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1. A supervised weighted similarity measure for gene expressions using biological knowledge

Author:
Ray, Shubhra Sankar; Misra, Sampa
Source:
Gene 2016 v.595 no.2 pp. 150-160
ISSN:
0378-1119
Subject:
algorithms,   etc   ; Saccharomyces cerevisiae; amino acid sequences; cell cycle; data collection; databases; genes; heat stress; yeasts;     Show all 9 Subjects
Abstract:
... A supervised similarity measure for Saccharomyces cerevisiae gene expressions is developed which can capture the gene similarity when multiple types of experimental conditions like cell cycle, heat shock are available for all the genes. The measure is called Weighted Pearson correlation (WPC), where the weights are systematically determined for each type of experiment by maximizing the positive pr ...
DOI:
10.1016/j.gene.2016.09.033

2. Horse-Expert: An aided expert system for diagnosing horse diseases

Author:
Qin, H.; Xiao, J.; Gao, X.; Wang, H.
Source:
Polish journal of veterinary sciences 2016 v.19 no.4 pp. 907-915
ISSN:
2300-2557
Subject:
algorithms,   etc   ; expert systems; experts; horse diseases; horses; uncertainty; veterinarians; veterinary clinics; China;     Show all 9 Subjects
Abstract:
... In contrast to the rapid development of the horse husbandry in China, the ability of horse veterinarians to diagnose diseases has not been improved and only a few domain experts have considerable expertise. At present, many expert systems have been developed for diseases diagnosis, but few for horse diseases diagnosis have been studied in depth. This paper presents the design and development of a ...
DOI:
10.1515/pjvs-2016-0112

3. Photon-by-Photon Hidden Markov Model Analysis for Microsecond Single-Molecule FRET Kinetics B

Author:
Pirchi, Menahem; Tsukanov, Roman; Khamis, Rashid; Tomov, Toma E.; Berger, Yaron; Khara, Dinesh C.; Volkov, Hadas; Haran, Gilad; Nir, Eyal
Source:
The Journal of physical chemistry 2016 v.120 no.51 pp. 13065-13075
ISSN:
1520-5207
Subject:
algorithms,   etc   ; Markov chain; biochemical compounds; data collection; energy transfer; fluorescence; magnesium; models; physical chemistry;     Show all 9 Subjects
Abstract:
... The function of biological macromolecules involves large-scale conformational dynamics spanning multiple time scales, from microseconds to seconds. Such conformational motions, which may involve whole domains or subunits of a protein, play a key role in allosteric regulation. There is an urgent need for experimental methods to probe the fastest of these motions. Single-molecule fluorescence experi ...
DOI:
10.1021/acs.jpcb.6b10726

4. An Evolutionary Algorithm Applied to Inventory Control for Natural Gasoline

Author:
Oteiza, Paola Patricia; Brignole, Nélida Beatriz
Source:
Industrial & Engineering Chemistry Research 2016 v.55 no.51 pp. 13062-13073
ISSN:
1520-5045
Subject:
algorithms,   etc   ; chemistry; engineering; gasoline; inventories;     Show all 5 Subjects
Abstract:
... A metaheuristic technique for controller design is explored, and its performance is assessed for a real-world case. An evolutionary algorithm for self-tuning systems is proposed to tune the optimal control settings in order to achieve the best overall performance to control accurately the volume of natural gasoline in a storage tank. For high-level optimization, a flexible iterative technique base ...
DOI:
10.1021/acs.iecr.6b01934

5. Systematic Generation, Analysis, and Characterization of 3D Micro-architected Metamaterials

Author:
Trifale, Ninad T.; Nauman, Eric A.; Yazawa, Kazuaki
Source:
ACS Applied Materials & Interfaces 2016 v.8 no.51 pp. 35534-35544
ISSN:
1944-8252
Subject:
algorithms,   etc   ; foams; mechanical properties; models; porosity; porous media; thermal conductivity; topology;     Show all 8 Subjects
Abstract:
... Controlling the unit-cell topology of microlattice structures can enable the customization of effective anisotropic material properties. A wide range of properties can be obtained by varying connectivity within the unit cell, which then can be further used to optimize structures specific to applications. A methodology for a systematic generation of microlattice structures is presented that focuses ...
DOI:
10.1021/acsami.6b10502

6. Clearcutting and Site Preparation, but Not Planting, Promoted Early Tree Regeneration in Boreal Alaska

Author:
Morimoto, Miho; Juday, Glenn; Young, Brian
Source:
Forests 2016 v.8 no.1
ISSN:
1999-4907
Subject:
algorithms,   etc   ; Betula pendula subsp. mandshurica; Picea glauca; Populus tremuloides; biomass production; boreal forests; clearcutting; energy; fuelwood; heat; landscapes; natural regeneration; planting; reforestation; seed trees; site preparation; stems; timber production; tree and stand measurements; Alaska;     Show all 20 Subjects
Abstract:
... The stand initiation stage decisively influences future forest structure and composition, particularly in the boreal forest which is a stand replacement disturbance driven system. In boreal Alaska, the conventional forest management paradigm has focused on the production of large-dimension timber, particularly white spruce (Picea glauca). However, energy generation and heating from wood is increas ...
DOI:
10.3390/f8010012

7. α-Cyperone of Cyperus rotundus is an effective candidate for reduction of inflammation by destabilization of microtubule fibers in brain

Author:
Azimi, Azam; Ghaffari, Seyed Mahmood; Riazi, Gholam Hossein; Arab, Seyed Shahriar; Tavakol, Mohammad Mehdi; Pooyan, Shahriar
Source:
Journal of ethnopharmacology 2016 v.194 pp. 219-227
ISSN:
0378-8741
Subject:
algorithms,   etc   ; Alzheimer disease; Cyperus rotundus; amino acids; binding sites; brain; chemotaxis; circular dichroism spectroscopy; cytokines; epilepsy; fluorescence; fluorescence emission spectroscopy; grasses; guanosine triphosphate; hydrolysis; hydrophobicity; inflammation; ingredients; ligands; microtubules; molecular models; phagocytosis; polymerization; temperate zones; traditional medicine; transmission electron microscopy; tubulin; weeds;     Show all 28 Subjects
Abstract:
... Cyperus rotundus L. (Cyperaceae), commonly known as purple nutsedge or nut grass is one of the most invasive and endemic weeds in tropical, subtropical and temperate regions. This plant has been extensively used in traditional medicine for anti-arthritic, antidiarrheal and antiplatelet properties as well as treatment for several CNS disorders such as epilepsy, depression and inflammatory disorders ...
DOI:
10.1016/j.jep.2016.06.058

8. Spatially-explicit forecasting of cyanobacteria assemblages in freshwater lakes by multi-objective hybrid evolutionary algorithms

Author:
Cao, Hongqing; Recknagel, Friedrich; Bartkow, Michael
Source:
Ecological modelling 2016 v.342 pp. 97-112
ISSN:
0304-3800
Subject:
algorithms,   etc   ; Anabaena; Cylindrospermopsis; freshwater lakes; models; population density; time series analysis; water quality; Queensland;     Show all 9 Subjects
Abstract:
... This paper proposes a novel multi-objective hybrid evolutionary algorithm (MOHEA) that allows spatially-explicit modelling of local outbreaks and dispersal of population density. The MOHEA was tested for modelling at once two cyanobacteria populations at one lake site, same population in two different lakes and same population at three different sites of one lake. All experiments with MOHEA utiliz ...
DOI:
10.1016/j.ecolmodel.2016.09.024

9. Synergistic Combination of CASE Algorithms and DFT Chemical Shift Predictions: A Powerful Approach for Structure Elucidation, Verification, and Revision

Author:
Buevich, Alexei V.; Elyashberg, Mikhail E.
Source:
Journal of natural products 2016 v.79 no.12 pp. 3105-3116
ISSN:
1520-6025
Subject:
algorithms,   etc   ; expert systems; nuclear magnetic resonance spectroscopy; organic compounds; prediction;     Show all 5 Subjects
Abstract:
... Structure elucidation of complex natural products and new organic compounds remains a challenging problem. To support this endeavor, CASE (computer-assisted structure elucidation) expert systems were developed. These systems are capable of generating a set of all possible structures consistent with an ensemble of 2D NMR data followed by selection of the most probable structure on the basis of empi ...
DOI:
10.1021/acs.jnatprod.6b00799

10. Detecting Road Intersections from GPS Traces Using Longest Common Subsequence Algorithm

Author:
Xie, Xingzhe; Liao, Wenzhi; Aghajan, Hamid; Veelaert, Peter; Philips, Wilfried
Source:
ISPRS international journal of geo-information 2016 v.6 no.1
ISSN:
2220-9964
Subject:
algorithms,   etc   ; dynamic programming; global positioning systems; planning; roads;     Show all 5 Subjects
Abstract:
... Intersections are important components of road networks, which are critical to both route planning and path optimization. Most existing methods define the intersections as locations where the road users change their moving directions and identify the intersections from GPS traces through analyzing the road users’ turning behaviors. However, these methods suffer from finding an appropriate threshol ...
DOI:
10.3390/ijgi6010001

11. Numerical Study of the Orientation of Cylindrical Particles in a Circulating Fluidized Bed

Author:
Cai, Jie; Peng, Zhengbiao; Wu, Charley; Zhao, Xiaobao; Yuan, Zhulin; Moghtaderi, Behdad; Doroodchi, Elham
Source:
Industrial & Engineering Chemistry Research 2016 v.55 no.50 pp. 12806-12817
ISSN:
1520-5045
Subject:
algorithms,   etc   ; Reynolds number; chemistry; engineering; fluidized beds; models; prediction; turbulent flow;     Show all 8 Subjects
Abstract:
... Orientation is pivotal in circulating fluidized beds using cylinder-shaped particles. This study developed a three-dimensional multiway coupling model for predicting the orientation of cylindrical particles in circulating fluidized beds. The coupling algorithm between motorial cylindrical particles and the turbulence was established by incorporating the correlation between Lagrangian time scales a ...

12. Probabilistic Fault Diagnosis Based on Monte Carlo and Nested-Loop Fisher Discriminant Analysis for Industrial Processes

Author:
Zhao, Chunhui; Wang, Wei; Gao, Furong
Source:
Industrial & Engineering Chemistry Research 2016 v.55 no.50 pp. 12896-12908
ISSN:
1520-5045
Subject:
algorithms,   etc   ; algebra; chemistry; discriminant analysis; engineering; models; probability;     Show all 7 Subjects
Abstract:
... In this study, a new discriminant analysis (DA)-based fault diagnosis method is proposed based on the idea of variable selection to overcome the drawbacks of the existing methods. It addresses three issues. One is that a prejudgment strategy should be developed that can determine whether it is suitable to perform DA on the fault data. Second, it should solve the dependence problem of faulty variab ...

13. Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform

Author:
Ibrahim, Yehia M.; Garimella, Sandilya V. B.; Prost, Spencer A.; Wojcik, Roza; Norheim, Randolph V.; Baker, Erin S.; Rusyn, Ivan; Smith, Richard D.
Source:
Analytical chemistry 2016 v.88 no.24 pp. 12152-12160
ISSN:
1520-6882
Subject:
algorithms,   etc   ; ions; petroleum; proteomics; refining; spectrometers;     Show all 6 Subjects
Abstract:
... Complex samples benefit from multidimensional measurements where higher resolution enables more complete characterization of biological and environmental systems. To address this challenge, we developed a drift tube-based ion mobility spectrometry-Orbitrap mass spectrometer (IMS-Orbitrap MS) platform. To circumvent the time scale disparity between the fast IMS separation and the much slower Orbitr ...
DOI:
10.1021/acs.analchem.6b03027
PubMed:
28193022
PubMed Central:
PMC6211177

14. Efficient Processing of Continuous Reverse <em>k</em> Nearest Neighbor on Moving Objects in Road Networks

Author:
Attique, Muhammad; Cho, Hyung-Ju; Jin, Rize; Chung, Tae-Sun
Source:
ISPRS international journal of geo-information 2016 v.5 no.12
ISSN:
2220-9964
Subject:
algorithms,   etc   ; monitoring; roads; traffic;     Show all 4 Subjects
Abstract:
... A reverse k nearest neighbor (RkNN) query retrieves all the data points that have q as one of their k closest points. In recent years, considerable research has been conducted into monitoring reverse k nearest neighbor queries. In this paper, we study the problem of continuous reverse nearest neighbor queries where both the query object q and data objects are moving. Existing state-of-the-art tech ...
DOI:
10.3390/ijgi5120247

15. Noise Reduction Method for Quantifying Nanoparticle Light Scattering in Low Magnification Dark-Field Microscope Far-Field Images

Author:
Sun, Dali; Fan, Jia; Liu, Chang; Liu, Yang; Bu, Yang; Lyon, Christopher J.; Hu, Ye
Source:
Analytical chemistry 2016 v.88 no.24 pp. 12001-12005
ISSN:
1520-6882
Subject:
algorithms,   etc   ; blood sampling; image analysis; labor; light scattering; nanoparticles; pancreatic neoplasms; patients;     Show all 8 Subjects
Abstract:
... Nanoparticles have become a powerful tool for cell imaging and biomolecule, cell and protein interaction studies, but are difficult to rapidly and accurately measure in most assays. Dark-field microscope (DFM) image analysis approaches used to quantify nanoparticles require high-magnification near-field (HN) images that are labor intensive due to a requirement for manual image selection and focal ...
DOI:
10.1021/acs.analchem.6b03661
PubMed:
28177210
PubMed Central:
PMC5300049

16. Vaccine safety evaluation: Practical aspects in assessing benefits and risks

Author:
Di Pasquale, Alberta; Bonanni, Paolo; Garçon, Nathalie; Stanberry, Lawrence R.; El-Hodhod, Mostafa; Tavares Da Silva, Fernanda
Source:
Vaccine 2016 v.34 no.52 pp. 6672-6680
ISSN:
0264-410X
Subject:
algorithms,   etc   ; adverse effects; autism; children; disease resurgence; encephalopathy; guidelines; health care workers; immunization; industry; infants; infectious diseases; monitoring; risk; safety assessment; stakeholders; vaccines; Europe; United States;     Show all 19 Subjects
Abstract:
... Vaccines are different from most medicines in that they are administered to large and mostly healthy populations including infants and children, so there is a low tolerance for potential risks or side-effects. In addition, the long-term benefits of immunisation in reducing or eliminating infectious diseases may induce complacency due to the absence of cases. However, as demonstrated in recent meas ...
DOI:
10.1016/j.vaccine.2016.10.039

17. Variations in the Abundance of Lipid Biomarker Ions in Mass Spectrometry Images Correlate to Tissue Density

Author:
Bilkey, Jade; Tata, Alessandra; McKee, Trevor D.; Porcari, Andreia M.; Bluemke, Emma; Woolman, Michael; Ventura, Manuela; Eberlin, Marcos N.; Zarrine-Afsar, Arash
Source:
Analytical chemistry 2016 v.88 no.24 pp. 12099-12107
ISSN:
1520-6882
Subject:
algorithms,   etc   ; biomarkers; breast neoplasms; electrospray ionization mass spectrometry; humans; image analysis; ions; lipids; mice; morphometry; neoplasm cells;     Show all 11 Subjects
Abstract:
... While mass spectrometry (MS) imaging is widely used to investigate the molecular composition of ex vivo slices of cancerous tumors, little is known about how variations in the cellular properties of cancer tissue can influence cancer biomarker ion images. To better understand the basis for variations in the abundances of cancer biomarker ions seen in MS images of relatively homogeneous ex vivo tum ...
DOI:
10.1021/acs.analchem.6b02767

18. A Line Graph-Based Continuous Range Query Method for Moving Objects in Networks

Author:
Zhang, Hengcai; Lu, Feng; Chen, Jie
Source:
ISPRS international journal of geo-information 2016 v.5 no.12
ISSN:
2220-9964
Subject:
algorithms,   etc   ; databases; decision support systems; mathematical theory;     Show all 4 Subjects
Abstract:
... The rapid growth of location-based services has motivated the development of continuous range queries in networks. Existing query algorithms usually adopt an expansion tree to reuse the previous query results to get better efficiency. However, the high maintenance costs of the traditional expansion tree lead to a sharp efficiency decrease. In this paper, we propose a line graph-based continuous ra ...
DOI:
10.3390/ijgi5120246

19. Adaptive unsupervised classification of polarimetric SAR images using the improved affinity propagation clustering algorithm

Author:
Hua, Wenqiang; Wang, Shuang; Liu, Hongying; Liu, Yachao; Jiao, Licheng
Source:
International journal of remote sensing 2016 v.37 no.24 pp. 6023-6040
ISSN:
1366-5901
Subject:
algorithms,   etc   ; data collection; polarimetry; remote sensing; synthetic aperture radar;     Show all 5 Subjects
Abstract:
... A robust automatic classification system is critical for polarimetric synthetic aperture radar (POLSAR) terrain processing. In most of the conventional classification methods, the number of classes could not be calculated before classification. In this article, we present a new unsupervised classification algorithm with an adaptive number of classes for POLSAR data which is capable of estimating t ...
DOI:
10.1080/01431161.2016.1253894

20. A modified vegetation backscattering model for leaf area index retrieval from SAR time series

Author:
Tao, Liangliang; Li, Jing; Jiang, Jinbao; Chen, Xi; Cai, Qingkong
Source:
International journal of remote sensing 2016 v.37 no.24 pp. 5884-5901
ISSN:
1366-5901
Subject:
algorithms,   etc   ; leaf area index; models; remote sensing; soil; time series analysis; vegetation; water content; China;     Show all 9 Subjects
Abstract:
... In this study, a semi-empirical modified vegetation backscattering model was developed to retrieve leaf area index (LAI) based on multi-temporal Radarsat-2 data and ground observations collected in China. This model combined the contribution of the vegetation and bare soil at the pixel level by adding vegetation coverage and the influence of bare soil on the total backscatter coefficients. Then, a ...
DOI:
10.1080/01431161.2016.1251627