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  • Articles  (10)
  • 2015-2019  (10)
  • Computer Science  (10)
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  • Articles  (10)
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  • 1
    Publication Date: 2015-06-02
    Description: Environment reconstruction is to rebuild the physical environment in the cyberspace using the sensory data collected by sensor networks, which is a fundamental method for human to understand the physical world in depth. A lot of basic scientific work such as nature discovery and organic evolution heavily relies on the environment reconstruction. However, gathering large amount of environmental data costs huge energy and storage space. The shortage of energy and storage resources has become a major problem in sensor networks for environment reconstruction applications. Motivated by exploiting the inherent feature of environmental data, in this paper, we design a novel data gathering protocol based on compressive sensing theory and time series analysis to further improve the resource efficiency. This protocol adapts the duty cycle and sensing probability of every sensor node according to the dynamic environment, which cannot only guarantee the reconstruction accuracy, but also save energy and storage resources. We implement the proposed protocol on a 51-node testbed and conduct the simulations based on three real datasets from Intel Indoor, GreenOrbs and Ocean Sense projects. Both the experiment and simulation performances demonstrate that our method significantly outperforms the conventional methods in terms of resource efficiency and reconstruction accuracy.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 2
    Publication Date: 2016-06-01
    Description: : Identifying chemical probes or seeking scaffolds for a specific biological target is important for protein function studies. Therefore, we create the Annotated Scaffold Database (ASDB), a computer-readable and systematic target-annotated scaffold database, to serve such needs. The scaffolds in ASDB were derived from public databases including ChEMBL, DrugBank and TCMSP, with a scaffold-based classification approach. Each scaffold was assigned with an InChIKey as its unique identifier, energy-minimized 3D conformations, and other calculated properties. A scaffold is also associated with drugs, natural products, drug targets and medical indications. The database can be retrieved through text or structure query tools. ASDB collects 333 601 scaffolds, which are associated with 4368 targets. The scaffolds consist of 3032 scaffolds derived from drugs and 5163 scaffolds derived from natural products. For given scaffolds, scaffold-target networks can be generated from the database to demonstrate the relations of scaffolds and targets. Availability and implementation: ASDB is freely available at http://www.rcdd.org.cn/asdb/ with the major web browsers. Contact: junxu@biochemomes.com or xujun9@mail.sysu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 3
    Publication Date: 2015-11-21
    Description: Despite appearing featureless to our eyes, the open ocean is a highly variable environment for polarization-sensitive viewers. Dynamic visual backgrounds coupled with predator encounters from all possible directions make this habitat one of the most challenging for camouflage. We tested open-ocean crypsis in nature by collecting more than 1500 videopolarimetry measurements from live fish from distinct habitats under a variety of viewing conditions. Open-ocean fish species exhibited camouflage that was superior to that of both nearshore fish and mirrorlike surfaces, with significantly higher crypsis at angles associated with predator detection and pursuit. Histological measurements revealed that specific arrangements of reflective guanine platelets in the fish's skin produce angle-dependent polarization modifications for polarocrypsis in the open ocean, suggesting a mechanism for natural selection to shape reflectance properties in this complex environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brady, Parrish C -- Gilerson, Alexander A -- Kattawar, George W -- Sullivan, James M -- Twardowski, Michael S -- Dierssen, Heidi M -- Gao, Meng -- Travis, Kort -- Etheredge, Robert Ian -- Tonizzo, Alberto -- Ibrahim, Amir -- Carrizo, Carlos -- Gu, Yalong -- Russell, Brandon J -- Mislinski, Kathryn -- Zhao, Shulei -- Cummings, Molly E -- New York, N.Y. -- Science. 2015 Nov 20;350(6263):965-9. doi: 10.1126/science.aad5284. Epub 2015 Nov 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Biology, University of Texas, Austin, TX 78712, USA. ; Optical Remote Sensing Laboratory, the City College of New York-CUNY, New York, NY 10031, USA. ; Department of Physics and Astronomy and Institute for Quantum Science and Engineering, Texas A&M University, College Station, TX 77843-4242, USA. ; Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL 34946, USA. ; Department of Marine Sciences, University of Connecticut Avery Point, 1080 Shennecossett Road, Groton, CT 06340-6048, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26586762" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Mimicry ; Blood Platelets/cytology ; Ecosystem ; Fishes/*physiology ; Oceans and Seas ; Predatory Behavior ; *Selection, Genetic ; Skin/anatomy & histology/blood supply ; Vision, Ocular
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2015-09-19
    Description: The enhancement of the functional properties of materials at reduced dimensions is crucial for continuous advancements in nanoelectronic applications. Here, we report that the scale reduction leads to the emergence of an important functional property, ferroelectricity, challenging the long-standing notion that ferroelectricity is inevitably suppressed at the scale of a few nanometers. A combination of theoretical calculations, electrical measurements, and structural analyses provides evidence of room-temperature ferroelectricity in strain-free epitaxial nanometer-thick films of otherwise nonferroelectric strontium titanate (SrTiO3). We show that electrically induced alignment of naturally existing polar nanoregions is responsible for the appearance of a stable net ferroelectric polarization in these films. This finding can be useful for the development of low-dimensional material systems with enhanced functional properties relevant to emerging nanoelectronic devices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, D -- Lu, H -- Gu, Y -- Choi, S-Y -- Li, S-D -- Ryu, S -- Paudel, T R -- Song, K -- Mikheev, E -- Lee, S -- Stemmer, S -- Tenne, D A -- Oh, S H -- Tsymbal, E Y -- Wu, X -- Chen, L-Q -- Gruverman, A -- Eom, C B -- New York, N.Y. -- Science. 2015 Sep 18;349(6254):1314-7. doi: 10.1126/science.aaa6442.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA. ; Department of Physics and Astronomy and Nebraska Center for Materials and Nanoscience, University of Nebraska, Lincoln, NE 68588, USA. ; Department of Materials Science and Engineering, Pennsylvania State University, University Park, PA 16802 USA. ; Department of Materials Modeling and Characterization, Korea Institute of Materials Science, Changwon 642-831, Korea. ; Department of Physics, Temple University, Philadelphia, PA 19122, USA. ; Department of Materials Science and Engineering, Pohang University of Science and Technology, Pohang 790-784, Korea. ; Materials Department, University of California-Santa Barbara, Santa Barbara, CA 93106-5050, USA. ; Department of Physics, Boise State University, Boise, ID 83725-1570, USA. ; Department of Physics and Astronomy and Nebraska Center for Materials and Nanoscience, University of Nebraska, Lincoln, NE 68588, USA. agruverman2@unl.edu eom@engr.wisc.edu. ; Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA. agruverman2@unl.edu eom@engr.wisc.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26383947" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2016-07-30
    Description: Motivation: The sequences among subgenomes in a polyploid species have high similarity, making it difficult to design genome-specific primers for sequence analysis. Results: We present GSP, a web-based platform to design genome-specific primers that distinguish subgenome sequences in a polyploid genome. GSP uses BLAST to extract homeologous sequences of the subgenomes in existing databases, performs a multiple sequence alignment, and design primers based on sequence variants in the alignment. An interactive primers diagram, a sequence alignment viewer and a virtual electrophoresis are displayed as parts of the primer design result. GSP also designs specific primers from multiple sequences uploaded by users. Availability and implementation: GSP is a user-friendly and efficient web platform freely accessible at http://probes.pw.usda.gov/GSP . Source code and command-line application are available at https://github.com/bioinfogenome/GSP . Contacts: yong.gu@ars.usda.gov or devin.coleman-derr@ars.usda.gov Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 2016-01-21
    Description: Current pathway analysis approaches are primarily dedicated to capturing deregulated pathways at the population level and cannot provide patient-specific pathway deregulation information. In this article, the authors present a simple approach, called individPath, to detect pathways with significantly disrupted intra-pathway relative expression orderings for each disease sample compared with the stable, normal intra-pathway relative expression orderings pre-determined in previously accumulated normal samples. Through the analysis of multiple microarray data sets for lung and breast cancer, the authors demonstrate individPath's effectiveness for detecting cancer-associated pathways with disrupted relative expression orderings at the individual level and dissecting the heterogeneity of pathway deregulation among different patients. The portable use of this simple approach in clinical contexts is exemplified by the identification of prognostic intra-pathway gene pair signatures to predict overall survival of resected early-stage lung adenocarcinoma patients and signatures to predict relapse-free survival of estrogen receptor-positive breast cancer patients after tamoxifen treatment.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 7
    Publication Date: 2016-03-17
    Description: Most of current gene expression signatures for cancer prognosis are based on risk scores, usually calculated as some summaries of expression levels of the signature genes, whose applications require presetting risk score thresholds and data normalization. In this study, we demonstrate the critical limitations of such type of signatures that the risk scores of samples will change greatly when they are normalized together with different samples, which would induce spurious risk classification and difficulty in clinical settings, and the risk scores of independent samples are incomparable if data normalization is not adopted. To overcome these limitations, we propose a rank-based method to extract a prognostic gene pair signature for overall survival of stage I non-small-cell lung cancer. The prognostic gene pair signature is verified in three integrated data sets detected by different laboratories with different microarray platforms. We conclude that, different from the type of signatures based on risk scores summarized from gene expression levels, the rank-based signatures could be robustly applied at the individualized level to independent clinical samples assessed in different laboratories.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 8
    Publication Date: 2018-01-19
    Description: A sharp increase in the frequency of earthquakes near Fox Creek, Alberta, began in December 2013 in response to hydraulic fracturing. Using a hydraulic fracturing database, we explore relationships between injection parameters and seismicity response. We show that induced earthquakes are associated with completions that used larger injection volumes (10 4 to 10 5 cubic meters) and that seismic productivity scales linearly with injection volume. Injection pressure and rate have an insignificant association with seismic response. Further findings suggest that geological factors play a prominent role in seismic productivity, as evidenced by spatial correlations. Together, volume and geological factors account for ~96% of the variability in the induced earthquake rate near Fox Creek. This result is quantified by a seismogenic index–modified frequency-magnitude distribution, providing a framework to forecast induced seismicity.
    Keywords: Geochemistry, Geophysics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2018-01-19
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2015-09-18
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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