriftsartikel (refereegranskat)abstract
- Passband broadening of an AWG (array waveguide grating) demultiplexer with an MMI (multimode interference) coupler connected at the end of a tapered input waveguide is considered. An explicit formula based on the field propagation of an approximate Hermit-Gaussian beam is used to calculate quickly and reliably the spectral response of the AWG demultiplexer. The widths of the input waveguide, the output waveguides and the MMI coupler are optimized. The optimal design is verified with the experimental measurement.
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| 6. |
- Liu, Jin-ming, et al.
(författare)
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Mid-term effects of lung volume reduction surgery on pulmonary function in patients with chronic obstructive pulmonary disease
- 2007
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Ingår i: Chinese Medical Journal. - Chinese Medical Association. - 0366-6999. ; 120:8, s. 658-662
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Tidskriftsartikel (refereegranskat)abstract
- Background Now lung volume reduction surgery (LVRS) has become one of the most effective methods for the management of some cases of severe chronic obstructive pulmonary disease (COPD). We evaluated the mid-term effects of LVRS on pulmonary function in patients with severe COPD. Methods Ten male patients with severe COPD aged 38-70 years underwent LVRS and their pulmonary function was assessed before, 3 months and 3 years after surgery. The spirometric and gas exchange parameters included residual volume, total lung capacity, inspiratory capacity, forced vital capacity, forced expiratory volume in one second, diffusion capacity for CO, and arterial blood gas. A 6-minute walk distance (6MWD) test was performed. Results As to preoperative assessment, most spirometric parameters and 6MWD were significantly improved after 3 months and slightly 3 years after LVRS. Gas exchange parameters were significantly improved 3 months after surgery, but returned to the preoperative levels after 3 years. Conclusions LVRS may significantly improve pulmonary function in patients with severe COPD indicating for LVRS. Mid-term pulmonary function 3 years after surgery can be decreased to the level at 3 months after surgery. Three years after LVRS, lung volume and pulmonary ventilation function can be significantly improved, but the improvement in gas exchange function was not significant.
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| 7. |
- Liu, Ming, et al.
(författare)
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A High-End Reconfigurable Computation Platform for Nuclear and Particle Physics Experiments
- 2011
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Ingår i: Computing in science & engineering (Print). - 1521-9615. ; 13:2, s. 52-63
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Tidskriftsartikel (refereegranskat)abstract
- A high-performance computation platform based on field-programmable gate arrays targets nuclear and particle physics experiment applications. The system can be constructed or scaled into a supercomputer-equivalent size for detector data processing by inserting compute nodes into advanced telecommunications computing architecture (ATCA) crates. Among the case study results are that one ATCA crate can provide a computation capability equivalent to hundreds of commodity PCs for Hades online particle track reconstruction and Cherenkov ring recognition.
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| 8. |
- Liu, Ming, et al.
(författare)
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ATCA-based Computation Platform for Data Acquisition and Triggering in Particle Physics Experiments
- 2008
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Ingår i: 2008 INTERNATIONAL CONFERENCE ON FIELD PROGRAMMABLE AND LOGIC APPLICATIONS, VOLS 1 AND 2. ; s. 287-292
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Konferensbidrag (refereegranskat)abstract
- An ATCA-based computation platform for data acquisition and trigger applications in nuclear and particle physics experiments has been developed. Each Compute Node (CN) which appears as a Field Replaceable Unit (FRU) in an ATCA shelf, features 5 Xilinx Virtex-4 FX60 FPGAs and up to 10 GBytes DDR2 memory. Connectivity is provided with 8 optical links and 5 Gigabit Ethernet ports, which are mounted on each board to receive data from detectors and forward results to outer shelves or PC farms with attached mass storage. Fast point-to-point on-board interconnections between FPGAs as well as the full-mesh shelf backplane provide flexibility and high bandwidth to partition algorithms and correlate results among them. The system represents a highly reconfigurable and scalable solution for multiple applications.
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| 9. |
- Liu, Ming, et al.
(författare)
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Hardware/Software co-design of a general-purpose computation platform in particle physics
- 2007
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Ingår i: ICFPT 2007 : International Conference On Field-Programmable Technology, Proceedings. - 978-1-4244-1471-0 ; s. 177-183
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Konferensbidrag (refereegranskat)abstract
- In this paper we present a hardware/software co-design based computation platform for online data processing in particle physics experiments. Our goal is to ease and accelerate the development and make it universal and scalable for multiple applications, on the premise of guaranteeing high communicating and processing capabilities. The entire computation network consists of quite a few interconnected compute nodes, each of which has multiple FPGAs to implement specific algorithms for data processing. High-speed communication features including RocketIO multi-gigabit transceiver and Gigabit Ethernet are supported by FPGAs to construct internal and external connections. An embedded Linux operating system is fitted on the PowerPC CPU core inside the Xilinx Virtex-4 FX FPGA. Thus programmers can access hardware resources via device drivers and write application programs to manage the system from the high level. Furthermore measurements have been executed using the development board to investigate both communicating and processing performances of the system. Results show that the computation platform is able to communicate at a UDP/IP data rate of around 400 Mbps per Ethernet link, and the event selection engine could process an event rate of 25%.
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| 10. |
- Liu, Ming, et al.
(författare)
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Trigger algorithm development on FPGA-based Compute Nodes
- 2009
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Ingår i: 2009 16th IEEE-NPSS Real Time Conference. - New York : IEEE. - 978-1-4244-5796-0 ; s. 478-484
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Konferensbidrag (refereegranskat)abstract
- Based on the ATCA computation architecture and Compute Nodes (CN), investigation and implementation work has been being executed for HADES and PANDA trigger algorithms. We present our designs for HADES track reconstruction processing, Cherenkov ring recognition, Time-Of-Flight processing, electromagnetic shower recognition.. and the PANDA straw tube tracking algorithm. They will appear as co-processors in the uniform system design to undertake the detector-specific computing. The algorithm principles will be explained and hardware designs are described in the paper. The current progress reveals the feasibility to implement these algorithms on FPGAs. Also experimental results demonstrate the performance speedup when compared to alternative software solutions, as well as the potential capability of high-speed parallel/pipelined processing in Data Acquisition and Trigger systems.
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