The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.

PubMed

Verde, Ignazio; Jenkins, Jerry; Dondini, Luca; Micali, Sabrina; Pagliarani, Giulia; Vendramin, Elisa; Paris, Roberta; Aramini, Valeria; Gazza, Laura; Rossini, Laura; Bassi, Daniele; Troggio, Michela; Shu, Shengqiang; Grimwood, Jane; Tartarini, Stefano; Dettori, Maria Teresa; Schmutz, Jeremy

2017-03-11

The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.

Quality and rigor of the concept mapping methodology: a pooled study analysis.

PubMed

Rosas, Scott R; Kane, Mary

2012-05-01

The use of concept mapping in research and evaluation has expanded dramatically over the past 20 years. Researchers in academic, organizational, and community-based settings have applied concept mapping successfully without the benefit of systematic analyses across studies to identify the features of a methodologically sound study. Quantitative characteristics and estimates of quality and rigor that may guide for future studies are lacking. To address this gap, we conducted a pooled analysis of 69 concept mapping studies to describe characteristics across study phases, generate specific indicators of validity and reliability, and examine the relationship between select study characteristics and quality indicators. Individual study characteristics and estimates were pooled and quantitatively summarized, describing the distribution, variation and parameters for each. In addition, variation in the concept mapping data collection in relation to characteristics and estimates was examined. Overall, results suggest concept mapping yields strong internal representational validity and very strong sorting and rating reliability estimates. Validity and reliability were consistently high despite variation in participation and task completion percentages across data collection modes. The implications of these findings as a practical reference to assess the quality and rigor for future concept mapping studies are discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

A high resolution radiation hybrid map of wheat chromosome 4A

USDA-ARS?s Scientific Manuscript database

Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequenc...

Quality of Individualised Education Programme Goals and Objectives for Preschool Children with Disabilities

ERIC Educational Resources Information Center

Rakap, Salih

2015-01-01

Individualised education programmes (IEPs) are the road maps for individualising services for children with disabilities, specifically through the development of high-quality child goals/objectives. High-quality IEP goals/objectives that are developed based on a comprehensive assessment of child functioning and directly connected to intervention…

Mapping of fluoride endemic areas and correlation studies of fluoride with other quality parameters of drinking water of Veppanapalli block of Dharmapuri district in Tamil Nadu.

PubMed

Karthikeyan, G; Sundarraj, A Shunmuga; Elango, K P

2003-10-01

193 drinking water samples from water sources of 27 panchayats of Veppanapalli block of Dharmapuri district of Tamil Nadu were analysed for chemical quality parameters. Based on the fluoride content of the water sources, fluoride maps differentiating regions with high / low fluoride levels were prepared using Isopleth mapping technique. The interdependence among the important chemical quality parameters were assessed using correlation studies. The experimental results of the application of linear and multiple regression equations on the influence of hardness, alkalinity, total dissolved solids and pH on fluoride are discussed.

An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize

USDA-ARS?s Scientific Manuscript database

In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73'×'Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, http:...

Total quality index of Agaricus bisporus mushrooms packed in modified atmosphere.

PubMed

Djekic, Ilija; Vunduk, Jovana; Tomašević, Igor; Kozarski, Maja; Petrovic, Predrag; Niksic, Miomir; Pudja, Predrag; Klaus, Anita

2017-07-01

The aim of this study was to develop a total quality index and examine the effects of modified atmosphere packaging (MAP) on the quality of Agaricus bisporus mushrooms stored for 22 days at 4 °C. Mushrooms were packaged under three MAPs: high nitrogen packaging (HNP), low carbon dioxide packaging (LCP) and low oxygen packaging (LOP). Passive MAP with air inside initially was used as the atmosphere treatment (AIR). This research revealed two phases in quality deterioration of A. bisporus mushrooms. During the first week, most of the quality parameters were not statistically different. Thereafter, odor intensities were stronger for all four types of packaging. Color difference and browning index values showed significantly lower color changes for AIR and LOP compared with HNP and LCP mushrooms. The best total quality index was calculated for LOP, followed by LCP and AIR. The findings of this study are useful with respect to examining two-component MAPs, separating the limiting factors (O 2 and CO 2 ) and evaluating quality deterioration effects and the total quality index of A. bisporus mushrooms. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Gradient Magnitude Similarity Deviation: A Highly Efficient Perceptual Image Quality Index.

PubMed

Xue, Wufeng; Zhang, Lei; Mou, Xuanqin; Bovik, Alan C

2014-02-01

It is an important task to faithfully evaluate the perceptual quality of output images in many applications, such as image compression, image restoration, and multimedia streaming. A good image quality assessment (IQA) model should not only deliver high quality prediction accuracy, but also be computationally efficient. The efficiency of IQA metrics is becoming particularly important due to the increasing proliferation of high-volume visual data in high-speed networks. We present a new effective and efficient IQA model, called gradient magnitude similarity deviation (GMSD). The image gradients are sensitive to image distortions, while different local structures in a distorted image suffer different degrees of degradations. This motivates us to explore the use of global variation of gradient based local quality map for overall image quality prediction. We find that the pixel-wise gradient magnitude similarity (GMS) between the reference and distorted images combined with a novel pooling strategy-the standard deviation of the GMS map-can predict accurately perceptual image quality. The resulting GMSD algorithm is much faster than most state-of-the-art IQA methods, and delivers highly competitive prediction accuracy. MATLAB source code of GMSD can be downloaded at http://www4.comp.polyu.edu.hk/~cslzhang/IQA/GMSD/GMSD.htm.

Mapping the categories of the Swedish primary health care version of ICD-10 to SNOMED CT concepts: Rule development and intercoder reliability in a mapping trial

PubMed Central

Vikström, Anna; Skånér, Ylva; Strender, Lars-Erik; Nilsson, Gunnar H

2007-01-01

Background Terminologies and classifications are used for different purposes and have different structures and content. Linking or mapping terminologies and classifications has been pointed out as a possible way to achieve various aims as well as to attain additional advantages in describing and documenting health care data. The objectives of this study were: • to explore and develop rules to be used in a mapping process • to evaluate intercoder reliability and the assessed degree of concordance when the 'Swedish primary health care version of the International Classification of Diseases version 10' (ICD-10) is matched to the Systematized Nomenclature of Medicine, Clinical Terms (SNOMED CT) • to describe characteristics in the coding systems that are related to obstacles to high quality mapping. Methods Mapping (interpretation, matching, assessment and rule development) was done by two coders. The Swedish primary health care version of ICD-10 with 972 codes was randomly divided into an allotment of three sets of categories, used in three mapping sequences, A, B and C. Mapping was done independently by the coders and new rules were developed between the sequences. Intercoder reliability was measured by comparing the results after each set. The extent of matching was assessed as either 'partly' or 'completely concordant' Results General principles for mapping were outlined before the first sequence, A. New mapping rules had significant impact on the results between sequences A - B (p < 0.01) and A - C (p < 0.001). The intercoder reliability in our study reached 83%. Obstacles to high quality mapping were mainly a lack of agreement by the coders due to structural and content factors in SNOMED CT and in the current ICD-10 version. The predominant reasons for this were difficulties in interpreting the meaning of the categories in the current ICD-10 version, and the presence of many related concepts in SNOMED CT. Conclusion Mapping from ICD-10-categories to SNOMED CT needs clear and extensive rules. It is possible to reach high intercoder reliability in mapping from ICD-10-categories to SNOMED CT. However, several obstacles to high quality mapping remain due to structure and content characteristics in both coding systems. PMID:17472757

Uav Photogrammetry: a Practical Solution for Challenging Mapping Projects

NASA Astrophysics Data System (ADS)

Saadatseresht, M.; Hashempour, A. H.; Hasanlou, M.

2015-12-01

We have observed huge attentions to application of unmanned aerial vehicle (UAV) in aerial mapping since a decade ago. Though, it has several advantages for handling time/cost/quality issues, there are a dozen of challenges in working with UAVs. In this paper, we; as the Robotic Photogrammetry Research Group (RPRG), will firstly review these challenges then show its advantages in three special practical projects. For each project, we will share our experiences through description of the UAV specifications, flight settings and processing steps. At the end, we will illustrate final result of each project and show how this technology could make unbelievable benefits to clients including 3D city realistic model in decimetre level, ultra high quality map production in several centimetre level, and accessing to a high risk and rough relief area for mapping aims.

Improving Low-Dose Blood-Brain Barrier Permeability Quantification Using Sparse High-Dose Induced Prior for Patlak Model

PubMed Central

Fang, Ruogu; Karlsson, Kolbeinn; Chen, Tsuhan; Sanelli, Pina C.

2014-01-01

Blood-brain-barrier permeability (BBBP) measurements extracted from the perfusion computed tomography (PCT) using the Patlak model can be a valuable indicator to predict hemorrhagic transformation in patients with acute stroke. Unfortunately, the standard Patlak model based PCT requires excessive radiation exposure, which raised attention on radiation safety. Minimizing radiation dose is of high value in clinical practice but can degrade the image quality due to the introduced severe noise. The purpose of this work is to construct high quality BBBP maps from low-dose PCT data by using the brain structural similarity between different individuals and the relations between the high- and low-dose maps. The proposed sparse high-dose induced (shd-Patlak) model performs by building a high-dose induced prior for the Patlak model with a set of location adaptive dictionaries, followed by an optimized estimation of BBBP map with the prior regularized Patlak model. Evaluation with the simulated low-dose clinical brain PCT datasets clearly demonstrate that the shd-Patlak model can achieve more significant gains than the standard Patlak model with improved visual quality, higher fidelity to the gold standard and more accurate details for clinical analysis. PMID:24200529

Mineral Potential Mapping in a Frontier Region

NASA Astrophysics Data System (ADS)

Ford, A.

2009-04-01

Mineral potential mapping using Geographic Information Systems (GIS) allows for rapid evaluation of spatial geoscience data and has the potential to delineate areas which may be prospective for hosting mineral deposits. Popular methods for evaluating digital data include weights of evidence, fuzzy logic and probabilistic neural networks. To date, such methods have been mostly applied to terrains that are well-studied, well-explored, and for which high-quality data is readily available. However, despite lacking protracted exploration histories and high-quality data, many frontier regions may have high-potential for hosting world-class mineral deposits and may benefit from mineral potential mapping exercises. Sovereign risk factors can limit the scope of previous work in a frontier region, and previous research in such areas is often limited and/or inaccessible, publicly available literature and data can be restricted, and any available data may also be unreliable. Mineral potential mapping using GIS in a frontier region presents many challenges in terms of the data availability (eg. non-existent information, lack of digital data) and data quality (eg. inaccuracy, incomplete coverage). The quality of the final mineral potential map is limited by the quality of the input data and as such, is affected by data availability and quality. Such issues are not limited to frontier regions, but they are often compounded by having multiple weaknesses within the same dataset, which is uncommon for data in more well-explored, data-rich areas. We show how mineral potential mapping can be successfully applied to frontier regions in order to delineate targets with high potential for hosting a mineral deposit despite the data challenges posed. Data is evaluated using the weights of evidence and fuzzy logic methods due to their effectiveness in dealing with incomplete geoscientific datasets. Weights of evidence may be employed as a data driven method for indirectly evaluating the quality of the data. In a frontier region, the quality of both the training data (mineral deposits) and evidential layers (geological features) may be questionable. Statistical measures can be used to verify whether the data exhibits logical inconsistencies which may be the result of inaccurate training data or inaccurate data in the evidential layer. Expert geological knowledge may be used to exclude, refine or modify such datasets for further analysis using an iterative weights of evidence process. After verification of the datasets using weights of evidence, fuzzy logic can be used to prepare a mineral potential map using expert geological knowledge. Fuzzy logic is suited to new areas where data availability may be poor, and allows a geologist to select the evidential layers they believe are the most critical for the particular ore deposit style being investigated, as specific deposit models for the area may not yet exist. These critical layers can then be quantified based on expert opinion. The results of the mineral potential mapping can be verified by their ability to predict known ore deposits within the study area.

Assessment and mapping of water pollution indices in zone-III of municipal corporation of hyderabad using remote sensing and geographic information system.

PubMed

Asadi, S S; Vuppala, Padmaja; Reddy, M Anji

2005-01-01

A preliminary survey of area under Zone-III of MCH was undertaken to assess the ground water quality, demonstrate its spatial distribution and correlate with the land use patterns using advance techniques of remote sensing and geographical information system (GIS). Twenty-seven ground water samples were collected and their chemical analysis was done to form the attribute database. Water quality index was calculated from the measured parameters, based on which the study area was classified into five groups with respect to suitability of water for drinking purpose. Thematic maps viz., base map, road network, drainage and land use/land cover were prepared from IRS ID PAN + LISS III merged satellite imagery forming the spatial database. Attribute database was integrated with spatial sampling locations map in Arc/Info and maps showing spatial distribution of water quality parameters were prepared in Arc View. Results indicated that high concentrations of total dissolved solids (TDS), nitrates, fluorides and total hardness were observed in few industrial and densely populated areas indicating deteriorated water quality while the other areas exhibited moderate to good water quality.

Forward and backward tone mapping of high dynamic range images based on subband architecture

NASA Astrophysics Data System (ADS)

Bouzidi, Ines; Ouled Zaid, Azza

2015-01-01

This paper presents a novel High Dynamic Range (HDR) tone mapping (TM) system based on sub-band architecture. Standard wavelet filters of Daubechies, Symlets, Coiflets and Biorthogonal were used to estimate the proposed system performance in terms of Low Dynamic Range (LDR) image quality and reconstructed HDR image fidelity. During TM stage, the HDR image is firstly decomposed in sub-bands using symmetrical analysis-synthesis filter bank. The transform coefficients are then rescaled using a predefined gain map. The inverse Tone Mapping (iTM) stage is straightforward. Indeed, the LDR image passes through the same sub-band architecture. But, instead of reducing the dynamic range, the LDR content is boosted to an HDR representation. Moreover, in our TM sheme, we included an optimization module to select the gain map components that minimize the reconstruction error, and consequently resulting in high fidelity HDR content. Comparisons with recent state-of-the-art methods have shown that our method provides better results in terms of visual quality and HDR reconstruction fidelity using objective and subjective evaluations.

An ultra-dense SNP linkage map for the octoploid, cultivated strawberry and its application in genetic research

USDA-ARS?s Scientific Manuscript database

We will present an ultra-dense genetic linkage map for the octoploid, cultivated strawberry (Fragaria x ananassa) consisting of over 13K Axiom® based SNP markers and 150 previously mapped reference SSR loci. The high quality of the map is demonstrated by the short sizes of each of the 28 linkage gro...

Process mapping as a framework for performance improvement in emergency general surgery.

PubMed

DeGirolamo, Kristin; D'Souza, Karan; Hall, William; Joos, Emilie; Garraway, Naisan; Sing, Chad Kim; McLaughlin, Patrick; Hameed, Morad

2017-12-01

Emergency general surgery conditions are often thought of as being too acute for the development of standardized approaches to quality improvement. However, process mapping, a concept that has been applied extensively in manufacturing quality improvement, is now being used in health care. The objective of this study was to create process maps for small bowel obstruction in an effort to identify potential areas for quality improvement. We used the American College of Surgeons Emergency General Surgery Quality Improvement Program pilot database to identify patients who received nonoperative or operative management of small bowel obstruction between March 2015 and March 2016. This database, patient charts and electronic health records were used to create process maps from the time of presentation to discharge. Eighty-eight patients with small bowel obstruction (33 operative; 55 nonoperative) were identified. Patients who received surgery had a complication rate of 32%. The processes of care from the time of presentation to the time of follow-up were highly elaborate and variable in terms of duration; however, the sequences of care were found to be consistent. We used data visualization strategies to identify bottlenecks in care, and they showed substantial variability in terms of operating room access. Variability in the operative care of small bowel obstruction is high and represents an important improvement opportunity in general surgery. Process mapping can identify common themes, even in acute care, and suggest specific performance improvement measures.

Process mapping as a framework for performance improvement in emergency general surgery.

PubMed

DeGirolamo, Kristin; D'Souza, Karan; Hall, William; Joos, Emilie; Garraway, Naisan; Sing, Chad Kim; McLaughlin, Patrick; Hameed, Morad

2018-02-01

Emergency general surgery conditions are often thought of as being too acute for the development of standardized approaches to quality improvement. However, process mapping, a concept that has been applied extensively in manufacturing quality improvement, is now being used in health care. The objective of this study was to create process maps for small bowel obstruction in an effort to identify potential areas for quality improvement. We used the American College of Surgeons Emergency General Surgery Quality Improvement Program pilot database to identify patients who received nonoperative or operative management of small bowel obstruction between March 2015 and March 2016. This database, patient charts and electronic health records were used to create process maps from the time of presentation to discharge. Eighty-eight patients with small bowel obstruction (33 operative; 55 nonoperative) were identified. Patients who received surgery had a complication rate of 32%. The processes of care from the time of presentation to the time of follow-up were highly elaborate and variable in terms of duration; however, the sequences of care were found to be consistent. We used data visualization strategies to identify bottlenecks in care, and they showed substantial variability in terms of operating room access. Variability in the operative care of small bowel obstruction is high and represents an important improvement opportunity in general surgery. Process mapping can identify common themes, even in acute care, and suggest specific performance improvement measures.

Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation

PubMed Central

Hardison, Ross C.

2017-01-01

Abstract The Roadmap Epigenomics Consortium has published whole-genome functional annotation maps in 127 human cell types by integrating data from studies of multiple epigenetic marks. These maps have been widely used for studying gene regulation in cell type-specific contexts and predicting the functional impact of DNA mutations on disease. Here, we present a new map of functional elements produced by applying a method called IDEAS on the same data. The method has several unique advantages and outperforms existing methods, including that used by the Roadmap Epigenomics Consortium. Using five categories of independent experimental datasets, we compared the IDEAS and Roadmap Epigenomics maps. While the overall concordance between the two maps is high, the maps differ substantially in the prediction details and in their consistency of annotation of a given genomic position across cell types. The annotation from IDEAS is uniformly more accurate than the Roadmap Epigenomics annotation and the improvement is substantial based on several criteria. We further introduce a pipeline that improves the reproducibility of functional annotation maps. Thus, we provide a high-quality map of candidate functional regions across 127 human cell types and compare the quality of different annotation methods in order to facilitate biomedical research in epigenomics. PMID:28973456

Hazard-Specific Vulnerability Mapping for Water Security in a Shale Gas Context

NASA Astrophysics Data System (ADS)

Allen, D. M.; Holding, S.; McKoen, Z.

2015-12-01

Northeast British Columbia (NEBC) is estimated to hold large reserves of unconventional natural gas and has experienced rapid growth in shale gas development activities over recent decades. Shale gas development has the potential to impact the quality and quantity of surface and ground water. Robust policies and sound water management are required to protect water security in relation to the water-energy nexus surrounding shale gas development. In this study, hazard-specific vulnerability mapping was conducted across NEBC to identify areas most vulnerable to water quality and quantity deterioration due to shale gas development. Vulnerability represents the combination of a specific hazard threat and the susceptibility of the water system to that threat. Hazard threats (i.e. potential contamination sources and water abstraction) were mapped spatially across the region. The shallow aquifer susceptibility to contamination was characterised using the DRASTIC aquifer vulnerability approach, while the aquifer susceptibility to abstraction was mapped according to aquifer productivity. Surface water susceptibility to contamination was characterised on a watershed basis to describe the propensity for overland flow (i.e. contaminant transport), while watershed discharge estimates were used to assess surface water susceptibility to water abstractions. The spatial distribution of hazard threats and susceptibility were combined to form hazard-specific vulnerability maps for groundwater quality, groundwater quantity, surface water quality and surface water quantity. The vulnerability maps identify priority areas for further research, monitoring and policy development. Priority areas regarding water quality occur where hazard threat (contamination potential) coincide with high aquifer susceptibility or high overland flow potential. Priority areas regarding water quantity occur where demand is estimated to represent a significant proportion of estimated supply. The identification of priority areas allows for characterization of the vulnerability of water security in the region. This vulnerability mapping approach, using the hazard threat and susceptibility indicators, can be applied to other shale gas areas to assess vulnerability to shale gas activities and support water security.

Leveraging electronic health record documentation for Failure Mode and Effects Analysis team identification

PubMed Central

Carson, Matthew B; Lee, Young Ji; Benacka, Corrine; Mutharasan, R. Kannan; Ahmad, Faraz S; Kansal, Preeti; Yancy, Clyde W; Anderson, Allen S; Soulakis, Nicholas D

2017-01-01

Objective: Using Failure Mode and Effects Analysis (FMEA) as an example quality improvement approach, our objective was to evaluate whether secondary use of orders, forms, and notes recorded by the electronic health record (EHR) during daily practice can enhance the accuracy of process maps used to guide improvement. We examined discrepancies between expected and observed activities and individuals involved in a high-risk process and devised diagnostic measures for understanding discrepancies that may be used to inform quality improvement planning. Methods: Inpatient cardiology unit staff developed a process map of discharge from the unit. We matched activities and providers identified on the process map to EHR data. Using four diagnostic measures, we analyzed discrepancies between expectation and observation. Results: EHR data showed that 35% of activities were completed by unexpected providers, including providers from 12 categories not identified as part of the discharge workflow. The EHR also revealed sub-components of process activities not identified on the process map. Additional information from the EHR was used to revise the process map and show differences between expectation and observation. Conclusion: Findings suggest EHR data may reveal gaps in process maps used for quality improvement and identify characteristics about workflow activities that can identify perspectives for inclusion in an FMEA. Organizations with access to EHR data may be able to leverage clinical documentation to enhance process maps used for quality improvement. While focused on FMEA protocols, findings from this study may be applicable to other quality activities that require process maps. PMID:27589944

SU-F-T-32: Evaluation of the Performance of a Multiple-Array-Diode Detector for Quality Assurance Tests in High-Dose-Rate Brachytherapy with Ir-192 Source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harpool, K; De La Fuente Herman, T; Ahmad, S

Purpose: To evaluate the performance of a two-dimensional (2D) array-diode- detector for geometric and dosimetric quality assurance (QA) tests of high-dose-rate (HDR) brachytherapy with an Ir-192-source. Methods: A phantom setup was designed that encapsulated a two-dimensional (2D) array-diode-detector (MapCheck2) and a catheter for the HDR brachytherapy Ir-192 source. This setup was used to perform both geometric and dosimetric quality assurance for the HDR-Ir192 source. The geometric tests included: (a) measurement of the position of the source and (b) spacing between different dwell positions. The dosimteric tests include: (a) linearity of output with time, (b) end effect and (c) relative dosemore » verification. The 2D-dose distribution measured with MapCheck2 was used to perform the previous tests. The results of MapCheck2 were compared with the corresponding quality assurance testes performed with Gafchromic-film and well-ionization-chamber. Results: The position of the source and the spacing between different dwell-positions were reproducible within 1 mm accuracy by measuring the position of maximal dose using MapCheck2 in contrast to the film which showed a blurred image of the dwell positions due to limited film sensitivity to irradiation. The linearity of the dose with dwell times measured from MapCheck2 was superior to the linearity measured with ionization chamber due to higher signal-to-noise ratio of the diode readings. MapCheck2 provided more accurate measurement of the end effect with uncertainty < 1.5% in comparison with the ionization chamber uncertainty of 3%. Although MapCheck2 did not provide absolute calibration dosimeter for the activity of the source, it provided accurate tool for relative dose verification in HDR-brachytherapy. Conclusion: The 2D-array-diode-detector provides a practical, compact and accurate tool to perform quality assurance for HDR-brachytherapy with an Ir-192 source. The diodes in MapCheck2 have high radiation sensitivity and linearity that is superior to Gafchromic-films and ionization chamber used for geometric and dosimetric QA in HDR-brachytherapy, respectively.« less

Using Value Stream Mapping to improve quality of care in low-resource facility settings.

PubMed

Ramaswamy, Rohit; Rothschild, Claire; Alabi, Funmi; Wachira, Eric; Muigai, Faith; Pearson, Nick

2017-11-01

Jacaranda Health (JH) is a Kenya-based organization that attempts to provide affordable, high-quality maternal and newborn healthcare through a chain of private health facilities in Nairobi. JH needed to adopted quality improvement as an organization-wide strategy to optimize effectiveness and efficiency. Value Stream Mapping, a Lean Management tool, was used to engage staff in prioritizing opportunities to improve clinical outcomes and patient-centered quality of care. Implementation was accomplished through a five-step process: (i) leadership engagement and commitment; (ii) staff training; (iii) team formation; (iv) process walkthrough; and (v) construction and validation. The Value Stream Map allowed the organization to come together and develop an end-to-end view of the process of care at JH and to select improvement opportunities for the entire system. The Value Stream Map is a simple visual tool that allows organizations to engage staff at all levels to gain commitment around quality improvement efforts. © The Author 2017. Published by Oxford University Press in association with the International Society for Quality in Health Care. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Improving depth maps of plants by using a set of five cameras

NASA Astrophysics Data System (ADS)

Kaczmarek, Adam L.

2015-03-01

Obtaining high-quality depth maps and disparity maps with the use of a stereo camera is a challenging task for some kinds of objects. The quality of these maps can be improved by taking advantage of a larger number of cameras. The research on the usage of a set of five cameras to obtain disparity maps is presented. The set consists of a central camera and four side cameras. An algorithm for making disparity maps called multiple similar areas (MSA) is introduced. The algorithm was specially designed for the set of five cameras. Experiments were performed with the MSA algorithm and the stereo matching algorithm based on the sum of sum of squared differences (sum of SSD, SSSD) measure. Moreover, the following measures were included in the experiments: sum of absolute differences (SAD), zero-mean SAD (ZSAD), zero-mean SSD (ZSSD), locally scaled SAD (LSAD), locally scaled SSD (LSSD), normalized cross correlation (NCC), and zero-mean NCC (ZNCC). Algorithms presented were applied to images of plants. Making depth maps of plants is difficult because parts of leaves are similar to each other. The potential usability of the described algorithms is especially high in agricultural applications such as robotic fruit harvesting.

High spatial resolution mapping of water quality and bathymetry with an autonomous underwater vehicle

NASA Astrophysics Data System (ADS)

Pampalone, Vincenzo; Milici, Barbara

2015-12-01

The drone Ecomapper AUV (Autonomous Underwater Vehicle) is a rare example of highly technological instrument in the environmental coastal monitoring field. The YSI EcoMapper is a one-man deployable, Autonomous Underwater Vehicle (AUV) designed to collect bathymetry and water quality data. The submarine-like vehicle follows a programmed course and employs sensors mounted in the nose to record pertinent information. Once the vehicle has started its mission, it operates independently of the user and utilizes GPS waypoints navigation to complete its programmed course. Throughout the course, the vehicle constantly steers toward the line drawn in the mission planning software (VectorMap), essentially following a more accurate road of coordinates instead of transversing waypoint-to-waypoint. It has been equipped with a Doppler Velocity Log (DVL) to increase its underwater navigation accuracy. Potential EcoMapper applications include baseline environmental mapping in freshwater, estuarine or near-coastal environments, bathymetric mapping, dissolved oxygen studies, event monitoring (algal blooms, storm impacts, low dissolved oxygen), non-point source studies, point-source dispersion mapping, security, search & rescue, inspection, shallow water mapping, thermal dissipation mapping of cooling outfalls, trace-dye studies. The AUV is used in the coastal area of the Augusta Bay (Italy), located in the eastern part of Sicily. Due to the heavy contamination generated by the several chemical and petrochemical industries active in the zone, the harbour was declared a Contaminated Site of National Interest. The ecomapper allows for a simultaneous data collection of water quality and bathymetric data providing a complete environmental mapping system of the Harbour.

Identification of stable QTLs for seed oil content by combined linkage and association mapping in Brassica napus.

PubMed

Sun, Fengming; Liu, Jing; Hua, Wei; Sun, Xingchao; Wang, Xinfa; Wang, Hanzhong

2016-11-01

Seed oil content is an important agricultural trait in rapeseed breeding. Although numerous quantitative trait locus (QTL) have been identified, most of them cannot be applied in practical breeding mainly due to environmental instability or large confidence intervals. The purpose of this study was to identify and validate high quality and more stable QTLs by combining linkage mapping and genome-wide association study (GWAS). For linkage mapping, we constructed two F 2 populations from crosses of high-oil content (∼50%) lines 6F313 and 61616 with a low-oil content (∼40%) line 51070. Two high density linkage maps spanned 1987cM (1659 bins) and 1856cM (1746 bins), respectively. For GWAS, we developed more than 34,000 high-quality SNP markers based on 227 accessions. Finally, 40 QTLs and 29 associations were established by linkage and association mapping in different environments. After merging the results, 32 consensus QTLs were obtained and 7 of them were identified by both mapping methods. Seven overlapping QTLs covered an average confidence interval of 183kb and explained the phenotypic variation of 10.23 to 24.45%. We further developed allele-specific PCR primers to identify each of the seven QTLs. These stable QTLs should be useful in gene cloning and practical breeding application. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Influence of modified atmosphere packaging on 'Star Ruby' grapefruit phytochemicals.

PubMed

Chaudhary, Priyanka R; Jayaprakasha, G K; Porat, Ron; Patil, Bhimanagouda S

2015-01-28

Modified atmosphere packaging (MAP) can extend the shelf life of salads, vegetables, and fruits by generating a storage environment with low O2, high CO2, and high humidity. The current study investigates the effect of modified atmosphere and humidity generated by two plastic films, microperforated bags (MIPBs) and macroperforated bags (MAPBs), on the levels of phytochemicals present in 'Star Ruby' grapefruits (Citrus paradisi, Macf.) stored for 16 weeks at 10 °C. Control fruits were stored without any packaging film. Juice samples were analyzed every 4 weeks for ascorbic acid, carotenoids, limonoids, flavonoids, and furocoumarins and assessed for quality parameters. MAP significantly reduced weight loss compared to control grapefruits. Control fruits had more β-carotene, lycopene, and furocoumarin compared with the fruits in MAP. Flavonoid content was highest in fruits stored in MAPB (P < 0.05), while fruits stored in MIPB showed no significant difference in flavonoid content compared to control (P > 0.05). The MAP treatments did not significantly affect ascorbic acid, limonoids, or fruit quality parameters, including total soluble solids, acidity, ripening ratio, decay and disorders, fruit taste, and off-flavors after 16 weeks of storage. These results suggest that MAP can be used to maintain the quality of 'Star Ruby' grapefruit with no detrimental effect on health-promoting phytochemicals.

CerebroMatic: A Versatile Toolbox for Spline-Based MRI Template Creation

PubMed Central

Wilke, Marko; Altaye, Mekibib; Holland, Scott K.

2017-01-01

Brain image spatial normalization and tissue segmentation rely on prior tissue probability maps. Appropriately selecting these tissue maps becomes particularly important when investigating “unusual” populations, such as young children or elderly subjects. When creating such priors, the disadvantage of applying more deformation must be weighed against the benefit of achieving a crisper image. We have previously suggested that statistically modeling demographic variables, instead of simply averaging images, is advantageous. Both aspects (more vs. less deformation and modeling vs. averaging) were explored here. We used imaging data from 1914 subjects, aged 13 months to 75 years, and employed multivariate adaptive regression splines to model the effects of age, field strength, gender, and data quality. Within the spm/cat12 framework, we compared an affine-only with a low- and a high-dimensional warping approach. As expected, more deformation on the individual level results in lower group dissimilarity. Consequently, effects of age in particular are less apparent in the resulting tissue maps when using a more extensive deformation scheme. Using statistically-described parameters, high-quality tissue probability maps could be generated for the whole age range; they are consistently closer to a gold standard than conventionally-generated priors based on 25, 50, or 100 subjects. Distinct effects of field strength, gender, and data quality were seen. We conclude that an extensive matching for generating tissue priors may model much of the variability inherent in the dataset which is then not contained in the resulting priors. Further, the statistical description of relevant parameters (using regression splines) allows for the generation of high-quality tissue probability maps while controlling for known confounds. The resulting CerebroMatic toolbox is available for download at http://irc.cchmc.org/software/cerebromatic.php. PMID:28275348

CerebroMatic: A Versatile Toolbox for Spline-Based MRI Template Creation.

PubMed

Wilke, Marko; Altaye, Mekibib; Holland, Scott K

2017-01-01

Brain image spatial normalization and tissue segmentation rely on prior tissue probability maps. Appropriately selecting these tissue maps becomes particularly important when investigating "unusual" populations, such as young children or elderly subjects. When creating such priors, the disadvantage of applying more deformation must be weighed against the benefit of achieving a crisper image. We have previously suggested that statistically modeling demographic variables, instead of simply averaging images, is advantageous. Both aspects (more vs. less deformation and modeling vs. averaging) were explored here. We used imaging data from 1914 subjects, aged 13 months to 75 years, and employed multivariate adaptive regression splines to model the effects of age, field strength, gender, and data quality. Within the spm/cat12 framework, we compared an affine-only with a low- and a high-dimensional warping approach. As expected, more deformation on the individual level results in lower group dissimilarity. Consequently, effects of age in particular are less apparent in the resulting tissue maps when using a more extensive deformation scheme. Using statistically-described parameters, high-quality tissue probability maps could be generated for the whole age range; they are consistently closer to a gold standard than conventionally-generated priors based on 25, 50, or 100 subjects. Distinct effects of field strength, gender, and data quality were seen. We conclude that an extensive matching for generating tissue priors may model much of the variability inherent in the dataset which is then not contained in the resulting priors. Further, the statistical description of relevant parameters (using regression splines) allows for the generation of high-quality tissue probability maps while controlling for known confounds. The resulting CerebroMatic toolbox is available for download at http://irc.cchmc.org/software/cerebromatic.php.

Characteristics of High-Quality Teachers

ERIC Educational Resources Information Center

Jones, Jason E.; Gulek, James C.

2010-01-01

The purpose of this study was to examine the characteristics of high-quality teachers who used a structured mathematics program for teaching, namely the Math Achievement Program (MAP[superscript 2]D), which demonstrated significant gains on student achievement as measured by California's Standards Test (CST) in mathematics. Specifically, the…

Neighbourhood Analysis to Foster Meaningful Learning Using Concept Mapping in Science Education

ERIC Educational Resources Information Center

Correia, P. R. M.; Cicuto, C. A. T.

2014-01-01

One critical aspect that hinders the systematic use of concept mapping in everyday classrooms is the difficulty of providing high-quality feedback to students so as to keep improving and revising their concept maps (Cmaps). The development of an innovative way to analyse, at a glance, students' Cmaps is presented to allow a diagnostic assessment…

Accurate estimation of short read mapping quality for next-generation genome sequencing

PubMed Central

Ruffalo, Matthew; Koyutürk, Mehmet; Ray, Soumya; LaFramboise, Thomas

2012-01-01

Motivation: Several software tools specialize in the alignment of short next-generation sequencing reads to a reference sequence. Some of these tools report a mapping quality score for each alignment—in principle, this quality score tells researchers the likelihood that the alignment is correct. However, the reported mapping quality often correlates weakly with actual accuracy and the qualities of many mappings are underestimated, encouraging the researchers to discard correct mappings. Further, these low-quality mappings tend to correlate with variations in the genome (both single nucleotide and structural), and such mappings are important in accurately identifying genomic variants. Approach: We develop a machine learning tool, LoQuM (LOgistic regression tool for calibrating the Quality of short read mappings, to assign reliable mapping quality scores to mappings of Illumina reads returned by any alignment tool. LoQuM uses statistics on the read (base quality scores reported by the sequencer) and the alignment (number of matches, mismatches and deletions, mapping quality score returned by the alignment tool, if available, and number of mappings) as features for classification and uses simulated reads to learn a logistic regression model that relates these features to actual mapping quality. Results: We test the predictions of LoQuM on an independent dataset generated by the ART short read simulation software and observe that LoQuM can ‘resurrect’ many mappings that are assigned zero quality scores by the alignment tools and are therefore likely to be discarded by researchers. We also observe that the recalibration of mapping quality scores greatly enhances the precision of called single nucleotide polymorphisms. Availability: LoQuM is available as open source at http://compbio.case.edu/loqum/. Contact: matthew.ruffalo@case.edu. PMID:22962451

Exploring the potential offered by legacy soil databases for ecosystem services mapping of Central African soils

NASA Astrophysics Data System (ADS)

Verdoodt, Ann; Baert, Geert; Van Ranst, Eric

2014-05-01

Central African soil resources are characterised by a large variability, ranging from stony, shallow or sandy soils with poor life-sustaining capabilities to highly weathered soils that recycle and support large amounts of biomass. Socio-economic drivers within this largely rural region foster inappropriate land use and management, threaten soil quality and finally culminate into a declining soil productivity and increasing food insecurity. For the development of sustainable land use strategies targeting development planning and natural hazard mitigation, decision makers often rely on legacy soil maps and soil profile databases. Recent development cooperation financed projects led to the design of soil information systems for Rwanda, D.R. Congo, and (ongoing) Burundi. A major challenge is to exploit these existing soil databases and convert them into soil inference systems through an optimal combination of digital soil mapping techniques, land evaluation tools, and biogeochemical models. This presentation aims at (1) highlighting some key characteristics of typical Central African soils, (2) assessing the positional, geographic and semantic quality of the soil information systems, and (3) revealing its potential impacts on the use of these datasets for thematic mapping of soil ecosystem services (e.g. organic carbon storage, pH buffering capacity). Soil map quality is assessed considering positional and semantic quality, as well as geographic completeness. Descriptive statistics, decision tree classification and linear regression techniques are used to mine the soil profile databases. Geo-matching as well as class-matching approaches are considered when developing thematic maps. Variability in inherent as well as dynamic soil properties within the soil taxonomic units is highlighted. It is hypothesized that within-unit variation in soil properties highly affects the use and interpretation of thematic maps for ecosystem services mapping. Results will mainly be based on analyses done in Rwanda, but can be complemented with ongoing research results or prospects for Burundi.

Improved Lunar Iron Map Obtained by the Kaguya Gamma-Ray Spectrometer

NASA Astrophysics Data System (ADS)

Naito, M.; Hasebe, N.; Nagaoka, H.; Shibamura, E.; Ohtake, M.; Kim, K. J.; Wöhler, C.; Berezhnoy, A. A.

2018-04-01

The lunar iron distribution is determined by the observation data of Kaguya Gamma-ray Spectrometer (KGRS). The excellent energy resolution of KGRS enables us to produce high quality FeO map with lower limit of about 3 wt%.

MISR Regional VBBE Map Projection

Atmospheric Science Data Center

2013-03-26

... Imagery:   Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

MISR Regional UAE2 Map Projection

Atmospheric Science Data Center

2013-03-26

... Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

DOE PAGES

Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei; ...

2015-08-17

Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report that EMRinger is a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

TU-FG-201-12: Designing a Risk-Based Quality Assurance Program for a Newly Implemented Y-90 Microspheres Procedure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vile, D; Zhang, L; Cuttino, L

2016-06-15

Purpose: To create a quality assurance program based upon a risk-based assessment of a newly implemented SirSpheres Y-90 procedure. Methods: A process map was created for a newly implemented SirSpheres procedure at a community hospital. The process map documented each step of this collaborative procedure, as well as the roles and responsibilities of each member. From the process map, different potential failure modes were determined as well as any current controls in place. From this list, a full failure mode and effects analysis (FMEA) was performed by grading each failure mode’s likelihood of occurrence, likelihood of detection, and potential severity.more » These numbers were then multiplied to compute the risk priority number (RPN) for each potential failure mode. Failure modes were then ranked based on their RPN. Additional controls were then added, with failure modes corresponding to the highest RPNs taking priority. Results: A process map was created that succinctly outlined each step in the SirSpheres procedure in its current implementation. From this, 72 potential failure modes were identified and ranked according to their associated RPN. Quality assurance controls and safety barriers were then added for failure modes associated with the highest risk being addressed first. Conclusion: A quality assurance program was created from a risk-based assessment of the SirSpheres process. Process mapping and FMEA were effective in identifying potential high-risk failure modes for this new procedure, which were prioritized for new quality assurance controls. TG 100 recommends the fault tree analysis methodology to design a comprehensive and effective QC/QM program, yet we found that by simply introducing additional safety barriers to address high RPN failure modes makes the whole process simpler and safer.« less

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

PubMed Central

Peng, Wenzhu; Xu, Jian; Zhang, Yan; Feng, Jianxin; Dong, Chuanju; Jiang, Likun; Feng, Jingyan; Chen, Baohua; Gong, Yiwen; Chen, Lin; Xu, Peng

2016-01-01

High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly. PMID:27225429

Soft bilateral filtering volumetric shadows using cube shadow maps

PubMed Central

Ali, Hatam H.; Sunar, Mohd Shahrizal; Kolivand, Hoshang

2017-01-01

Volumetric shadows often increase the realism of rendered scenes in computer graphics. Typical volumetric shadows techniques do not provide a smooth transition effect in real-time with conservation on crispness of boundaries. This research presents a new technique for generating high quality volumetric shadows by sampling and interpolation. Contrary to conventional ray marching method, which requires extensive time, this proposed technique adopts downsampling in calculating ray marching. Furthermore, light scattering is computed in High Dynamic Range buffer to generate tone mapping. The bilateral interpolation is used along a view rays to smooth transition of volumetric shadows with respect to preserving-edges. In addition, this technique applied a cube shadow map to create multiple shadows. The contribution of this technique isreducing the number of sample points in evaluating light scattering and then introducing bilateral interpolation to improve volumetric shadows. This contribution is done by removing the inherent deficiencies significantly in shadow maps. This technique allows obtaining soft marvelous volumetric shadows, having a good performance and high quality, which show its potential for interactive applications. PMID:28632740

Signalling maps in cancer research: construction and data analysis

PubMed Central

Kondratova, Maria; Sompairac, Nicolas; Barillot, Emmanuel; Zinovyev, Andrei

2018-01-01

Abstract Generation and usage of high-quality molecular signalling network maps can be augmented by standardizing notations, establishing curation workflows and application of computational biology methods to exploit the knowledge contained in the maps. In this manuscript, we summarize the major aims and challenges of assembling information in the form of comprehensive maps of molecular interactions. Mainly, we share our experience gained while creating the Atlas of Cancer Signalling Network. In the step-by-step procedure, we describe the map construction process and suggest solutions for map complexity management by introducing a hierarchical modular map structure. In addition, we describe the NaviCell platform, a computational technology using Google Maps API to explore comprehensive molecular maps similar to geographical maps and explain the advantages of semantic zooming principles for map navigation. We also provide the outline to prepare signalling network maps for navigation using the NaviCell platform. Finally, several examples of cancer high-throughput data analysis and visualization in the context of comprehensive signalling maps are presented. PMID:29688383

MISR Regional SAMUM Map Projection

Atmospheric Science Data Center

2017-03-29

... Regional Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data  |  ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

Map Downloads | USDA Plant Hardiness Zone Map

Science.gov Websites

formats. National, regional, and state maps are available under the View Maps section. Print Quality Maps dpi Graphic TIF 222 MB US Map 300 dpi Adobe Photoshop PS 25 MB *Print quality maps are very large | Non-Discrimination Statement | Information Quality | USA.gov | Whitehouse.gov

An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum).

PubMed

Han, Koeun; Jeong, Hee-Jin; Yang, Hee-Bum; Kang, Sung-Min; Kwon, Jin-Kyung; Kim, Seungill; Choi, Doil; Kang, Byoung-Cheorl

2016-04-01

Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there are few studies on QTL mapping of horticultural traits in pepper (Capsicum spp.) due to the lack of high-density molecular maps and the sequence information. In this study, an ultra-high-density map and 120 recombinant inbred lines (RILs) derived from a cross between C. annuum'Perennial' and C. annuum'Dempsey' were used for QTL mapping of horticultural traits. Parental lines and RILs were resequenced at 18× and 1× coverage, respectively. Using a sliding window approach, an ultra-high-density bin map containing 2,578 bins was constructed. The total map length of the map was 1,372 cM, and the average interval between bins was 0.53 cM. A total of 86 significant QTLs controlling 17 horticultural traits were detected. Among these, 32 QTLs controlling 13 traits were major QTLs. Our research shows that the construction of bin maps using low-coverage sequence is a powerful method for QTL mapping, and that the short intervals between bins are helpful for fine-mapping of QTLs. Furthermore, bin maps can be used to improve the quality of reference genomes by elucidating the genetic order of unordered regions and anchoring unassigned scaffolds to linkage groups. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Enhanced visual perception through tone mapping

NASA Astrophysics Data System (ADS)

Harrison, Andre; Mullins, Linda L.; Raglin, Adrienne; Etienne-Cummings, Ralph

2016-05-01

Tone mapping operators compress high dynamic range images to improve the picture quality on a digital display when the dynamic range of the display is lower than that of the image. However, tone mapping operators have been largely designed and evaluated based on the aesthetic quality of the resulting displayed image or how perceptually similar the compressed image appears relative to the original scene. They also often require per image tuning of parameters depending on the content of the image. In military operations, however, the amount of information that can be perceived is more important than the aesthetic quality of the image and any parameter adjustment needs to be as automated as possible regardless of the content of the image. We have conducted two studies to evaluate the perceivable detail of a set of tone mapping algorithms, and we apply our findings to develop and test an automated tone mapping algorithm that demonstrates a consistent improvement in the amount of perceived detail. An automated, and thereby predictable, tone mapping method enables a consistent presentation of perceivable features, can reduce the bandwidth required to transmit the imagery, and can improve the accessibility of the data by reducing the needed expertise of the analyst(s) viewing the imagery.

Urban and regional land use analysis: CARETS and census cities experiment package

NASA Technical Reports Server (NTRS)

Alexander, R. (Principal Investigator); Lins, H. F., Jr.

1974-01-01

The author has identified the following significant results. The most significant finding has been the ability of the S-190B data to produce land use maps not far removed from the quality of high altitude aircraft photography generated maps.

MISR Regional INTEX-B Map Projection

Atmospheric Science Data Center

2016-09-28

... Regional Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data  |  ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

MISR Regional GoMACCS Map Projection

Atmospheric Science Data Center

2017-03-29

... Regional Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data  |  ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

High-resolution maps of forest-urban watersheds present an opportunity for ecologists and managers

EPA Science Inventory

Dense populations of people and abundant impervious surfaces contribute to poor water quality and increased flooding in forest-urban watersheds. Green infrastructure mitigates these effects, but precisely quantifying benefits is difficult because most land cover maps rely on coar...

Local adaptive tone mapping for video enhancement

NASA Astrophysics Data System (ADS)

Lachine, Vladimir; Dai, Min (.

2015-03-01

As new technologies like High Dynamic Range cameras, AMOLED and high resolution displays emerge on consumer electronics market, it becomes very important to deliver the best picture quality for mobile devices. Tone Mapping (TM) is a popular technique to enhance visual quality. However, the traditional implementation of Tone Mapping procedure is limited by pixel's value to value mapping, and the performance is restricted in terms of local sharpness and colorfulness. To overcome the drawbacks of traditional TM, we propose a spatial-frequency based framework in this paper. In the proposed solution, intensity component of an input video/image signal is split on low pass filtered (LPF) and high pass filtered (HPF) bands. Tone Mapping (TM) function is applied to LPF band to improve the global contrast/brightness, and HPF band is added back afterwards to keep the local contrast. The HPF band may be adjusted by a coring function to avoid noise boosting and signal overshooting. Colorfulness of an original image may be preserved or enhanced by chroma components correction by means of saturation function. Localized content adaptation is further improved by dividing an image to a set of non-overlapped regions and modifying each region individually. The suggested framework allows users to implement a wide range of tone mapping applications with perceptional local sharpness and colorfulness preserved or enhanced. Corresponding hardware circuit may be integrated in camera, video or display pipeline with minimal hardware budget

A Hierarchical and Distributed Approach for Mapping Large Applications to Heterogeneous Grids using Genetic Algorithms

NASA Technical Reports Server (NTRS)

Sanyal, Soumya; Jain, Amit; Das, Sajal K.; Biswas, Rupak

2003-01-01

In this paper, we propose a distributed approach for mapping a single large application to a heterogeneous grid environment. To minimize the execution time of the parallel application, we distribute the mapping overhead to the available nodes of the grid. This approach not only provides a fast mapping of tasks to resources but is also scalable. We adopt a hierarchical grid model and accomplish the job of mapping tasks to this topology using a scheduler tree. Results show that our three-phase algorithm provides high quality mappings, and is fast and scalable.

Method for the visualization of landform by mapping using low altitude UAV application

NASA Astrophysics Data System (ADS)

Sharan Kumar, N.; Ashraf Mohamad Ismail, Mohd; Sukor, Nur Sabahiah Abdul; Cheang, William

2018-05-01

Unmanned Aerial Vehicle (UAV) and Digital Photogrammetry are evolving drastically in mapping technology. The significance and necessity for digital landform mapping are developing with years. In this study, a mapping workflow is applied to obtain two different input data sets which are the orthophoto and DSM. A fine flying technology is used to capture Low Altitude Aerial Photography (LAAP). Low altitude UAV (Drone) with the fixed advanced camera was utilized for imagery while computerized photogrammetry handling using Photo Scan was applied for cartographic information accumulation. The data processing through photogrammetry and orthomosaic processes is the main applications. High imagery quality is essential for the effectiveness and nature of normal mapping output such as 3D model, Digital Elevation Model (DEM), Digital Surface Model (DSM) and Ortho Images. The exactitude of Ground Control Points (GCP), flight altitude and the resolution of the camera are essential for good quality DEM and Orthophoto.

Proposed DoD (Department of Defense) Internet Protocol Standard.

DTIC Science & Technology

1982-07-06

parameters fall into two categories: service quality parameters and service options. Service quality parameters influence the transmission service provided...Corporation 6 July 1982 -7- TM-7172/481/OO o Service Quality Parameters - Precedence : attempts preferential treatment for high importance datagrams...select the transmission quality. IP passes the type of service (TOS) command set for service quality to the SNP where it is mapped into subnetwork

A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection.

PubMed

Jones, David B; Jerry, Dean R; Khatkar, Mehar S; Raadsma, Herman W; Zenger, Kyall R

2013-11-20

The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for this species in order to select for improved pearl quality, but many economic traits under selection are complex, polygenic and confounded with environmental factors, limiting the accuracy of selection. The incorporation of a marker-assisted selection (MAS) breeding approach would greatly benefit pearl breeding programs by allowing the direct selection of genes responsible for pearl quality. However, before MAS can be incorporated, substantial genomic resources such as genetic linkage maps need to be generated. The construction of a high-density genetic linkage map for P. maxima is not only essential for unravelling the genomic architecture of complex pearl quality traits, but also provides indispensable information on the genome structure of pearl oysters. A total of 1,189 informative genome-wide single nucleotide polymorphisms (SNPs) were incorporated into linkage map construction. The final linkage map consisted of 887 SNPs in 14 linkage groups, spans a total genetic distance of 831.7 centimorgans (cM), and covers an estimated 96% of the P. maxima genome. Assessment of sex-specific recombination across all linkage groups revealed limited overall heterochiasmy between the sexes (i.e. 1.15:1 F/M map length ratio). However, there were pronounced localised differences throughout the linkage groups, whereby male recombination was suppressed near the centromeres compared to female recombination, but inflated towards telomeric regions. Mean values of LD for adjacent SNP pairs suggest that a higher density of markers will be required for powerful genome-wide association studies. Finally, numerous nacre biomineralization genes were localised providing novel positional information for these genes. This high-density SNP genetic map is the first comprehensive linkage map for any pearl oyster species. It provides an essential genomic tool facilitating studies investigating the genomic architecture of complex trait variation and identifying quantitative trait loci for economically important traits useful in genetic selection programs within the P. maxima pearling industry. Furthermore, this map provides a foundation for further research aiming to improve our understanding of the dynamic process of biomineralization, and pearl oyster evolution and synteny.

Deriving health utilities from the MacNew Heart Disease Quality of Life Questionnaire.

PubMed

Chen, Gang; McKie, John; Khan, Munir A; Richardson, Jeff R

2015-10-01

Quality of life is included in the economic evaluation of health services by measuring the preference for health states, i.e. health state utilities. However, most intervention studies include a disease-specific, not a utility, instrument. Consequently, there has been increasing use of statistical mapping algorithms which permit utilities to be estimated from a disease-specific instrument. The present paper provides such algorithms between the MacNew Heart Disease Quality of Life Questionnaire (MacNew) instrument and six multi-attribute utility (MAU) instruments, the Euroqol (EQ-5D), the Short Form 6D (SF-6D), the Health Utilities Index (HUI) 3, the Quality of Wellbeing (QWB), the 15D (15 Dimension) and the Assessment of Quality of Life (AQoL-8D). Heart disease patients and members of the healthy public were recruited from six countries. Non-parametric rank tests were used to compare subgroup utilities and MacNew scores. Mapping algorithms were estimated using three separate statistical techniques. Mapping algorithms achieved a high degree of precision. Based on the mean absolute error and the intra class correlation the preferred mapping is MacNew into SF-6D or 15D. Using the R squared statistic the preferred mapping is MacNew into AQoL-8D. The algorithms reported in this paper enable MacNew data to be mapped into utilities predicted from any of six instruments. This permits studies which have included the MacNew to be used in cost utility analyses which, in turn, allows the comparison of services with interventions across the health system. © The European Society of Cardiology 2014.

Identification of milling and baking quality QTL in multiple soft wheat mapping populations.

PubMed

Cabrera, Antonio; Guttieri, Mary; Smith, Nathan; Souza, Edward; Sturbaum, Anne; Hua, Duc; Griffey, Carl; Barnett, Marla; Murphy, Paul; Ohm, Herb; Uphaus, Jim; Sorrells, Mark; Heffner, Elliot; Brown-Guedira, Gina; Van Sanford, David; Sneller, Clay

2015-11-01

Two mapping approaches were use to identify and validate milling and baking quality QTL in soft wheat. Two LG were consistently found important for multiple traits and we recommend the use marker-assisted selection on specific markers reported here. Wheat-derived food products require a range of characteristics. Identification and understanding of the genetic components controlling end-use quality of wheat is important for crop improvement. We assessed the underlying genetics controlling specific milling and baking quality parameters of soft wheat including flour yield, softness equivalent, flour protein, sucrose, sodium carbonate, water absorption and lactic acid, solvent retention capacities in a diversity panel and five bi-parental mapping populations. The populations were genotyped with SSR and DArT markers, with markers specific for the 1BL.1RS translocation and sucrose synthase gene. Association analysis and composite interval mapping were performed to identify quantitative trait loci (QTL). High heritability was observed for each of the traits evaluated, trait correlations were consistent over populations, and transgressive segregants were common in all bi-parental populations. A total of 26 regions were identified as potential QTL in the diversity panel and 74 QTL were identified across all five bi-parental mapping populations. Collinearity of QTL from chromosomes 1B and 2B was observed across mapping populations and was consistent with results from the association analysis in the diversity panel. Multiple regression analysis showed the importance of the two 1B and 2B regions and marker-assisted selection for the favorable alleles at these regions should improve quality.

Geospatial distribution modeling and determining suitability of groundwater quality for irrigation purpose using geospatial methods and water quality index (WQI) in Northern Ethiopia

NASA Astrophysics Data System (ADS)

Gidey, Amanuel

2018-06-01

Determining suitability and vulnerability of groundwater quality for irrigation use is a key alarm and first aid for careful management of groundwater resources to diminish the impacts on irrigation. This study was conducted to determine the overall suitability of groundwater quality for irrigation use and to generate their spatial distribution maps in Elala catchment, Northern Ethiopia. Thirty-nine groundwater samples were collected to analyze and map the water quality variables. Atomic absorption spectrophotometer, ultraviolet spectrophotometer, titration and calculation methods were used for laboratory groundwater quality analysis. Arc GIS, geospatial analysis tools, semivariogram model types and interpolation methods were used to generate geospatial distribution maps. Twelve and eight water quality variables were used to produce weighted overlay and irrigation water quality index models, respectively. Root-mean-square error, mean square error, absolute square error, mean error, root-mean-square standardized error, measured values versus predicted values were used for cross-validation. The overall weighted overlay model result showed that 146 km2 areas are highly suitable, 135 km2 moderately suitable and 60 km2 area unsuitable for irrigation use. The result of irrigation water quality index confirms 10.26% with no restriction, 23.08% with low restriction, 20.51% with moderate restriction, 15.38% with high restriction and 30.76% with the severe restriction for irrigation use. GIS and irrigation water quality index are better methods for irrigation water resources management to achieve a full yield irrigation production to improve food security and to sustain it for a long period, to avoid the possibility of increasing environmental problems for the future generation.

Discourse-Centric Learning Analytics: Mapping the Terrain

ERIC Educational Resources Information Center

Knight, Simon; Littleton, Karen

2015-01-01

There is an increasing interest in developing learning analytic techniques for the analysis, and support of, high-quality learning discourse. This paper maps the terrain of discourse-centric learning analytics (DCLA), outlining the distinctive contribution of DCLA and outlining a definition for the field moving forwards. It is our claim that DCLA…

Statistical Properties of Differences between Low and High Resolution CMAQ Runs with Matched Initial and Boundary Conditions

EPA Science Inventory

The difficulty in assessing errors in numerical models of air quality is a major obstacle to improving their ability to predict and retrospectively map air quality. In this paper, using simulation outputs from the Community Multi-scale Air Quality Model (CMAQ), the statistic...

Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

PubMed Central

2012-01-01

Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource for tetraploid cotton genome assembly, for cloning genes related to superior agronomic traits, and for further comparative genomic analyses in Gossypium. PMID:23046547

A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq)

PubMed Central

Li, Min; Li, Yujuan; Wang, Ying; Ma, Xiangjian; Zhang, Yuan; Tan, Feng; Wu, Rongling

2016-01-01

As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive “Yanjiang” variety as the female parent with the salt-tolerant “9901” variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq), leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for “Yanjiang”, 47.41-fold for “9901”, and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs). The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree. PMID:27327501

Tracking the polio virus down the Congo River: a case study on the use of Google Earth™ in public health planning and mapping

PubMed Central

Kamadjeu, Raoul

2009-01-01

Background The use of GIS in public health is growing, a consequence of a rapidly evolving technology and increasing accessibility to a wider audience. Google Earth™ (GE) is becoming an important mapping infrastructure for public health. However, generating traditional public health maps for GE is still beyond the reach of most public health professionals. In this paper, we explain, through the example of polio eradication activities in the Democratic Republic of Congo, how we used GE Earth as a planning tool and we share the methods used to generate public health maps. Results The use of GE improved field operations and resulted in better dispatch of vaccination teams and allocation of resources. It also allowed the creation of maps of high quality for advocacy, training and to help understand the spatiotemporal relationship between all the entities involved in the polio outbreak and response. Conclusion GE has the potential of making mapping available to a new set of public health users in developing countries. High quality and free satellite imagery, rich features including Keyhole Markup Language or image overlay provide a flexible but yet powerful platform that set it apart from traditional GIS tools and this power is still to be fully harnessed by public health professionals. PMID:19161606

Development of new mapping standards for geological surveys in Greenland

NASA Astrophysics Data System (ADS)

Mätzler, Eva; langley, Kirsty; Hollis, Julie; Heide-Jørgensen, Helene

2017-04-01

The current official topographic and geological maps of Greenland are in scale of 1:250:000 and 1:500.000 respectively, allowing only very limited amount of detail. The maps are outdated, and periglacial landscapes have changed significantly since the acquisition date. Hence, new affordable mapping products of high quality are in demand that can be available within a restricted time frame. In order to fulfill those demands a new mapping standard based on satellite imagery was developed, where classifications are mainly carried out with algorithms suitable for automatization. A Digital Elevation Model (ArcticDEM) was applied allowing examination of topographic and geological structures and 3D visualizing. Information on topographic features and lithology was extracted based on analysis of spectral characteristics from different multispectral data sources (Landsat 8, ASTER, WorldView-3) partly combined with the DEM. A first product is completed, and validation was carried out by field surveys. Field and remotely sensed data were integrated into a GIS database, and derived data will be freely available providing a valuable tool for planning and carrying out mineral exploration and other field activities. This study offers a method for generating up-to-date, low-cost and high quality mapping products suitable for Arctic regions, where accessibility is restricted due to remoteness and lack of infrastructure.

Mapping mental health service access: achieving equity through quality improvement.

PubMed

Green, Stuart A; Poots, Alan J; Marcano-Belisario, Jose; Samarasundera, Edgar; Green, John; Honeybourne, Emmi; Barnes, Ruth

2013-06-01

Improving access to psychological therapies (IAPTs) services deliver evidence-based care to people with depression and anxiety. A quality improvement (QI) initiative was undertaken by an IAPT service to improve referrals providing an opportunity to evaluate equitable access. QI methodologies were used by the clinical team to improve referrals to the service. The collection of geo-coded data allowed referrals to be mapped to small geographical areas according to deprivation. A total of 6078 patients were referred to the IAPT service during the period of analysis and mapped to 120 unique lower super output areas (LSOAs). The average weekly referral rate rose from 17 during the baseline phase to 43 during the QI implementation phase. Spatial analysis demonstrated all 15 of the high deprivation/low referral LSOAs were converted to high deprivation/high or medium referral LSOAs following the QI initiative. This work highlights the importance of QI in developing clinical services aligned to the needs of the population through the analysis of routine data matched to health needs. Mapping can be utilized to communicate complex information to inform the planning and organization of clinical service delivery and evaluate the progress and sustainability of QI initiatives.

Path integration guided with a quality map for shape reconstruction in the fringe reflection technique

NASA Astrophysics Data System (ADS)

Jing, Xiaoli; Cheng, Haobo; Wen, Yongfu

2018-04-01

A new local integration algorithm called quality map path integration (QMPI) is reported for shape reconstruction in the fringe reflection technique. A quality map is proposed to evaluate the quality of gradient data locally, and functions as a guideline for the integrated path. The presented method can be employed in wavefront estimation from its slopes over the general shaped surface with slope noise equivalent to that in practical measurements. Moreover, QMPI is much better at handling the slope data with local noise, which may be caused by the irregular shapes of the surface under test. The performance of QMPI is discussed by simulations and experiment. It is shown that QMPI not only improves the accuracy of local integration, but can also be easily implemented with no iteration compared to Southwell zonal reconstruction (SZR). From an engineering point-of-view, the proposed method may also provide an efficient and stable approach for different shapes with high-precise demand.

Interpretation of fingerprint image quality features extracted by self-organizing maps

NASA Astrophysics Data System (ADS)

Danov, Ivan; Olsen, Martin A.; Busch, Christoph

2014-05-01

Accurate prediction of fingerprint quality is of significant importance to any fingerprint-based biometric system. Ensuring high quality samples for both probe and reference can substantially improve the system's performance by lowering false non-matches, thus allowing finer adjustment of the decision threshold of the biometric system. Furthermore, the increasing usage of biometrics in mobile contexts demands development of lightweight methods for operational environment. A novel two-tier computationally efficient approach was recently proposed based on modelling block-wise fingerprint image data using Self-Organizing Map (SOM) to extract specific ridge pattern features, which are then used as an input to a Random Forests (RF) classifier trained to predict the quality score of a propagated sample. This paper conducts an investigative comparative analysis on a publicly available dataset for the improvement of the two-tier approach by proposing additionally three feature interpretation methods, based respectively on SOM, Generative Topographic Mapping and RF. The analysis shows that two of the proposed methods produce promising results on the given dataset.

Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing

PubMed Central

Guo, Yinshan; Xing, Huiyang; Zhao, Yuhui; Liu, Zhendong; Li, Kun; Guo, Xiuwu

2017-01-01

Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape. PMID:28746364

Modeling the distribution of white spruce (Picea glauca) for Alaska with high accuracy: an open access role-model for predicting tree species in last remaining wilderness areas

Treesearch

Bettina Ohse; Falk Huettmann; Stefanie M. Ickert-Bond; Glenn P. Juday

2009-01-01

Most wilderness areas still lack accurate distribution information on tree species. We met this need with a predictive GIS modeling approach, using freely available digital data and computer programs to efficiently obtain high-quality species distribution maps. Here we present a digital map with the predicted distribution of white spruce (Picea glauca...

Using Google Earth as an innovative tool for community mapping.

PubMed

Lefer, Theodore B; Anderson, Matthew R; Fornari, Alice; Lambert, Anastasia; Fletcher, Jason; Baquero, Maria

2008-01-01

Maps are used to track diseases and illustrate the social context of health problems. However, commercial mapping software requires special training. This article illustrates how nonspecialists used Google Earth, a free program, to create community maps. The Bronx, New York, is characterized by high levels of obesity and diabetes. Residents and medical students measured the variety and quality of food and exercise sources around a residency training clinic and a student-run free clinic, using Google Earth to create maps with minimal assistance. Locations were identified using street addresses or simply by pointing to them on a map. Maps can be shared via e-mail, viewed online with Google Earth or Google Maps, and the data can be incorporated into other mapping software.

A standard photomap of ovarian nurse cell chromosomes and inversion polymorphism in Anopheles beklemishevi.

PubMed

Artemov, Gleb N; Gordeev, Mikhail I; Kokhanenko, Alina A; Moskaev, Anton V; Velichevskaya, Alena I; Stegniy, Vladimir N; Sharakhov, Igor V; Sharakhova, Maria V

2018-03-27

Anopheles beklemishevi is a member of the Maculipennis group of malaria mosquitoes that has the most northern distribution among other members of the group. Although a cytogenetic map for the larval salivary gland chromosomes of this species has been developed, a high-quality standard cytogenetic photomap that enables genomics and population genetics studies of this mosquito at the adult stage is still lacking. In this study, a cytogenetic map for the polytene chromosomes of An. beklemishevi from ovarian nurse cells was developed using high-resolution digital imaging from field collected mosquitoes. PCR-amplified DNA probes for fluorescence in situ hybridization (FISH) were designed based on the genome of An. atroparvus. The DNA probe obtained by microdissection procedures from the breakpoint region was labelled in a DOP-PCR reaction. Population analysis was performed on 371 specimens collected in 18 locations. We report the development of a high-quality standard photomap for the polytene chromosomes from ovarian nurse cells of An. beklemishevi. To confirm the suitability of the map for physical mapping, several PCR-amplified probes were mapped to the chromosomes of An. beklemishevi using FISH. In addition, we identified and mapped DNA probes to flanking regions of the breakpoints of two inversions on chromosome X of this species. Inversion polymorphism was determined in 13 geographically distant populations of An. beklemishevi. Four polymorphic inversions were detected. The positions of common chromosomal inversions were indicated on the map. The study constructed a standard photomap for ovarian nurse cell chromosomes of An. beklemishevi and tested its suitability for physical genome mapping and population studies. Cytogenetic analysis determined inversion polymorphism in natural populations of An. beklemishevi related to this species' adaptation.

Evaluation of color mapping algorithms in different color spaces

NASA Astrophysics Data System (ADS)

Bronner, Timothée.-Florian; Boitard, Ronan; Pourazad, Mahsa T.; Nasiopoulos, Panos; Ebrahimi, Touradj

2016-09-01

The color gamut supported by current commercial displays is only a subset of the full spectrum of colors visible by the human eye. In High-Definition (HD) television technology, the scope of the supported colors covers 35.9% of the full visible gamut. For comparison, Ultra High-Definition (UHD) television, which is currently being deployed on the market, extends this range to 75.8%. However, when reproducing content with a wider color gamut than that of a television, typically UHD content on HD television, some original color information may lie outside the reproduction capabilities of the television. Efficient gamut mapping techniques are required in order to fit the colors of any source content into the gamut of a given display. The goal of gamut mapping is to minimize the distortion, in terms of perceptual quality, when converting video from one color gamut to another. It is assumed that the efficiency of gamut mapping depends on the color space in which it is computed. In this article, we evaluate 14 gamut mapping techniques, 12 combinations of two projection methods across six color spaces as well as R'G'B' Clipping and wrong gamut interpretation. Objective results, using the CIEDE2000 metric, show that the R'G'B' Clipping is slightly outperformed by only one combination of color space and projection method. However, analysis of images shows that R'G'B' Clipping can result in loss of contrast in highly saturated images, greatly impairing the quality of the mapped image.

Criteria to Extract High-Quality Protein Data Bank Subsets for Structure Users.

PubMed

Carugo, Oliviero; Djinović-Carugo, Kristina

2016-01-01

It is often necessary to build subsets of the Protein Data Bank to extract structural trends and average values. For this purpose it is mandatory that the subsets are non-redundant and of high quality. The first problem can be solved relatively easily at the sequence level or at the structural level. The second, on the contrary, needs special attention. It is not sufficient, in fact, to consider the crystallographic resolution and other feature must be taken into account: the absence of strings of residues from the electron density maps and from the files deposited in the Protein Data Bank; the B-factor values; the appropriate validation of the structural models; the quality of the electron density maps, which is not uniform; and the temperature of the diffraction experiments. More stringent criteria produce smaller subsets, which can be enlarged with more tolerant selection criteria. The incessant growth of the Protein Data Bank and especially of the number of high-resolution structures is allowing the use of more stringent selection criteria, with a consequent improvement of the quality of the subsets of the Protein Data Bank.

The Effect of Map Boundary on Estimates of Landscape Resistance to Animal Movement

PubMed Central

Koen, Erin L.; Garroway, Colin J.; Wilson, Paul J.; Bowman, Jeff

2010-01-01

Background Artificial boundaries on a map occur when the map extent does not cover the entire area of study; edges on the map do not exist on the ground. These artificial boundaries might bias the results of animal dispersal models by creating artificial barriers to movement for model organisms where there are no barriers for real organisms. Here, we characterize the effects of artificial boundaries on calculations of landscape resistance to movement using circuit theory. We then propose and test a solution to artificially inflated resistance values whereby we place a buffer around the artificial boundary as a substitute for the true, but unknown, habitat. Methodology/Principal Findings We randomly assigned landscape resistance values to map cells in the buffer in proportion to their occurrence in the known map area. We used circuit theory to estimate landscape resistance to organism movement and gene flow, and compared the output across several scenarios: a habitat-quality map with artificial boundaries and no buffer, a map with a buffer composed of randomized habitat quality data, and a map with a buffer composed of the true habitat quality data. We tested the sensitivity of the randomized buffer to the possibility that the composition of the real but unknown buffer is biased toward high or low quality. We found that artificial boundaries result in an overestimate of landscape resistance. Conclusions/Significance Artificial map boundaries overestimate resistance values. We recommend the use of a buffer composed of randomized habitat data as a solution to this problem. We found that resistance estimated using the randomized buffer did not differ from estimates using the real data, even when the composition of the real data was varied. Our results may be relevant to those interested in employing Circuitscape software in landscape connectivity and landscape genetics studies. PMID:20668690

Mapping Gnss Restricted Environments with a Drone Tandem and Indirect Position Control

NASA Astrophysics Data System (ADS)

Cledat, E.; Cucci, D. A.

2017-08-01

The problem of autonomously mapping highly cluttered environments, such as urban and natural canyons, is intractable with the current UAV technology. The reason lies in the absence or unreliability of GNSS signals due to partial sky occlusion or multi-path effects. High quality carrier-phase observations are also required in efficient mapping paradigms, such as Assisted Aerial Triangulation, to achieve high ground accuracy without the need of dense networks of ground control points. In this work we consider a drone tandem in which the first drone flies outside the canyon, where GNSS constellation is ideal, visually tracks the second drone and provides an indirect position control for it. This enables both autonomous guidance and accurate mapping of GNSS restricted environments without the need of ground control points. We address the technical feasibility of this concept considering preliminary real-world experiments in comparable conditions and we perform a mapping accuracy prediction based on a simulation scenario.

Food production and service in UK hospitals.

PubMed

Ahmed, Mohamed; Jones, Eleri; Redmond, Elizabeth; Hewedi, Mahmoud; Wingert, Andreas; Gad El Rab, Mohamed

2015-01-01

The purpose of this paper is to apply value stream mapping holistically to hospital food production/service systems focused on high-quality food. Multiple embedded case study of three (two private-sector and one public-sector) hospitals in the UK. The results indicated various issues affecting hospital food production including: the menu and nutritional considerations; food procurement; food production; foodservice; patient perceptions/expectations. Value stream mapping is a new approach for food production systems in UK hospitals whether private or public hospitals. The paper identifies opportunities for enhancing hospital food production systems. The paper provides a theoretical basis for process enhancement of hospital food production and the provision of high-quality hospital food.

Filter methods to preserve local contrast and to avoid artifacts in gamut mapping

NASA Astrophysics Data System (ADS)

Meili, Marcel; Küpper, Dennis; Barańczuk, Zofia; Caluori, Ursina; Simon, Klaus

2010-01-01

Contrary to high dynamic range imaging, the preservation of details and the avoidance of artifacts is not explicitly considered in popular color management systems. An effective way to overcome these difficulties is image filtering. In this paper we investigate several image filter concepts for detail preservation as part of a practical gamut mapping strategy. In particular we define four concepts including various image filters and check their performance with a psycho-visual test. Additionally, we compare our performance evaluation to two image quality measures with emphasis on local contrast. Surprisingly, the most simple filter concept performs highly efficient and achieves an image quality which is comparable to the more established but slower methods.

Echo Mapping of Active Galactic Nuclei

NASA Technical Reports Server (NTRS)

Peterson, B. M.; Horne, K.

2004-01-01

Echo mapping makes use of the intrinsic variability of the continuum source in active galactic nuclei to map out the distribution and kinematics of line-emitting gas from its light travel time-delayed response to continuum changes. Echo mapping experiments have yielded sizes for the broad line-emitting region in about three dozen AGNs. The dynamics of the line-emitting gas seem to be dominated by the gravity of the central black hole, enabling measurement of the black-hole masses in AGNs. We discuss requirements for future echo-mapping experiments that will yield the high quality velocity-delay maps of the broad-line region that are needed to determine its physical nature.

Avoiding Design Fixation: Transformation and Abstraction in Mapping from Source to Target

ERIC Educational Resources Information Center

Goldschmidt, Gabriela

2011-01-01

Designers try to "enlist" whatever they can to help themselves arrive at high quality, novel and original designs. When stimuli are used for this purpose, usually provided at the onset of the design process, these stimuli, or sources, may have one of two effects: they may enhance the design search and contribute to a high-quality, creative design,…

Genetic mapping of FAD2 genes and their relative contribution towards oil quality in peanut (Arachis hypogaea L.)

USDA-ARS?s Scientific Manuscript database

Improvement of oil quality is the major research objective in peanut because of its high economic impact on growers/traders and several health benefits to consumers. Fatty acid desaturase (FAD) genes are known to control quality traits but their position on the peanut genome and their relative contr...

Meat Quality Derived from High Inclusion of a Micro-Alga or Insect Meal as an Alternative Protein Source in Poultry Diets: A Pilot Study

PubMed Central

Neumann, Carmen; Velten, Susanne; Liebert, Frank

2018-01-01

The effects on meat quality resulting from alternative dietary protein sources (Spirulina and Hermetia meal) in poultry diets are studied to determine the overall suitability of these ingredients considering state-of-the-art packaging practices—highly oxygenated modified atmosphere packaging (HiOx MAP). We monitored standard slaughterhouse parameters, such as live weight, carcass weight, dressed yield, and pH at 20 min and 24 h post mortem. In addition, we studied the effects that 3 and 7-day storage in HiOx MAP has on the overall product physico-chemical and sensory properties. In addition to previously supported effects of HiOx MAP, we found that meat quality could be improved when Spirulina replaces 50% of the soy protein in broiler diets; however, this substitution results in a dark reddish-yellowish meat colour. On the other hand, the substitution with Hermetia larval meal results in a product that does not differ from the standard fed control group, with the exception that the breast filet has a more intense flavour that decreases over storage time. All-in-all Spirulina and Hermetia meal have the potential to replace soybean meal in broiler diets without deteriorating meat quality. PMID:29518048

LIHE Spectral Dynamics and Jaguar Data Acquisition System Measurement Assurance Results 2014.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Covert, Timothy T.; Willis, Michael David; Radtke, Gregg Arthur

2015-06-01

The Light Initiated High Explosive (LIHE) facility performs high rigor, high consequence impulse testing for the nuclear weapons (NW) community. To support the facility mission, LIHE's extensive data acquisition system (DAS) is comprised of several discrete components as well as a fully integrated system. Due to the high consequence and high rigor of the testing performed at LIHE, a measurement assurance plan (MAP) was developed in collaboration with NW system customers to meet their data quality needs and to provide assurance of the robustness of the LIHE DAS. While individual components of the DAS have been calibrated by the SNLmore » Primary Standards Laboratory (PSL), the integrated nature of this complex system requires verification of the complete system, from end-to-end. This measurement assurance plan (MAP) report documents the results of verification and validation procedures used to ensure that the data quality meets customer requirements.« less

Using optical mapping data for the improvement of vertebrate genome assemblies.

PubMed

Howe, Kerstin; Wood, Jonathan M D

2015-01-01

Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. Because it is not subject to cloning, amplification, hybridisation or sequencing bias, it is ideally suited to the improvement of fragmented genome assemblies that can no longer be improved by classical methods. In addition, its low cost and rapid turnaround make it equally useful during the scaffolding process of de novo assembly from high throughput sequencing reads. We describe how optical mapping has been used in practice to produce high quality vertebrate genome assemblies. In particular, we detail the efforts undertaken by the Genome Reference Consortium (GRC), which maintains the reference genomes for human, mouse, zebrafish and chicken, and uses different optical mapping platforms for genome curation.

New segmentation-based tone mapping algorithm for high dynamic range image

NASA Astrophysics Data System (ADS)

Duan, Weiwei; Guo, Huinan; Zhou, Zuofeng; Huang, Huimin; Cao, Jianzhong

2017-07-01

The traditional tone mapping algorithm for the display of high dynamic range (HDR) image has the drawback of losing the impression of brightness, contrast and color information. To overcome this phenomenon, we propose a new tone mapping algorithm based on dividing the image into different exposure regions in this paper. Firstly, the over-exposure region is determined using the Local Binary Pattern information of HDR image. Then, based on the peak and average gray of the histogram, the under-exposure and normal-exposure region of HDR image are selected separately. Finally, the different exposure regions are mapped by differentiated tone mapping methods to get the final result. The experiment results show that the proposed algorithm achieve the better performance both in visual quality and objective contrast criterion than other algorithms.

The chimeric mapping problem: algorithmic strategies and performance evaluation on synthetic genomic data.

PubMed

Greenberg, D; Istrail, S

1994-09-01

The Human Genome Project requires better software for the creation of physical maps of chromosomes. Current mapping techniques involve breaking large segments of DNA into smaller, more-manageable pieces, gathering information on all the small pieces, and then constructing a map of the original large piece from the information about the small pieces. Unfortunately, in the process of breaking up the DNA some information is lost and noise of various types is introduced; in particular, the order of the pieces is not preserved. Thus, the map maker must solve a combinatorial problem in order to reconstruct the map. Good software is indispensable for quick, accurate reconstruction. The reconstruction is complicated by various experimental errors. A major source of difficulty--which seems to be inherent to the recombination technology--is the presence of chimeric DNA clones. It is fairly common for two disjoint DNA pieces to form a chimera, i.e., a fusion of two pieces which appears as a single piece. Attempts to order chimera will fail unless they are algorithmically divided into their constituent pieces. Despite consensus within the genomic mapping community of the critical importance of correcting chimerism, algorithms for solving the chimeric clone problem have received only passing attention in the literature. Based on a model proposed by Lander (1992a, b) this paper presents the first algorithms for analyzing chimerism. We construct physical maps in the presence of chimerism by creating optimization functions which have minimizations which correlate with map quality. Despite the fact that these optimization functions are invariably NP-complete our algorithms are guaranteed to produce solutions which are close to the optimum. The practical import of using these algorithms depends on the strength of the correlation of the function to the map quality as well as on the accuracy of the approximations. We employ two fundamentally different optimization functions as a means of avoiding biases likely to decorrelate the solutions from the desired map. Experiments on simulated data show that both our algorithm which minimizes the number of chimeric fragments in a solution and our algorithm which minimizes the maximum number of fragments per clone in a solution do, in fact, correlate to high quality solutions. Furthermore, tests on simulated data using parameters set to mimic real experiments show that that the algorithms have the potential to find high quality solutions with real data. We plan to test our software against real data from the Whitehead Institute and from Los Alamos Genomic Research Center in the near future.

Next Generation Mapping of Enological Traits in an F2 Interspecific Grapevine Hybrid Family

PubMed Central

Sun, Qi; Manns, David C.; Sacks, Gavin L.; Mansfield, Anna Katharine; Luby, James J.; Londo, Jason P.; Reisch, Bruce I.; Cadle-Davidson, Lance E.; Fennell, Anne Y.

2016-01-01

In winegrapes (Vitis spp.), fruit quality traits such as berry color, total soluble solids content (SS), malic acid content (MA), and yeast assimilable nitrogen (YAN) affect fermentation or wine quality, and are important traits in selecting new hybrid winegrape cultivars. Given the high genetic diversity and heterozygosity of Vitis species and their tendency to exhibit inbreeding depression, linkage map construction and quantitative trait locus (QTL) mapping has relied on F1 families with the use of simple sequence repeat (SSR) and other markers. This study presents the construction of a genetic map by single nucleotide polymorphisms identified through genotyping-by-sequencing (GBS) technology in an F2 mapping family of 424 progeny derived from a cross between the wild species V. riparia Michx. and the interspecific hybrid winegrape cultivar, ‘Seyval’. The resulting map has 1449 markers spanning 2424 cM in genetic length across 19 linkage groups, covering 95% of the genome with an average distance between markers of 1.67 cM. Compared to an SSR map previously developed for this F2 family, these results represent an improved map covering a greater portion of the genome with higher marker density. The accuracy of the map was validated using the well-studied trait berry color. QTL affecting YAN, MA and SS related traits were detected. A joint MA and SS QTL spans a region with candidate genes involved in the malate metabolism pathway. We present an analytical pipeline for calling intercross GBS markers and a high-density linkage map for a large F2 family of the highly heterozygous Vitis genus. This study serves as a model for further genetic investigations of the molecular basis of additional unique characters of North American hybrid wine cultivars and to enhance the breeding process by marker-assisted selection. The GBS protocols for identifying intercross markers developed in this study can be adapted for other heterozygous species. PMID:26974672

Scalable and High-Throughput Execution of Clinical Quality Measures from Electronic Health Records using MapReduce and the JBoss® Drools Engine

PubMed Central

Peterson, Kevin J.; Pathak, Jyotishman

2014-01-01

Automated execution of electronic Clinical Quality Measures (eCQMs) from electronic health records (EHRs) on large patient populations remains a significant challenge, and the testability, interoperability, and scalability of measure execution are critical. The High Throughput Phenotyping (HTP; http://phenotypeportal.org) project aligns with these goals by using the standards-based HL7 Health Quality Measures Format (HQMF) and Quality Data Model (QDM) for measure specification, as well as Common Terminology Services 2 (CTS2) for semantic interpretation. The HQMF/QDM representation is automatically transformed into a JBoss® Drools workflow, enabling horizontal scalability via clustering and MapReduce algorithms. Using Project Cypress, automated verification metrics can then be produced. Our results show linear scalability for nine executed 2014 Center for Medicare and Medicaid Services (CMS) eCQMs for eligible professionals and hospitals for >1,000,000 patients, and verified execution correctness of 96.4% based on Project Cypress test data of 58 eCQMs. PMID:25954459

Differentiating the Spatiotemporal Distribution of Natural and Anthropogenic Processes on River Water-Quality Variation Using a Self-Organizing Map With Factor Analysis.

PubMed

Wang, Yeuh-Bin; Liu, Chen-Wuing; Lee, Jin-Jing

2015-08-01

To elucidate the historical improvement and advanced measure of river water quality in the Taipei metropolitan area, this study applied the self-organizing map (SOM) technique with factor analysis (FA) to differentiate the spatiotemporal distribution of natural and anthropogenic processes on river water-quality variation spanning two decades. The SOM clustered river water quality into five groups: very low pollution, low pollution, moderate pollution, high pollution, and very high pollution. FA was then used to extract four latent factors that dominated water quality from 1991 to 2011 including three anthropogenic process factors (organic, industrial, and copper pollution) and one natural process factor [suspended solids (SS) pollution]. The SOM revealed that the water quality improved substantially over time. However, the downstream river water quality was still classified as high pollution because of an increase in anthropogenic activity. FA showed the spatiotemporal pattern of each factor score decreasing over time, but the organic pollution factor downstream of the Tamsui River, as well as the SS factor scores in the upstream major tributary (the Dahan Stream), remained within the high pollution level. Therefore, we suggest that public sewage-treatment plants should be upgraded from their current secondary biological processing to advanced treatment processing. The conservation of water and soil must also be reinforced to decrease the SS loading of the Dahan Stream from natural erosion processes in the future.

Mapping the Medical Literature for High Quality Studies and Reviews for Age-specific Clinical Specialties

PubMed Central

Stevens, Adrienne L.; Wilczynski, Nancy L.; McKibbon, K. Ann; Haynes, R. Brian

2001-01-01

Objective: To identify a journal subset that publishes reports of high quality studies and reviews relating to age-specific clinical specialties, such as pediatrics and geriatrics. Design: Handsearch of 172 journals using explicit criteria to determine methodologic quality for generating evidence for clinical practice. Main outcome measure: Frequency of high quality articles and their top yielding journals. Results: Between 17% and 33% of articles published in age-specific specialties are of high quality for clinical use. Top yielding journals for the specialties ranged from 16 to 130. Conclusion: Handsearch of the clinical literature for the year 2000 reveals that high quality articles for some age-specific specialties are concentrated in a small subset of journals (eg, obstetrics), whereas articles for other specialties are widely scattered among a large number of journals (eg, adult medicine).

Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei

PubMed Central

Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Li, Fuhua; Chen, Xiaohan; Zhao, Yongzhen; Huang, Long; Zheng, Hongkun; Xiang, Jianhai

2015-01-01

The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species. PMID:26503227

Muscle Activity Map Reconstruction from High Density Surface EMG Signals With Missing Channels Using Image Inpainting and Surface Reconstruction Methods.

PubMed

Ghaderi, Parviz; Marateb, Hamid R

2017-07-01

The aim of this study was to reconstruct low-quality High-density surface EMG (HDsEMG) signals, recorded with 2-D electrode arrays, using image inpainting and surface reconstruction methods. It is common that some fraction of the electrodes may provide low-quality signals. We used variety of image inpainting methods, based on partial differential equations (PDEs), and surface reconstruction methods to reconstruct the time-averaged or instantaneous muscle activity maps of those outlier channels. Two novel reconstruction algorithms were also proposed. HDsEMG signals were recorded from the biceps femoris and brachial biceps muscles during low-to-moderate-level isometric contractions, and some of the channels (5-25%) were randomly marked as outliers. The root-mean-square error (RMSE) between the original and reconstructed maps was then calculated. Overall, the proposed Poisson and wave PDE outperformed the other methods (average RMSE 8.7 μV rms ± 6.1 μV rms and 7.5 μV rms ± 5.9 μV rms ) for the time-averaged single-differential and monopolar map reconstruction, respectively. Biharmonic Spline, the discrete cosine transform, and the Poisson PDE outperformed the other methods for the instantaneous map reconstruction. The running time of the proposed Poisson and wave PDE methods, implemented using a Vectorization package, was 4.6 ± 5.7 ms and 0.6 ± 0.5 ms, respectively, for each signal epoch or time sample in each channel. The proposed reconstruction algorithms could be promising new tools for reconstructing muscle activity maps in real-time applications. Proper reconstruction methods could recover the information of low-quality recorded channels in HDsEMG signals.

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

PubMed Central

2013-01-01

Background As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. Results Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. Conclusions Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing. PMID:23800011

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.).

PubMed

Guo, Yinshan; Shi, Guangli; Liu, Zhendong; Zhao, Yuhui; Yang, Xiaoxu; Zhu, Junchi; Li, Kun; Guo, Xiuwu

2015-01-01

In this study, 149 F1 plants from the interspecific cross between 'Red Globe' (Vitis vinifera L.) and 'Shuangyou' (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for 'Red Globe,' 63.65 for 'Shuangyou,' and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape.

Applications of Skylab EREP photographs to mapping landforms and environmental geomorphology in the Great Plains and Midwest

NASA Technical Reports Server (NTRS)

Morrison, R. B.; Lineback, J. A.; Fuller, H. K.; Rinkenberger, R. K.

1975-01-01

The following evaluations of Skylab photographs were undertaken: (1) the 1290 Skylab S190A and S190B photographs of Illinois, Iowa, Kansas, Missouri, Nebraska, and South Dakota were evaluated in detail in terms of coverage, cloud cover, photographic quality, endlap, detectability of roads and stereorelief, and utility for geomorphologic mapping, and (2) the utility of the Skylab photos were tested for interpretive analytic mapping of geomorphologic features over large areas representative of different parts of this region. Photointerpretative maps of analytic geomorphology were obtained for various test areas representative of the varied landscapes in the region. These maps are useful for regional land-use planning, ground-water exploration, and other environmental geomorphologic-geologic applications. Compared with LANDSAT-1 MSS images, Skylab photos afford almost as extensive overviews of large areas but in considerably greater detail, and for many SL photos, moderate stereorelief. However, repetitive multiseasonal, cloud-free coverage by high-quality photos is very limited and many areas have no coverage at all.

Adaption to High Altitude: An Evaluation of the Storage Quality of Suspended Red Blood Cells Prepared from the Whole Blood of Tibetan Plateau Migrants

PubMed Central

Wang, Hong; Li, Xiaojuan; He, Zeng; Gangla, Meiduo; Zhang, Jingdan; Han, Dingding; Liu, Jiaxin

2015-01-01

Hypoxia has been reported to cause the significant enhancement of hemoglobin (Hb) and hematocrit (Hct), which stabilizes at relatively high levels after an individual ascends to a high altitude. However, the quality of the suspended red blood cells (SRBCs) obtained from individuals at high altitudes such as Tibetan plateau migrants after storage has not been studied. In this study, we compared the storage quality of SRBCs prepared from Tibetan plateau and Deyang lowland populations by adding a normal volume of mannitol-adenine-phosphate (MAP), which is a common additive solution used in blood storage in Asian countries. The storage cell characteristics were examined on days1, 7, 14 and 35.We found higher Hct and Hb levels and viscosity in the high altitude samples. The metabolic rates, including those for electrolytes and lactate, were higher in plateau SRBCs than in lowland SRBCs; these findings were consistent with the higher osmotic fragility and hemolysis of plateau SRBCs throughout the entire storage period. In addition, the reduction rates of 2,3-diphosphoglycerate (2,3-DPG) and oxygen tension to attain 50% oxygen saturation of Hb (P50) in plateau SRBCs were higher than those in lowland SRBCs, and the oxygen delivering capacity in plateau SRBCs was weaker than that in lowland SRBCs. We concluded that the storage quality of plateau SRBCs was inferior to that of lowland SRBCs when using the same concentration of MAP. We suggested that the optimal formula, including the MAP concentration or even a new additive solution, to store the plateau SRBCs must be assessed and regulated. PMID:26637115

2010-2011 Performance of the AirNow Satellite Data Processor

NASA Astrophysics Data System (ADS)

Pasch, A. N.; DeWinter, J. L.; Haderman, M. D.; van Donkelaar, A.; Martin, R. V.; Szykman, J.; White, J. E.; Dickerson, P.; Zahn, P. H.; Dye, T. S.

2012-12-01

The U.S. Environmental Protection Agency's (EPA) AirNow program provides maps of real time hourly Air Quality Index (AQI) conditions and daily AQI forecasts nationwide (http://www.airnow.gov). The public uses these maps to make health-based decisions. The usefulness of the AirNow air quality maps depends on the accuracy and spatial coverage of air quality measurements. Currently, the maps use only ground-based measurements, which have significant gaps in coverage in some parts of the United States. As a result, contoured AQI levels have high uncertainty in regions far from monitors. To improve the usefulness of air quality maps, scientists at EPA, Dalhousie University, and Sonoma Technology, Inc. have been working in collaboration with the National Aeronautics and Space Administration (NASA) and the National Oceanic and Atmospheric Administration (NOAA) to incorporate satellite-estimated surface PM2.5 concentrations into the maps via the AirNow Satellite Data Processor (ASDP). These satellite estimates are derived using NASA/NOAA satellite aerosol optical depth (AOD) retrievals and GEOS-Chem modeled ratios of surface PM2.5 concentrations to AOD. GEOS-Chem is a three-dimensional chemical transport model for atmospheric composition driven by meteorological input from the Goddard Earth Observing System (GOES). The ASDP can fuse multiple PM2.5 concentration data sets to generate AQI maps with improved spatial coverage. The goal of ASDP is to provide more detailed AQI information in monitor-sparse locations and augment monitor-dense locations with more information. We will present a statistical analysis for 2010-2011 of the ASDP predictions of PM2.5 focusing on performance at validation sites. In addition, we will present several case studies evaluating the ASDP's performance for multiple regions and seasons, focusing specifically on days when large spatial gradients in AQI and wildfire smoke impact were observed.

The Adventure of the Deceitful Numbers

ERIC Educational Resources Information Center

Andrade-Molina, Melissa

2017-01-01

This article addresses access to high-quality education under a neoliberal mentality. It engages at both the discursive and material levels, by mapping how taken-for-granted truths about neoliberal policies circulate through the media. The media--newspapers, network channels, and news websites--have correlated quality education with socioeconomic…

Strategy and Quality Maps in Higher Education

ERIC Educational Resources Information Center

Kettunen, Juha

2011-01-01

The purpose of this study is to investigate the integration of strategic management and quality assurance in higher education. The study presents how the value chain can be described in the strategy and quality maps, which are, respectively graphical representations of the strategic plan and the quality assurance system. The quality map is a new…

How to use concept mapping to identify barriers and facilitators of an electronic quality improvement intervention.

PubMed

van Engen-Verheul, Mariëtte; Peek, Niels; Vromen, Tom; Jaspers, Monique; de Keizer, Nicolette

2015-01-01

Systematic quality improvement (QI) interventions are increasingly used to change complex health care systems. Results of randomized clinical trials can provide quantitative evidence whether QI interventions were effective but they do not teach us why and how QI was (not) achieved. Qualitative research methods can answer these questions but typically involve only a small group of respondents against high resources. Concept mapping methodology overcomes these drawbacks by integrating results from qualitative group sessions with multivariate statistical analysis to represent ideas of diverse stakeholders visually on maps in an efficient way. This paper aims to describe how to use concept mapping to qualitatively gain insight into barriers and facilitators of an electronic QI intervention and presents experiences with the method from an ongoing case study to evaluate a QI system in the field of cardiac rehabilitation in the Netherlands.

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

PubMed Central

Kujur, Alice; Upadhyaya, Hari D.; Shree, Tanima; Bajaj, Deepak; Das, Shouvik; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20–0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9–39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement. PMID:25942004

Assessing Volunteered Geographic Information (vgi) Quality Based on CONTRIBUTORS' Mapping Behaviours

NASA Astrophysics Data System (ADS)

Bégin, D.; Devillers, R.; Roche, S.

2013-05-01

VGI changed the mapping landscape by allowing people that are not professional cartographers to contribute to large mapping projects, resulting at the same time in concerns about the quality of the data produced. While a number of early VGI studies used conventional methods to assess data quality, such approaches are not always well adapted to VGI. Since VGI is a user-generated content, we posit that features and places mapped by contributors largely reflect contributors' personal interests. This paper proposes studying contributors' mapping processes to understand the characteristics and quality of the data produced. We argue that contributors' behaviour when mapping reflects contributors' motivation and individual preferences in selecting mapped features and delineating mapped areas. Such knowledge of contributors' behaviour could allow for the derivation of information about the quality of VGI datasets. This approach was tested using a sample area from OpenStreetMap, leading to a better understanding of data completeness for contributor's preferred features.

QTL mapping for grain yield, flowering time, and stay-green traits in sorghum with genotyping-by-sequencing markers

USDA-ARS?s Scientific Manuscript database

Molecular breeding can complement traditional breeding approaches to achieve genetic gains in a more efficient way. In the present study, genetic mapping was conducted in a sorghum recombinant inbred line (RIL) population developed from Tx436 (a non-stay-green high food quality inbred) × 00MN7645 (a...

A Two-Stage Framework for 3D Face Reconstruction from RGBD Images.

PubMed

Wang, Kangkan; Wang, Xianwang; Pan, Zhigeng; Liu, Kai

2014-08-01

This paper proposes a new approach for 3D face reconstruction with RGBD images from an inexpensive commodity sensor. The challenges we face are: 1) substantial random noise and corruption are present in low-resolution depth maps; and 2) there is high degree of variability in pose and face expression. We develop a novel two-stage algorithm that effectively maps low-quality depth maps to realistic face models. Each stage is targeted toward a certain type of noise. The first stage extracts sparse errors from depth patches through the data-driven local sparse coding, while the second stage smooths noise on the boundaries between patches and reconstructs the global shape by combining local shapes using our template-based surface refinement. Our approach does not require any markers or user interaction. We perform quantitative and qualitative evaluations on both synthetic and real test sets. Experimental results show that the proposed approach is able to produce high-resolution 3D face models with high accuracy, even if inputs are of low quality, and have large variations in viewpoint and face expression.

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

PubMed

Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair; Stewart, Chip; Garrison, Erik P; Marth, Gabor T

2014-01-01

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

PubMed Central

Lee, Wan-Ping; Stromberg, Michael P.; Ward, Alistair; Stewart, Chip; Garrison, Erik P.; Marth, Gabor T.

2014-01-01

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). PMID:24599324

Selection and quality assessment of Landsat data for the North American forest dynamics forest history maps of the US

USGS Publications Warehouse

Schleeweis, Karen; Goward, Samuel N.; Huang, Chengquan; Dwyer, John L.; Dungan, Jennifer L.; Lindsey, Mary A.; Michaelis, Andrew; Rishmawi, Khaldoun; Masek, Jeffery G.

2016-01-01

Using the NASA Earth Exchange platform, the North American Forest Dynamics (NAFD) project mapped forest history wall-to-wall, annually for the contiguous US (1986–2010) using the Vegetation Change Tracker algorithm. As with any effort to identify real changes in remotely sensed time-series, data gaps, shifts in seasonality, misregistration, inconsistent radiometry and cloud contamination can be sources of error. We discuss the NAFD image selection and processing stream (NISPS) that was designed to minimize these sources of error. The NISPS image quality assessments highlighted issues with the Landsat archive and metadata including inadequate georegistration, unreliability of the pre-2009 L5 cloud cover assessments algorithm, missing growing-season imagery and paucity of clear views. Assessment maps of Landsat 5–7 image quantities and qualities are presented that offer novel perspectives on the growing-season archive considered for this study. Over 150,000+ Landsat images were considered for the NAFD project. Optimally, one high quality cloud-free image in each year or a total of 12,152 images would be used. However, to accommodate data gaps and cloud/shadow contamination 23,338 images were needed. In 220 specific path-row image years no acceptable images were found resulting in data gaps in the annual national map products.

Fusion of Kinect depth data with trifocal disparity estimation for near real-time high quality depth maps generation

NASA Astrophysics Data System (ADS)

Boisson, Guillaume; Kerbiriou, Paul; Drazic, Valter; Bureller, Olivier; Sabater, Neus; Schubert, Arno

2014-03-01

Generating depth maps along with video streams is valuable for Cinema and Television production. Thanks to the improvements of depth acquisition systems, the challenge of fusion between depth sensing and disparity estimation is widely investigated in computer vision. This paper presents a new framework for generating depth maps from a rig made of a professional camera with two satellite cameras and a Kinect device. A new disparity-based calibration method is proposed so that registered Kinect depth samples become perfectly consistent with disparities estimated between rectified views. Also, a new hierarchical fusion approach is proposed for combining on the flow depth sensing and disparity estimation in order to circumvent their respective weaknesses. Depth is determined by minimizing a global energy criterion that takes into account the matching reliability and the consistency with the Kinect input. Thus generated depth maps are relevant both in uniform and textured areas, without holes due to occlusions or structured light shadows. Our GPU implementation reaches 20fps for generating quarter-pel accurate HD720p depth maps along with main view, which is close to real-time performances for video applications. The estimated depth is high quality and suitable for 3D reconstruction or virtual view synthesis.

You

ERIC Educational Resources Information Center

Walker, Kathrin C.; Saito, Rebecca N.

2011-01-01

Research demonstrates that involvement in high-quality youth programs benefits young people personally, socially, and academically. Yet many families--particularly low-income and minority families--are unsatisfied with the quality, affordability, and availability of options in their communities. Participation rates are especially low for youth who…

Using ESRI Online Mapping Tools to Support STEM Learning through Analysis of the Impact of Land Use/Land Cover Change on Water Quality

NASA Astrophysics Data System (ADS)

Powley, C.; Alian, S.; Mayer, A.

2017-12-01

In the 2004 National Water Quality Report to the Congress, the US EPA states that about 44% of the streams, 64% of lakes and 30% of estuaries that were assessed were not suitable for basic use like fishing and swimming. Pollutants from nonpoint sources are most likely the cause. The needs of landowners to use their land for other uses is enormous and most are likely willing to forgo the potential damage to achieve monetary gains. These are difficult decisions as there are many positive gains in commercialized development, although this comes with a cost. So it is imperative for all entities to work together in developing an awareness that benefits all stakeholders. We used this water quality management context to prepare lessons for high school students to map water quality problem areas in Rifle River and the West Branch in Ogemaw County, Michigan based on field samples and by using ESRI online data entry and mapping tools. The students also used Long Term Hydrologic Impact Analysis (L-THIA) to evaluate the impacts of different land use/cover types, developing an understanding of the implication of land management on surface water quality.

Toward shrimp consumption without chemicals: Combined effects of freezing and modified atmosphere packaging (MAP) on some quality characteristics of Giant Red Shrimp (Aristaeomorpha foliacea) during storage.

PubMed

Bono, Gioacchino; Okpala, Charles Odilichukwu R; Alberio, Giuseppina R A; Messina, Concetta M; Santulli, Andrea; Giacalone, Gabriele; Spagna, Giovanni

2016-04-15

The combined effects of freezing and modified atmosphere packaging (MAP) (100% N2 and 50% N2+50% CO2) on some quality characteristics of Giant Red Shrimp (GRS) (Aristaeomorpha foliacea) was studied during 12-month storage. In particular, the quality characteristics determined proximal and gas compositions, melanosis scores, pH, total volatile basic-nitrogen (TVB-N), thiobarbituric acid (TBA) as well as free amino acid (FAA). In addition, the emergent data were compared to those subject to vacuum packaging as well as conventional preservative method of sulphite treatment (SUL). Most determined qualities exhibited quantitative differences with storage. By comparisons, while pH and TVB-N statistically varied between treatments (P<0.05) and TBA that ranged between ∼0.15 and 0.30 mg MDA/kg appeared least at end of storage for 100% N2 treated-group, the latter having decreased melanosis scores showed such treatments with high promise to keep the colour of GRS sample hence, potential replacement for SUL group. By comparisons also, while some individual FAA values showed increases especially at the 100% N2-treated group, the total FAAs statistically differed with storage (P<0.05). The combination of freezing and MAP treatments as preservative treatment method shows high promise to influence some quality characteristics of GRS samples of this study. Copyright © 2015 Elsevier Ltd. All rights reserved.

National Atlas of the United States Maps

USGS Publications Warehouse

,

2001-01-01

The "National Atlas of the United States of America®", published by the U.S. Geological Survey (USGS) in 1970, is out of print, but many of its maps can be purchased separately. Maps that span facing pages in the atlas are printed on one sheet. Maps dated after 1970 and before 1997 are either revisions of original atlas maps or new maps published in the original atlas format. The USGS and its partners in government and industry began work on a new "National Atlas" in 1997. Though most new atlas products are designed for the World Wide Web, we are continuing our tradition of printing high-quality maps of America. In 1998, the first completely redesigned maps of the "National Atlas of the United States®" were published.

Dementia care mapping: an approach to quality audit of services for people with dementia in two health districts.

PubMed

Younger, D; Martin, G W

2000-11-01

The audit reported in this paper and submitted to the Psychiatry of Old Age Management group, assessed six units within each of two health districts in the UK. Using a nonparticipatory observation method in the units selected, the aim was to measure quality and the environment of care. Dependency levels of the clients/residents were also estimated to give a clearer picture of the setting and the care requirements. This was intended to establish a baseline for the units mapped and to enable care developments to be focussed upon intended outcomes. Results led to a number of observations related to the levels of interaction between staff and clients/residents, the need for a wider range of activities to promote person-centred care, and a suggested route to the improvement in quality of life for this vulnerable group of people. Assessment of dependency levels linked to the results of the mapping showed that high dependency does not lead automatically to a lower quality of person centred care.

Fast and Accurate Construction of Ultra-Dense Consensus Genetic Maps Using Evolution Strategy Optimization

PubMed Central

Mester, David; Ronin, Yefim; Schnable, Patrick; Aluru, Srinivas; Korol, Abraham

2015-01-01

Our aim was to develop a fast and accurate algorithm for constructing consensus genetic maps for chip-based SNP genotyping data with a high proportion of shared markers between mapping populations. Chip-based genotyping of SNP markers allows producing high-density genetic maps with a relatively standardized set of marker loci for different mapping populations. The availability of a standard high-throughput mapping platform simplifies consensus analysis by ignoring unique markers at the stage of consensus mapping thereby reducing mathematical complicity of the problem and in turn analyzing bigger size mapping data using global optimization criteria instead of local ones. Our three-phase analytical scheme includes automatic selection of ~100-300 of the most informative (resolvable by recombination) markers per linkage group, building a stable skeletal marker order for each data set and its verification using jackknife re-sampling, and consensus mapping analysis based on global optimization criterion. A novel Evolution Strategy optimization algorithm with a global optimization criterion presented in this paper is able to generate high quality, ultra-dense consensus maps, with many thousands of markers per genome. This algorithm utilizes "potentially good orders" in the initial solution and in the new mutation procedures that generate trial solutions, enabling to obtain a consensus order in reasonable time. The developed algorithm, tested on a wide range of simulated data and real world data (Arabidopsis), outperformed two tested state-of-the-art algorithms by mapping accuracy and computation time. PMID:25867943

Evaluation of radiometric and geometric characteristics of LANDSAT-D imaging system

NASA Technical Reports Server (NTRS)

Bender, L. U.; Podwysocki, M. H.; Rowan, L.; Salisbury, J. (Principal Investigator)

1983-01-01

Problems, accomplishments, and significant results associated with the evaluation of the LANDSAT-D thematic mapper system are outlined. The higher resolution (over MSS) causes the TM data to approach more closely the quality of high altitude photographs. Thus far, it appears that the data can be used for map inspection and in certain instances for limited map revision. Image maps can be made at a scale of 1:100,000 and perhaps up to 1:62,500. It was also shown that TM data can help locate rocks containing minerals with high hydroxol content, such as clays, gypsum, alunite, and sericite.

Automated map sharpening by maximization of detail and connectivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terwilliger, Thomas C.; Sobolev, Oleg V.; Afonine, Pavel V.

An algorithm for automatic map sharpening is presented that is based on optimization of the detail and connectivity of the sharpened map. The detail in the map is reflected in the surface area of an iso-contour surface that contains a fixed fraction of the volume of the map, where a map with high level of detail has a high surface area. The connectivity of the sharpened map is reflected in the number of connected regions defined by the same iso-contour surfaces, where a map with high connectivity has a small number of connected regions. By combining these two measures inmore » a metric termed the `adjusted surface area', map quality can be evaluated in an automated fashion. This metric was used to choose optimal map-sharpening parameters without reference to a model or other interpretations of the map. Map sharpening by optimization of the adjusted surface area can be carried out for a map as a whole or it can be carried out locally, yielding a locally sharpened map. To evaluate the performance of various approaches, a simple metric based on map–model correlation that can reproduce visual choices of optimally sharpened maps was used. The map–model correlation is calculated using a model withBfactors (atomic displacement factors; ADPs) set to zero. Finally, this model-based metric was used to evaluate map sharpening and to evaluate map-sharpening approaches, and it was found that optimization of the adjusted surface area can be an effective tool for map sharpening.« less

Automated map sharpening by maximization of detail and connectivity

DOE PAGES

Terwilliger, Thomas C.; Sobolev, Oleg V.; Afonine, Pavel V.; ...

2018-05-18

An algorithm for automatic map sharpening is presented that is based on optimization of the detail and connectivity of the sharpened map. The detail in the map is reflected in the surface area of an iso-contour surface that contains a fixed fraction of the volume of the map, where a map with high level of detail has a high surface area. The connectivity of the sharpened map is reflected in the number of connected regions defined by the same iso-contour surfaces, where a map with high connectivity has a small number of connected regions. By combining these two measures inmore » a metric termed the `adjusted surface area', map quality can be evaluated in an automated fashion. This metric was used to choose optimal map-sharpening parameters without reference to a model or other interpretations of the map. Map sharpening by optimization of the adjusted surface area can be carried out for a map as a whole or it can be carried out locally, yielding a locally sharpened map. To evaluate the performance of various approaches, a simple metric based on map–model correlation that can reproduce visual choices of optimally sharpened maps was used. The map–model correlation is calculated using a model withBfactors (atomic displacement factors; ADPs) set to zero. Finally, this model-based metric was used to evaluate map sharpening and to evaluate map-sharpening approaches, and it was found that optimization of the adjusted surface area can be an effective tool for map sharpening.« less

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

PubMed Central

Ganal, Martin W.; Durstewitz, Gregor; Polley, Andreas; Bérard, Aurélie; Buckler, Edward S.; Charcosset, Alain; Clarke, Joseph D.; Graner, Eva-Maria; Hansen, Mark; Joets, Johann; Le Paslier, Marie-Christine; McMullen, Michael D.; Montalent, Pierre; Rose, Mark; Schön, Chris-Carolin; Sun, Qi; Walter, Hildrun; Martin, Olivier C.; Falque, Matthieu

2011-01-01

SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations – IBM (B73×Mo17) and LHRF (F2×F252) – were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding. PMID:22174790

Major quality trait analysis and QTL detection in hexaploid wheat in humid rain-fed agriculture.

PubMed

Li, H M; Tang, Z X; Zhang, H Q; Yan, B J; Ren, Z L

2013-05-21

Humid rain-fed agriculture is a special environment for wheat (Triticum aestivum) culture that tends to negatively affect wheat yield and quality. To identify quality characters of wheat in a humid environment, we conducted quality analysis and quantitative trait loci (QTL) detection in a recombinant inbred line whose parent had a high level of quality for several years. We found that high-quality wheat had less gluten content and lower protein content. Apparently, wheat quality and associated quantity traits were in a dynamic state of equilibrium. We detected 83 QTL for 10 wheat quality traits in this recombinant inbred line population. Nine QTL were detected in both evaluation years; Q.DT.scau-2A, linked to Xwmc522-2A, was detected at the same genetic location in both years. Other QTL for different traits were detected simultaneously in more than one location. Consequently, there appeared to be pleiotropic genes that control wheat quality. Based on previous studies and our research on QTL analysis of grain protein content, we conclude that there must be one or more genes for grain protein content on chromosome 6B, whose expression was little affected by environment. We constructed a consensus map and projected the QTL on it. It was useful for choosing optimal markers for marker-assisted breeding and map-based cloning.

The First Genetic Map in Sweet Osmanthus (Osmanthus fragrans Lour.) Using Specific Locus Amplified Fragment Sequencing

PubMed Central

He, Yanxia; Yuan, Wangjun; Dong, Meifang; Han, Yuanji; Shang, Fude

2017-01-01

Osmanthus fragrans is an ornamental plant of substantial commercial value, and no genetic linkage maps of this species have previously been reported. Specific-locus amplified fragment sequencing (SLAF-seq) is a recently developed technology that allows massive single nucleotide polymorphisms (SNPs) to be identified and high-resolution genotyping. In our current research, we generated the first genetic map of O. fragrans using SLAF-seq, which is composed with 206.92 M paired-end reads and 173,537 SLAF markers. Among total 90,715 polymorphic SLAF markers, 15,317 polymorphic SLAFs could be used for genetic map construction. The integrated map contained 14,189 high quality SLAFs that were grouped in 23 genetic linkage groups, with a total length of 2962.46 cM and an average distance of 0.21 cM between two adjacent markers. In addition, 23,664 SNPs were identified from the mapped markers. As far as we know, this is the first of the genetic map of O. fragrans. Our results are further demonstrate that SLAF-seq is a very effective method for developing markers and constructing high-density linkage maps. The SNP markers and the genetic map reported in this study should be valuable resource in future research. PMID:29018460

Very High Quality Crystals of Wide-Gap II-VI Semiconductors: What for?

DTIC Science & Technology

2001-01-01

the reciprocal space mapping , by the etch pit density (EPD) measurements (to determine the density of dislocations) and by the measurement of the width...crystals. The EPD was in the range 5 x 1 + 104 cmn2 for Cdl.,ZnxTe crystals and about 104 cmz for ZnTe. The reciprocal space mapping of the crystals

A statistically valid method for using FIA plots to guide spectral class rejection in producing stratification maps

Treesearch

Michael L. Hoppus; Andrew J. Lister

2002-01-01

A Landsat TM classification method (iterative guided spectral class rejection) produced a forest cover map of southern West Virginia that provided the stratification layer for producing estimates of timberland area from Forest Service FIA ground plots using a stratified sampling technique. These same high quality and expensive FIA ground plots provided ground reference...

Can the theoretical domains framework account for the implementation of clinical quality interventions?

PubMed

Lipworth, Wendy; Taylor, Natalie; Braithwaite, Jeffrey

2013-12-21

The health care quality improvement movement is a complex enterprise. Implementing clinical quality initiatives requires attitude and behaviour change on the part of clinicians, but this has proven to be difficult. In an attempt to solve this kind of behavioural challenge, the theoretical domains framework (TDF) has been developed. The TDF consists of 14 domains from psychological and organisational theory said to influence behaviour change. No systematic research has been conducted into the ways in which clinical quality initiatives map on to the domains of the framework. We therefore conducted a qualitative mapping experiment to determine to what extent, and in what ways, the TDF is relevant to the implementation of clinical quality interventions. We conducted a thematic synthesis of the qualitative literature exploring clinicians' perceptions of various clinical quality interventions. We analysed and synthesised 50 studies in total, in five domains of clinical quality interventions: clinical quality interventions in general, structural interventions, audit-type interventions, interventions aimed at making practice more evidence-based, and risk management interventions. Data were analysed thematically, followed by synthesis of these themes into categories and concepts, which were then mapped to the domains of the TDF. Our results suggest that the TDF is highly relevant to the implementation of clinical quality interventions. It can be used to map most, if not all, of the attitudinal and behavioural barriers and facilitators of uptake of clinical quality interventions. Each of these 14 domains appeared to be relevant to many different types of clinical quality interventions. One possible additional domain might relate to perceived trustworthiness of those instituting clinical quality interventions. The TDF can be usefully applied to a wide range of clinical quality interventions. Because all 14 of the domains emerged as relevant, and we did not identify any obvious differences between different kinds of clinical quality interventions, our findings support an initially broad approach to identifying barriers and facilitators, followed by a "drilling down" to what is most contextually salient. In future, it may be possible to establish a model of clinical quality policy implementation using the TDF.

Can the theoretical domains framework account for the implementation of clinical quality interventions?

PubMed Central

2013-01-01

Background The health care quality improvement movement is a complex enterprise. Implementing clinical quality initiatives requires attitude and behaviour change on the part of clinicians, but this has proven to be difficult. In an attempt to solve this kind of behavioural challenge, the theoretical domains framework (TDF) has been developed. The TDF consists of 14 domains from psychological and organisational theory said to influence behaviour change. No systematic research has been conducted into the ways in which clinical quality initiatives map on to the domains of the framework. We therefore conducted a qualitative mapping experiment to determine to what extent, and in what ways, the TDF is relevant to the implementation of clinical quality interventions. Methods We conducted a thematic synthesis of the qualitative literature exploring clinicians’ perceptions of various clinical quality interventions. We analysed and synthesised 50 studies in total, in five domains of clinical quality interventions: clinical quality interventions in general, structural interventions, audit-type interventions, interventions aimed at making practice more evidence-based, and risk management interventions. Data were analysed thematically, followed by synthesis of these themes into categories and concepts, which were then mapped to the domains of the TDF. Results Our results suggest that the TDF is highly relevant to the implementation of clinical quality interventions. It can be used to map most, if not all, of the attitudinal and behavioural barriers and facilitators of uptake of clinical quality interventions. Each of these 14 domains appeared to be relevant to many different types of clinical quality interventions. One possible additional domain might relate to perceived trustworthiness of those instituting clinical quality interventions. Conclusions The TDF can be usefully applied to a wide range of clinical quality interventions. Because all 14 of the domains emerged as relevant, and we did not identify any obvious differences between different kinds of clinical quality interventions, our findings support an initially broad approach to identifying barriers and facilitators, followed by a “drilling down” to what is most contextually salient. In future, it may be possible to establish a model of clinical quality policy implementation using the TDF. PMID:24359085

Correlation-based perfusion mapping using time-resolved MR angiography: A feasibility study for patients with suspicions of steno-occlusive craniocervical arteries.

PubMed

Nam, Yoonho; Jang, Jinhee; Park, Sonya Youngju; Choi, Hyun Seok; Jung, So-Lyung; Ahn, Kook-Jin; Kim, Bum-Soo

2018-05-22

To explore the feasibility of using correlation-based time-delay (CTD) maps produced from time-resolved MR angiography (TRMRA) to diagnose perfusion abnormalities in patients suspected to have steno-occlusive lesions in the craniocervical arteries. Twenty-seven patients who were suspected to have steno-occlusive lesions in the craniocervical arteries underwent both TRMRA and brain single-photon emission computed tomography (SPECT). TRMRA was performed on the supra-aortic area after intravenous injection of a 0.03 mmol/kg gadolinium-based contrast agent. Time-to-peak (TTP) maps and CTD maps of the brain were automatically generated from TRMRA data, and their quality was assessed. Detection of perfusion abnormalities was compared between CTD maps and the time-series maximal intensity projection (MIP) images from TRMRA and TTP maps. Correlation coefficients between quantitative changes in SPECT and parametric maps for the abnormal perfusion areas were calculated. The CTD maps were of significantly superior quality than TTP maps (p < 0.01). For perfusion abnormality detection, CTD maps (kappa 0.84, 95% confidence interval [CI] 0.67-1.00) showed better agreement with SPECT than TTP maps (0.66, 0.46-0.85). For perfusion deficit detection, CTD maps showed higher accuracy (85.2%, 95% CI 66.3-95.8) than MIP images (66.7%, 46-83.5), with marginal significance (p = 0.07). In abnormal perfusion areas, correlation coefficients between SPECT and CTD (r = 0.74, 95% CI 0.34-0.91) were higher than those between SPECT and TTP (r = 0.66, 0.20-0.88). CTD maps generated from TRMRA were of high quality and offered good diagnostic performance for detecting perfusion abnormalities associated with steno-occlusive arterial lesions in the craniocervical area. • Generation of perfusion parametric maps from time-resolved MR angiography is clinically useful. • Correlation-based delay maps can be used to detect perfusion abnormalities associated with steno-occlusive craniocervical arteries. • Estimation of correlation-based delay is robust for low signal-to-noise 4D MR data.

A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping.

PubMed

Wen, Qing; Kim, Chang-Sik; Hamilton, Peter W; Zhang, Shu-Dong

2016-05-11

Gene expression connectivity mapping has gained much popularity recently with a number of successful applications in biomedical research testifying its utility and promise. Previously methodological research in connectivity mapping mainly focused on two of the key components in the framework, namely, the reference gene expression profiles and the connectivity mapping algorithms. The other key component in this framework, the query gene signature, has been left to users to construct without much consensus on how this should be done, albeit it has been an issue most relevant to end users. As a key input to the connectivity mapping process, gene signature is crucially important in returning biologically meaningful and relevant results. This paper intends to formulate a standardized procedure for constructing high quality gene signatures from a user's perspective. We describe a two-stage process for making quality gene signatures using gene expression data as initial inputs. First, a differential gene expression analysis comparing two distinct biological states; only the genes that have passed stringent statistical criteria are considered in the second stage of the process, which involves ranking genes based on statistical as well as biological significance. We introduce a "gene signature progression" method as a standard procedure in connectivity mapping. Starting from the highest ranked gene, we progressively determine the minimum length of the gene signature that allows connections to the reference profiles (drugs) being established with a preset target false discovery rate. We use a lung cancer dataset and a breast cancer dataset as two case studies to demonstrate how this standardized procedure works, and we show that highly relevant and interesting biological connections are returned. Of particular note is gefitinib, identified as among the candidate therapeutics in our lung cancer case study. Our gene signature was based on gene expression data from Taiwan female non-smoker lung cancer patients, while there is evidence from independent studies that gefitinib is highly effective in treating women, non-smoker or former light smoker, advanced non-small cell lung cancer patients of Asian origin. In summary, we introduced a gene signature progression method into connectivity mapping, which enables a standardized procedure for constructing high quality gene signatures. This progression method is particularly useful when the number of differentially expressed genes identified is large, and when there is a need to prioritize them to be included in the query signature. The results from two case studies demonstrate that the approach we have developed is capable of obtaining pertinent candidate drugs with high precision.

An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus)

PubMed Central

2014-01-01

Background Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Results Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. Conclusions The integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A large proportion of the markers in the integrated map are SSRs, InDels and SNPs, which are easily transferable across laboratories. Moreover, the populations used to construct the integrated map include all three watermelon subspecies, making this integrated map useful for the selection of breeding traits, identification of QTL, MAS, analysis of germplasm and commercial hybrid seed detection. PMID:24443961

Covariance and correlation estimation in electron-density maps.

PubMed

Altomare, Angela; Cuocci, Corrado; Giacovazzo, Carmelo; Moliterni, Anna; Rizzi, Rosanna

2012-03-01

Quite recently two papers have been published [Giacovazzo & Mazzone (2011). Acta Cryst. A67, 210-218; Giacovazzo et al. (2011). Acta Cryst. A67, 368-382] which calculate the variance in any point of an electron-density map at any stage of the phasing process. The main aim of the papers was to associate a standard deviation to each pixel of the map, in order to obtain a better estimate of the map reliability. This paper deals with the covariance estimate between points of an electron-density map in any space group, centrosymmetric or non-centrosymmetric, no matter the correlation between the model and target structures. The aim is as follows: to verify if the electron density in one point of the map is amplified or depressed as an effect of the electron density in one or more other points of the map. High values of the covariances are usually connected with undesired features of the map. The phases are the primitive random variables of our probabilistic model; the covariance changes with the quality of the model and therefore with the quality of the phases. The conclusive formulas show that the covariance is also influenced by the Patterson map. Uncertainty on measurements may influence the covariance, particularly in the final stages of the structure refinement; a general formula is obtained taking into account both phase and measurement uncertainty, valid at any stage of the crystal structure solution.

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.)

PubMed Central

Guo, Yinshan; Shi, Guangli; Liu, Zhendong; Zhao, Yuhui; Yang, Xiaoxu; Zhu, Junchi; Li, Kun; Guo, Xiuwu

2015-01-01

In this study, 149 F1 plants from the interspecific cross between ‘Red Globe’ (Vitis vinifera L.) and ‘Shuangyou’ (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for ‘Red Globe,’ 63.65 for ‘Shuangyou,’ and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape. PMID:26089826

Scales of heterogeneity of water quality in rivers: Insights from high resolution maps based on integrated geospatial, sensor and ROV technologies

EPA Science Inventory

While the spatial heterogeneity of many aquatic ecosystems is acknowledged, rivers are often mistakenly described as homogenous and well-mixed. The collection and visualization of attributes like water quality is key to our perception and management of these ecosystems. The ass...

Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing

USDA-ARS?s Scientific Manuscript database

Predicted rising global temperatures due to climate change have generated a demand for crops that are resistant to yield and quality losses from heat stress. Broccoli (Brassica oleracea var. italica) is a cool weather crop with high temperatures during production decreasing both head quality and yie...

Effect of packaging atmospheres on storage quality characteristics of heavily marbled beef longissimus steaks.

PubMed

Yang, Xiaoyin; Zhang, Yimin; Zhu, Lixian; Han, Mingshan; Gao, Shujuan; Luo, Xin

2016-07-01

The objective of this study was to investigate the effects of modified atmosphere packaging (MAP) systems on shelf-life and quality of beef steaks with high marbling. Four packaging types were used including 80% O2 MAP (80% O2+20% CO2), 50% O2 MAP (50% O2+30% CO2+20% N2), carbon monoxide MAP (0.4% CO+30% CO2+69.6% N2) and vacuum packaging (VP). Steaks were displayed under simulated retail conditions at 4°C for 12days. Purge loss, pH, color stability, oxidative stability and microbial counts were monitored. Aerobically packaged steaks exhibited a bright-red color at the first 4days. However, discoloration and oxidation became major factors limiting their shelf-life to 8days. Compared with aerobic packaging, anaerobic packaging extended shelf-life of heavily marbled beef steaks, due to better color stability, together with lower oxidation and microbial populations. Among all packaging methods, CO-MAP had the best preservation for steaks, with more red color than other packaging types. Copyright © 2016 Elsevier Ltd. All rights reserved.

Earth mapping - aerial or satellite imagery comparative analysis

NASA Astrophysics Data System (ADS)

Fotev, Svetlin; Jordanov, Dimitar; Lukarski, Hristo

Nowadays, solving the tasks for revision of existing map products and creation of new maps requires making a choice of the land cover image source. The issue of the effectiveness and cost of the usage of aerial mapping systems versus the efficiency and cost of very-high resolution satellite imagery is topical [1, 2, 3, 4]. The price of any remotely sensed image depends on the product (panchromatic or multispectral), resolution, processing level, scale, urgency of task and on whether the needed image is available in the archive or has to be requested. The purpose of the present work is: to make a comparative analysis between the two approaches for mapping the Earth having in mind two parameters: quality and cost. To suggest an approach for selection of the map information sources - airplane-based or spacecraft-based imaging systems with very-high spatial resolution. Two cases are considered: area that equals approximately one satellite scene and area that equals approximately the territory of Bulgaria.

Chromosomes 3B and 4D are associated with several milling and baking quality traits in a soft white spring wheat (Triticum aestivum L.) population.

PubMed

Carter, A H; Garland-Campbell, K; Morris, C F; Kidwell, K K

2012-04-01

Wheat is marketed based on end-use quality characteristics and better knowledge of the underlying genetics of specific quality parameters is essential to enhance the breeding process. A set of 188 recombinant inbred lines from a 'Louise' by 'Penawawa' mapping population was grown in two crop years at two locations in the Pacific Northwest region of the United States and data were collected on 17 end-use quality traits using established quality analysis protocols. Using an established genetic linkage map, composite interval mapping was used to identify QTL associated with 16 of the 17 quality traits. QTL were found on 13 of the 21 wheat chromosomes. A large number of QTL were located on chromosomes 3B and 4D and coincided with traits for milling quality and starch functionality. Chromosome 3B contained 10 QTL, which were localized to a 26.2 cM region. Chromosome 4D contained 7 QTL, all of which were located on an 18.8 cM region of this chromosome. The majority of the alleles for superior end-use quality were associated with the cultivar Louise. The identified QTL detected remained highly significant independent of grain yield and protein quantity. The identification of these QTL for end-use quality gives key insight into the relationship and complexity of end-use quality traits. It also improves our understanding of these relationships, thereby allowing plant breeders to make valuable gains from selection for these important traits.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

PubMed

Zheng, Qi; Grice, Elizabeth A

2016-10-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

Water Deficit and Salinity Stress Reveal Many Specific QTL for Plant Growth and Fruit Quality Traits in Tomato

PubMed Central

Diouf, Isidore A.; Derivot, Laurent; Bitton, Frédérique; Pascual, Laura; Causse, Mathilde

2018-01-01

Quality is a key trait in plant breeding, especially for fruit and vegetables. Quality involves several polygenic components, often influenced by environmental conditions with variable levels of genotype × environment interaction that must be considered in breeding strategies aiming to improve quality. In order to assess the impact of water deficit and salinity on tomato fruit quality, we evaluated a multi-parent advanced generation intercross (MAGIC) tomato population in contrasted environmental conditions over 2 years, one year in control vs. drought condition and the other in control vs. salt condition. Overall 250 individual lines from the MAGIC population—derived from eight parental lines covering a large diversity in cultivated tomato—were used to identify QTL in both experiments for fruit quality and yield component traits (fruit weight, number of fruit, Soluble Solid Content, firmness), phenology traits (time to flower and ripe) and a vegetative trait, leaf length. All the traits showed a large genotype variation (33–86% of total phenotypic variation) in both experiments and high heritability whatever the year or treatment. Significant genotype × treatment interactions were detected for five of the seven traits over the 2 years of experiments. QTL were mapped using 1,345 SNP markers. A total of 54 QTL were found among which 15 revealed genotype × environment interactions and 65% (35 QTL) were treatment specific. Confidence intervals of the QTL were projected on the genome physical map and allowed identifying regions carrying QTL co-localizations, suggesting pleiotropic regulation. We then applied a strategy for candidate gene detection based on the high resolution mapping offered by the MAGIC population, the allelic effect of each parental line at the QTL and the sequence information of the eight parental lines. PMID:29559986

Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits

PubMed Central

Albert, Elise; Segura, Vincent; Gricourt, Justine; Bonnefoi, Julien; Derivot, Laurent; Causse, Mathilde

2016-01-01

Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses. PMID:27856709

A fruit quality gene map of Prunus

PubMed Central

2009-01-01

Background Prunus fruit development, growth, ripening, and senescence includes major biochemical and sensory changes in texture, color, and flavor. The genetic dissection of these complex processes has important applications in crop improvement, to facilitate maximizing and maintaining stone fruit quality from production and processing through to marketing and consumption. Here we present an integrated fruit quality gene map of Prunus containing 133 genes putatively involved in the determination of fruit texture, pigmentation, flavor, and chilling injury resistance. Results A genetic linkage map of 211 markers was constructed for an intraspecific peach (Prunus persica) progeny population, Pop-DG, derived from a canning peach cultivar 'Dr. Davis' and a fresh market cultivar 'Georgia Belle'. The Pop-DG map covered 818 cM of the peach genome and included three morphological markers, 11 ripening candidate genes, 13 cold-responsive genes, 21 novel EST-SSRs from the ChillPeach database, 58 previously reported SSRs, 40 RAFs, 23 SRAPs, 14 IMAs, and 28 accessory markers from candidate gene amplification. The Pop-DG map was co-linear with the Prunus reference T × E map, with 39 SSR markers in common to align the maps. A further 158 markers were bin-mapped to the reference map: 59 ripening candidate genes, 50 cold-responsive genes, and 50 novel EST-SSRs from ChillPeach, with deduced locations in Pop-DG via comparative mapping. Several candidate genes and EST-SSRs co-located with previously reported major trait loci and quantitative trait loci for chilling injury symptoms in Pop-DG. Conclusion The candidate gene approach combined with bin-mapping and availability of a community-recognized reference genetic map provides an efficient means of locating genes of interest in a target genome. We highlight the co-localization of fruit quality candidate genes with previously reported fruit quality QTLs. The fruit quality gene map developed here is a valuable tool for dissecting the genetic architecture of fruit quality traits in Prunus crops. PMID:19995417

Deblurring adaptive optics retinal images using deep convolutional neural networks.

PubMed

Fei, Xiao; Zhao, Junlei; Zhao, Haoxin; Yun, Dai; Zhang, Yudong

2017-12-01

The adaptive optics (AO) can be used to compensate for ocular aberrations to achieve near diffraction limited high-resolution retinal images. However, many factors such as the limited aberration measurement and correction accuracy with AO, intraocular scatter, imaging noise and so on will degrade the quality of retinal images. Image post processing is an indispensable and economical method to make up for the limitation of AO retinal imaging procedure. In this paper, we proposed a deep learning method to restore the degraded retinal images for the first time. The method directly learned an end-to-end mapping between the blurred and restored retinal images. The mapping was represented as a deep convolutional neural network that was trained to output high-quality images directly from blurry inputs without any preprocessing. This network was validated on synthetically generated retinal images as well as real AO retinal images. The assessment of the restored retinal images demonstrated that the image quality had been significantly improved.

Deblurring adaptive optics retinal images using deep convolutional neural networks

PubMed Central

Fei, Xiao; Zhao, Junlei; Zhao, Haoxin; Yun, Dai; Zhang, Yudong

2017-01-01

The adaptive optics (AO) can be used to compensate for ocular aberrations to achieve near diffraction limited high-resolution retinal images. However, many factors such as the limited aberration measurement and correction accuracy with AO, intraocular scatter, imaging noise and so on will degrade the quality of retinal images. Image post processing is an indispensable and economical method to make up for the limitation of AO retinal imaging procedure. In this paper, we proposed a deep learning method to restore the degraded retinal images for the first time. The method directly learned an end-to-end mapping between the blurred and restored retinal images. The mapping was represented as a deep convolutional neural network that was trained to output high-quality images directly from blurry inputs without any preprocessing. This network was validated on synthetically generated retinal images as well as real AO retinal images. The assessment of the restored retinal images demonstrated that the image quality had been significantly improved. PMID:29296496

BikeMaps.org: A Global Tool for Collision and Near Miss Mapping

PubMed Central

Nelson, Trisalyn A.; Denouden, Taylor; Jestico, Benjamin; Laberee, Karen; Winters, Meghan

2015-01-01

There are many public health benefits to cycling, such as chronic disease reduction and improved air quality. Real and perceived concerns about safety are primary barriers to new ridership. Due to limited forums for official reporting of cycling incidents, lack of comprehensive data is limiting our ability to study cycling safety and conduct surveillance. Our goal is to introduce BikeMaps.org, a new website developed by the authors for crowd-source mapping of cycling collisions and near misses. BikeMaps.org is a global mapping system that allows citizens to map locations of cycling incidents and report on the nature of the event. Attributes collected are designed for spatial modeling research on predictors of safety and risk, and to aid surveillance and planning. Released in October 2014, within 2 months the website had more than 14,000 visitors and mapping in 14 countries. Collisions represent 38% of reports (134/356) and near misses 62% (222/356). In our pilot city, Victoria, Canada, citizens mapped data equivalent to about 1 year of official cycling collision reports within 2 months via BikeMaps.org. Using report completeness as an indicator, early reports indicate that data are of high quality with 50% being fully attributed and another 10% having only one missing attribute. We are advancing this technology, with the development of a mobile App, improved data visualization, real-time altering of hazard reports, and automated open-source tools for data sharing. Researchers and citizens interested in utilizing the BikeMaps.org technology can get involved by encouraging citizen mapping in their region. PMID:25870852

BikeMaps.org: A Global Tool for Collision and Near Miss Mapping.

PubMed

Nelson, Trisalyn A; Denouden, Taylor; Jestico, Benjamin; Laberee, Karen; Winters, Meghan

2015-01-01

There are many public health benefits to cycling, such as chronic disease reduction and improved air quality. Real and perceived concerns about safety are primary barriers to new ridership. Due to limited forums for official reporting of cycling incidents, lack of comprehensive data is limiting our ability to study cycling safety and conduct surveillance. Our goal is to introduce BikeMaps.org, a new website developed by the authors for crowd-source mapping of cycling collisions and near misses. BikeMaps.org is a global mapping system that allows citizens to map locations of cycling incidents and report on the nature of the event. Attributes collected are designed for spatial modeling research on predictors of safety and risk, and to aid surveillance and planning. Released in October 2014, within 2 months the website had more than 14,000 visitors and mapping in 14 countries. Collisions represent 38% of reports (134/356) and near misses 62% (222/356). In our pilot city, Victoria, Canada, citizens mapped data equivalent to about 1 year of official cycling collision reports within 2 months via BikeMaps.org. Using report completeness as an indicator, early reports indicate that data are of high quality with 50% being fully attributed and another 10% having only one missing attribute. We are advancing this technology, with the development of a mobile App, improved data visualization, real-time altering of hazard reports, and automated open-source tools for data sharing. Researchers and citizens interested in utilizing the BikeMaps.org technology can get involved by encouraging citizen mapping in their region.

Cause-and-effect mapping of critical events.

PubMed

Graves, Krisanne; Simmons, Debora; Galley, Mark D

2010-06-01

Health care errors are routinely reported in the scientific and public press and have become a major concern for most Americans. In learning to identify and analyze errors health care can develop some of the skills of a learning organization, including the concept of systems thinking. Modern experts in improving quality have been working in other high-risk industries since the 1920s making structured organizational changes through various frameworks for quality methods including continuous quality improvement and total quality management. When using these tools, it is important to understand systems thinking and the concept of processes within organization. Within these frameworks of improvement, several tools can be used in the analysis of errors. This article introduces a robust tool with a broad analytical view consistent with systems thinking, called CauseMapping (ThinkReliability, Houston, TX, USA), which can be used to systematically analyze the process and the problem at the same time. Copyright 2010 Elsevier Inc. All rights reserved.

Combinatorial materials synthesis and high-throughput screening: an integrated materials chip approach to mapping phase diagrams and discovery and optimization of functional materials.

PubMed

Xiang, X D

Combinatorial materials synthesis methods and high-throughput evaluation techniques have been developed to accelerate the process of materials discovery and optimization and phase-diagram mapping. Analogous to integrated circuit chips, integrated materials chips containing thousands of discrete different compositions or continuous phase diagrams, often in the form of high-quality epitaxial thin films, can be fabricated and screened for interesting properties. Microspot x-ray method, various optical measurement techniques, and a novel evanescent microwave microscope have been used to characterize the structural, optical, magnetic, and electrical properties of samples on the materials chips. These techniques are routinely used to discover/optimize and map phase diagrams of ferroelectric, dielectric, optical, magnetic, and superconducting materials.

User’s manual for the Automated Data Assurance and Management application developed for quality control of Everglades Depth Estimation Network water-level data

USGS Publications Warehouse

Petkewich, Matthew D.; Daamen, Ruby C.; Roehl, Edwin A.; Conrads, Paul

2016-09-29

The generation of Everglades Depth Estimation Network (EDEN) daily water-level and water-depth maps is dependent on high quality real-time data from over 240 water-level stations. To increase the accuracy of the daily water-surface maps, the Automated Data Assurance and Management (ADAM) tool was created by the U.S. Geological Survey as part of Greater Everglades Priority Ecosystems Science. The ADAM tool is used to provide accurate quality-assurance review of the real-time data from the EDEN network and allows estimation or replacement of missing or erroneous data. This user’s manual describes how to install and operate the ADAM software. File structure and operation of the ADAM software is explained using examples.

Bacterial pathogen gene abundance and relation to recreational water quality at seven Great Lakes beaches.

PubMed

Oster, Ryan J; Wijesinghe, Rasanthi U; Haack, Sheridan K; Fogarty, Lisa R; Tucker, Taaja R; Riley, Stephen C

2014-12-16

Quantitative assessment of bacterial pathogens, their geographic variability, and distribution in various matrices at Great Lakes beaches are limited. Quantitative PCR (qPCR) was used to test for genes from E. coli O157:H7 (eaeO157), shiga-toxin producing E. coli (stx2), Campylobacter jejuni (mapA), Shigella spp. (ipaH), and a Salmonella enterica-specific (SE) DNA sequence at seven Great Lakes beaches, in algae, water, and sediment. Overall, detection frequencies were mapA>stx2>ipaH>SE>eaeO157. Results were highly variable among beaches and matrices; some correlations with environmental conditions were observed for mapA, stx2, and ipaH detections. Beach seasonal mean mapA abundance in water was correlated with beach seasonal mean log10 E. coli concentration. At one beach, stx2 gene abundance was positively correlated with concurrent daily E. coli concentrations. Concentration distributions for stx2, ipaH, and mapA within algae, sediment, and water were statistically different (Non-Detect and Data Analysis in R). Assuming 10, 50, or 100% of gene copies represented viable and presumably infective cells, a quantitative microbial risk assessment tool developed by Michigan State University indicated a moderate probability of illness for Campylobacter jejuni at the study beaches, especially where recreational water quality criteria were exceeded. Pathogen gene quantification may be useful for beach water quality management.

Genetic complexity of miscanthus cell wall composition and biomass quality for biofuels.

PubMed

van der Weijde, Tim; Kamei, Claire L Alvim; Severing, Edouard I; Torres, Andres F; Gomez, Leonardo D; Dolstra, Oene; Maliepaard, Chris A; McQueen-Mason, Simon J; Visser, Richard G F; Trindade, Luisa M

2017-05-25

Miscanthus sinensis is a high yielding perennial grass species with great potential as a bioenergy feedstock. One of the challenges that currently impedes commercial cellulosic biofuel production is the technical difficulty to efficiently convert lignocellulosic biomass into biofuel. The development of feedstocks with better biomass quality will improve conversion efficiency and the sustainability of the value-chain. Progress in the genetic improvement of biomass quality may be substantially expedited by the development of genetic markers associated to quality traits, which can be used in a marker-assisted selection program. To this end, a mapping population was developed by crossing two parents of contrasting cell wall composition. The performance of 182 F1 offspring individuals along with the parents was evaluated in a field trial with a randomized block design with three replicates. Plants were phenotyped for cell wall composition and conversion efficiency characters in the second and third growth season after establishment. A new SNP-based genetic map for M. sinensis was built using a genotyping-by-sequencing (GBS) approach, which resulted in 464 short-sequence uniparental markers that formed 16 linkage groups in the male map and 17 linkage groups in the female map. A total of 86 QTLs for a variety of biomass quality characteristics were identified, 20 of which were detected in both growth seasons. Twenty QTLs were directly associated to different conversion efficiency characters. Marker sequences were aligned to the sorghum reference genome to facilitate cross-species comparisons. Analyses revealed that for some traits previously identified QTLs in sorghum occurred in homologous regions on the same chromosome. In this work we report for the first time the genetic mapping of cell wall composition and bioconversion traits in the bioenergy crop miscanthus. These results are a first step towards the development of marker-assisted selection programs in miscanthus to improve biomass quality and facilitate its use as feedstock for biofuel production.

Rapid mapping of schistosomiasis and other neglected tropical diseases in the context of integrated control programmes in Africa

PubMed Central

BROOKER, S.; KABATEREINE, N. B.; GYAPONG, J. O.; STOTHARD, J. R.; UTZINGER, J.

2009-01-01

SUMMARY There is growing interest and commitment to the control of schistosomiasis and other so-called neglected tropical diseases (NTDs). Resources for control are inevitably limited, necessitating assessment methods that can rapidly and accurately identify and map high-risk communities so that interventions can be targeted in a spatially-explicit and cost-effective manner. Here, we review progress made with (i) mapping schistosomiasis across Africa using available epidemiological data and more recently, climate-based risk prediction; (ii) the development and use of morbidity questionnaires for rapid identification of high-risk communities of urinary schistosomiasis; and (iii) innovative sampling-based approaches for intestinal schistosomiasis, using the lot quality assurance sampling technique. Experiences are also presented for the rapid mapping of other NTDs, including onchocerciasis, loiasis and lymphatic filariasis. Future directions for an integrated rapid mapping approach targeting multiple NTDs simultaneously are outlined, including potential challenges in developing an integrated survey tool. The lessons from the mapping of human helminth infections may also be relevant for the rapid mapping of malaria as its control efforts are intensified. PMID:19450373

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willard, H.F.; Cremers, F.; Mandel, J.L.

A high-quality integrated genetic and physical map of the X chromosome from telomere to telomere, based primarily on YACs formatted with probes and STSs, is increasingly close to reality. At the Fifth International X Chromosome Workshop, organized by A.M. Poustka and D. Schlessinger in Heidelberg, Germany, April 24--27, 1994, substantial progress was recorded on extension and refinement of the physical map, on the integration of genetic and cytogenetic data, on attempts to use the map to direct gene searches, and on nascent large-scale sequencing efforts. This report summarizes physical and genetic mapping information presented at the workshop and/or published sincemore » the reports of the fourth International X Chromosome Workshop. The principle aim of the workshop was to derive a consensus map of the chromosome, in terms of physical contigs emphasizing the location of genes and microsatellite markers. The resulting map is presented and updates previous versions. This report also updates the list of highly informative microsatellites. The text highlights the working state of the map, the genes known to reside on the X, and the progress toward integration of various types of data.« less

Combined effect of MAP and active compounds on fresh blue fish burger.

PubMed

Del Nobile, M A; Corbo, M R; Speranza, B; Sinigaglia, M; Conte, A; Caroprese, M

2009-11-15

The combined effects of three essential oils [thymol, lemon extract and grapefruit seed extract (GFSE)] and modified atmosphere packaging conditions (MAP) on quality retention of blue fish burgers was studied and discussed. In particular, samples were packaged in air and in three different gas mix compositions: 30:40:30 O(2):CO(2):N(2), 50:50 O(2):CO(2) and 5:95 O(2):CO(2). During a 28-day storage period at 4 degrees C, the nutritional, microbiological and sensorial quality of the packed products was assessed. The potential development of biogenic amines was also evaluated. The obtained results highlight the possibility to improve the microbial quality of blue fish burgers by using very small amount of thymol (110ppm), GFSE (100ppm) and lemon extract (120ppm) in combination with MAP. Based primarily on microbiological results, the combined use of the tested natural preservatives and a packaging system characterized by a high CO(2)-concentration, was able to guarantee the microbial acceptability of fish burgers until the 28th day of storage at 4 degrees C. On the other hand, results from sensory analyses showed that sensorial quality was the sub-index that limited the burgers shelf life (to about 22-23days), even if the proposed strategy was also effective in minimizing the sensory quality loss of the product having no effect on its nutritional quality.

MAGSAT anomaly map and continental drift

NASA Technical Reports Server (NTRS)

Lemouel, J. L. (Principal Investigator); Galdeano, A.; Ducruix, J.

1981-01-01

Anomaly maps of high quality are needed to display unambiguously the so called long wave length anomalies. The anomalies were analyzed in terms of continental drift and the nature of their sources is discussed. The map presented confirms the thinness of the oceanic magnetized layer. Continental magnetic anomalies are characterized by elongated structures generally of east-west trend. Paleomagnetic reconstruction shows that the anomalies found in India, Australia, and Antarctic exhibit a fair consistency with the African anomalies. It is also shown that anomalies are locked under the continents and have a fixed geometry.

Evidence of Water Quality Degradation in Lower Mekong Basin Revealed by Self-Organizing Map

PubMed Central

Chea, Ratha; Grenouillet, Gaël; Lek, Sovan

2016-01-01

To reach a better understanding of the spatial variability of water quality in the Lower Mekong Basin (LMB), the Self-Organizing Map (SOM) was used to classify 117 monitoring sites and hotspots of pollution within the basin identified according to water quality indicators and US-EPA guidelines. Four different clusters were identified based on their similar physicochemical characteristics. The majority of sites in upper (Laos and Thailand) and middle part (Cambodia) of the basin were grouped in two clusters, considered as good quality water with high DO and low nutrient levels. The other two clusters were mostly composed of sites in Mekong delta (Vietnam) and few sites in upstream tributaries (i.e., northwestern Thailand, Tonle Sap Lake, and swamps close to Vientiane), known for moderate to poor quality of water and characterized by high nutrient and dissolved solid levels. Overall, we found that the water in the mainstream was less polluted than its tributaries; eutrophication and salinity could be key factors affecting water quality in LMB. Moreover, the seasonal variation of water quality seemed to be less marked than spatial variation occurring along the longitudinal gradient of Mekong River. Significant degradations were mainly associated with human disturbance and particularly apparent in sites distributed along the man-made canals in Vietnam delta where population growth and agricultural development are intensive. PMID:26731522

Validation of projective mapping as potential sensory screening tool for application by the honeybush herbal tea industry.

PubMed

Moelich, Erika Ilette; Muller, Magdalena; Joubert, Elizabeth; Næs, Tormod; Kidd, Martin

2017-09-01

Honeybush herbal tea is produced from the endemic South African Cyclopia species. Plant material subjected to a high-temperature oxidation step ("fermentation") forms the bulk of production. Production lags behind demand forcing tea merchants to use blends of available material to supply local and international markets. The distinct differences in the sensory profiles of the herbal tea produced from the different Cyclopia species require that special care is given to blending to ensure a consistent, high quality product. Although conventional descriptive sensory analysis (DSA) is highly effective in providing a detailed sensory profile of herbal tea infusions, industry requires a method that is more time- and cost-effective. Recent advances in sensory science have led to the development of rapid profiling methodologies. The question is whether projective mapping can successfully be used for the sensory characterisation of herbal tea infusions. Trained assessors performed global and partial projective mapping to determine the validity of this technique for the sensory characterisation of infusions of five Cyclopia species. Similar product configurations were obtained when comparing results of DSA and global and partial projective mapping. Comparison of replicate sessions showed RV coefficients >0.8. A similarity index, based on multifactor analysis, was calculated to determine assessor repeatability. Global projective mapping, demonstrated to be a valid method for providing a broad sensory characterisation of Cyclopia species, is thus suitable as a rapid quality control method of honeybush infusions. Its application by the honeybush industry could improve the consistency of the sensory profile of blended products. Copyright © 2017 Elsevier Ltd. All rights reserved.

Event-Based Tone Mapping for Asynchronous Time-Based Image Sensor

PubMed Central

Simon Chane, Camille; Ieng, Sio-Hoi; Posch, Christoph; Benosman, Ryad B.

2016-01-01

The asynchronous time-based neuromorphic image sensor ATIS is an array of autonomously operating pixels able to encode luminance information with an exceptionally high dynamic range (>143 dB). This paper introduces an event-based methodology to display data from this type of event-based imagers, taking into account the large dynamic range and high temporal accuracy that go beyond available mainstream display technologies. We introduce an event-based tone mapping methodology for asynchronously acquired time encoded gray-level data. A global and a local tone mapping operator are proposed. Both are designed to operate on a stream of incoming events rather than on time frame windows. Experimental results on real outdoor scenes are presented to evaluate the performance of the tone mapping operators in terms of quality, temporal stability, adaptation capability, and computational time. PMID:27642275

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework

PubMed Central

Zheng, Qi; Grice, Elizabeth A.

2016-01-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost. PMID:27706155

Integration of remote sensing and geographic information systems for Great Lakes water quality monitoring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lathrop, R.G. Jr.

1988-01-01

The utility of three operational satellite remote sensing systems, namely, the Landsat Thematic Mapper (TM), the SPOT High Resolution Visible (HRV) sensors and the NOAA Advanced Very High Resolution Radiometer (AVHRR), were evaluated as a means of estimating water quality and surface temperature. Empirical calibration through linear regression techniques was used to relate near-simultaneously acquired satellite radiance/reflectance data and water quality observations obtained in Green Bay and the nearshore waters of Lake Michigan. Four dates of TM and one date each of SPOT and AVHRR imagery/surface reference data were acquired and analyzed. Highly significant relationships were identified between the TMmore » and SPOT data and secchi disk depth, nephelometric turbidity, chlorophyll a, total suspended solids (TSS), absorbance, and surface temperature (TM only). The AVHRR data were not analyzed independently but were used for comparison with the TM data. Calibrated water quality image maps were input to a PC-based raster GIS package, EPPL7. Pattern interpretation and spatial analysis techniques were used to document the circulation dynamics and model mixing processes in Green Bay. A GIS facilitates the retrieval, query and spatial analysis of mapped information and provides the framework for an integrated operational monitoring system for the Great Lakes.« less

Harvesting geographic features from heterogeneous raster maps

NASA Astrophysics Data System (ADS)

Chiang, Yao-Yi

2010-11-01

Raster maps offer a great deal of geospatial information and are easily accessible compared to other geospatial data. However, harvesting geographic features locked in heterogeneous raster maps to obtain the geospatial information is challenging. This is because of the varying image quality of raster maps (e.g., scanned maps with poor image quality and computer-generated maps with good image quality), the overlapping geographic features in maps, and the typical lack of metadata (e.g., map geocoordinates, map source, and original vector data). Previous work on map processing is typically limited to a specific type of map and often relies on intensive manual work. In contrast, this thesis investigates a general approach that does not rely on any prior knowledge and requires minimal user effort to process heterogeneous raster maps. This approach includes automatic and supervised techniques to process raster maps for separating individual layers of geographic features from the maps and recognizing geographic features in the separated layers (i.e., detecting road intersections, generating and vectorizing road geometry, and recognizing text labels). The automatic technique eliminates user intervention by exploiting common map properties of how road lines and text labels are drawn in raster maps. For example, the road lines are elongated linear objects and the characters are small connected-objects. The supervised technique utilizes labels of road and text areas to handle complex raster maps, or maps with poor image quality, and can process a variety of raster maps with minimal user input. The results show that the general approach can handle raster maps with varying map complexity, color usage, and image quality. By matching extracted road intersections to another geospatial dataset, we can identify the geocoordinates of a raster map and further align the raster map, separated feature layers from the map, and recognized features from the layers with the geospatial dataset. The road vectorization and text recognition results outperform state-of-art commercial products, and with considerably less user input. The approach in this thesis allows us to make use of the geospatial information of heterogeneous maps locked in raster format.

Response of antioxidant activity and sensory quality in fresh-cut pear as affected by high O2,active packaging compared with low O2 packaging

USDA-ARS?s Scientific Manuscript database

Effects of active modified atmosphere packaging (MAP, initial O2/CO2: 5/5; 30/5; 80/0) and passive packaging (initial O2/CO2: 20.8/0 (air)) on the antioxidant capacity and sensory quality of fresh-cut ‘Yaoshan’ pear stored at 4C for 12 days were investigated. Samples stored in high O2 (30% and 80%) ...

Mapping gully-affected areas in the region of Taroudannt, Morocco based on Object-Based Image Analysis (OBIA)

NASA Astrophysics Data System (ADS)

d'Oleire-Oltmanns, Sebastian; Marzolff, Irene; Tiede, Dirk; Blaschke, Thomas

2015-04-01

The need for area-wide landform mapping approaches, especially in terms of land degradation, can be ascribed to the fact that within area-wide landform mapping approaches, the (spatial) context of erosional landforms is considered by providing additional information on the physiography neighboring the distinct landform. This study presents an approach for the detection of gully-affected areas by applying object-based image analysis in the region of Taroudannt, Morocco, which is highly affected by gully erosion while simultaneously representing a major region of agro-industry with a high demand of arable land. Various sensors provide readily available high-resolution optical satellite data with a much better temporal resolution than 3D terrain data which lead to the development of an area-wide mapping approach to extract gully-affected areas using only optical satellite imagery. The classification rule-set was developed with a clear focus on virtual spatial independence within the software environment of eCognition Developer. This allows the incorporation of knowledge about the target objects under investigation. Only optical QuickBird-2 satellite data and freely-available OpenStreetMap (OSM) vector data were used as input data. The OSM vector data were incorporated in order to mask out plantations and residential areas. Optical input data are more readily available for a broad range of users compared to terrain data, which is considered to be a major advantage. The methodology additionally incorporates expert knowledge and freely-available vector data in a cyclic object-based image analysis approach. This connects the two fields of geomorphology and remote sensing. The classification results allow conclusions on the current distribution of gullies. The results of the classification were checked against manually delineated reference data incorporating expert knowledge based on several field campaigns in the area, resulting in an overall classification accuracy of 62%. The error of omission accounts for 38% and the error of commission for 16%, respectively. Additionally, a manual assessment was carried out to assess the quality of the applied classification algorithm. The limited error of omission contributes with 23% to the overall error of omission and the limited error of commission contributes with 98% to the overall error of commission. This assessment improves the results and confirms the high quality of the developed approach for area-wide mapping of gully-affected areas in larger regions. In the field of landform mapping, the overall quality of the classification results is often assessed with more than one method to incorporate all aspects adequately.

Quality-assurance and data-management plan for water-quality activities in the Kansas Water Science Center, 2014

USGS Publications Warehouse

Rasmussen, Teresa J.; Bennett, Trudy J.; Foster, Guy M.; Graham, Jennifer L.; Putnam, James E.

2014-01-01

As the Nation’s largest water, earth, and biological science and civilian mapping information agency, the U.S. Geological Survey is relied on to collect high-quality data, and produce factual and impartial interpretive reports. This quality-assurance and data-management plan provides guidance for water-quality activities conducted by the Kansas Water Science Center. Policies and procedures are documented for activities related to planning, collecting, storing, documenting, tracking, verifying, approving, archiving, and disseminating water-quality data. The policies and procedures described in this plan complement quality-assurance plans for continuous water-quality monitoring, surface-water, and groundwater activities in Kansas.

Mapping of chlorophyll a distributions in coastal zones

NASA Technical Reports Server (NTRS)

Johnson, R. W.

1978-01-01

It is pointed out that chlorophyll a is an important environmental parameter for monitoring water quality, nutrient loads, and pollution effects in coastal zones. High chlorophyll a concentrations occur in areas which have high nutrient inflows from sources such as sewage treatment plants and industrial wastes. Low chlorophyll a concentrations may be due to the addition of toxic substances from industrial wastes or other sources. Remote sensing provides an opportunity to assess distributions of water quality parameters, such as chlorophyll a. A description is presented of the chlorophyll a analysis and a quantitative mapping of the James River, Virginia. An approach considered by Johnson (1977) was used in the analysis. An application of the multiple regression analysis technique to a data set collected over the New York Bight, an environmentally different area of the coastal zone, is also discussed.

Application of terrestrial laser scanning to the development and updating of the base map

NASA Astrophysics Data System (ADS)

Klapa, Przemysław; Mitka, Bartosz

2017-06-01

The base map provides basic information about land to individuals, companies, developers, design engineers, organizations, and government agencies. Its contents include spatial location data for control network points, buildings, land lots, infrastructure facilities, and topographic features. As the primary map of the country, it must be developed in accordance with specific laws and regulations and be continuously updated. The base map is a data source used for the development and updating of derivative maps and other large scale cartographic materials such as thematic or topographic maps. Thanks to the advancement of science and technology, the quality of land surveys carried out by means of terrestrial laser scanning (TLS) matches that of traditional surveying methods in many respects. This paper discusses the potential application of output data from laser scanners (point clouds) to the development and updating of cartographic materials, taking Poland's base map as an example. A few research sites were chosen to present the method and the process of conducting a TLS land survey: a fragment of a residential area, a street, the surroundings of buildings, and an undeveloped area. The entire map that was drawn as a result of the survey was checked by comparing it to a map obtained from PODGiK (pol. Powiatowy Ośrodek Dokumentacji Geodezyjnej i Kartograficznej - Regional Centre for Geodetic and Cartographic Records) and by conducting a field inspection. An accuracy and quality analysis of the conducted fieldwork and deskwork yielded very good results, which provide solid grounds for predicating that cartographic materials based on a TLS point cloud are a reliable source of information about land. The contents of the map that had been created with the use of the obtained point cloud were very accurately located in space (x, y, z). The conducted accuracy analysis and the inspection of the performed works showed that high quality is characteristic of TLS surveys. The accuracy of determining the location of the various map contents has been estimated at 0.02-0.03 m. The map was developed in conformity with the applicable laws and regulations as well as with best practice requirements.

Fusion of High Resolution Multispectral Imagery in Vulnerable Coastal and Land Ecosystems.

PubMed

Ibarrola-Ulzurrun, Edurne; Gonzalo-Martin, Consuelo; Marcello-Ruiz, Javier; Garcia-Pedrero, Angel; Rodriguez-Esparragon, Dionisio

2017-01-25

Ecosystems provide a wide variety of useful resources that enhance human welfare, but these resources are declining due to climate change and anthropogenic pressure. In this work, three vulnerable ecosystems, including shrublands, coastal areas with dunes systems and areas of shallow water, are studied. As far as these resources' reduction is concerned, remote sensing and image processing techniques could contribute to the management of these natural resources in a practical and cost-effective way, although some improvements are needed for obtaining a higher quality of the information available. An important quality improvement is the fusion at the pixel level. Hence, the objective of this work is to assess which pansharpening technique provides the best fused image for the different types of ecosystems. After a preliminary evaluation of twelve classic and novel fusion algorithms, a total of four pansharpening algorithms was analyzed using six quality indices. The quality assessment was implemented not only for the whole set of multispectral bands, but also for the subset of spectral bands covered by the wavelength range of the panchromatic image and outside of it. A better quality result is observed in the fused image using only the bands covered by the panchromatic band range. It is important to highlight the use of these techniques not only in land and urban areas, but a novel analysis in areas of shallow water ecosystems. Although the algorithms do not show a high difference in land and coastal areas, coastal ecosystems require simpler algorithms, such as fast intensity hue saturation, whereas more heterogeneous ecosystems need advanced algorithms, as weighted wavelet ' à trous ' through fractal dimension maps for shrublands and mixed ecosystems. Moreover, quality map analysis was carried out in order to study the fusion result in each band at the local level. Finally, to demonstrate the performance of these pansharpening techniques, advanced Object-Based (OBIA) support vector machine classification was applied, and a thematic map for the shrubland ecosystem was obtained, which corroborates wavelet ' à trous ' through fractal dimension maps as the best fusion algorithm for this ecosystem.

Fusion of High Resolution Multispectral Imagery in Vulnerable Coastal and Land Ecosystems

PubMed Central

Ibarrola-Ulzurrun, Edurne; Gonzalo-Martin, Consuelo; Marcello-Ruiz, Javier; Garcia-Pedrero, Angel; Rodriguez-Esparragon, Dionisio

2017-01-01

Ecosystems provide a wide variety of useful resources that enhance human welfare, but these resources are declining due to climate change and anthropogenic pressure. In this work, three vulnerable ecosystems, including shrublands, coastal areas with dunes systems and areas of shallow water, are studied. As far as these resources’ reduction is concerned, remote sensing and image processing techniques could contribute to the management of these natural resources in a practical and cost-effective way, although some improvements are needed for obtaining a higher quality of the information available. An important quality improvement is the fusion at the pixel level. Hence, the objective of this work is to assess which pansharpening technique provides the best fused image for the different types of ecosystems. After a preliminary evaluation of twelve classic and novel fusion algorithms, a total of four pansharpening algorithms was analyzed using six quality indices. The quality assessment was implemented not only for the whole set of multispectral bands, but also for the subset of spectral bands covered by the wavelength range of the panchromatic image and outside of it. A better quality result is observed in the fused image using only the bands covered by the panchromatic band range. It is important to highlight the use of these techniques not only in land and urban areas, but a novel analysis in areas of shallow water ecosystems. Although the algorithms do not show a high difference in land and coastal areas, coastal ecosystems require simpler algorithms, such as fast intensity hue saturation, whereas more heterogeneous ecosystems need advanced algorithms, as weighted wavelet ‘à trous’ through fractal dimension maps for shrublands and mixed ecosystems. Moreover, quality map analysis was carried out in order to study the fusion result in each band at the local level. Finally, to demonstrate the performance of these pansharpening techniques, advanced Object-Based (OBIA) support vector machine classification was applied, and a thematic map for the shrubland ecosystem was obtained, which corroborates wavelet ‘à trous’ through fractal dimension maps as the best fusion algorithm for this ecosystem. PMID:28125055

Effect of modified atmosphere packaging (MAP) on quality of Sea Buckthorn during postharvest storage

USDA-ARS?s Scientific Manuscript database

Modified atmosphere packaging (MAP) has been used to retain the quality of postharvest produce. In the present study the effect of MAP on quality of berry fruit of Sea buckthorn (Hippophae rhamnoides L., a hardy, deciduous shrub, native to Asia) during refrigerated storage was investigated. Sea buck...

Color, lipid oxidation, sensory quality, and aroma compounds of beef steaks displayed under different levels of oxygen in a modified atmosphere package.

PubMed

Resconi, Virginia Celia; Escudero, Ana; Beltrán, José Antonio; Olleta, José Luis; Sañudo, Carlos; Campo, María del Mar

2012-01-01

High oxygen modified atmosphere packaging (MAP) is currently used by the industry to maintain an attractive color in fresh meat. However, it can also promote lipid oxidation and sensory changes. The aim of this study was to compare the quality of beef steaks displayed under different levels of oxygen. For that purpose, meat was stored with 50%, 60%, and 80% of oxygen for 4 and 8 d at retail conditions. A control treatment with steaks vacuum packaged, without exposure to retail display, was included, and color, lipid oxidation, organoleptic characteristics, and aroma compounds were analyzed. Steaks displayed under high oxygen MAP with 50% of oxygen showed the lowest color stability, according to hue values. Higher oxygen levels did not necessarily correspond with higher rancidity levels in the raw meat. Thiobarbituric Acid Reacting Substances (TBARS) values were higher than 2.2 mg malonaldehyde (MDA)/kg muscle in all the samples displayed for 8 d at retail conditions. These samples exhibited the highest intensities of rancid and the least intense beef odors and flavors. The ketones: 2,3-butanedione, 2-octanone, 2,3-pentanedione, 2-heptanone, 4-methyl-2-pentanone, and the aldehydes: pentanal, 2-methyl-butanal, and 2-furfurylthiol, 1-octen-3-ol and 2-methylpropyl-acetate, were proposed as candidates for the aroma differences between the cooked beef steaks stored under vacuum and high oxygen packs. High oxygen modified atmosphere packaging (MAP) is used to increase shelf-life and color at the retail level. However, oxygen deteriorates faster some quality attributes, being a contributor to lipid oxidation that could be perceived at consumption. This study attempts to find the best gas composition in a MAP in order to maintain the color, minimizing the oxidation. Aromatically relevant chemicals have been analyzed by gas olfactometry-gas chromatography as a key to measure beef oxidation after display. © 2011 Institute of Food Technologists®

Eliminating expression of erucic acid-encoding loci allows the identification of "hidden" QTL contributing to oil quality fractions and oil content in Brassica juncea (Indian mustard).

PubMed

Jagannath, Arun; Sodhi, Yashpal Singh; Gupta, Vibha; Mukhopadhyay, Arundhati; Arumugam, Neelakantan; Singh, Indira; Rohatgi, Soma; Burma, Pradeep Kumar; Pradhan, Akshay Kumar; Pental, Deepak

2011-04-01

Oil content and oil quality fractions (viz., oleic, linoleic and linolenic acid) are strongly influenced by the erucic acid pathway in oilseed Brassicas. Low levels of erucic acid in seed oil increases oleic acid content to nutritionally desirable levels, but also increases the linoleic and linolenic acid fractions and reduces oil content in Indian mustard (Brassica juncea). Analysis of phenotypic variability for oil quality fractions among a high-erucic Indian variety (Varuna), a low-erucic east-European variety (Heera) and a zero-erucic Indian variety (ZE-Varuna) developed by backcross breeding in this study indicated that lower levels of linoleic and linolenic acid in Varuna are due to substrate limitation caused by an active erucic acid pathway and not due to weaker alleles or enzyme limitation. To identify compensatory loci that could be used to increase oil content and maintain desirable levels of oil quality fractions under zero-erucic conditions, we performed Quantitative Trait Loci (QTL) mapping for the above traits on two independent F1 doubled haploid (F1DH) mapping populations developed from a cross between Varuna and Heera. One of the populations comprised plants segregating for erucic acid content (SE) and was used earlier for construction of a linkage map and QTL mapping of several yield-influencing traits in B. juncea. The second population consisted of zero-erucic acid individuals (ZE) for which, an Amplified Fragment Length Polymorphism (AFLP)-based framework linkage map was constructed in the present study. By QTL mapping for oil quality fractions and oil content in the ZE population, we detected novel loci contributing to the above traits. These loci did not co-localize with mapped locations of the fatty acid desaturase 2 (FAD2), fatty acid desaturase 3 (FAD3) or fatty acid elongase (FAE) genes unlike those of the SE population wherein major QTL were found to coincide with mapped locations of the FAE genes. Some of the new loci identified in the ZE population could be detected as 'weak' contributors (with LOD < 2.5) in the SE population in which their contribution to the traits was "masked" due to pleiotropic effects of erucic acid genes. The novel loci identified in this study could now be used to improve oil quality parameters and oil content in B. juncea under zero-erucic conditions.

Maintenance of safety and quality of refrigerated ready-to-cook seasoned ground beef product (meatball) by combining gamma irradiation with modified atmosphere packaging.

PubMed

Gunes, Gurbuz; Ozturk, Aylin; Yilmaz, Neriman; Ozcelik, Beraat

2011-08-01

Meatballs were prepared by mixing ground beef and spices and inoculated with E. coli O157:H7, L. monocytogenes, and S. enteritidis before packaged in modified atmosphere (3% O₂ + 50% CO₂ + 47% N₂) or aerobic conditions. The packaged samples were irradiated at 0.75, 1.5, and 3 kGy doses and stored at 4 °C for 21 d. Survival of the pathogens, total plate count, lipid oxidation, color change, and sensory quality were analyzed during storage. Irradiation at 3 kGy inactivated all the inoculated (approximately 10⁶ CFU/g) S. enteritidis and L. monocytogenes cells in the samples. The inoculated (approximately 10⁶ CFU/g) E. coli O157:H7 cells were totally inactivated by 1.5 kGy irradiation. D¹⁰-values for E. coli O157:H7, S. enteritidis, and L. monocytogenes were 0.24, 0.43, and 0.41 kGy in MAP and 0.22, 0.39, and 0.39 kGy in aerobic packages, respectively. Irradiation at 1.5 and 3 kGy resulted in 0.13 and 0.36 mg MDA/kg increase in 2-thiobarbituric acid-reactive substances (TBARS) reaching 1.02 and 1.49 MDA/kg, respectively, on day 1. Irradiation also caused significant loss of color and sensory quality in aerobic packages. However, MAP effectively inhibited the irradiation-induced quality degradations during 21-d storage. Thus, combining irradiation (3 kGy) and MAP (3% O₂ + 50% CO₂ + 47% N₂) controlled the safety risk due to the potential pathogens and maintained qualities of meatballs during 21-d refrigerated storage. Combined use of gamma irradiation and modified atmosphere packaging (MAP) can maintain quality and safety of seasoned ground beef (meatball). Seasoned ground beef can be irradiated at 3 kGy and packaged in MAP with 3% O₂ + 50% CO₂ + 47% N₂ gas mixture in a high barrier packaging materials. These treatments can significantly decrease risk due to potential pathogens including E. coli O157:H7, L. monocytogenes, and S. enteritidis in the product. The MAP would reduce the undesirable effects of irradiation on quality, and extend the shelf life of the product for up to 21 d at 3 °C. © 2011 Institute of Food Technologists®

OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

PubMed

Verzotto, Davide; M Teo, Audrey S; Hillmer, Axel M; Nagarajan, Niranjan

2016-01-01

Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences. We introduce a novel seed-and-extend glocal (short for global-local) alignment method, OPTIMA (and a sliding-window extension for overlap alignment, OPTIMA-Overlap), which is the first to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic with respect to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests. We show that OPTIMA and OPTIMA-Overlap outperform other state-of-the-art approaches (1.6-2 times more sensitive) and are more efficient (170-200 %) and precise in their alignments (nearly 99 % precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust, provide improved sensitivity and guarantee high precision.

Urban-scale mapping of PM2.5 distribution via data fusion between high-density sensor network and MODIS Aerosol Optical Depth

NASA Astrophysics Data System (ADS)

Ba, Yu Tao; xian Liu, Bao; Sun, Feng; Wang, Li hua; Tang, Yu jia; Zhang, Da wei

2017-04-01

High-resolution mapping of PM2.5 is the prerequisite for precise analytics and subsequent anti-pollution interventions. Considering the large variances of particulate distribution, urban-scale mapping is challenging either with ground-based fixed stations, with satellites or via models. In this study, a dynamic fusion method between high-density sensor network and MODIS Aerosol Optical Depth (AOD) was introduced. The sensor network was deployed in Beijing ( > 1000 fixed monitors across 16000 km2 area) to provide raw observations with high temporal resolution (sampling interval < 1 hour), high spatial resolution in flat areas ( < 1 km), and low spatial resolution in mountainous areas ( > 5 km). The MODIS AOD was calibrated to provide distribution map with low temporal resolution (daily) and moderate spatial resolution ( = 3 km). By encoding the data quality and defects (e.g. could, reflectance, abnormal), a hybrid interpolation procedure with cross-validation generated PM2.5 distribution with both high temporal and spatial resolution. Several no-pollutant and high-pollution periods were tested to validate the proposed fusion method for capturing the instantaneous patterns of PM2.5 emission.

Evaluation of karst water quality as an early reference of land suitability mapping for vaname shrimp (Litopenaeusvannamei) culture media

NASA Astrophysics Data System (ADS)

Wildan, D. M.; Affandi, R.; Pratiwi, N. T. M.; Krisanti, M.; Ayu, I. P.; Iswantari, A.

2017-01-01

Vaname shrimp (Litopenaeusvannamei) is one of the excellent fishery commodities in Indonesia. Vaname shrimp farming can be conducted in low salinity water. Low salinity water sources which could be used as culture media is karst water because it has a high mineral. The research was aimedto evaluate land suitability mapping for pond as the vaname shrimpculture mediaseen from the water quality. Research was conducted in May and August 2016. Water sampling was conducted in several locations; Ancol-Jakarta (seawater), Ciseeng-Bogor (karst water salinity), Ciampea-Bogor (karst freshwater), and Situ Gede Bogor (freshwater). Evaluating the suitability of karst water quality for vaname shrimp culture media, done by the results of karst water quality analysis compared with seawater and SNI 01-7246-2006 on shrimp vaname culture media. The results showed that Karst water of Ciseeng and Ciampea could not directly use as vaname shrimp culture media. It is needed water quality treatment of ozonation and aeration of karst water to improve water quality. Ozonation and aeration treatments were able to improve the quality of karst water up to approach the living quality standard of vaname shrimp media.

QTL mapping for fruit quality in Citrus using DArTseq markers.

PubMed

Curtolo, Maiara; Cristofani-Yaly, Mariângela; Gazaffi, Rodrigo; Takita, Marco Aurélio; Figueira, Antonio; Machado, Marcos Antonio

2017-04-12

Citrus breeding programs have many limitations associated with the species biology and physiology, requiring the incorporation of new biotechnological tools to provide new breeding possibilities. Diversity Arrays Technology (DArT) markers, combined with next-generation sequencing, have wide applicability in the construction of high-resolution genetic maps and in quantitative trait locus (QTL) mapping. This study aimed to construct an integrated genetic map using full-sib progeny derived from Murcott tangor and Pera sweet orange and DArTseq™ molecular markers and to perform QTL mapping of twelve fruit quality traits. A controlled Murcott x Pera crossing was conducted at the Citrus Germplasm Repository at the Sylvio Moreira Citrus Centre of the Agronomic Institute (IAC) located in Cordeirópolis, SP, in 1997. In 2012, 278 F 1 individuals out of a family of 312 confirmed hybrid individuals were analyzed for fruit traits and genotyped using the DArTseq markers. Using OneMap software to obtain the integrated genetic map, we considered only the DArT loci that showed no segregation deviation. The likelihood ratio and the genomic information from the available Citrus sinensis L. Osbeck genome were used to determine the linkage groups (LGs). The resulting integrated map contained 661 markers in 13 LGs, with a genomic coverage of 2,774 cM and a mean density of 0.23 markers/cM. The groups were assigned to the nine Citrus haploid chromosomes; however, some of the chromosomes were represented by two LGs due the lack of information for a single integration, as in cases where markers segregated in a 3:1 fashion. A total of 19 QTLs were identified through composite interval mapping (CIM) of the 12 analyzed fruit characteristics: fruit diameter (cm), height (cm), height/diameter ratio, weight (g), rind thickness (cm), segments per fruit, total soluble solids (TSS, %), total titratable acidity (TTA, %), juice content (%), number of seeds, TSS/TTA ratio and number of fruits per box. The genomic sequence (pseudochromosomes) of C. sinensis was compared to the genetic map, and synteny was clearly identified. Further analysis of the map regions with the highest LOD scores enabled the identification of putative genes that could be associated with the fruit quality characteristics. An integrated linkage map of Murcott tangor and Pera sweet orange using DArTseq™ molecular markers was established and it was useful to perform QTL mapping of twelve fruit quality traits. The next generation sequences data allowed the comparison between the linkage map and the genomic sequence (pseudochromosomes) of C. sinensis and the identification of genes that may be responsible for phenotypic traits in Citrus. The obtained linkage map was used to assign sequences that had not been previously assigned to a position in the reference genome.

Evaluation of arctic multibeam sonar data quality using nadir crossover error analysis and compilation of a full-resolution data product

NASA Astrophysics Data System (ADS)

Flinders, Ashton F.; Mayer, Larry A.; Calder, Brian A.; Armstrong, Andrew A.

2014-05-01

We document a new high-resolution multibeam bathymetry compilation for the Canada Basin and Chukchi Borderland in the Arctic Ocean - United States Arctic Multibeam Compilation (USAMBC Version 1.0). The compilation preserves the highest native resolution of the bathymetric data, allowing for more detailed interpretation of seafloor morphology than has been previously possible. The compilation was created from multibeam bathymetry data available through openly accessible government and academic repositories. Much of the new data was collected during dedicated mapping cruises in support of the United States effort to map extended continental shelf regions beyond the 200 nm Exclusive Economic Zone. Data quality was evaluated using nadir-beam crossover-error statistics, making it possible to assess the precision of multibeam depth soundings collected from a wide range of vessels and sonar systems. Data were compiled into a single high-resolution grid through a vertical stacking method, preserving the highest quality data source in any specific grid cell. The crossover-error analysis and method of data compilation can be applied to other multi-source multibeam data sets, and is particularly useful for government agencies targeting extended continental shelf regions but with limited hydrographic capabilities. Both the gridded compilation and an easily distributed geospatial PDF map are freely available through the University of New Hampshire's Center for Coastal and Ocean Mapping (ccom.unh.edu/theme/law-sea). The geospatial pdf is a full resolution, small file-size product that supports interpretation of Arctic seafloor morphology without the need for specialized gridding/visualization software.

2D and 3D visualization methods of endoscopic panoramic bladder images

NASA Astrophysics Data System (ADS)

Behrens, Alexander; Heisterklaus, Iris; Müller, Yannick; Stehle, Thomas; Gross, Sebastian; Aach, Til

2011-03-01

While several mosaicking algorithms have been developed to compose endoscopic images of the internal urinary bladder wall into panoramic images, the quantitative evaluation of these output images in terms of geometrical distortions have often not been discussed. However, the visualization of the distortion level is highly desired for an objective image-based medical diagnosis. Thus, we present in this paper a method to create quality maps from the characteristics of transformation parameters, which were applied to the endoscopic images during the registration process of the mosaicking algorithm. For a global first view impression, the quality maps are laid over the panoramic image and highlight image regions in pseudo-colors according to their local distortions. This illustration supports then surgeons to identify geometrically distorted structures easily in the panoramic image, which allow more objective medical interpretations of tumor tissue in shape and size. Aside from introducing quality maps in 2-D, we also discuss a visualization method to map panoramic images onto a 3-D spherical bladder model. Reference points are manually selected by the surgeon in the panoramic image and the 3-D model. Then the panoramic image is mapped by the Hammer-Aitoff equal-area projection onto the 3-D surface using texture mapping. Finally the textured bladder model can be freely moved in a virtual environment for inspection. Using a two-hemisphere bladder representation, references between panoramic image regions and their corresponding space coordinates within the bladder model are reconstructed. This additional spatial 3-D information thus assists the surgeon in navigation, documentation, as well as surgical planning.

Creating cinematic wide gamut HDR-video for the evaluation of tone mapping operators and HDR-displays

NASA Astrophysics Data System (ADS)

Froehlich, Jan; Grandinetti, Stefan; Eberhardt, Bernd; Walter, Simon; Schilling, Andreas; Brendel, Harald

2014-03-01

High quality video sequences are required for the evaluation of tone mapping operators and high dynamic range (HDR) displays. We provide scenic and documentary scenes with a dynamic range of up to 18 stops. The scenes are staged using professional film lighting, make-up and set design to enable the evaluation of image and material appearance. To address challenges for HDR-displays and temporal tone mapping operators, the sequences include highlights entering and leaving the image, brightness changing over time, high contrast skin tones, specular highlights and bright, saturated colors. HDR-capture is carried out using two cameras mounted on a mirror-rig. To achieve a cinematic depth of field, digital motion picture cameras with Super-35mm size sensors are used. We provide HDR-video sequences to serve as a common ground for the evaluation of temporal tone mapping operators and HDR-displays. They are available to the scientific community for further research.

Analysis and quality control of carbohydrates in therapeutic proteins with fluorescence HPLC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Kun; Huang, Jian; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054

Conbercept is an Fc fusion protein with very complicated carbohydrate profiles which must be carefully monitored through manufacturing process. Here, we introduce an optimized fluorescence derivatization high-performance liquid chromatographic method for glycan mapping in conbercept. Compared with conventional glycan analysis method, this method has much better resolution and higher reproducibility making it excellent for product quality control.

Talbot-Lau x-ray deflectometry phase-retrieval methods for electron density diagnostics in high-energy density experiments.

PubMed

Valdivia, Maria Pia; Stutman, Dan; Stoeckl, Christian; Mileham, Chad; Begishev, Ildar A; Bromage, Jake; Regan, Sean P

2018-01-10

Talbot-Lau x-ray interferometry uses incoherent x-ray sources to measure refraction index changes in matter. These measurements can provide accurate electron density mapping through phase retrieval. An adaptation of the interferometer has been developed in order to meet the specific requirements of high-energy density experiments. This adaptation is known as a moiré deflectometer, which allows for single-shot capabilities in the form of interferometric fringe patterns. The moiré x-ray deflectometry technique requires a set of object and reference images in order to provide electron density maps, which can be costly in the high-energy density environment. In particular, synthetic reference phase images obtained ex situ through a phase-scan procedure, can provide a feasible solution. To test this procedure, an object phase map was retrieved from a single-shot moiré image obtained from a plasma-produced x-ray source. A reference phase map was then obtained from phase-stepping measurements using a continuous x-ray tube source in a small laboratory setting. The two phase maps were used to retrieve an electron density map. A comparison of the moiré and phase-stepping phase-retrieval methods was performed to evaluate single-exposure plasma electron density mapping for high-energy density and other transient plasma experiments. It was found that a combination of phase-retrieval methods can deliver accurate refraction angle mapping. Once x-ray backlighter quality is optimized, the ex situ method is expected to deliver electron density mapping with improved resolution. The steps necessary for improved diagnostic performance are discussed.

Use of modified atmosphere packaging to preserve mushroom quality during storage.

PubMed

Palacios, Irene; Moro, Carlos; Lozano, Miguel; D'Arrigo, Matilde; Guillamón, Eva; García-Lafuente, Ana; Villares, Ana

2011-09-01

Mushrooms have attracted much attention due to their excellent nutritional and sensory properties. However, they are highly perishable and rapidly lose their organoleptic characteristics. Many methods have been employed for mushroom storage, such as packaging, blanching, canning, or freeze drying. Among them, modified atmosphere packaging (MAP) has been widely employed for preserving fresh mushrooms. MAP provides an affordable packaging system that partly avoids enzymatic browning, fermentation and other biochemical processes by maintaining a controlled gas atmosphere. Several factors, including optimum CO2 and O2 partial pressures, permeability, package material, thickness, or product weight, must be considered in order to design a suitable modified atmosphere package for mushrooms. Thus, different strategies are available to preserve mushroom quality after harvest. The article presents some promising patents on use of modified atmosphere packaging to preserve mushroom quality during storage.

Accessing groundwater quality in lower part of Nagapattinam district, Southern India: using hydrogeochemistry and GIS interpolation techniques

NASA Astrophysics Data System (ADS)

Gnanachandrasamy, G.; Ramkumar, T.; Venkatramanan, S.; Vasudevan, S.; Chung, S. Y.; Bagyaraj, M.

2015-03-01

The aim of this present study was to evaluate groundwater quality in the lower part of Nagapattinam district, Tamil Nadu, Southern India. A detailed geochemical study of groundwater region is described, and the origin of the chemical composition of groundwater has been qualitatively evaluated, using observations over a period of two seasons premonsoon (June) and monsoon (November) in the year of 2010. To attempt this goal, samples were analysed for various physico-chemical parameters such as temperature, pH, salinity, Na+, Ca2+, K+, Mg2+, Cl-, HCO3 - and SO4 2-. The abundance of major cations concentration in groundwater is as Na > Ca > Mg > K, while that of anions is Cl > SO4 > HCO3. The Piper trilinear diagram indicates Ca-Cl2 facies, and according to USSL diagram, most of the sample exhibits high salinity hazard (C3S1) type in both seasons. It indicates that high salinity (C3) and low sodium (S1) are moderately suitable for irrigation purposes. Gibbs boomerang exhibits most of the samples mainly controlled by evaporation and weathering process sector in both seasons. Irrigation status of the groundwater samples indicates that it was moderately suitable for agricultural purpose. ArcGIS 9.3 software was used for the generation of various thematic maps and the final groundwater quality map. An interpolation technique inverse distance weighting was used to obtain the spatial distribution of groundwater quality parameters. The final map classified the ground quality in the study area. The results of this research show that the development of the management strategies for the aquifer system is vitally necessary.

Effect of high carbon dioxide atmosphere packaging and soluble gas stabilization pre-treatment on the shelf-life and quality of chicken drumsticks.

PubMed

Al-Nehlawi, A; Saldo, J; Vega, L F; Guri, S

2013-05-01

The effects of an aerobic modified atmosphere packaging (MAP) (70% CO2, 15% O2 and 15% N2) with and without a CO2 3-h soluble gas stabilization (SGS) pre-treatment of chicken drumsticks were determined for various package and product quality characteristics. The CO2 dissolved into drumsticks was determined. The equilibrium between CO2 dissolved in drumsticks and CO2 in head space was reached within 48h after packaging, showing highest values of CO2 in SGS pre-treated samples. This greater availability of CO2 resulted in lower counts of TAB and Pseudomonas in SGS than in MAP drumsticks. Package collapse was significantly reduced in SGS samples. The average of CO2 dissolved in the MAP treatment was 567mg CO2kg(-1) of chicken and, 361mg CO2kg(-1) of chicken during the MAP treatment, in SGS pre-treated samples. This difference could be the quantity of CO2 dissolved during SGS pre-treatment. These results highlight the advantages of using SGS versus traditional MAP for chicken products preservation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits.

PubMed

Albert, Elise; Segura, Vincent; Gricourt, Justine; Bonnefoi, Julien; Derivot, Laurent; Causse, Mathilde

2016-12-01

Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination.

PubMed

Li, Gang; Hillier, LaDeana W; Grahn, Robert A; Zimin, Aleksey V; David, Victor A; Menotti-Raymond, Marilyn; Middleton, Rondo; Hannah, Steven; Hendrickson, Sher; Makunin, Alex; O'Brien, Stephen J; Minx, Pat; Wilson, Richard K; Lyons, Leslie A; Warren, Wesley C; Murphy, William J

2016-06-01

High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location. Copyright © 2016 Li et al.

Association mapping of seed quality traits using the Canadian flax (Linum usitatissimum L.) core collection.

PubMed

Soto-Cerda, Braulio J; Duguid, Scott; Booker, Helen; Rowland, Gordon; Diederichsen, Axel; Cloutier, Sylvie

2014-04-01

The identification of stable QTL for seed quality traits by association mapping of a diverse panel of linseed accessions establishes the foundation for assisted breeding and future fine mapping in linseed. Linseed oil is valued for its food and non-food applications. Modifying its oil content and fatty acid (FA) profiles to meet market needs in a timely manner requires clear understanding of their quantitative trait loci (QTL) architectures, which have received little attention to date. Association mapping is an efficient approach to identify QTL in germplasm collections. In this study, we explored the quantitative nature of seed quality traits including oil content (OIL), palmitic acid, stearic acid, oleic acid, linoleic acid (LIO) linolenic acid (LIN) and iodine value in a flax core collection of 390 accessions assayed with 460 microsatellite markers. The core collection was grown in a modified augmented design at two locations over 3 years and phenotypic data for all seven traits were obtained from all six environments. Significant phenotypic diversity and moderate to high heritability for each trait (0.73-0.99) were observed. Most of the candidate QTL were stable as revealed by multivariate analyses. Nine candidate QTL were identified, varying from one for OIL to three for LIO and LIN. Candidate QTL for LIO and LIN co-localized with QTL previously identified in bi-parental populations and some mapped nearby genes known to be involved in the FA biosynthesis pathway. Fifty-eight percent of the QTL alleles were absent (private) in the Canadian cultivars suggesting that the core collection possesses QTL alleles potentially useful to improve seed quality traits. The candidate QTL identified herein will establish the foundation for future marker-assisted breeding in linseed.

Landsat Image Map Production Methods at the U. S. Geological Survey

USGS Publications Warehouse

Kidwell, R.D.; Binnie, D.R.; Martin, S.

1987-01-01

To maintain consistently high quality in satellite image map production, the U. S. Geological Survey (USGS) has developed standard procedures for the photographic and digital production of Landsat image mosaics, and for lithographic printing of multispectral imagery. This paper gives a brief review of the photographic, digital, and lithographic procedures currently in use for producing image maps from Landsat data. It is shown that consistency in the printing of image maps is achieved by standardizing the materials and procedures that affect the image detail and color balance of the final product. Densitometric standards are established by printing control targets using the pressplates, inks, pre-press proofs, and paper to be used for printing.

The MAP Autonomous Mission Control System

NASA Technical Reports Server (NTRS)

Breed, Juile; Coyle, Steven; Blahut, Kevin; Dent, Carolyn; Shendock, Robert; Rowe, Roger

2000-01-01

The Microwave Anisotropy Probe (MAP) mission is the second mission in NASA's Office of Space Science low-cost, Medium-class Explorers (MIDEX) program. The Explorers Program is designed to accomplish frequent, low cost, high quality space science investigations utilizing innovative, streamlined, efficient management, design and operations approaches. The MAP spacecraft will produce an accurate full-sky map of the cosmic microwave background temperature fluctuations with high sensitivity and angular resolution. The MAP spacecraft is planned for launch in early 2001, and will be staffed by only single-shift operations. During the rest of the time the spacecraft must be operated autonomously, with personnel available only on an on-call basis. Four (4) innovations will work cooperatively to enable a significant reduction in operations costs for the MAP spacecraft. First, the use of a common ground system for Spacecraft Integration and Test (I&T) as well as Operations. Second, the use of Finite State Modeling for intelligent autonomy. Third, the integration of a graphical planning engine to drive the autonomous systems without an intermediate manual step. And fourth, the ability for distributed operations via Web and pager access.

Guided filter-based fusion method for multiexposure images

NASA Astrophysics Data System (ADS)

Hou, Xinglin; Luo, Haibo; Qi, Feng; Zhou, Peipei

2016-11-01

It is challenging to capture a high-dynamic range (HDR) scene using a low-dynamic range camera. A weighted sum-based image fusion (IF) algorithm is proposed so as to express an HDR scene with a high-quality image. This method mainly includes three parts. First, two image features, i.e., gradients and well-exposedness are measured to estimate the initial weight maps. Second, the initial weight maps are refined by a guided filter, in which the source image is considered as the guidance image. This process could reduce the noise in initial weight maps and preserve more texture consistent with the original images. Finally, the fused image is constructed by a weighted sum of source images in the spatial domain. The main contributions of this method are the estimation of the initial weight maps and the appropriate use of the guided filter-based weight maps refinement. It provides accurate weight maps for IF. Compared to traditional IF methods, this algorithm avoids image segmentation, combination, and the camera response curve calibration. Furthermore, experimental results demonstrate the superiority of the proposed method in both subjective and objective evaluations.

Fast mapping algorithm of lighting spectrum and GPS coordinates for a large area

NASA Astrophysics Data System (ADS)

Lin, Chih-Wei; Hsu, Ke-Fang; Hwang, Jung-Min

2016-09-01

In this study, we propose a fast rebuild technology for evaluating light quality in large areas. Outdoor light quality, which is measured by illuminance uniformity and the color rendering index, is difficult to conform after improvement. We develop an algorithm for a lighting quality mapping system and coordinates using a micro spectrometer and GPS tracker integrated with a quadcopter or unmanned aerial vehicle. After cruising at a constant altitude, lighting quality data is transmitted and immediately mapped to evaluate the light quality in a large area.

Two dimensional thermal and charge mapping of power thyristors

NASA Technical Reports Server (NTRS)

Hu, S. P.; Rabinovici, B. M.

1975-01-01

The two dimensional static and dynamic current density distributions within the junction of semiconductor power switching devices and in particular the thyristors were obtained. A method for mapping the thermal profile of the device junctions with fine resolution using an infrared beam and measuring the attenuation through the device as a function of temperature were developed. The results obtained are useful in the design and quality control of high power semiconductor switching devices.

Automated mapping of the ocean floor using the theory of intrinsic random functions of order k

USGS Publications Warehouse

David, M.; Crozel, D.; Robb, James M.

1986-01-01

High-quality contour maps can be computer drawn from single track echo-sounding data by combining Universal Kriging and the theory of intrinsic random function of order K (IRFK). These methods interpolate values among the closely spaced points that lie along relatively widely spaced lines. The technique provides a variance which can be contoured as a quantitative measure of map precision. The technique can be used to evaluate alternative survey trackline configurations and data collection intervals, and can be applied to other types of oceanographic data. ?? 1986 D. Reidel Publishing Company.

Radar systems for the water resources mission, volume 2

NASA Technical Reports Server (NTRS)

Moore, R. K.; Claassen, J. P.; Erickson, R. L.; Fong, R. K. T.; Hanson, B. C.; Komen, M. J.; Mcmillan, S. B.; Parashar, S. K.

1976-01-01

The application of synthetic aperture radar (SAR) in monitoring and managing earth resources was examined. The function of spaceborne radar is to provide maps and map imagery to be used for earth resource and oceanographic applications. Spaceborne radar has the capability of mapping the entire United States regardless of inclement weather; however, the imagery must have a high degree of resolution to be meaningful. Attaining this resolution is possible with the SAR system. Imagery of the required quality must first meet mission parameters in the following areas: antenna patterns, azimuth and range ambiguities, coverage, and angle of incidence.

Remote sensing of land use and water quality relationships - Wisconsin shore, Lake Michigan

NASA Technical Reports Server (NTRS)

Haugen, R. K.; Marlar, T. L.

1976-01-01

This investigation assessed the utility of remote sensing techniques in the study of land use-water quality relationships in an east central Wisconsin test area. The following types of aerial imagery were evaluated: high altitude (60,000 ft) color, color infrared, multispectral black and white, and thermal; low altitude (less than 5000 ft) color infrared, multispectral black and white, thermal, and passive microwave. A non-imaging hand-held four-band radiometer was evaluated for utility in providing data on suspended sediment concentrations. Land use analysis includes the development of mapping and quantification methods to obtain baseline data for comparison to water quality variables. Suspended sediment loads in streams, determined from water samples, were related to land use differences and soil types in three major watersheds. A multiple correlation coefficient R of 0.85 was obtained for the relationship between the 0.6-0.7 micrometer incident and reflected radiation data from the hand-held radiometer and concurrent ground measurements of suspended solids in streams. Applications of the methods and baseline data developed in this investigation include: mapping and quantification of land use; input to watershed runoff models; estimation of effects of land use changes on stream sedimentation; and remote sensing of suspended sediment content of streams. High altitude color infrared imagery was found to be the most acceptable remote sensing technique for the mapping and measurement of land use types.

The use of process mapping in healthcare quality improvement projects.

PubMed

Antonacci, Grazia; Reed, Julie E; Lennox, Laura; Barlow, James

2018-05-01

Introduction Process mapping provides insight into systems and processes in which improvement interventions are introduced and is seen as useful in healthcare quality improvement projects. There is little empirical evidence on the use of process mapping in healthcare practice. This study advances understanding of the benefits and success factors of process mapping within quality improvement projects. Methods Eight quality improvement projects were purposively selected from different healthcare settings within the UK's National Health Service. Data were gathered from multiple data-sources, including interviews exploring participants' experience of using process mapping in their projects and perceptions of benefits and challenges related to its use. These were analysed using inductive analysis. Results Eight key benefits related to process mapping use were reported by participants (gathering a shared understanding of the reality; identifying improvement opportunities; engaging stakeholders in the project; defining project's objectives; monitoring project progress; learning; increased empathy; simplicity of the method) and five factors related to successful process mapping exercises (simple and appropriate visual representation, information gathered from multiple stakeholders, facilitator's experience and soft skills, basic training, iterative use of process mapping throughout the project). Conclusions Findings highlight benefits and versatility of process mapping and provide practical suggestions to improve its use in practice.

The DosiMap, a new 2D scintillating dosimeter for IMRT quality assurance: characterization of two Cerenkov discrimination methods.

PubMed

Frelin, A M; Fontbonne, J M; Ban, G; Colin, J; Labalme, M; Batalla, A; Vela, A; Boher, P; Braud, M; Leroux, T

2008-05-01

New radiation therapy techniques such as IMRT present significant efficiency due to their highly conformal dose distributions. A consequence of the complexity of their dose distributions (high gradients, small irradiation fields, low dose distribution, ...) is the requirement for better precision quality assurance than in classical radiotherapy in order to compare the conformation of the delivered dose with the planned dose distribution and to guarantee the quality of the treatment. Currently this control is mostly performed by matrices of ionization chambers, diode detectors, dosimetric films, portal imaging, or dosimetric gels. Another approach is scintillation dosimetry, which has been developed in the last 15 years mainly through scintillating fiber devices. Despite having many advantages over other methods it is still at an experimental level for routine dosimetry because the Cerenkov radiation produced under irradiation represents an important stem effect. A new 2D water equivalent scintillating dosimeter, the DosiMap, and two different Cerenkov discrimination methods were developed with the collaboration of the Laboratoire de Physique Corpusculaire of Caen, the Comprehensive Cancer Center François Baclesse, and the ELDIM Co., in the frame of the MAESTRO European project. The DosiMap consists of a plastic scintillating sheet placed inside a transparent polystyrene phantom. The light distribution produced under irradiation is recorded by a CCD camera. Our first Cerenkov discrimination technique is subtractive. It uses a chessboard pattern placed in front of the scintillator, which provides a background signal containing only Cerenkov light. Our second discrimination technique is colorimetric. It performs a spectral analysis of the light signal, which allows the unfolding of the Cerenkov radiation and the scintillation. Tests were carried out with our DosiMap prototype and the performances of the two discrimination methods were assessed. The comparison of the dose measurements performed with the DosiMap and with dosimetric films for three different irradiation configurations showed discrepancies smaller than 3.5% for a 2 mm spatial resolution. Two innovative discrimination solutions were demonstrated to separate the scintillation from the Cerenkov radiation. It was also shown that the DosiMap, which is water equivalent, fast, and user friendly, is a very promising tool for radiotherapy quality assurance.

The diploid genome sequence of an Asian individual

PubMed Central

Wang, Jun; Wang, Wei; Li, Ruiqiang; Li, Yingrui; Tian, Geng; Goodman, Laurie; Fan, Wei; Zhang, Junqing; Li, Jun; Zhang, Juanbin; Guo, Yiran; Feng, Binxiao; Li, Heng; Lu, Yao; Fang, Xiaodong; Liang, Huiqing; Du, Zhenglin; Li, Dong; Zhao, Yiqing; Hu, Yujie; Yang, Zhenzhen; Zheng, Hancheng; Hellmann, Ines; Inouye, Michael; Pool, John; Yi, Xin; Zhao, Jing; Duan, Jinjie; Zhou, Yan; Qin, Junjie; Ma, Lijia; Li, Guoqing; Yang, Zhentao; Zhang, Guojie; Yang, Bin; Yu, Chang; Liang, Fang; Li, Wenjie; Li, Shaochuan; Li, Dawei; Ni, Peixiang; Ruan, Jue; Li, Qibin; Zhu, Hongmei; Liu, Dongyuan; Lu, Zhike; Li, Ning; Guo, Guangwu; Zhang, Jianguo; Ye, Jia; Fang, Lin; Hao, Qin; Chen, Quan; Liang, Yu; Su, Yeyang; san, A.; Ping, Cuo; Yang, Shuang; Chen, Fang; Li, Li; Zhou, Ke; Zheng, Hongkun; Ren, Yuanyuan; Yang, Ling; Gao, Yang; Yang, Guohua; Li, Zhuo; Feng, Xiaoli; Kristiansen, Karsten; Wong, Gane Ka-Shu; Nielsen, Rasmus; Durbin, Richard; Bolund, Lars; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian

2009-01-01

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics. PMID:18987735

Star-spot distributions and chromospheric activity on the RS CVn type eclipsing binary SV Cam

NASA Astrophysics Data System (ADS)

Şenavcı, H. V.; Bahar, E.; Montes, D.; Zola, S.; Hussain, G. A. J.; Frasca, A.; Işık, E.; Yörükoǧlu, O.

2018-06-01

Using a time series of high-resolution spectra and high-quality multi-colour photometry, we reconstruct surface maps of the primary component of the RS CVn type rapidly rotating eclipsing binary, SV Cam (F9V + K4V). We measure a mass ratio, q, of 0.641(2) using our highest quality spectra and obtain surface brightness maps of the primary component, which exhibit predominantly high-latitude spots located between 60° - 70° latitudes with a mean filling factor of ˜35%. This is also indicated by the R-band light curve inversion, subjected to rigourous numerical tests. The spectral subtraction of the Hα line reveals strong activity of the secondary component. The excess Hα absorption detected near the secondary minimum hints to the presence of cool material partially obscuring the primary star. The flux ratios of Ca II IRT excess emission indicate that the contribution of chromospheric plage regions associated with star-spots is dominant, even during the passage of the filament-like absorption feature.

Does Value Stream Mapping affect the structure, process, and outcome quality in care facilities? A systematic review.

PubMed

Nowak, Marina; Pfaff, Holger; Karbach, Ute

2017-08-24

Quality improvement within health and social care facilities is needed and has to be evidence-based and patient-centered. Value Stream Mapping, a method of Lean management, aims to increase the patients' value and quality of care by a visualization and quantification of the care process. The aim of this research is to examine the effectiveness of Value Stream Mapping on structure, process, and outcome quality in care facilities. A systematic review is conducted. PubMed, EBSCOhost, including Business Source Complete, Academic Search Complete, PSYCInfo, PSYNDX, SocINDEX with Full Text, Web of Knowledge, and EMBASE ScienceDirect are searched in February 2016. All peer-reviewed papers evaluating Value Stream Mapping and published in English or German from January 2000 are included. For data synthesis, all study results are categorized into Donabedian's model of structure, process, and outcome quality. To assess and interpret the effectiveness of Value Stream Mapping, the frequencies of the results statistically examined are considered. Of the 903 articles retrieved, 22 studies fulfill the inclusion criteria. Of these, 11 studies are used to answer the research question. Value Stream Mapping has positive effects on the time dimension of process and outcome quality. It seems to reduce non-value-added time (e.g., waiting time) and length of stay. All study designs are before and after studies without control, and methodologically sophisticated studies are missing. For a final conclusion about Value Stream Mapping's effectiveness, more research with improved methodology is needed. Despite this lack of evidence, Value Stream Mapping has the potential to improve quality of care on the time dimension. The contextual influence has to be investigated to make conclusions about the relationship between different quality domains when applying Value Stream Mapping. However, for using this review's conclusion, the limitation of including heterogeneous and potentially biased results has to be considered.

Accuracy Assessment of Professional Grade Unmanned Systems for High Precision Airborne Mapping

NASA Astrophysics Data System (ADS)

Mostafa, M. M. R.

2017-08-01

Recently, sophisticated multi-sensor systems have been implemented on-board modern Unmanned Aerial Systems. This allows for producing a variety of mapping products for different mapping applications. The resulting accuracies match the traditional well engineered manned systems. This paper presents the results of a geometric accuracy assessment project for unmanned systems equipped with multi-sensor systems for direct georeferencing purposes. There are a number of parameters that either individually or collectively affect the quality and accuracy of a final airborne mapping product. This paper focuses on identifying and explaining these parameters and their mutual interaction and correlation. Accuracy Assessment of the final ground object positioning accuracy is presented through real-world 8 flight missions that were flown in Quebec, Canada. The achievable precision of map production is addressed in some detail.

Combined modified atmosphere packaging and low temperature storage delay lignification and improve the defense response of minimally processed water bamboo shoot.

PubMed

Song, Lili; Chen, Hangjun; Gao, Haiyan; Fang, Xiangjun; Mu, Honglei; Yuan, Ya; Yang, Qian; Jiang, Yueming

2013-09-04

Minimally processed water bamboo shoot (WBS) lignifies and deteriorates rapidly at room temperature, which limits greatly its marketability. This study was to investigate the effect of modified atmosphere packaging (MAP) on the sensory quality index, lignin formation, production of radical oxygen species (ROS) and activities of scavenging enzymes, membrane integrity and energy status of minimally processed WBS when packaged with or without the sealed low-density polyethylene (LDPE) bags, and then stored at 20°C for 9 days or 2°C for 60 days. The sensory quality of minimally processed WBS decreased quickly after 6 days of storage at 20°C. Low temperature storage maintained a higher sensory quality index within the first 30 days, but exhibited higher contents of lignin and hydrogen peroxide (H2O2) as compared with non-MAP shoots at 20°C. Combined MAP and low temperature storage not only maintained good sensory quality after 30 days, but also reduced significantly the increases in lignin content, superoxide anion (O2.-) production rate, H2O2 content and membrane permeability, maintained high activities of superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX), and reduced the increase in activities of lipase, phospholipase D (PLD) and lipoxygenase (LOX). Furthermore, the minimally processed WBS under MAP condition exhibited higher energy charge (EC) and lower adenosine monophosphate (AMP) content by the end of storage (60 days) at 2°C than those without MAP or stored for 9 days at 20°C. These results indicated that MAP in combination with low temperature storage reduced lignification of minimally processed WBS, which was closely associated with maintenance of energy status and enhanced activities of antioxidant enzymes, as well as reduced alleviation of membrane damage caused by ROS.

Combined modified atmosphere packaging and low temperature storage delay lignification and improve the defense response of minimally processed water bamboo shoot

PubMed Central

2013-01-01

Background Minimally processed water bamboo shoot (WBS) lignifies and deteriorates rapidly at room temperature, which limits greatly its marketability. This study was to investigate the effect of modified atmosphere packaging (MAP) on the sensory quality index, lignin formation, production of radical oxygen species (ROS) and activities of scavenging enzymes, membrane integrity and energy status of minimally processed WBS when packaged with or without the sealed low-density polyethylene (LDPE) bags, and then stored at 20°C for 9 days or 2°C for 60 days. Results The sensory quality of minimally processed WBS decreased quickly after 6 days of storage at 20°C. Low temperature storage maintained a higher sensory quality index within the first 30 days, but exhibited higher contents of lignin and hydrogen peroxide (H2O2) as compared with non-MAP shoots at 20°C. Combined MAP and low temperature storage not only maintained good sensory quality after 30 days, but also reduced significantly the increases in lignin content, superoxide anion (O2.-) production rate, H2O2 content and membrane permeability, maintained high activities of superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX), and reduced the increase in activities of lipase, phospholipase D (PLD) and lipoxygenase (LOX). Furthermore, the minimally processed WBS under MAP condition exhibited higher energy charge (EC) and lower adenosine monophosphate (AMP) content by the end of storage (60 days) at 2°C than those without MAP or stored for 9 days at 20°C. Conclusion These results indicated that MAP in combination with low temperature storage reduced lignification of minimally processed WBS, which was closely associated with maintenance of energy status and enhanced activities of antioxidant enzymes, as well as reduced alleviation of membrane damage caused by ROS. PMID:24006941

Optimized multiple linear mappings for single image super-resolution

NASA Astrophysics Data System (ADS)

Zhang, Kaibing; Li, Jie; Xiong, Zenggang; Liu, Xiuping; Gao, Xinbo

2017-12-01

Learning piecewise linear regression has been recognized as an effective way for example learning-based single image super-resolution (SR) in literature. In this paper, we employ an expectation-maximization (EM) algorithm to further improve the SR performance of our previous multiple linear mappings (MLM) based SR method. In the training stage, the proposed method starts with a set of linear regressors obtained by the MLM-based method, and then jointly optimizes the clustering results and the low- and high-resolution subdictionary pairs for regression functions by using the metric of the reconstruction errors. In the test stage, we select the optimal regressor for SR reconstruction by accumulating the reconstruction errors of m-nearest neighbors in the training set. Thorough experimental results carried on six publicly available datasets demonstrate that the proposed SR method can yield high-quality images with finer details and sharper edges in terms of both quantitative and perceptual image quality assessments.

Evaluation of local free carrier concentrations in individual heavily-doped GaN:Si micro-rods by micro-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Mohajerani, M. S.; Khachadorian, S.; Schimpke, T.; Nenstiel, C.; Hartmann, J.; Ledig, J.; Avramescu, A.; Strassburg, M.; Hoffmann, A.; Waag, A.

2016-02-01

Three-dimensional III-nitride micro-structures are being developed as a promising candidate for the future opto-electrical devices. In this study, we demonstrate a quick and straight-forward method to locally evaluate free-carrier concentrations and a crystalline quality in individual GaN:Si micro-rods. By employing micro-Raman mapping and analyzing lower frequency branch of A1(LO)- and E1(LO)-phonon-plasmon-coupled modes (LPP-), the free carrier concentrations are determined in axial and planar configurations, respectively. Due to a gradual doping profile along the micro-rods, a highly spatially resolved mapping on the sidewall is exploited to reconstruct free carrier concentration profile along the GaN:Si micro-rods. Despite remarkably high free carrier concentrations above 1 × 1020 cm-3, the micro-rods reveal an excellent crystalline quality, without a doping-induced stress.

Global Atmosphere Watch Workshop on Measurement-Model ...

EPA Pesticide Factsheets

The World Meteorological Organization’s (WMO) Global Atmosphere Watch (GAW) Programme coordinates high-quality observations of atmospheric composition from global to local scales with the aim to drive high-quality and high-impact science while co-producing a new generation of products and services. In line with this vision, GAW’s Scientific Advisory Group for Total Atmospheric Deposition (SAG-TAD) has a mandate to produce global maps of wet, dry and total atmospheric deposition for important atmospheric chemicals to enable research into biogeochemical cycles and assessments of ecosystem and human health effects. The most suitable scientific approach for this activity is the emerging technique of measurement-model fusion for total atmospheric deposition. This technique requires global-scale measurements of atmospheric trace gases, particles, precipitation composition and precipitation depth, as well as predictions of the same from global/regional chemical transport models. The fusion of measurement and model results requires data assimilation and mapping techniques. The objective of the GAW Workshop on Measurement-Model Fusion for Global Total Atmospheric Deposition (MMF-GTAD), an initiative of the SAG-TAD, was to review the state-of-the-science and explore the feasibility and methodology of producing, on a routine retrospective basis, global maps of atmospheric gas and aerosol concentrations as well as wet, dry and total deposition via measurement-model

3D single point imaging with compressed sensing provides high temporal resolution R 2* mapping for in vivo preclinical applications.

PubMed

Rioux, James A; Beyea, Steven D; Bowen, Chris V

2017-02-01

Purely phase-encoded techniques such as single point imaging (SPI) are generally unsuitable for in vivo imaging due to lengthy acquisition times. Reconstruction of highly undersampled data using compressed sensing allows SPI data to be quickly obtained from animal models, enabling applications in preclinical cellular and molecular imaging. TurboSPI is a multi-echo single point technique that acquires hundreds of images with microsecond spacing, enabling high temporal resolution relaxometry of large-R 2 * systems such as iron-loaded cells. TurboSPI acquisitions can be pseudo-randomly undersampled in all three dimensions to increase artifact incoherence, and can provide prior information to improve reconstruction. We evaluated the performance of CS-TurboSPI in phantoms, a rat ex vivo, and a mouse in vivo. An algorithm for iterative reconstruction of TurboSPI relaxometry time courses does not affect image quality or R 2 * mapping in vitro at acceleration factors up to 10. Imaging ex vivo is possible at similar acceleration factors, and in vivo imaging is demonstrated at an acceleration factor of 8, such that acquisition time is under 1 h. Accelerated TurboSPI enables preclinical R 2 * mapping without loss of data quality, and may show increased specificity to iron oxide compared to other sequences.

Deciphering Natural Allelic Variation in Switchgrass for Biomass Yield and Quality Using a Nested Association Mapping Population

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saha, Malay C.; Brummer, E. Charles; Kaeppler, Shawn

Switchgrass (Panicum virgatum L.) is a C4 grass with high biomass yield potential and a model species for bioenergy feedstock development. Understanding the genetic basis of quantitative traits is essential to facilitate genome-enabled breeding programs. The nested association mapping (NAM) analysis combines the best features of both bi-parental and association analyses and can provide high power and high resolution in QTL detection and will ensure significant improvements in biomass yield and quality. To develop a NAM population of switchgrass, 15 highly diverse genotypes with specific characteristics were selected from a diversity panel and crossed to a recurrent parent, AP13, amore » genotype selected for whole genome sequencing and parent of a mapping population. Ten genotypes from each of the 15 F1 families were then chain crossed. Progenies form each family were randomly selected to develop the NAM population. The switchgrass NAM population consists of a total of 2000 genotypes from 15 families. All the progenies, founder parents, F1 parents (n=2350) were evaluated in replicated field trials at Ardmore, OK and Knoxville, TN. Phenotypic data on plant height, tillering ability, regrowth, flowering time, and biomass yield were collected. Dried biomass samples were also analyzed using prediction equations of NIRS at the Noble Foundation and for lignin content, S/G ratio, and sugar release characteristics at the NREL. Genomic shotgun sequencing of 15 switchgrass NAM founder parental genomes at JGI produced 28-66 Gb high-quality sequence data. Alignment of these sequences with the reference genome, AP13 (v3.0), revealed that up to 99% of the genomic sequences mapped to the reference genome. A total of 2,149 individuals from NAM populations were sequenced by exome capture and two sets of 15 SNP matrices (one for each family) were generated. QTL associated with important traits have been identified and verified in breeding populations. The QTL detected and their associated markers can be used in molecular breeding programs to facilitate development of improved switchgrass cultivars for biofuel production.« less

Assessment of aggregate quality and petrographic properties' influence on rock quality: A case study from Nordland county, Norway

NASA Astrophysics Data System (ADS)

Kløve Keiding, Jakob; Erichsen, Eyolf; Heldal, Tom; Aslaksen Aasly, Kari

2017-04-01

Good access to construction materials is crucial for future infrastructure development and continued economic growth. In Norway >80 % of construction materials come from crushed aggregates and represent an growing share of the consumption. Although recycling to some extend can cover the need for construction materials, economic growth, increasing population and urbanization necessitates exploitation of new rock resources in Norway as well as many other parts of the world. Aggregates must fulfill a number of technical requirements to ensure high quality and long life expectancy of new roads, buildings and structures. Aggregates also have to be extracted near the consumer market. Particularly for road construction strict criteria are in place for wearing course for roads with high traffic density. Thus knowledge of mechanical rock quality is paramount for both exploitation as well as future resource and land-use planning but is often not assessed or mapped beyond the quarry scale. The Geological survey of Norway runs a database with information about crushed aggregate deposits from >1500 Norwegian quarries and sample sites. Here we use mechanical test analyses from the database to assess the aggregate quality in the Nordland county, Norway. Maps have been produced linking bed rock geology with rock quality parameters. The survey documents that the county is challenged in meeting the requirements for roads with high traffic density and especially in the middle parts of the county many samples have weak mechanical properties. This to some degree reflect that weak Cambro-Silurian rocks like phyllite, schist, carbonate and greenstone are abundant in Nordland. Typically mechanically stronger rock types such as gabbro, monzonite and granite are also exposed in large parts of the county, but are also characterized by relative poor or very variable mechanical test quality. Preliminary results indicate that many intrinsic parameters influence the mechanical rock strength, but variable degrees of deformation in the different tectonostratigraphic units exposed in Nordland affects the rock mechanical properties and is a prominent feature of our mapping. Unsurprisingly rock type, mineralogy, grain size and rock texture are all important factors that have a major control on the mechanical behaviour of the rocks. However, this assessment shows that there is an intricate interaction between these parameters and the resulting mechanical properties at present making it difficult to assess mechanical quality accurately only based on petrographic examination.

A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera.

PubMed

Shi, Yuan Yuan; Sun, Liang Xian; Huang, Zachary Y; Wu, Xiao Bo; Zhu, Yong Qiang; Zheng, Hua Jun; Zeng, Zhi Jiang

2013-01-01

The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. F2 workers (N = 103) were genotyped for 126,990 single nucleotide polymorphisms (SNPs). After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM) with the largest linkage group (180 loci) measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.

Global and Local Gravity Field Models of the Moon Using GRAIL Primary and Extended Mission Data

NASA Technical Reports Server (NTRS)

Goossens, Sander; Lemoine, Frank G.; Sabaka, Terence J.; Nicholas, Joseph B.; Mazarico, Erwan; Rowlands, David D.; Loomis, Bryant D.; Chinn, Douglas S.; Neumann, Gregory A.; Smith, David E.;

Emergency Response Damage Assessment using Satellite Remote Sensing Data

NASA Astrophysics Data System (ADS)

Clandillon, Stephen; Yésou, Hervé; Schneiderhan, Tobias; de Boissezon, Hélène; de Fraipont, Paul

2013-04-01

During disasters rescue and relief organisations need quick access to reliable and accurate information to be better equipped to do their job. It is increasingly felt that satellites offer a unique near real time (NRT) tool to aid disaster management. A short introduction to the International Charter 'Space and Major Disasters', in operation since 2000 promoting worldwide cooperation among member space agencies, will be given as it is the foundation on which satellite-based, emergency response, damage assessment has been built. Other complementary mechanisms will also be discussed. The user access, triggering mechanism, an essential component for this user-driven service, will be highlighted with its 24/7 single access point. Then, a clear distinction will be made between data provision and geo-information delivery mechanisms to underline the user need for geo-information that is easily integrated into their working environments. Briefly, the path to assured emergency response product quality will be presented beginning with user requirements, expressed early-on, for emergency response value-adding services. Initiatives were then established, supported by national and European institutions, to develop the sector, with SERTIT and DLR being key players, providing support to decision makers in headquarters and relief teams in the field. To consistently meet the high quality levels demanded by users, rapid mapping has been transformed via workflow and quality control standardisation to improve both speed and quality. As such, SERTIT located in Alsace, France, and DLR/ZKI from Bavaria, Germany, join their knowledge in this presentation to report about recent standards as both have ISO certified their rapid mapping services based on experienced, well-trained, 24/7 on-call teams and established systems providing the first crisis analysis product in 6 hours after satellite data reception. The three main product types provided are then outlined: up-to-date pre-event reference maps, disaster extent maps and damage assessment or intensity/grading maps. With Google and open-sourced information the need for the reference maps has diminished, but not altogether, as damage extent and assessment products also require coherent reference geo-information which often has to be produced internally. Increasingly users need up-to-date, highly detailed, customised products; it is in damage assessment that an operator's working environment, geomatic skills and experience can often provide the highest levels of value-adding while adapting to user requests. Accordingly, DLR and SERTIT are involved in R&D work integrating data, e.g. TerraSAR-X and Pléiades sources plus Sentinel simulated data, which have interesting emergency mapping capacities. Their close interaction with the research sector is essential to be at the cutting-edge of the field, implementing effective and efficient analysis methods. Future R&D challenges to further improve the quality of the damage mapping service will be highlighted. Finally, this presentation will show some practical examples and thus how at present, space-based rapid mapping, which has more than 10 years of experience, has come to being able to provide, if rapidly programmed and acquired, geo-information linked to disaster extent and damage assessment from overview scales down to the street level and this with an ever increasing array of satellite data sources.

Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

PubMed Central

Nunes, José de Ribamar da Silva; Liu, Shikai; Pértille, Fábio; Perazza, Caio Augusto; Villela, Priscilla Marqui Schmidt; de Almeida-Val, Vera Maria Fonseca; Hilsdorf, Alexandre Wagner Silva; Liu, Zhanjiang; Coutinho, Luiz Lehmann

2017-01-01

Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs. PMID:28387238

A Practical Framework for Cartographic Design

NASA Astrophysics Data System (ADS)

Denil, Mark

2018-05-01

Creation of a map artifact that can be recognized, accepted, read, and absorbed is the cartographer's chief responsibility. This involves bringing coherence and order out of chaos and randomness through the construction of map artifacts that mediate processes of social communication. Maps are artifacts, first and foremost: they are artifacts with particular formal attributes. It is the formal aspects of the map artifact that allows it to invoke and sustain a reading as a map. This paper examines Cartographic Design as the sole means at the cartographer's disposal for constructing the meaning bearing artifacts we know as maps, by placing it in a center of a practical analytic framework. The framework draws together the Theoretic and Craft aspects of map making, and examines how Style and Taste operate through the rubric of a schema of Mapicity to produce high quality maps. The role of the Cartographic Canon, and the role of Critique, are also explored, and a few design resources are identified.

Assessment of groundwater vulnerability in the coastal region of Oman using DRASTIC index method in GIS environment.

PubMed

Jamrah, Ahmad; Al-Futaisi, Ahmed; Rajmohan, Natarajan; Al-Yaroubi, Saif

2008-12-01

A study was carried out to develop a vulnerability map for Barka region in the North Batina of Oman using DRASTIC vulnerability index method in GIS environment. DRASTIC layers were created using data from published reports and the seven DRASTIC layers were processed by the ArcGIS geographic information system. Finally, DRASTIC maps were created for 1995 and 2004 to understand the long-term changes in the vulnerability index. DRASTIC vulnerability maps were evaluated using groundwater quality data such as chemical and biological parameters. DRASTIC vulnerability maps of 1995 and 2004 indicate that the northern part of Barka is more vulnerable to pollution than southern part and the central part of Barka also shows high relative vulnerability which is mostly related to the high conductivity values. Moreover, the changes in water level due to high abstraction rate of groundwater reflect in the vulnerability maps and low vulnerability area is increased in the southern part during 2004 compared to 1995. Moreover, regional distribution maps of nitrate, chloride and total and fecal coliforms are well correlated with DRASTIC vulnerability maps. In contrast to this, even though DRASTIC method predicted the central part of the study region is highly vulnerable, both chemical and biological parameters show lower concentrations in this region compared to coastal belt, which is mainly due to agricultural and urban development. In Barka, urban development and agricultural activities are very high in coastal region compared to southern and central part of the study area. Hence, this study concluded that DRASTIC method is also applicable in coastal region having ubiquitous contamination sources.

Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq).

PubMed

Qian, Wei; Fan, Guiyan; Liu, Dandan; Zhang, Helong; Wang, Xiaowu; Wu, Jian; Xu, Zhaosheng

2017-04-04

Cultivated spinach (Spinacia oleracea L.) is one of the most widely cultivated types of leafy vegetable in the world, and it has a high nutritional value. Spinach is also an ideal plant for investigating the mechanism of sex determination because it is a dioecious species with separate male and female plants. Some reports on the sex labeling and localization of spinach in the study of molecular markers have surfaced. However, there have only been two reports completed on the genetic map of spinach. The lack of rich and reliable molecular markers and the shortage of high-density linkage maps are important constraints in spinach research work. In this study, a high-density genetic map of spinach based on the Specific-locus Amplified Fragment Sequencing (SLAF-seq) technique was constructed; the sex-determining gene was also finely mapped. Through bio-information analysis, 50.75 Gb of data in total was obtained, including 207.58 million paired-end reads. Finally, 145,456 high-quality SLAF markers were obtained, with 27,800 polymorphic markers and 4080 SLAF markers were finally mapped onto the genetic map after linkage analysis. The map spanned 1,125.97 cM with an average distance of 0.31 cM between the adjacent marker loci. It was divided into 6 linkage groups corresponding to the number of spinach chromosomes. Besides, the combination of Bulked Segregation Analysis (BSA) with SLAF-seq technology(super-BSA) was employed to generate the linkage markers with the sex-determining gene. Combined with the high-density genetic map of spinach, the sex-determining gene X/Y was located at the position of the linkage group (LG) 4 (66.98 cM-69.72 cM and 75.48 cM-92.96 cM), which may be the ideal region for the sex-determining gene. A high-density genetic map of spinach based on the SLAF-seq technique was constructed with a backcross (BC 1 ) population (which is the highest density genetic map of spinach reported at present). At the same time, the sex-determining gene X/Y was mapped to LG4 with super-BSA. This map will offer a suitable basis for further study of spinach, such as gene mapping, map-based cloning of Specific genes, quantitative trait locus (QTL) mapping and marker-assisted selection (MAS). It will also provide an efficient reference for studies on the mechanism of sex determination in other dioecious plants.

An improved dehazing algorithm of aerial high-definition image

NASA Astrophysics Data System (ADS)

Jiang, Wentao; Ji, Ming; Huang, Xiying; Wang, Chao; Yang, Yizhou; Li, Tao; Wang, Jiaoying; Zhang, Ying

2016-01-01

For unmanned aerial vehicle(UAV) images, the sensor can not get high quality images due to fog and haze weather. To solve this problem, An improved dehazing algorithm of aerial high-definition image is proposed. Based on the model of dark channel prior, the new algorithm firstly extracts the edges from crude estimated transmission map and expands the extracted edges. Then according to the expended edges, the algorithm sets a threshold value to divide the crude estimated transmission map into different areas and makes different guided filter on the different areas compute the optimized transmission map. The experimental results demonstrate that the performance of the proposed algorithm is substantially the same as the one based on dark channel prior and guided filter. The average computation time of the new algorithm is around 40% of the one as well as the detection ability of UAV image is improved effectively in fog and haze weather.

Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat

PubMed Central

Holtz, Yan; Ardisson, Morgane; Ranwez, Vincent; Besnard, Alban; Leroy, Philippe; Poux, Gérard; Roumet, Pierre; Viader, Véronique; Santoni, Sylvain; David, Jacques

2016-01-01

Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays. PMID:27171472

A system and method for online high-resolution mapping of gastric slow-wave activity.

PubMed

Bull, Simon H; O'Grady, Gregory; Du, Peng; Cheng, Leo K

2014-11-01

High-resolution (HR) mapping employs multielectrode arrays to achieve spatially detailed analyses of propagating bioelectrical events. A major current limitation is that spatial analyses must currently be performed "off-line" (after experiments), compromising timely recording feedback and restricting experimental interventions. These problems motivated development of a system and method for "online" HR mapping. HR gastric recordings were acquired and streamed to a novel software client. Algorithms were devised to filter data, identify slow-wave events, eliminate corrupt channels, and cluster activation events. A graphical user interface animated data and plotted electrograms and maps. Results were compared against off-line methods. The online system analyzed 256-channel serosal recordings with no unexpected system terminations with a mean delay 18 s. Activation time marking sensitivity was 0.92; positive predictive value was 0.93. Abnormal slow-wave patterns including conduction blocks, ectopic pacemaking, and colliding wave fronts were reliably identified. Compared to traditional analysis methods, online mapping had comparable results with equivalent coverage of 90% of electrodes, average RMS errors of less than 1 s, and CC of activation maps of 0.99. Accurate slow-wave mapping was achieved in near real-time, enabling monitoring of recording quality and experimental interventions targeted to dysrhythmic onset. This work also advances the translation of HR mapping toward real-time clinical application.

UAS close range remote sensing for mapping coastal environments

NASA Astrophysics Data System (ADS)

Papakonstantinou, Apostolos; Topouzelis, Kostantinos; Doukari, Michaela

2017-09-01

Coastline change and marine litter concentration in shoreline zones are two different emerging problems indicating the vulnerability as well as the quality of a coastal environment. Both problems present spatiotemporal changes due to weather and anthropogenic factors. Traditionally spatiotemporal changes in coastal environments are monitored using high-resolution satellite images and manned surveys. The last years, Unmanned Aerial Systems (UAS) are used as additional tool for monitoring environmental phenomena in sensitive coastal areas. In this study, two different case studies for mapping emerging coastal phenomena i.e. coastline changes and marine litter in Lesvos island, are presented. Both phenomena have increasing interest among scientists monitoring sensitive coastal areas. This paper outlines the integration of UAS for data acquisition and Structure from Motion (SfM) pipeline for the visualization of selected coastal areas in the Aegean Sea. The followed UAS-SfM methodology produces very detailed orthophoto maps. This high resolution spatial information is used for mapping and detecting primarily, marine litter on coastal and underwater zones and secondly, coastline changes and coastal erosion. More specific the produced orthophoto maps analyzed through GIS and with the use of the appropriate cartographic techniques the objective environmental parameters were mapped. Results showed that UAS-SfM pipeline produces geoinformation with high accuracy and spatial resolution that helps scientists to map with confidence environmental changes that take place in shoreline zones.

High-confidence coding and noncoding transcriptome maps

PubMed Central

2017-01-01

The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap 2.0, The Cancer Genome Atlas, and GTEx projects, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalog that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of noncoding genomes. PMID:28396519

Influence of pansharpening techniques in obtaining accurate vegetation thematic maps

NASA Astrophysics Data System (ADS)

Ibarrola-Ulzurrun, Edurne; Gonzalo-Martin, Consuelo; Marcello-Ruiz, Javier

2016-10-01

In last decades, there have been a decline in natural resources, becoming important to develop reliable methodologies for their management. The appearance of very high resolution sensors has offered a practical and cost-effective means for a good environmental management. In this context, improvements are needed for obtaining higher quality of the information available in order to get reliable classified images. Thus, pansharpening enhances the spatial resolution of the multispectral band by incorporating information from the panchromatic image. The main goal in the study is to implement pixel and object-based classification techniques applied to the fused imagery using different pansharpening algorithms and the evaluation of thematic maps generated that serve to obtain accurate information for the conservation of natural resources. A vulnerable heterogenic ecosystem from Canary Islands (Spain) was chosen, Teide National Park, and Worldview-2 high resolution imagery was employed. The classes considered of interest were set by the National Park conservation managers. 7 pansharpening techniques (GS, FIHS, HCS, MTF based, Wavelet `à trous' and Weighted Wavelet `à trous' through Fractal Dimension Maps) were chosen in order to improve the data quality with the goal to analyze the vegetation classes. Next, different classification algorithms were applied at pixel-based and object-based approach, moreover, an accuracy assessment of the different thematic maps obtained were performed. The highest classification accuracy was obtained applying Support Vector Machine classifier at object-based approach in the Weighted Wavelet `à trous' through Fractal Dimension Maps fused image. Finally, highlight the difficulty of the classification in Teide ecosystem due to the heterogeneity and the small size of the species. Thus, it is important to obtain accurate thematic maps for further studies in the management and conservation of natural resources.

Mapping with Small UAS: A Point Cloud Accuracy Assessment

NASA Astrophysics Data System (ADS)

Toth, Charles; Jozkow, Grzegorz; Grejner-Brzezinska, Dorota

2015-12-01

Interest in using inexpensive Unmanned Aerial System (UAS) technology for topographic mapping has recently significantly increased. Small UAS platforms equipped with consumer grade cameras can easily acquire high-resolution aerial imagery allowing for dense point cloud generation, followed by surface model creation and orthophoto production. In contrast to conventional airborne mapping systems, UAS has limited ground coverage due to low flying height and limited flying time, yet it offers an attractive alternative to high performance airborne systems, as the cost of the sensors and platform, and the flight logistics, is relatively low. In addition, UAS is better suited for small area data acquisitions and to acquire data in difficult to access areas, such as urban canyons or densely built-up environments. The main question with respect to the use of UAS is whether the inexpensive consumer sensors installed in UAS platforms can provide the geospatial data quality comparable to that provided by conventional systems. This study aims at the performance evaluation of the current practice of UAS-based topographic mapping by reviewing the practical aspects of sensor configuration, georeferencing and point cloud generation, including comparisons between sensor types and processing tools. The main objective is to provide accuracy characterization and practical information for selecting and using UAS solutions in general mapping applications. The analysis is based on statistical evaluation as well as visual examination of experimental data acquired by a Bergen octocopter with three different image sensor configurations, including a GoPro HERO3+ Black Edition, a Nikon D800 DSLR and a Velodyne HDL-32. In addition, georeferencing data of varying quality were acquired and evaluated. The optical imagery was processed by using three commercial point cloud generation tools. Comparing point clouds created by active and passive sensors by using different quality sensors, and finally, by different commercial software tools, provides essential information for the performance validation of UAS technology.

Does the process map influence the outcome of quality improvement work? A comparison of a sequential flow diagram and a hierarchical task analysis diagram.

PubMed

Colligan, Lacey; Anderson, Janet E; Potts, Henry W W; Berman, Jonathan

2010-01-07

Many quality and safety improvement methods in healthcare rely on a complete and accurate map of the process. Process mapping in healthcare is often achieved using a sequential flow diagram, but there is little guidance available in the literature about the most effective type of process map to use. Moreover there is evidence that the organisation of information in an external representation affects reasoning and decision making. This exploratory study examined whether the type of process map - sequential or hierarchical - affects healthcare practitioners' judgments. A sequential and a hierarchical process map of a community-based anti coagulation clinic were produced based on data obtained from interviews, talk-throughs, attendance at a training session and examination of protocols and policies. Clinic practitioners were asked to specify the parts of the process that they judged to contain quality and safety concerns. The process maps were then shown to them in counter-balanced order and they were asked to circle on the diagrams the parts of the process where they had the greatest quality and safety concerns. A structured interview was then conducted, in which they were asked about various aspects of the diagrams. Quality and safety concerns cited by practitioners differed depending on whether they were or were not looking at a process map, and whether they were looking at a sequential diagram or a hierarchical diagram. More concerns were identified using the hierarchical diagram compared with the sequential diagram and more concerns were identified in relation to clinical work than administrative work. Participants' preference for the sequential or hierarchical diagram depended on the context in which they would be using it. The difficulties of determining the boundaries for the analysis and the granularity required were highlighted. The results indicated that the layout of a process map does influence perceptions of quality and safety problems in a process. In quality improvement work it is important to carefully consider the type of process map to be used and to consider using more than one map to ensure that different aspects of the process are captured.

A heuristic multi-criteria classification approach incorporating data quality information for choropleth mapping

PubMed Central

Sun, Min; Wong, David; Kronenfeld, Barry

2016-01-01

Despite conceptual and technology advancements in cartography over the decades, choropleth map design and classification fail to address a fundamental issue: estimates that are statistically indifferent may be assigned to different classes on maps or vice versa. Recently, the class separability concept was introduced as a map classification criterion to evaluate the likelihood that estimates in two classes are statistical different. Unfortunately, choropleth maps created according to the separability criterion usually have highly unbalanced classes. To produce reasonably separable but more balanced classes, we propose a heuristic classification approach to consider not just the class separability criterion but also other classification criteria such as evenness and intra-class variability. A geovisual-analytic package was developed to support the heuristic mapping process to evaluate the trade-off between relevant criteria and to select the most preferable classification. Class break values can be adjusted to improve the performance of a classification. PMID:28286426

Experiments to Distribute Map Generalization Processes

NASA Astrophysics Data System (ADS)

Berli, Justin; Touya, Guillaume; Lokhat, Imran; Regnauld, Nicolas

2018-05-01

Automatic map generalization requires the use of computationally intensive processes often unable to deal with large datasets. Distributing the generalization process is the only way to make them scalable and usable in practice. But map generalization is a highly contextual process, and the surroundings of a generalized map feature needs to be known to generalize the feature, which is a problem as distribution might partition the dataset and parallelize the processing of each part. This paper proposes experiments to evaluate the past propositions to distribute map generalization, and to identify the main remaining issues. The past propositions to distribute map generalization are first discussed, and then the experiment hypotheses and apparatus are described. The experiments confirmed that regular partitioning was the quickest strategy, but also the less effective in taking context into account. The geographical partitioning, though less effective for now, is quite promising regarding the quality of the results as it better integrates the geographical context.

Predefined Redundant Dictionary for Effective Depth Maps Representation

NASA Astrophysics Data System (ADS)

Sebai, Dorsaf; Chaieb, Faten; Ghorbel, Faouzi

2016-01-01

The multi-view video plus depth (MVD) video format consists of two components: texture and depth map, where a combination of these components enables a receiver to generate arbitrary virtual views. However, MVD presents a very voluminous video format that requires a compression process for storage and especially for transmission. Conventional codecs are perfectly efficient for texture images compression but not for intrinsic depth maps properties. Depth images indeed are characterized by areas of smoothly varying grey levels separated by sharp discontinuities at the position of object boundaries. Preserving these characteristics is important to enable high quality view synthesis at the receiver side. In this paper, sparse representation of depth maps is discussed. It is shown that a significant gain in sparsity is achieved when particular mixed dictionaries are used for approximating these types of images with greedy selection strategies. Experiments are conducted to confirm the effectiveness at producing sparse representations, and competitiveness, with respect to candidate state-of-art dictionaries. Finally, the resulting method is shown to be effective for depth maps compression and represents an advantage over the ongoing 3D high efficiency video coding compression standard, particularly at medium and high bitrates.

Protecting water quality in the watershed

DOE Office of Scientific and Technical Information (OSTI.GOV)

James, C.R.; Johnson, K.E.; Stewart, E.H.

1994-08-01

This article highlights the water quality component of a watershed management plan being developed for the San Francisco (CA) Water Department. The physical characteristics of the 63,000-acre watersheds were analyzed for source and transport vulnerability for five groups of water quality parameters--particulates, THM precursors, microorganisms (Giardia and cryptosporidium), nutrients (nitrogen and phosphorus), and synthetic organic chemicals--and vulnerability zones were mapped. Mapping was achieved through the use of an extensive geographic information system (GIS) database. Each water quality vulnerability zone map was developed based on five watershed physical characteristics--soils, slope, vegetation, wildlife concentration, and proximity to water bodies--and their relationships tomore » each of the five groups of water quality parameters. An approach to incorporate the watershed physical characteristics information into the five water quality vulnerability zone maps was defined and verified. The composite approach was based in part on information gathered from existing watershed management plans.« less

Temporal reliability of ultra-high field resting-state MRI for single-subject sensorimotor and language mapping.

PubMed

Branco, Paulo; Seixas, Daniela; Castro, São Luís

2018-03-01

Resting-state fMRI is a well-suited technique to map functional networks in the brain because unlike task-based approaches it requires little collaboration from subjects. This is especially relevant in clinical settings where a number of subjects cannot comply with task demands. Previous studies using conventional scanner fields have shown that resting-state fMRI is able to map functional networks in single subjects, albeit with moderate temporal reliability. Ultra-high resolution (7T) imaging provides higher signal-to-noise ratio and better spatial resolution and is thus well suited to assess the temporal reliability of mapping results, and to determine if resting-state fMRI can be applied in clinical decision making including preoperative planning. We used resting-state fMRI at ultra-high resolution to examine whether the sensorimotor and language networks are reliable over time - same session and one week after. Resting-state networks were identified for all subjects and sessions with good accuracy. Both networks were well delimited within classical regions of interest. Mapping was temporally reliable at short and medium time-scales as demonstrated by high values of overlap in the same session and one week after for both networks. Results were stable independently of data quality metrics and physiological variables. Taken together, these findings provide strong support for the suitability of ultra-high field resting-state fMRI mapping at the single-subject level. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Road Extraction from AVIRIS Using Spectral Mixture and Q-Tree Filter Techniques

NASA Technical Reports Server (NTRS)

Gardner, Margaret E.; Roberts, Dar A.; Funk, Chris; Noronha, Val

2001-01-01

Accurate road location and condition information are of primary importance in road infrastructure management. Additionally, spatially accurate and up-to-date road networks are essential in ambulance and rescue dispatch in emergency situations. However, accurate road infrastructure databases do not exist for vast areas, particularly in areas with rapid expansion. Currently, the US Department of Transportation (USDOT) extends great effort in field Global Positioning System (GPS) mapping and condition assessment to meet these informational needs. This methodology, though effective, is both time-consuming and costly, because every road within a DOT's jurisdiction must be field-visited to obtain accurate information. Therefore, the USDOT is interested in identifying new technologies that could help meet road infrastructure informational needs more effectively. Remote sensing provides one means by which large areas may be mapped with a high standard of accuracy and is a technology with great potential in infrastructure mapping. The goal of our research is to develop accurate road extraction techniques using high spatial resolution, fine spectral resolution imagery. Additionally, our research will explore the use of hyperspectral data in assessing road quality. Finally, this research aims to define the spatial and spectral requirements for remote sensing data to be used successfully for road feature extraction and road quality mapping. Our findings will facilitate the USDOT in assessing remote sensing as a new resource in infrastructure studies.

Anatomical accuracy of brain connections derived from diffusion MRI tractography is inherently limited.

PubMed

Thomas, Cibu; Ye, Frank Q; Irfanoglu, M Okan; Modi, Pooja; Saleem, Kadharbatcha S; Leopold, David A; Pierpaoli, Carlo

2014-11-18

Tractography based on diffusion-weighted MRI (DWI) is widely used for mapping the structural connections of the human brain. Its accuracy is known to be limited by technical factors affecting in vivo data acquisition, such as noise, artifacts, and data undersampling resulting from scan time constraints. It generally is assumed that improvements in data quality and implementation of sophisticated tractography methods will lead to increasingly accurate maps of human anatomical connections. However, assessing the anatomical accuracy of DWI tractography is difficult because of the lack of independent knowledge of the true anatomical connections in humans. Here we investigate the future prospects of DWI-based connectional imaging by applying advanced tractography methods to an ex vivo DWI dataset of the macaque brain. The results of different tractography methods were compared with maps of known axonal projections from previous tracer studies in the macaque. Despite the exceptional quality of the DWI data, none of the methods demonstrated high anatomical accuracy. The methods that showed the highest sensitivity showed the lowest specificity, and vice versa. Additionally, anatomical accuracy was highly dependent upon parameters of the tractography algorithm, with different optimal values for mapping different pathways. These results suggest that there is an inherent limitation in determining long-range anatomical projections based on voxel-averaged estimates of local fiber orientation obtained from DWI data that is unlikely to be overcome by improvements in data acquisition and analysis alone.

A High-Resolution InDel (Insertion–Deletion) Markers-Anchored Consensus Genetic Map Identifies Major QTLs Governing Pod Number and Seed Yield in Chickpea

PubMed Central

Srivastava, Rishi; Singh, Mohar; Bajaj, Deepak; Parida, Swarup K.

2016-01-01

Development and large-scale genotyping of user-friendly informative genome/gene-derived InDel markers in natural and mapping populations is vital for accelerating genomics-assisted breeding applications of chickpea with minimal resource expenses. The present investigation employed a high-throughput whole genome next-generation resequencing strategy in low and high pod number parental accessions and homozygous individuals constituting the bulks from each of two inter-specific mapping populations [(Pusa 1103 × ILWC 46) and (Pusa 256 × ILWC 46)] to develop non-erroneous InDel markers at a genome-wide scale. Comparing these high-quality genomic sequences, 82,360 InDel markers with reference to kabuli genome and 13,891 InDel markers exhibiting differentiation between low and high pod number parental accessions and bulks of aforementioned mapping populations were developed. These informative markers were structurally and functionally annotated in diverse coding and non-coding sequence components of genome/genes of kabuli chickpea. The functional significance of regulatory and coding (frameshift and large-effect mutations) InDel markers for establishing marker-trait linkages through association/genetic mapping was apparent. The markers detected a greater amplification (97%) and intra-specific polymorphic potential (58–87%) among a diverse panel of cultivated desi, kabuli, and wild accessions even by using a simpler cost-efficient agarose gel-based assay implicating their utility in large-scale genetic analysis especially in domesticated chickpea with narrow genetic base. Two high-density inter-specific genetic linkage maps generated using aforesaid mapping populations were integrated to construct a consensus 1479 InDel markers-anchored high-resolution (inter-marker distance: 0.66 cM) genetic map for efficient molecular mapping of major QTLs governing pod number and seed yield per plant in chickpea. Utilizing these high-density genetic maps as anchors, three major genomic regions harboring each of pod number and seed yield robust QTLs (15–28% phenotypic variation explained) were identified on chromosomes 2, 4, and 6. The integration of genetic and physical maps at these QTLs mapped on chromosomes scaled-down the long major QTL intervals into high-resolution short pod number and seed yield robust QTL physical intervals (0.89–2.94 Mb) which were essentially got validated in multiple genetic backgrounds of two chickpea mapping populations. The genome-wide InDel markers including natural allelic variants and genomic loci/genes delineated at major six especially in one colocalized novel congruent robust pod number and seed yield robust QTLs mapped on a high-density consensus genetic map were found most promising in chickpea. These functionally relevant molecular tags can drive marker-assisted genetic enhancement to develop high-yielding cultivars with increased seed/pod number and yield in chickpea. PMID:27695461

Comparison of PV signal quality using a novel circular mapping and ablation catheter versus a standard circular mapping catheter.

PubMed

von Bary, Christian; Fredersdorf-Hahn, Sabine; Heinicke, Norbert; Jungbauer, Carsten; Schmid, Peter; Riegger, Günter A; Weber, Stefan

2011-08-01

Recently, new catheter technologies have been developed for atrial fibrillation (AF) ablation. We investigate the diagnostic accuracy of a circular mapping and pulmonary vein ablation catheter (PVAC) compared with a standard circular mapping catheter (Orbiter) and the influence of filter settings on signal quality. After reconstruction of the left atrium by three-dimensional atriography, baseline PV potentials (PVP) were recorded consecutively with PVAC and Orbiter in 20 patients with paroxysmal AF. PVPs were compared and attributed to predefined anatomical PV segments. Ablation was performed in 80 PVs using the PVAC. If isolation of the PVs was assumed, signal assessment of each PV was repeated with the Orbiter. If residual PV potentials could be uncovered, different filter settings were tested to improve mapping quality of the PVAC. Ablation was continued until complete PV isolation (PVI) was confirmed with the Orbiter. Baseline mapping demonstrated a good correlation between the Orbiter and PVAC. Mapping accuracy using the PVAC for mapping and ablation was 94% (74 of 79 PVs). Additional mapping with the Orbiter improved the PV isolation rate to 99%. Adjustment of filter settings failed to improve quality of the PV signals compared with standard filter settings. Using the PVAC as a stand-alone strategy for mapping and ablation, one should be aware that in some cases, different signal morphology mimics PVI isolation. Adjustment of filter settings failed to improve signal quality. The use of an additional mapping catheter is recommended to become familiar with the particular signal morphology during the first PVAC cases or whenever there is a doubt about successful isolation of the pulmonary veins.

High resolution mapping of development in the wildland-urban interface using object based image extraction.

PubMed

Caggiano, Michael D; Tinkham, Wade T; Hoffman, Chad; Cheng, Antony S; Hawbaker, Todd J

2016-10-01

The wildland-urban interface (WUI), the area where human development encroaches on undeveloped land, is expanding throughout the western United States resulting in increased wildfire risk to homes and communities. Although census based mapping efforts have provided insights into the pattern of development and expansion of the WUI at regional and national scales, these approaches do not provide sufficient detail for fine-scale fire and emergency management planning, which requires maps of individual building locations. Although fine-scale maps of the WUI have been developed, they are often limited in their spatial extent, have unknown accuracies and biases, and are costly to update over time. In this paper we assess a semi-automated Object Based Image Analysis (OBIA) approach that utilizes 4-band multispectral National Aerial Image Program (NAIP) imagery for the detection of individual buildings within the WUI. We evaluate this approach by comparing the accuracy and overall quality of extracted buildings to a building footprint control dataset. In addition, we assessed the effects of buffer distance, topographic conditions, and building characteristics on the accuracy and quality of building extraction. The overall accuracy and quality of our approach was positively related to buffer distance, with accuracies ranging from 50 to 95% for buffer distances from 0 to 100 m. Our results also indicate that building detection was sensitive to building size, with smaller outbuildings (footprints less than 75 m 2 ) having detection rates below 80% and larger residential buildings having detection rates above 90%. These findings demonstrate that this approach can successfully identify buildings in the WUI in diverse landscapes while achieving high accuracies at buffer distances appropriate for most fire management applications while overcoming cost and time constraints associated with traditional approaches. This study is unique in that it evaluates the ability of an OBIA approach to extract highly detailed data on building locations in a WUI setting.

High resolution mapping of development in the wildland-urban interface using object based image extraction

USGS Publications Warehouse

Caggiano, Michael D.; Tinkham, Wade T.; Hoffman, Chad; Cheng, Antony S.; Hawbaker, Todd J.

2016-01-01

The wildland-urban interface (WUI), the area where human development encroaches on undeveloped land, is expanding throughout the western United States resulting in increased wildfire risk to homes and communities. Although census based mapping efforts have provided insights into the pattern of development and expansion of the WUI at regional and national scales, these approaches do not provide sufficient detail for fine-scale fire and emergency management planning, which requires maps of individual building locations. Although fine-scale maps of the WUI have been developed, they are often limited in their spatial extent, have unknown accuracies and biases, and are costly to update over time. In this paper we assess a semi-automated Object Based Image Analysis (OBIA) approach that utilizes 4-band multispectral National Aerial Image Program (NAIP) imagery for the detection of individual buildings within the WUI. We evaluate this approach by comparing the accuracy and overall quality of extracted buildings to a building footprint control dataset. In addition, we assessed the effects of buffer distance, topographic conditions, and building characteristics on the accuracy and quality of building extraction. The overall accuracy and quality of our approach was positively related to buffer distance, with accuracies ranging from 50 to 95% for buffer distances from 0 to 100 m. Our results also indicate that building detection was sensitive to building size, with smaller outbuildings (footprints less than 75 m2) having detection rates below 80% and larger residential buildings having detection rates above 90%. These findings demonstrate that this approach can successfully identify buildings in the WUI in diverse landscapes while achieving high accuracies at buffer distances appropriate for most fire management applications while overcoming cost and time constraints associated with traditional approaches. This study is unique in that it evaluates the ability of an OBIA approach to extract highly detailed data on building locations in a WUI setting.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

PubMed

Kisand, Veljo; Lettieri, Teresa

2013-04-01

De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize unknown bacteria with modest effort.

Two-dimensional T2 distribution mapping in rock core plugs with optimal k-space sampling.

PubMed

Xiao, Dan; Balcom, Bruce J

2012-07-01

Spin-echo single point imaging has been employed for 1D T(2) distribution mapping, but a simple extension to 2D is challenging since the time increase is n fold, where n is the number of pixels in the second dimension. Nevertheless 2D T(2) mapping in fluid saturated rock core plugs is highly desirable because the bedding plane structure in rocks often results in different pore properties within the sample. The acquisition time can be improved by undersampling k-space. The cylindrical shape of rock core plugs yields well defined intensity distributions in k-space that may be efficiently determined by new k-space sampling patterns that are developed in this work. These patterns acquire 22.2% and 11.7% of the k-space data points. Companion density images may be employed, in a keyhole imaging sense, to improve image quality. T(2) weighted images are fit to extract T(2) distributions, pixel by pixel, employing an inverse Laplace transform. Images reconstructed with compressed sensing, with similar acceleration factors, are also presented. The results show that restricted k-space sampling, in this application, provides high quality results. Copyright © 2012 Elsevier Inc. All rights reserved.

A Tool for Creating Regionally Calibrated High-Resolution Land Cover Data Sets for the West African Sahel: Using Machine Learning to Scale Up Hand-Classified Maps in a Data-Sparse Environment

NASA Astrophysics Data System (ADS)

Van Gordon, M.; Van Gordon, S.; Min, A.; Sullivan, J.; Weiner, Z.; Tappan, G. G.

2017-12-01

Using support vector machine (SVM) learning and high-accuracy hand-classified maps, we have developed a publicly available land cover classification tool for the West African Sahel. Our classifier produces high-resolution and regionally calibrated land cover maps for the Sahel, representing a significant contribution to the data available for this region. Global land cover products are unreliable for the Sahel, and accurate land cover data for the region are sparse. To address this gap, the U.S. Geological Survey and the Regional Center for Agriculture, Hydrology and Meteorology (AGRHYMET) in Niger produced high-quality land cover maps for the region via hand-classification of Landsat images. This method produces highly accurate maps, but the time and labor required constrain the spatial and temporal resolution of the data products. By using these hand-classified maps alongside SVM techniques, we successfully increase the resolution of the land cover maps by 1-2 orders of magnitude, from 2km-decadal resolution to 30m-annual resolution. These high-resolution regionally calibrated land cover datasets, along with the classifier we developed to produce them, lay the foundation for major advances in studies of land surface processes in the region. These datasets will provide more accurate inputs for food security modeling, hydrologic modeling, analyses of land cover change and climate change adaptation efforts. The land cover classification tool we have developed will be publicly available for use in creating additional West Africa land cover datasets with future remote sensing data and can be adapted for use in other parts of the world.

A Single Molecule Scaffold for the Maize Genome

PubMed Central

Zhou, Shiguo; Wei, Fusheng; Nguyen, John; Bechner, Mike; Potamousis, Konstantinos; Goldstein, Steve; Pape, Louise; Mehan, Michael R.; Churas, Chris; Pasternak, Shiran; Forrest, Dan K.; Wise, Roger; Ware, Doreen; Wing, Rod A.; Waterman, Michael S.; Livny, Miron; Schwartz, David C.

2009-01-01

About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars. PMID:19936062

A physical map of the bovine genome

PubMed Central

Snelling, Warren M; Chiu, Readman; Schein, Jacqueline E; Hobbs, Matthew; Abbey, Colette A; Adelson, David L; Aerts, Jan; Bennett, Gary L; Bosdet, Ian E; Boussaha, Mekki; Brauning, Rudiger; Caetano, Alexandre R; Costa, Marcos M; Crawford, Allan M; Dalrymple, Brian P; Eggen, André; Everts-van der Wind, Annelie; Floriot, Sandrine; Gautier, Mathieu; Gill, Clare A; Green, Ronnie D; Holt, Robert; Jann, Oliver; Jones, Steven JM; Kappes, Steven M; Keele, John W; de Jong, Pieter J; Larkin, Denis M; Lewin, Harris A; McEwan, John C; McKay, Stephanie; Marra, Marco A; Mathewson, Carrie A; Matukumalli, Lakshmi K; Moore, Stephen S; Murdoch, Brenda; Nicholas, Frank W; Osoegawa, Kazutoyo; Roy, Alice; Salih, Hanni; Schibler, Laurent; Schnabel, Robert D; Silveri, Licia; Skow, Loren C; Smith, Timothy PL; Sonstegard, Tad S; Taylor, Jeremy F; Tellam, Ross; Van Tassell, Curtis P; Williams, John L; Womack, James E; Wye, Natasja H; Yang, George; Zhao, Shaying

2007-01-01

Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project. Results A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly. Conclusion Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans. PMID:17697342

Demystifying process mapping: a key step in neurosurgical quality improvement initiatives.

PubMed

McLaughlin, Nancy; Rodstein, Jennifer; Burke, Michael A; Martin, Neil A

2014-08-01

Reliable delivery of optimal care can be challenging for care providers. Health care leaders have integrated various business tools to assist them and their teams in ensuring consistent delivery of safe and top-quality care. The cornerstone to all quality improvement strategies is the detailed understanding of the current state of a process, captured by process mapping. Process mapping empowers caregivers to audit how they are currently delivering care to subsequently strategically plan improvement initiatives. As a community, neurosurgery has clearly shown dedication to enhancing patient safety and delivering quality care. A care redesign strategy named NERVS (Neurosurgery Enhanced Recovery after surgery, Value, and Safety) is currently being developed and piloted within our department. Through this initiative, a multidisciplinary team led by a clinician neurosurgeon has process mapped the way care is currently being delivered throughout the entire episode of care. Neurosurgeons are becoming leaders in quality programs, and their education on the quality improvement strategies and tools is essential. The authors present a comprehensive review of process mapping, demystifying its planning, its building, and its analysis. The particularities of using process maps, initially a business tool, in the health care arena are discussed, and their specific use in an academic neurosurgical department is presented.

Uncertainty Assessment and Weight Map Generation for Efficient Fusion of Tandem-X and CARTOSAT-1 Dems

NASA Astrophysics Data System (ADS)

Bagheri, H.; Schmitt, M.; Zhu, X. X.

2017-05-01

Recently, with InSAR data provided by the German TanDEM-X mission, a new global, high-resolution Digital Elevation Model (DEM) has been produced by the German Aerospace Center (DLR) with unprecedented height accuracy. However, due to SAR-inherent sensor specifics, its quality decreases over urban areas, making additional improvement necessary. On the other hand, DEMs derived from optical remote sensing imagery, such as Cartosat-1 data, have an apparently greater resolution in urban areas, making their fusion with TanDEM-X elevation data a promising perspective. The objective of this paper is two-fold: First, the height accuracies of TanDEM-X and Cartosat-1 elevation data over different land types are empirically evaluated in order to analyze the potential of TanDEM-XCartosat- 1 DEM data fusion. After the quality assessment, urban DEM fusion using weighted averaging is investigated. In this experiment, both weight maps derived from the height error maps delivered with the DEM data, as well as more sophisticated weight maps predicted by a procedure based on artificial neural networks (ANNs) are compared. The ANN framework employs several features that can describe the height residual performance to predict the weights used in the subsequent fusion step. The results demonstrate that especially the ANN-based framework is able to improve the quality of the final DEM through data fusion.

Evaluation of the AirNow Satellite Data Processor for 2010-2012

NASA Astrophysics Data System (ADS)

Pasch, A. N.; DeWinter, J. L.; Dye, T.; Haderman, M.; Zahn, P. H.; Szykman, J.; White, J. E.; Dickerson, P.; van Donkelaar, A.; Martin, R.

2013-12-01

The U.S. Environmental Protection Agency's (EPA) AirNow program provides the public with real-time and forecasted air quality conditions. Millions of people each day use information from AirNow to protect their health. The AirNow program (http://www.airnow.gov) reports ground-level ozone (O3) and fine particulate matter (PM2.5) with a standardized index called the Air Quality Index (AQI). AirNow aggregates information from over 130 state, local, and federal air quality agencies and provides tools for over 2,000 agency staff responsible for monitoring, forecasting, and communicating local air quality. Each hour, AirNow systems generate thousands of maps and products. The usefulness of the AirNow air quality maps depends on the accuracy and spatial coverage of air quality measurements. Currently, the maps use only ground-based measurements, which have significant gaps in coverage in some parts of the United States. As a result, contoured AQI levels have high uncertainty in regions far from monitors. To improve the usefulness of air quality maps, scientists at EPA, Dalhousie University, and Sonoma Technology, Inc., in collaboration with the National Aeronautics and Space Administration (NASA) and the National Oceanic and Atmospheric Administration (NOAA), have completed a project to incorporate satellite-estimated surface PM2.5 concentrations into the maps via the AirNow Satellite Data Processor (ASDP). These satellite estimates are derived using NASA/NOAA satellite aerosol optical depth (AOD) retrievals and GEOS-Chem modeled ratios of surface PM2.5 concentrations to AOD. GEOS-Chem is a three-dimensional chemical transport model for atmospheric composition driven by meteorological input from the Goddard Earth Observing System (GEOS). The ASDP can fuse multiple PM2.5 concentration data sets to generate AQI maps with improved spatial coverage. The goals of ASDP are to provide more detailed AQI information in monitor-sparse locations and to augment monitor-dense locations with more information. The ASDP system uses a weighted-average approach using uncertainty information about each data set. Recent improvements in the estimation of the uncertainty of interpolated ground-based monitor data have allowed for a more complete characterization of the uncertainty of the surface measurements. We will present a statistical analysis for 2010-2012 of the ASDP predictions of PM2.5 focusing on performance at validation sites. In addition, we will present several case studies evaluating the ASDP's performance for multiple regions and seasons, focusing specifically on days when large spatial gradients in AQI and wildfire smoke impacts were observed.

Threshold automatic selection hybrid phase unwrapping algorithm for digital holographic microscopy

NASA Astrophysics Data System (ADS)

Zhou, Meiling; Min, Junwei; Yao, Baoli; Yu, Xianghua; Lei, Ming; Yan, Shaohui; Yang, Yanlong; Dan, Dan

2015-01-01

Conventional quality-guided (QG) phase unwrapping algorithm is hard to be applied to digital holographic microscopy because of the long execution time. In this paper, we present a threshold automatic selection hybrid phase unwrapping algorithm that combines the existing QG algorithm and the flood-filled (FF) algorithm to solve this problem. The original wrapped phase map is divided into high- and low-quality sub-maps by selecting a threshold automatically, and then the FF and QG unwrapping algorithms are used in each level to unwrap the phase, respectively. The feasibility of the proposed method is proved by experimental results, and the execution speed is shown to be much faster than that of the original QG unwrapping algorithm.

A combined geostatistical-optimization model for the optimal design of a groundwater quality monitoring network

NASA Astrophysics Data System (ADS)

Kolosionis, Konstantinos; Papadopoulou, Maria P.

2017-04-01

Monitoring networks provide essential information for water resources management especially in areas with significant groundwater exploitation due to extensive agricultural activities. In this work, a simulation-optimization framework is developed based on heuristic optimization methodologies and geostatistical modeling approaches to obtain an optimal design for a groundwater quality monitoring network. Groundwater quantity and quality data obtained from 43 existing observation locations at 3 different hydrological periods in Mires basin in Crete, Greece will be used in the proposed framework in terms of Regression Kriging to develop the spatial distribution of nitrates concentration in the aquifer of interest. Based on the existing groundwater quality mapping, the proposed optimization tool will determine a cost-effective observation wells network that contributes significant information to water managers and authorities. The elimination of observation wells that add little or no beneficial information to groundwater level and quality mapping of the area can be obtain using estimations uncertainty and statistical error metrics without effecting the assessment of the groundwater quality. Given the high maintenance cost of groundwater monitoring networks, the proposed tool could used by water regulators in the decision-making process to obtain a efficient network design that is essential.

Visualizing the Quality of Vectur Features - a Proposal for Cadastral Maps

NASA Astrophysics Data System (ADS)

Navratil, G.; Leopoldseder, V.

2017-09-01

A well-known problem of geographical information is the communication of the quality level. It can be either done verbally / numerically or it can be done graphically. The graphical form is especially useful if the quality has a spatial variation because the spatial distribution is visualized as well. The problem of spatial variation of quality is an issue for cadastral maps. Non-experts cannot determine the quality at a specific location. Therefore a visual representation was tested for the Austrian cadastre. A map sheet was redesigned to give some indication of cadastral quality and presented to both experts and non-experts. The paper presents the result of the interviews.

US Topo Maps 2014: Program updates and research

USGS Publications Warehouse

Fishburn, Kristin A.

2014-01-01

The U. S. Geological Survey (USGS) US Topo map program is now in year two of its second three-year update cycle. Since the program was launched in 2009, the product and the production system tools and processes have undergone enhancements that have made the US Topo maps a popular success story. Research and development continues with structural and content product enhancements, streamlined and more fully automated workflows, and the evaluation of a GIS-friendly US Topo GIS Packet. In addition, change detection methodologies are under evaluation to further streamline product maintenance and minimize resource expenditures for production in the future. The US Topo map program will continue to evolve in the years to come, providing traditional map users and Geographic Information System (GIS) analysts alike with a convenient, freely available product incorporating nationally consistent data that are quality assured to high standards.

Experiences with Acquiring Highly Redundant Spatial Data to Support Driverless Vehicle Technologies

NASA Astrophysics Data System (ADS)

Koppanyi, Z.; Toth, C. K.

2018-05-01

As vehicle technology is moving towards higher autonomy, the demand for highly accurate geospatial data is rapidly increasing, as accurate maps have a huge potential of increasing safety. In particular, high definition 3D maps, including road topography and infrastructure, as well as city models along the transportation corridors represent the necessary support for driverless vehicles. In this effort, a vehicle equipped with high-, medium- and low-resolution active and passive cameras acquired data in a typical traffic environment, represented here by the OSU campus, where GPS/GNSS data are available along with other navigation sensor data streams. The data streams can be used for two purposes. First, high-definition 3D maps can be created by integrating all the sensory data, and Data Analytics/Big Data methods can be tested for automatic object space reconstruction. Second, the data streams can support algorithmic research for driverless vehicle technologies, including object avoidance, navigation/positioning, detecting pedestrians and bicyclists, etc. Crucial cross-performance analyses on map database resolution and accuracy with respect to sensor performance metrics to achieve economic solution for accurate driverless vehicle positioning can be derived. These, in turn, could provide essential information on optimizing the choice of geospatial map databases and sensors' quality to support driverless vehicle technologies. The paper reviews the data acquisition and primary data processing challenges and performance results.

Bacterial pathogen gene abundance and relation to recreational water quality at seven Great Lakes beaches

USGS Publications Warehouse

Oster, Ryan J.; Wijesinghe, Rasanthi U.; Fogarty, Lisa Reynolds; Haack, Sheridan K.; Fogarty, Lisa R.; Tucker, Taaja R.; Riley, Stephen

2014-01-01

Quantitative assessment of bacterial pathogens, their geographic variability, and distribution in various matrices at Great Lakes beaches are limited. Quantitative PCR (qPCR) was used to test for genes from E. coli O157:H7 (eaeO157), shiga-toxin producing E. coli (stx2), Campylobacter jejuni (mapA), Shigella spp. (ipaH), and a Salmonella enterica-specific (SE) DNA sequence at seven Great Lakes beaches, in algae, water, and sediment. Overall, detection frequencies were mapA>stx2>ipaH>SE>eaeO157. Results were highly variable among beaches and matrices; some correlations with environmental conditions were observed for mapA, stx2, and ipaH detections. Beach seasonal mean mapA abundance in water was correlated with beach seasonal mean log10E. coli concentration. At one beach, stx2 gene abundance was positively correlated with concurrent daily E. coli concentrations. Concentration distributions for stx2, ipaH, and mapA within algae, sediment, and water were statistically different (Non-Detect and Data Analysis in R). Assuming 10, 50, or 100% of gene copies represented viable and presumably infective cells, a quantitative microbial risk assessment tool developed by Michigan State University indicated a moderate probability of illness for Campylobacter jejuni at the study beaches, especially where recreational water quality criteria were exceeded. Pathogen gene quantification may be useful for beach water quality management.

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

PubMed Central

Wright, Imogen A.; Travers, Simon A.

2014-01-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

Towards the XML schema measurement based on mapping between XML and OO domain

NASA Astrophysics Data System (ADS)

Rakić, Gordana; Budimac, Zoran; Heričko, Marjan; Pušnik, Maja

2017-07-01

Measuring quality of IT solutions is a priority in software engineering. Although numerous metrics for measuring object-oriented code already exist, measuring quality of UML models or XML Schemas is still developing. One of the research questions in the overall research leaded by ideas described in this paper is whether we can apply already defined object-oriented design metrics on XML schemas based on predefined mappings. In this paper, basic ideas for mentioned mapping are presented. This mapping is prerequisite for setting the future approach to XML schema quality measuring with object-oriented metrics.

Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.

PubMed Central

Allegre, Mathilde; Argout, Xavier; Boccara, Michel; Fouet, Olivier; Roguet, Yolande; Bérard, Aurélie; Thévenin, Jean Marc; Chauveau, Aurélie; Rivallan, Ronan; Clement, Didier; Courtois, Brigitte; Gramacho, Karina; Boland-Augé, Anne; Tahi, Mathias; Umaharan, Pathmanathan; Brunel, Dominique; Lanaud, Claire

2012-01-01

Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr. PMID:22210604

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data

PubMed Central

2014-01-01

Background The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms. Results In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic variation positions. To measure robustness, we introduced a new definition for a correctly mapped read taking into account not only the expected start position of the read but also the end position and the number of indels and substitutions. We developed CuReSim, a new read simulator, that is able to generate customized benchmark data for any kind of HTS technology by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool to evaluate the mapping quality of the CuReSim simulated reads, are freely available. We applied our benchmark procedure to evaluate 14 mappers in the context of whole genome sequencing of small genomes with Ion Torrent data for which such a comparison has not yet been established. Conclusions A benchmark procedure to compare HTS data mappers is introduced with a new definition for the mapping correctness as well as tools to generate simulated reads and evaluate mapping quality. The application of this procedure to Ion Torrent data from the whole genome sequencing of small genomes has allowed us to validate our benchmark procedure and demonstrate that it is helpful for selecting a mapper based on the intended application, questions to be addressed, and the technology used. This benchmark procedure can be used to evaluate existing or in-development mappers as well as to optimize parameters of a chosen mapper for any application and any sequencing platform. PMID:24708189

Addressing the Needs of a Developing Nation: Electronic Maps of Mathematical Learning Resources Accessible via the Internet

ERIC Educational Resources Information Center

Fathurrohman, Maman; Porter, Anne

2012-01-01

Teaching and learning of mathematics are integral parts of societies throughout the world. The fundamental or core nature of mathematics, its compulsory acquisition, requires high quality mathematics learning experiences. Moreover it is highly desirable that the emergence of new technology positively influences learning experiences in mathematics.…

River-quality assessment of the Truckee and Carson River system, California and Nevada; hydrologic characteristics

USGS Publications Warehouse

Brown, W. M.; Nowlin, J.O.; Smith, L.H.; Flint, M.R.

1986-01-01

A study of the Truckee and Carson Rivers was begun in October 1978 to assess the cause and effect relations between human and natural actions, and the quality of water at different times and places along the rivers. This report deals with the compilation of basic hydrologic data and the presentation of some of the new data collected during the study. Topographic, flow, and chemical data, data from recent time-of-travel studies, and new data on river mileages and drainage areas that were determined using new , high-resolution maps, are included. The report is a guide to locating maps, aerial photographs, computer files, and reports that relate to the rivers and their basins. It describes methods for compiling and expressing hydrologic information for ease of reading and understanding by the many users of water-related data. Text, tabular data, and colored plates with detailed maps and hydrographs are extensively cross referenced. (USGS)

Quality control of the paracetamol drug by chemometrics and imaging spectroscopy in the near infrared region

NASA Astrophysics Data System (ADS)

Baptistao, Mariana; Rocha, Werickson Fortunato de Carvalho; Poppi, Ronei Jesus

2011-09-01

In this work, it was used imaging spectroscopy and chemometric tools for the development and analysis of paracetamol and excipients in pharmaceutical formulations. It was also built concentration maps to study the distribution of the drug in the tablets surface. Multivariate models based on PLS regression were developed for paracetamol and excipients concentrations prediction. For the construction of the models it was used 31 samples in the tablet form containing the active principle in a concentration range of 30.0-90.0% (w/w) and errors below to 5% were obtained for validation samples. Finally, the study of the distribution in the drug was performed through the distribution maps of concentration of active principle and excipients. The analysis of maps showed the complementarity between the active principle and excipients in the tablets. The region with a high concentration of a constituent must have, necessarily, absence or low concentration of the other one. Thus, an alternative method for the paracetamol drug quality monitoring is presented.

MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data.

PubMed

Murillo, Gabriel H; You, Na; Su, Xiaoquan; Cui, Wei; Reilly, Muredach P; Li, Mingyao; Ning, Kang; Cui, Xinping

2016-05-15

Single nucleotide variant (SNV) detection procedures are being utilized as never before to analyze the recent abundance of high-throughput DNA sequencing data, both on single and multiple sample datasets. Building on previously published work with the single sample SNV caller genotype model selection (GeMS), a multiple sample version of GeMS (MultiGeMS) is introduced. Unlike other popular multiple sample SNV callers, the MultiGeMS statistical model accounts for enzymatic substitution sequencing errors. It also addresses the multiple testing problem endemic to multiple sample SNV calling and utilizes high performance computing (HPC) techniques. A simulation study demonstrates that MultiGeMS ranks highest in precision among a selection of popular multiple sample SNV callers, while showing exceptional recall in calling common SNVs. Further, both simulation studies and real data analyses indicate that MultiGeMS is robust to low-quality data. We also demonstrate that accounting for enzymatic substitution sequencing errors not only improves SNV call precision at low mapping quality regions, but also improves recall at reference allele-dominated sites with high mapping quality. The MultiGeMS package can be downloaded from https://github.com/cui-lab/multigems xinping.cui@ucr.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

CryoSat-2 altimetry derived Arctic bathymetry map: first results and validation

NASA Astrophysics Data System (ADS)

Andersen, O. B.; Abulaitijiang, A.; Cancet, M.; Knudsen, P.

2017-12-01

The Technical University of Denmark (DTU), DTU Space has been developing high quality high resolution gravity fields including the new highly accurate CryoSat-2 radar altimetry satellite data which extends the global coverage of altimetry data up to latitude 88°. With its exceptional Synthetic Aperture Radar (SAR) mode being operating throughout the Arctic Ocean, leads, i.e., the ocean surface heights, is used to retrieve the sea surface height with centimeter-level range precision. Combined with the long repeat cycle ( 369 days), i.e., dense cross-track coverage, the high-resolution Arctic marine gravity can be modelled using the CryoSat-2 altimetry. Further, the polar gap can be filled by the available ArcGP product, thus yielding the complete map of the Arctic bathymetry map. In this presentation, we will make use of the most recent DTU17 marine gravity, to derive the arctic bathymetry map using inversion based on best available hydrographic maps. Through the support of ESA a recent evaluation of existing hydrographic models of the Arctic Ocean Bathymetry models (RTOPO, GEBCO, IBCAO etc) and various inconsistencies have been identified and means to rectify these inconsistencies have been taken prior to perform the inversion using altimetry. Simultaneously DTU Space has been placing great effort on the Arctic data screening, filtering, and de-noising using various altimetry retracking solutions and classifications. All the pre-processing contributed to the fine modelling of Actic gravity map. Thereafter, the arctic marine gravity grids will eventually be translated (downward continuation operation) to a new altimetry enhanced Arctic bathymetry map using appropriate band-pass filtering.

Rocking curve imaging of high quality sapphire crystals in backscattering geometry

DOE PAGES

Jafari, A.; European Synchrotron Radiation Facility; Univ. of Liege,; ...

2017-01-23

Here, we report on the characterization of high quality sapphire single crystals suitable for high-resolution X-ray optics at high energy. Investigations using rocking curve imaging reveal the crystals to be of uniformly good quality at the level of ~10 -4 in lattice parameter variations, deltad/d. But, investigations using backscattering rocking curve imaging with lattice spacing resolution of deltad/d ~ 5.10 -8 shows very diverse quality maps for all crystals. Our results highlight nearly ideal areas with edge length of 0.2-0.5 mm in most crystals, but a comparison of the back re ection peak positions shows that even neighboring ideal areasmore » exhibit a relative difference in the lattice parameters on the order of deltad/d = 10-20.10 -8; this is several times larger than the rocking curve width. Furthermore, the stress-strain analysis suggests that an extremely stringent limit on the strain at a level of ~100 kPa in the growth process is required in order to produce crystals with large areas of the quality required for X-ray optics at high energy.« less

Air quality mapping using GIS and economic evaluation of health impact for Mumbai City, India.

PubMed

Kumar, Awkash; Gupta, Indrani; Brandt, Jørgen; Kumar, Rakesh; Dikshit, Anil Kumar; Patil, Rashmi S

2016-05-01

Mumbai, a highly populated city in India, has been selected for air quality mapping and assessment of health impact using monitored air quality data. Air quality monitoring networks in Mumbai are operated by National Environment Engineering Research Institute (NEERI), Maharashtra Pollution Control Board (MPCB), and Brihanmumbai Municipal Corporation (BMC). A monitoring station represents air quality at a particular location, while we need spatial variation for air quality management. Here, air quality monitored data of NEERI and BMC were spatially interpolated using various inbuilt interpolation techniques of ArcGIS. Inverse distance weighting (IDW), Kriging (spherical and Gaussian), and spline techniques have been applied for spatial interpolation for this study. The interpolated results of air pollutants sulfur dioxide (SO2), nitrogen dioxide (NO2) and suspended particulate matter (SPM) were compared with air quality data of MPCB in the same region. Comparison of results showed good agreement for predicted values using IDW and Kriging with observed data. Subsequently, health impact assessment of a ward was carried out based on total population of the ward and air quality monitored data within the ward. Finally, health cost within a ward was estimated on the basis of exposed population. This study helps to estimate the valuation of health damage due to air pollution. Operating more air quality monitoring stations for measurement of air quality is highly resource intensive in terms of time and cost. The appropriate spatial interpolation techniques can be used to estimate concentration where air quality monitoring stations are not available. Further, health impact assessment for the population of the city and estimation of economic cost of health damage due to ambient air quality can help to make rational control strategies for environmental management. The total health cost for Mumbai city for the year 2012, with a population of 12.4 million, was estimated as USD8000 million.

A novel intra-operative, high-resolution atrial mapping approach.

PubMed

Yaksh, Ameeta; van der Does, Lisette J M E; Kik, Charles; Knops, Paul; Oei, Frans B S; van de Woestijne, Pieter C; Bekkers, Jos A; Bogers, Ad J J C; Allessie, Maurits A; de Groot, Natasja M S

2015-12-01

A new technique is demonstrated for extensive high-resolution intra-operative atrial mapping that will facilitate the localization of atrial fibrillation (AF) sources and identification of the substrate perpetuating AF. Prior to the start of extra-corporal circulation, a 8 × 24-electrode array (2-mm inter-electrode distance) is placed subsequently on all the right and left epicardial atrial sites, including Bachmann's bundle, for recording of unipolar electrograms during sinus rhythm and (induced) AF. AF is induced by high-frequency pacing at the right atrial free wall. A pacemaker wire stitched to the right atrium serves as a reference signal. The indifferent pole is connected to a steal wire fixed to subcutaneous tissue. Electrograms are recorded by a computerized mapping system and, after amplification (gain 1000), filtering (bandwidth 0.5-400 Hz), sampling (1 kHz) and analogue to digital conversion (16 bits), automatically stored on hard disk. During the mapping procedure, real-time visualization secures electrogram quality. Analysis will be performed offline. This technique was performed in 168 patients of 18 years and older, with coronary and/or structural heart disease, with or without AF, electively scheduled for cardiac surgery and a ventricular ejection fraction above 40 %. The mean duration of the entire mapping procedure including preparation time was 9 ± 2 min. Complications related to the mapping procedure during or after cardiac surgery were not observed. We introduce the first epicardial atrial mapping approach with a high resolution of ≥1728 recording sites which can be performed in a procedure time of only 9±2 mins. This mapping technique can potentially identify areas responsible for initiation and persistence of AF and hopefully can individualize both diagnosis and therapy of AF.

Genetic Dissection of End-Use Quality Traits in Adapted Soft White Winter Wheat

PubMed Central

Jernigan, Kendra L.; Godoy, Jayfred V.; Huang, Meng; Zhou, Yao; Morris, Craig F.; Garland-Campbell, Kimberly A.; Zhang, Zhiwu; Carter, Arron H.

2018-01-01

Soft white wheat is used in domestic and foreign markets for various end products requiring specific quality profiles. Phenotyping for end-use quality traits can be costly, time-consuming and destructive in nature, so it is advantageous to use molecular markers to select experimental lines with superior traits. An association mapping panel of 469 soft white winter wheat cultivars and advanced generation breeding lines was developed from regional breeding programs in the U.S. Pacific Northwest. This panel was genotyped on a wheat-specific 90 K iSelect single nucleotide polymorphism (SNP) chip. A total of 15,229 high quality SNPs were selected and combined with best linear unbiased predictions (BLUPs) from historical phenotypic data of the genotypes in the panel. Genome-wide association mapping was conducted using the Fixed and random model Circulating Probability Unification (FarmCPU). A total of 105 significant marker-trait associations were detected across 19 chromosomes. Potentially new loci for total flour yield, lactic acid solvent retention capacity, flour sodium dodecyl sulfate sedimentation and flour swelling volume were also detected. Better understanding of the genetic factors impacting end-use quality enable breeders to more effectively discard poor quality germplasm and increase frequencies of favorable end-use quality alleles in their breeding populations. PMID:29593752

Visualization for genomics: the Microbial Genome Viewer.

PubMed

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Inverse Tone Mapping Based upon Retina Response

PubMed Central

Huo, Yongqing; Yang, Fan; Brost, Vincent

2014-01-01

The development of high dynamic range (HDR) display arouses the research of inverse tone mapping methods, which expand dynamic range of the low dynamic range (LDR) image to match that of HDR monitor. This paper proposed a novel physiological approach, which could avoid artifacts occurred in most existing algorithms. Inspired by the property of the human visual system (HVS), this dynamic range expansion scheme performs with a low computational complexity and a limited number of parameters and obtains high-quality HDR results. Comparisons with three recent algorithms in the literature also show that the proposed method reveals more important image details and produces less contrast loss and distortion. PMID:24744678

Cross-entropy embedding of high-dimensional data using the neural gas model.

PubMed

Estévez, Pablo A; Figueroa, Cristián J; Saito, Kazumi

2005-01-01

A cross-entropy approach to mapping high-dimensional data into a low-dimensional space embedding is presented. The method allows to project simultaneously the input data and the codebook vectors, obtained with the Neural Gas (NG) quantizer algorithm, into a low-dimensional output space. The aim of this approach is to preserve the relationship defined by the NG neighborhood function for each pair of input and codebook vectors. A cost function based on the cross-entropy between input and output probabilities is minimized by using a Newton-Raphson method. The new approach is compared with Sammon's non-linear mapping (NLM) and the hierarchical approach of combining a vector quantizer such as the self-organizing feature map (SOM) or NG with the NLM recall algorithm. In comparison with these techniques, our method delivers a clear visualization of both data points and codebooks, and it achieves a better mapping quality in terms of the topology preservation measure q(m).

Application of the Risk-Based Early Warning Method in a Fracture-Karst Water Source, North China.

PubMed

Guo, Yongli; Wu, Qing; Li, Changsuo; Zhao, Zhenhua; Sun, Bin; He, Shiyi; Jiang, Guanghui; Zhai, Yuanzheng; Guo, Fang

2018-03-01

  The paper proposes a risk-based early warning considering characteristics of fracture-karst aquifer in North China and applied it in a super-large fracture-karst water source. Groundwater vulnerability, types of land use, water abundance, transmissivity and spatial temporal variation of groundwater quality were chosen as indexes of the method. Weights of factors were obtained by using AHP method based on relative importance of factors, maps of factors were zoned by GIS, early warning map was conducted based on extension theory with the help of GIS, ENVI+IDL. The early warning map fused five factors very well, serious and tremendous warning areas are mainly located in northwest and east with high or relatively high transmissivity and groundwater pollutant loading, and obviously deteriorated or deteriorated trend of petroleum. The early warning map warns people where more attention should be paid, and the paper guides decision making to take appropriate protection actions in different warning levels areas.

Using an ultrasound elasticity microscope to map three-dimensional strain in a porcine cornea.

PubMed

Hollman, Kyle W; Shtein, Roni M; Tripathy, Sakya; Kim, Kang

2013-08-01

An ultrasound elasticity microscope was used to map 3-D strain volume in an ex vivo porcine cornea to illustrate its ability to measure the mechanical properties of this tissue. Mechanical properties of the cornea play an important role in its function and, therefore, also in ophthalmic diseases such as kerataconus and corneal ectasia. The ultrasound elasticity microscope combines a tightly focused high-frequency transducer with confocal scanning to produce high-quality speckle over the entire volume of tissue. This system and the analysis were able to generate volume maps of compressional strain in all three directions for porcine corneal tissue, more information than any previous study has reported. Strain volume maps indicated features of the cornea and mechanical behavior as expected. These results constitute a step toward better understanding of corneal mechanics and better treatment of corneal diseases. Copyright © 2013 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

High-resolution imaging of SNR IC443 and W44 with the Sardinia Radio Telescope

NASA Astrophysics Data System (ADS)

Egron, E.; Pellizzoni, A.; Iacolina, M. N.; Loru, S.; Marongiu, M.; Righini, S.; Cardillo, M.; Giuliani, A.; Mulas, S.; Murtas, G.; Simeone, D.

2017-02-01

We present single-dish imaging of the well-known Supernova Remnants (SNRs) IC443 and W44 at 1.5 GHz and 7 GHz with the recently commissioned 64-m diameter Sardinia Radio Telescope (SRT). Our images were obtained through on-the-fly mapping techniques, providing antenna beam oversampling, automatic baseline subtraction and radio-frequency interference removal. It results in high-quality maps of the SNRs at 7 GHz, which are usually lacking and not easily achievable through interferometry at this frequency due to the very large SNR structures. SRT continuum maps of our targets are consistent with VLA maps carried out at lower frequencies (at 324 MHz and 1.4 GHz), providing a view of the complex filamentary morphology. New estimates of the total flux density are given within 3% and 5% error at 1.5 GHz and 7 GHz respectively, in addition to flux measurements in different regions of the SNRs.

Strategy for reliable strain measurement in InAs/GaAs materials from high-resolution Z-contrast STEM images

NASA Astrophysics Data System (ADS)

Vatanparast, Maryam; Vullum, Per Erik; Nord, Magnus; Zuo, Jian-Min; Reenaas, Turid W.; Holmestad, Randi

2017-09-01

Geometric phase analysis (GPA), a fast and simple Fourier space method for strain analysis, can give useful information on accumulated strain and defect propagation in multiple layers of semiconductors, including quantum dot materials. In this work, GPA has been applied to high resolution Z-contrast scanning transmission electron microscopy (STEM) images. Strain maps determined from different g vectors of these images are compared to each other, in order to analyze and assess the GPA technique in terms of accuracy. The SmartAlign tool has been used to improve the STEM image quality getting more reliable results. Strain maps from template matching as a real space approach are compared with strain maps from GPA, and it is discussed that a real space analysis is a better approach than GPA for aberration corrected STEM images.

Reciprocal Space Mapping of Macromolecular Crystals in the Home Laboratory

NASA Technical Reports Server (NTRS)

Snell, Edward H.; Fewster, P. F.; Andrew, Norman; Boggon, T. J.; Judge, Russell A.; Pusey, Marc A.

1999-01-01

Reciprocal space mapping techniques are used widely by the materials science community to provide physical information about their crystal samples. We have used similar methods at synchrotron sources to look at the quality of macromolecular crystals produced both on the ground and under microgravity conditions. The limited nature of synchrotron time has led us to explore the use of a high resolution materials research diffractometer to perform similar measurements in the home laboratory. Although the available intensity is much reduced due to the beam conditioning necessary for high reciprocal space resolution, lower resolution data can be collected in the same detail as the synchrotron source. Experiments can be optimized at home to make most benefit from the synchrotron time available. Preliminary results including information on the mosaicity and the internal strains from reciprocal space maps will be presented.

GRDC. A Collaborative Framework for Radiological Background and Contextual Data Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brian J. Quiter; Ramakrishnan, Lavanya; Mark S. Bandstra

The Radiation Mobile Analysis Platform (RadMAP) is unique in its capability to collect both high quality radiological data from both gamma-ray detectors and fast neutron detectors and a broad array of contextual data that includes positioning and stance data, high-resolution 3D radiological data from weather sensors, LiDAR, and visual and hyperspectral cameras. The datasets obtained from RadMAP are both voluminous and complex and require analyses from highly diverse communities within both the national laboratory and academic communities. Maintaining a high level of transparency will enable analysis products to further enrich the RadMAP dataset. It is in this spirit of openmore » and collaborative data that the RadMAP team proposed to collect, calibrate, and make available online data from the RadMAP system. The Berkeley Data Cloud (BDC) is a cloud-based data management framework that enables web-based data browsing visualization, and connects curated datasets to custom workflows such that analysis products can be managed and disseminated while maintaining user access rights. BDC enables cloud-based analyses of large datasets in a manner that simulates real-time data collection, such that BDC can be used to test algorithm performance on real and source-injected datasets. Using the BDC framework, a subset of the RadMAP datasets have been disseminated via the Gamma Ray Data Cloud (GRDC) that is hosted through the National Energy Research Science Computing (NERSC) Center, enabling data access to over 40 users at 10 institutions.« less

ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

PubMed

Fooshee, David; Andronico, Alessio; Baldi, Pierre

2013-11-25

Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon's AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu .

Evaluation of multi-resolution satellite sensors for assessing water quality and bottom depth of Lake Garda.

PubMed

Giardino, Claudia; Bresciani, Mariano; Cazzaniga, Ilaria; Schenk, Karin; Rieger, Patrizia; Braga, Federica; Matta, Erica; Brando, Vittorio E

2014-12-15

In this study we evaluate the capabilities of three satellite sensors for assessing water composition and bottom depth in Lake Garda, Italy. A consistent physics-based processing chain was applied to Moderate Resolution Imaging Spectroradiometer (MODIS), Landsat-8 Operational Land Imager (OLI) and RapidEye. Images gathered on 10 June 2014 were corrected for the atmospheric effects with the 6SV code. The computed remote sensing reflectance (Rrs) from MODIS and OLI were converted into water quality parameters by adopting a spectral inversion procedure based on a bio-optical model calibrated with optical properties of the lake. The same spectral inversion procedure was applied to RapidEye and to OLI data to map bottom depth. In situ measurements of Rrs and of concentrations of water quality parameters collected in five locations were used to evaluate the models. The bottom depth maps from OLI and RapidEye showed similar gradients up to 7 m (r = 0.72). The results indicate that: (1) the spatial and radiometric resolutions of OLI enabled mapping water constituents and bottom properties; (2) MODIS was appropriate for assessing water quality in the pelagic areas at a coarser spatial resolution; and (3) RapidEye had the capability to retrieve bottom depth at high spatial resolution. Future work should evaluate the performance of the three sensors in different bio-optical conditions.

Factors Affecting Quality and Health Promoting Compounds during Growth and Postharvest Life of Sweet Cherry (Prunus avium L.)

PubMed Central

Correia, Sofia; Schouten, Rob; Silva, Ana P.; Gonçalves, Berta

2017-01-01

Sweet cherries are attractive fruits due to their taste, color, nutritional value, and beneficial health effects. Sweet cherry is a highly perishable fruit and all quality attributes and the level of health promoting compounds are affected by growth conditions, picking, packing, transport, and storage. During production, the correct combination of scion × rootstock will produce fruits with higher firmness, weight, sugars, vitamins, and phenolic compounds that boost the fruit antioxidant activity. Orchard management, such as applying drip irrigation and summer pruning, will increase fruit sugar levels and total phenolic content, while application of growth regulators can result in improved storability, increased red coloring, increased fruit size, and reduced cracking. Salicylic acid, oxalic acid, acetylsalicylic acid, and methyl salicylate are promising growth regulators as they also increase total phenolics, anthocyanins, and induce higher activity of antioxidant enzymes. These growth regulators are now also applied as fruit coatings that improve shelf-life with higher antioxidant enzyme activities and total phenolics. Optimizing storage and transport conditions, such as hydro cooling with added CaCl2, chain temperature and relative humidity control, are crucial for slowing down decay of quality attributes and increasing the antioxidant capacity. Application of controlled atmosphere during storage is successful in delaying quality attributes, but lowers ascorbic acid levels. The combination of low temperature storage in combination with modified atmosphere packaging (MAP) is successful in reducing the incidence of fruit decay, while preserving taste attributes and stem color with a higher antioxidant capacity. A new trend in MAP is the use of biodegradable films such as micro-perforated polylactic acid film that combine significant retention of quality attributes, high consumer acceptability, and a reduced environmental footprint. Another trend is to replace MAP with fruit edible coatings. Edible coatings, such as various lipid composite coatings, have advantages in retaining quality attributes and increasing the antioxidant activity (chitosan) and are regarded as approved food additives, although studies regarding consumer acceptance are needed. The recent publication of the sweet cherry genome will likely increase the identification of more candidate genes involved in growing and maintaining health related compounds and quality attributes. PMID:29312407

Map showing general chemical quality of surface water in the Richfield Quadrangle, Utah

USGS Publications Warehouse

Price, Don

1980-01-01

This is one of a series of maps that describe the geology and related natural resources of the Richfield 2° quadrangle, Utah. The purpose of this map is to show the general chemical quality of surface water in the area by ranges of dissolved-solids concentrations.Data used to compile this map were collected by the U.S. Geological Survey in cooperation with the Utah Department of Natural Resources, Division of Water Rights. In those areas where little or no surface-water-quality data are available, ranges of dissolved-solids concentrations of the water are inferred on the basis of such factors as geology (Stokes, 1964), precipitation, topography, known ground-water quality, and water uses – all of which affect the chemical quality of surface water.Additional information about the chemical quality of surface water in various parts of the Richfield 2° quadrangle may be found in the following reports: Hahl and Cabell (1965), Hahl and Mundorff (1968), Stephens (1974, 1976), Cruff and Mower (1976), and Cruff(1977)

Large Scale Textured Mesh Reconstruction from Mobile Mapping Images and LIDAR Scans

NASA Astrophysics Data System (ADS)

Boussaha, M.; Vallet, B.; Rives, P.

2018-05-01

The representation of 3D geometric and photometric information of the real world is one of the most challenging and extensively studied research topics in the photogrammetry and robotics communities. In this paper, we present a fully automatic framework for 3D high quality large scale urban texture mapping using oriented images and LiDAR scans acquired by a terrestrial Mobile Mapping System (MMS). First, the acquired points and images are sliced into temporal chunks ensuring a reasonable size and time consistency between geometry (points) and photometry (images). Then, a simple, fast and scalable 3D surface reconstruction relying on the sensor space topology is performed on each chunk after an isotropic sampling of the point cloud obtained from the raw LiDAR scans. Finally, the algorithm proposed in (Waechter et al., 2014) is adapted to texture the reconstructed surface with the images acquired simultaneously, ensuring a high quality texture with no seams and global color adjustment. We evaluate our full pipeline on a dataset of 17 km of acquisition in Rouen, France resulting in nearly 2 billion points and 40000 full HD images. We are able to reconstruct and texture the whole acquisition in less than 30 computing hours, the entire process being highly parallel as each chunk can be processed independently in a separate thread or computer.

SU-E-T-420: Failure Effects Mode Analysis for Trigeminal Neuralgia Frameless Radiosurgery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Howe, J

2015-06-15

Purpose: Functional radiosurgery has been used successfully in the treatment of trigeminal neuralgia but presents significant challenges to ensuring the high prescription dose is delivered accurately. A review of existing practice should help direct the focus of quality improvement for this treatment regime. Method: Failure modes and effects analysis was used to identify the processes in preparing radiosurgery treatment for TN. The map was developed by a multidisciplinary team including: neurosurgeon, radiation oncology, physicist and therapist. Potential failure modes were identified for each step in the process map as well as potential causes and end effect. A risk priority numbermore » was assigned to each cause. Results: The process map identified 66 individual steps (see attached supporting document). Corrective actions were developed for areas of high risk priority number. Wrong site treatment is at higher risk for trigeminal neuralgia treatment due to the lack of site specific pathologic imaging on MR and CT – additional site specific checks were implemented to minimize the risk of wrong site treatment. Failed collision checks resulted from an insufficient collision model in the treatment planning system and a plan template was developed to address this problem. Conclusion: Failure modes and effects analysis is an effective tool for developing quality improvement in high risk radiotherapy procedures such as functional radiosurgery.« less

Genome-Wide Single-Nucleotide Polymorphisms Discovery and High-Density Genetic Map Construction in Cauliflower Using Specific-Locus Amplified Fragment Sequencing

PubMed Central

Zhao, Zhenqing; Gu, Honghui; Sheng, Xiaoguang; Yu, Huifang; Wang, Jiansheng; Huang, Long; Wang, Dan

2016-01-01

Molecular markers and genetic maps play an important role in plant genomics and breeding studies. Cauliflower is an important and distinctive vegetable; however, very few molecular resources have been reported for this species. In this study, a novel, specific-locus amplified fragment (SLAF) sequencing strategy was employed for large-scale single nucleotide polymorphism (SNP) discovery and high-density genetic map construction in a double-haploid, segregating population of cauliflower. A total of 12.47 Gb raw data containing 77.92 M pair-end reads were obtained after processing and 6815 polymorphic SLAFs between the two parents were detected. The average sequencing depths reached 52.66-fold for the female parent and 49.35-fold for the male parent. Subsequently, these polymorphic SLAFs were used to genotype the population and further filtered based on several criteria to construct a genetic linkage map of cauliflower. Finally, 1776 high-quality SLAF markers, including 2741 SNPs, constituted the linkage map with average data integrity of 95.68%. The final map spanned a total genetic length of 890.01 cM with an average marker interval of 0.50 cM, and covered 364.9 Mb of the reference genome. The markers and genetic map developed in this study could provide an important foundation not only for comparative genomics studies within Brassica oleracea species but also for quantitative trait loci identification and molecular breeding of cauliflower. PMID:27047515

A fast optimization approach for treatment planning of volumetric modulated arc therapy.

PubMed

Yan, Hui; Dai, Jian-Rong; Li, Ye-Xiong

2018-05-30

Volumetric modulated arc therapy (VMAT) is widely used in clinical practice. It not only significantly reduces treatment time, but also produces high-quality treatment plans. Current optimization approaches heavily rely on stochastic algorithms which are time-consuming and less repeatable. In this study, a novel approach is proposed to provide a high-efficient optimization algorithm for VMAT treatment planning. A progressive sampling strategy is employed for beam arrangement of VMAT planning. The initial beams with equal-space are added to the plan in a coarse sampling resolution. Fluence-map optimization and leaf-sequencing are performed for these beams. Then, the coefficients of fluence-maps optimization algorithm are adjusted according to the known fluence maps of these beams. In the next round the sampling resolution is doubled and more beams are added. This process continues until the total number of beams arrived. The performance of VMAT optimization algorithm was evaluated using three clinical cases and compared to those of a commercial planning system. The dosimetric quality of VMAT plans is equal to or better than the corresponding IMRT plans for three clinical cases. The maximum dose to critical organs is reduced considerably for VMAT plans comparing to those of IMRT plans, especially in the head and neck case. The total number of segments and monitor units are reduced for VMAT plans. For three clinical cases, VMAT optimization takes < 5 min accomplished using proposed approach and is 3-4 times less than that of the commercial system. The proposed VMAT optimization algorithm is able to produce high-quality VMAT plans efficiently and consistently. It presents a new way to accelerate current optimization process of VMAT planning.

Mapping transmission risk of Lassa fever in West Africa: the importance of quality control, sampling bias, and error weighting.

PubMed

Peterson, A Townsend; Moses, Lina M; Bausch, Daniel G

2014-01-01

Lassa fever is a disease that has been reported from sites across West Africa; it is caused by an arenavirus that is hosted by the rodent M. natalensis. Although it is confined to West Africa, and has been documented in detail in some well-studied areas, the details of the distribution of risk of Lassa virus infection remain poorly known at the level of the broader region. In this paper, we explored the effects of certainty of diagnosis, oversampling in well-studied region, and error balance on results of mapping exercises. Each of the three factors assessed in this study had clear and consistent influences on model results, overestimating risk in southern, humid zones in West Africa, and underestimating risk in drier and more northern areas. The final, adjusted risk map indicates broad risk areas across much of West Africa. Although risk maps are increasingly easy to develop from disease occurrence data and raster data sets summarizing aspects of environments and landscapes, this process is highly sensitive to issues of data quality, sampling design, and design of analysis, with macrogeographic implications of each of these issues and the potential for misrepresenting real patterns of risk.

A System and Method for Online High-Resolution Mapping of Gastric Slow-Wave Activity

PubMed Central

Bull, Simon H.; O’Grady, Gregory; Du, Peng

2015-01-01

High-resolution (HR) mapping employs multielectrode arrays to achieve spatially detailed analyses of propagating bioelectrical events. A major current limitation is that spatial analyses must currently be performed “off-line” (after experiments), compromising timely recording feedback and restricting experimental interventions. These problems motivated development of a system and method for “online” HR mapping. HR gastric recordings were acquired and streamed to a novel software client. Algorithms were devised to filter data, identify slow-wave events, eliminate corrupt channels, and cluster activation events. A graphical user interface animated data and plotted electrograms and maps. Results were compared against off-line methods. The online system analyzed 256-channel serosal recordings with no unexpected system terminations with a mean delay 18 s. Activation time marking sensitivity was 0.92; positive predictive value was 0.93. Abnormal slow-wave patterns including conduction blocks, ectopic pacemaking, and colliding wave fronts were reliably identified. Compared to traditional analysis methods, online mapping had comparable results with equivalent coverage of 90% of electrodes, average RMS errors of less than 1 s, and CC of activation maps of 0.99. Accurate slow-wave mapping was achieved in near real-time, enabling monitoring of recording quality and experimental interventions targeted to dysrhythmic onset. This work also advances the translation of HR mapping toward real-time clinical application. PMID:24860024

Assessment of tropospheric delay mapping function models in Egypt: Using PTD database model

NASA Astrophysics Data System (ADS)

Abdelfatah, M. A.; Mousa, Ashraf E.; El-Fiky, Gamal S.

2018-06-01

For space geodetic measurements, estimates of tropospheric delays are highly correlated with site coordinates and receiver clock biases. Thus, it is important to use the most accurate models for the tropospheric delay to reduce errors in the estimates of the other parameters. Both the zenith delay value and mapping function should be assigned correctly to reduce such errors. Several mapping function models can treat the troposphere slant delay. The recent models were not evaluated for the Egyptian local climate conditions. An assessment of these models is needed to choose the most suitable one. The goal of this paper is to test the quality of global mapping function which provides high consistency with precise troposphere delay (PTD) mapping functions. The PTD model is derived from radiosonde data using ray tracing, which consider in this paper as true value. The PTD mapping functions were compared, with three recent total mapping functions model and another three separate dry and wet mapping function model. The results of the research indicate that models are very close up to zenith angle 80°. Saastamoinen and 1/cos z model are behind accuracy. Niell model is better than VMF model. The model of Black and Eisner is a good model. The results also indicate that the geometric range error has insignificant effect on slant delay and the fluctuation of azimuth anti-symmetric is about 1%.

Influence of PA6 nanocomposite films on the stability of vacuum-aged beef loins during storage in modified atmospheres.

PubMed

Picouet, P A; Fernandez, A; Realini, C E; Lloret, E

2014-01-01

A masterbatch of polyamide 6 (PA6) containing dispersed nanoclays, was used to fabricate a novel multilayer film for vacuum packed meat. Performance of the nanocomposite was compared to a control PA6 multilayer and a high barrier commercial film. Addition of nanoclays improved oxygen barrier properties, UV-blocking capability and stiffness. Beef loins were vacuum-aged using the three films for 0 7, 14 and 21 days at 2°C. After each ageing time, beef steaks were packaged in commercial trays and high oxygen atmosphere and stored at 4°C for 9 days. Beef quality parameters and gas content were studied during display time in MAP (1, 3, 6 and 9 d). Beef quality parameters were not influenced by the packaging materials used during ageing and the performance of nanocomposites was comparable to high barrier films. Ageing had a positive impact on the stabilization of redness up to day 6 in MAP. Thereafter, oxymyoglobin content and oxidation levels were negatively influenced by ageing. © 2013.

Detection of Thermal Erosion Gullies from High-Resolution Images Using Deep Learning

NASA Astrophysics Data System (ADS)

Huang, L.; Liu, L.; Jiang, L.; Zhang, T.; Sun, Y.

2017-12-01

Thermal erosion gullies, one type of thermokarst landforms, develop due to thawing of ice-rich permafrost. Mapping the location and extent of thermal erosion gullies can help understand the spatial distribution of thermokarst landforms and their temporal evolution. Remote sensing images provide an effective way for mapping thermokarst landforms, especially thermokarst lakes. However, thermal erosion gullies are challenging to map from remote sensing images due to their small sizes and significant variations in geometric/radiometric properties. It is feasible to manually identify these features, as a few previous studies have carried out. However manual methods are labor-intensive, therefore, cannot be used for a large study area. In this work, we conduct automatic mapping of thermal erosion gullies from high-resolution images by using Deep Learning. Our study area is located in Eboling Mountain (Qinghai, China). Within a 6 km2 peatland area underlain by ice-rich permafrost, at least 20 thermal erosional gullies are well developed. The image used is a 15-cm-resolution Digital Orthophoto Map (DOM) generated in July 2016. First, we extracted 14 gully patches and ten non-gully patches as training data. And we performed image augmentation. Next, we fine-tuned the pre-trained model of DeepLab, a deep-learning algorithm for semantic image segmentation based on Deep Convolutional Neural Networks. Then, we performed inference on the whole DOM and obtained intermediate results in forms of polygons for all identified gullies. At last, we removed misidentified polygons based on a few pre-set criteria on the size and shape of each polygon. Our final results include 42 polygons. Validated against field measurements using GPS, most of the gullies are detected correctly. There are 20 false detections due to the small number and low quality of training images. We also found three new gullies that missed in the field observations. This study shows that (1) despite a challenging mapping task, DeepLab can detect small, irregular-shaped thermal erosion gullies with high accuracy. (2) Automatic detection is critical for mapping thermal erosion gully since manual mapping or field work may miss some targets even in a relatively small region. (3) The quantity and quality of training data are crucial for detection accuracy.

Multi-Depth-Map Raytracing for Efficient Large-Scene Reconstruction.

PubMed

Arikan, Murat; Preiner, Reinhold; Wimmer, Michael

2016-02-01

With the enormous advances of the acquisition technology over the last years, fast processing and high-quality visualization of large point clouds have gained increasing attention. Commonly, a mesh surface is reconstructed from the point cloud and a high-resolution texture is generated over the mesh from the images taken at the site to represent surface materials. However, this global reconstruction and texturing approach becomes impractical with increasing data sizes. Recently, due to its potential for scalability and extensibility, a method for texturing a set of depth maps in a preprocessing and stitching them at runtime has been proposed to represent large scenes. However, the rendering performance of this method is strongly dependent on the number of depth maps and their resolution. Moreover, for the proposed scene representation, every single depth map has to be textured by the images, which in practice heavily increases processing costs. In this paper, we present a novel method to break these dependencies by introducing an efficient raytracing of multiple depth maps. In a preprocessing phase, we first generate high-resolution textured depth maps by rendering the input points from image cameras and then perform a graph-cut based optimization to assign a small subset of these points to the images. At runtime, we use the resulting point-to-image assignments (1) to identify for each view ray which depth map contains the closest ray-surface intersection and (2) to efficiently compute this intersection point. The resulting algorithm accelerates both the texturing and the rendering of the depth maps by an order of magnitude.

Multibeam mapping of the Los Angeles, California Margin

USGS Publications Warehouse

Gardner, James V.; Dartnell, Peter

2002-01-01

The Los Angeles, California Margin was mapped using multibeam echosounders during three separate surveys (Figure 1). In 1996, the USGS surveyed the shelf and slope in Santa Monica Bay from Pt. Dume to south of the Palos Verdes Peninsula. The mapping was accomplished using a Kongsberg Simrad EM1000 multibeam sonar system that provided high-quality bathymetry and quantitative backscatter. In 1998, the USGS continued the mapping to the south and surveyed the outer shelf, slope, and proximal basin off Long Beach and Newport using a Kongsberg Simrad EM300 multibeam sonar system. In 1999, the Los Angeles Margin mapping was completed with the surveying of the inner Long Beach shelf from the Palos Verdes Peninsula, south to Newport. This survey used a dual Kongsberg Simrad EM3000D multibeam sonar system. These three surveys were conducted to support USGS projects studying marine pollution and geohazards along the Los Angeles Margin.

Quality changes of fresh filled pasta during storage: influence of modified atmosphere packaging on microbial growth and sensory properties.

PubMed

Sanguinetti, A M; Del Caro, A; Mangia, N P; Secchi, N; Catzeddu, P; Piga, A

2011-02-01

This study evaluated the shelf life of fresh pasta filled with cheese subjected to modified atmosphere packaging (MAP) or air packaging (AP). After a pasteurization treatment, fresh pasta was packaged under a 50/50 N(2)/CO(2) ratio or in air (air batch). Changes in microbial growth, in-package gas composition, chemical-physical parameters and sensory attributes were monitored for 42 days at 4 (°)C. The pasteurization treatment resulted in suitable microbiological reduction. MAP allowed a mold-free shelf life of the fresh filled pasta of 42 days, whereas air-packaged samples got spoilt between 7 and 14 days. The hurdle approach used (MAP and low storage temperature) prevented the growth of pathogens and alterative microorganisms. MAP samples maintained a high microbiological standard throughout the storage period. The panel judged MAP fresh pasta above the acceptability threshold throughout the shelf life.

The HEMP QSO Monitoring Project

NASA Astrophysics Data System (ADS)

Welsh, William F.; Robinson, E. L.

2000-02-01

Many AGN are highly variable sources. Some of these show a pronounced time delay between variations seen in their optical continuum and in their emission lines. ``Echo mapping'' is a technique that uses these time delays to measure the geometry and kinematics of the gas inside the AGN, near the supermassive black hole. The technique is immensely powerful, but the results so far have been modest due to relatively low quality data. We have initiated a long--term project to echo map QSOs. We will examine nearby (but intrinsically faint) QSOs as well as QSOs at high redshift. The high--z QSOs present a problem: it is not known ahead of time which of these are variable sources. Thus we have started a campaign to monitor about 60 high-redshift QSOs for the purpose of determining their variability characteristics. We request SSTO time on the 0.9m telescope for long--term monitoring of high--redshift QSOs to: (i) test their suitability as viable echo mapping candidates; and (ii) measure (for the first time) their variability properties, which is of intrinsic value itself.

How Fit is Your Citizen Science Data?

NASA Astrophysics Data System (ADS)

Fischer, H. A.; Gerber, L. R.; Wentz, E. A.

2017-12-01

Data quality and accuracy is a fundamental concern with utilizing citizen science data. Although many methods can be used to assess quality and accuracy, these methods may not be sufficient to qualify citizen science data for widespread use in scientific research. While Data Fitness For Use (DFFU) does not provide a blanket assessment of data quality, it does assesses the data's ability to be used for a specific application, within a given area (Devillers and Bédard 2007). The STAAq (Spatial, Temporal, Aptness, and Accuracy) assessment was developed to assess the fitness for use of citizen science data, this assessment can be used on a stand alone dataset or be used to compare multiple datasets. The citizen science data used in this assessment was collected by volunteers of the Map of Life- Denali project, which is a tourist-centric citizen science project developed through a partnership with Arizona State University, Map of Life at Yale University, and Denali National Park and Preserve. Volunteers use the offline version of the Map of Life app to record their wildlife, insect, and plant observations in the park. To test the STAAq assessment data from different sources- Map of Life- Denali, Ride Observe and Record, and NPS wildlife surveys- were compared to determined which dataset is most fit for use for a specific research question; What is the recent Grizzly bear distribution in areas of high visitor use in Denali National Park and Preserve? These datasets were compared and ranked according to how well they performed in each of the components of the STAAq assessment. These components include spatial scale, temporal scale, aptness, and application. The Map of Life- Denali data and the ROAR program data were most for use for this research question. The STAAq assessment can be adjusted to assess the fitness for use of a single dataset or being used to compare any number of datasets. This data fitness for use assessment provides a means to assess data fitness instead of data quality for citizen science data.

Improvement of the cost-benefit analysis algorithm for high-rise construction projects

NASA Astrophysics Data System (ADS)

Gafurov, Andrey; Skotarenko, Oksana; Plotnikov, Vladimir

2018-03-01

The specific nature of high-rise investment projects entailing long-term construction, high risks, etc. implies a need to improve the standard algorithm of cost-benefit analysis. An improved algorithm is described in the article. For development of the improved algorithm of cost-benefit analysis for high-rise construction projects, the following methods were used: weighted average cost of capital, dynamic cost-benefit analysis of investment projects, risk mapping, scenario analysis, sensitivity analysis of critical ratios, etc. This comprehensive approach helped to adapt the original algorithm to feasibility objectives in high-rise construction. The authors put together the algorithm of cost-benefit analysis for high-rise construction projects on the basis of risk mapping and sensitivity analysis of critical ratios. The suggested project risk management algorithms greatly expand the standard algorithm of cost-benefit analysis in investment projects, namely: the "Project analysis scenario" flowchart, improving quality and reliability of forecasting reports in investment projects; the main stages of cash flow adjustment based on risk mapping for better cost-benefit project analysis provided the broad range of risks in high-rise construction; analysis of dynamic cost-benefit values considering project sensitivity to crucial variables, improving flexibility in implementation of high-rise projects.

High-Density Genetic Map Construction and Stem Total Polysaccharide Content-Related QTL Exploration for Chinese Endemic Dendrobium (Orchidaceae)

PubMed Central

Lu, Jiangjie; Liu, Yuyang; Xu, Jing; Mei, Ziwei; Shi, Yujun; Liu, Pengli; He, Jianbo; Wang, Xiaotong; Meng, Yijun; Feng, Shangguo; Shen, Chenjia; Wang, Huizhong

2018-01-01

Plants of the Dendrobium genus are orchids with not only ornamental value but also high medicinal value. To understand the genetic basis of variations in active ingredients of the stem total polysaccharide contents (STPCs) among different Dendrobium species, it is of paramount importance to understand the mechanism of STPC formation and identify genes affecting its process at the whole genome level. Here, we report the first high-density single-nucleotide polymorphism (SNP) integrated genetic map with a good genome coverage of Dendrobium. The specific-locus amplified fragment sequencing (SLAF-seq) technology led to identification of 7,013,400 SNPs from 1,503,626 high-quality SLAF markers from two parents (Dendrobium moniliforme ♀ × Dendrobium officinale ♂) and their interspecific F1 hybrid population. The final genetic map contained 8, 573 SLAF markers, covering 19 linkage groups (LGs). This genetic map spanned a length of 2,737.49 cM, where the average distance between markers is 0.32 cM. In total, 5 quantitative trait loci (QTL) related to STPC were identified, 3 of which have candidate genes within the confidence intervals of these stable QTLs based on the D. officinale genome sequence. This study will build a foundation up for the mapping of other medicinal-related traits and provide an important reference for the molecular breeding of these Chinese herb. PMID:29636767

Use of Thematic Mapper for water quality assessment

NASA Technical Reports Server (NTRS)

Horn, E. M.; Morrissey, L. A.

1984-01-01

The evaluation of simulated TM data obtained on an ER-2 aircraft at twenty-five predesignated sample sites for mapping water quality factors such as conductivity, pH, suspended solids, turbidity, temperature, and depth, is discussed. Using a multiple regression for the seven TM bands, an equation is developed for the suspended solids. TM bands 1, 2, 3, 4, and 6 are used with logarithm conductivity in a multiple regression. The assessment of regression equations for a high coefficient of determination (R-squared) and statistical significance is considered. Confidence intervals about the mean regression point are calculated in order to assess the robustness of the regressions used for mapping conductivity, turbidity, and suspended solids, and by regressing random subsamples of sites and comparing the resultant range of R-squared, cross validation is conducted.

The quality of radiation care: the results of focus group interviews and concept mapping to explore the patient's perspective.

PubMed

Nijman, Jessica L; Sixma, Herman; van Triest, Baukelien; Keus, Ronald B; Hendriks, Michelle

2012-01-01

In this study, we explore the quality aspects of radiation care from the patient's perspective in order to develop a draft Consumer Quality Index (CQI) Radiation Care instrument. Four focus group discussions with (former) cancer patients were held to explore the aspects determining the quality of radiation care. The list of aspects generated was categorised based on similarity and importance in a concept mapping procedure. Four focus group discussions revealed seven main themes related to the quality of radiation care: information provision, a patient-centred approach, professional competence, planning and waiting times, accessibility, cooperation and communication, and follow-up care. Results of concept mapping procedures revealed which items the patients considered to be most important. A radiation oncologist who is up to date about the patient's file is of paramount importance for cancer patients receiving radiotherapy. The quality aspects found through focus group discussions provided useful insight into how patients experience radiation care. Furthermore, concept mapping made these results more solid. To evaluate the quality of radiation care from the patient's perspective, these quality aspects will be guiding in the development of a CQI Radiation Care. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

AIR QUALITY MODELING AT COARSE-TO-FINE SCALES IN URBAN AREAS

EPA Science Inventory

Urban air toxics control strategies are moving towards a community based modeling approach, with an emphasis on assessing those areas that experience high air toxic concentration levels, the so-called "hot spots". This approach will require information that accurately maps and...

Displaying Geographically-Based Domestic Statistics

NASA Technical Reports Server (NTRS)

Quann, J.; Dalton, J.; Banks, M.; Helfer, D.; Szczur, M.; Winkert, G.; Billingsley, J.; Borgstede, R.; Chen, J.; Chen, L.;

Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays).

PubMed

Wang, Baobao; Liu, Han; Liu, Zhipeng; Dong, Xiaomei; Guo, Jinjie; Li, Wei; Chen, Jing; Gao, Chi; Zhu, Yanbin; Zheng, Xinmei; Chen, Zongliang; Chen, Jian; Song, Weibin; Hauck, Andrew; Lai, Jinsheng

2018-01-18

Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested. Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs). We demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.

Perspectives on the methods of a large systematic mapping of maternal health interventions.

PubMed

Chersich, Matthew; Becerril-Montekio, Victor; Becerra-Posada, Francisco; Dumbaugh, Mari; Kavanagh, Josephine; Blaauw, Duane; Thwala, Siphiwe; Kern, Elinor; Penn-Kekana, Loveday; Vargas, Emily; Mlotshwa, Langelihle; Dhana, Ashar; Mannava, Priya; Portela, Anayda; Tristan, Mario; Rees, Helen; Bijlmakers, Leon

2016-08-25

Mapping studies describe a broad body of literature, and differ from classical systematic reviews, which assess more narrowly-defined questions and evaluate the quality of the studies included in the review. While the steps involved in mapping studies have been described previously, a detailed qualitative account of the methodology could inform the design of future mapping studies. Describe the perspectives of a large research team on the methods used and collaborative experiences in a study that mapped the literature published on maternal health interventions in low- and middle-income countries (2292 full text articles included, after screening 35,048 titles and abstracts in duplicate). Fifteen members of the mapping team, drawn from eight countries, provided their experiences and perspectives of the study in response to a list of questions and probes. The responses were collated and analysed thematically following a grounded theory approach. The objectives of the mapping evolved over time, posing difficulties in ensuring a uniform understanding of the purpose of the mapping among the team members. Ambiguity of some study variables and modifications in data extraction codes were the main threats to the quality of data extraction. The desire for obtaining detailed information on a few topics needed to be weighed against the benefits of collecting more superficial data on a wider range of topics. Team members acquired skills in systematic review methodology and software, and a broad knowledge of maternal health literature. Participation in analysis and dissemination was lower than during the screening of articles for eligibility and data coding. Though all respondents believed the workload involved was high, study outputs were viewed as novel and important contributions to evidence. Overall, most believed there was a favourable balance between the amount of work done and the project's outputs. A large mapping of literature is feasible with a committed team aiming to build their research capacity, and with a limited, simplified set of data extraction codes. In the team's view, the balance between the time spent on the review, and the outputs and skills acquired was favourable. Assessments of the value of a mapping need, however, to take into account the limitations inherent in such exercises, especially the exclusion of grey literature and of assessments of the quality of the studies identified.

Understanding and Mapping Water Quality for Lawrence, MA

EPA Pesticide Factsheets

EPA has created new maps of the lower Merrimack River that provide an overview of historic water quality data (E. coli concentrations); flood zones, precipitation, and combined sewer overflows (CSOs).

Genome-Wide QTL Mapping for Wheat Processing Quality Parameters in a Gaocheng 8901/Zhoumai 16 Recombinant Inbred Line Population.

PubMed

Jin, Hui; Wen, Weie; Liu, Jindong; Zhai, Shengnan; Zhang, Yan; Yan, Jun; Liu, Zhiyong; Xia, Xianchun; He, Zhonghu

2016-01-01

Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.). In the present study, a recombinant inbred line (RIL) population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs) for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA), and Mixolab parameters using the wheat 90 and 660 K single nucleotide polymorphism (SNP) chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90 and 660 K SNP assays spanned a total length of 4121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6596 new SNP markers were anchored to the bread wheat linkage map, with 1046 and 5550 markers from the 90 and 660 K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP) technique for improvement of processing quality in bread wheat.

Genome-Wide QTL Mapping for Wheat Processing Quality Parameters in a Gaocheng 8901/Zhoumai 16 Recombinant Inbred Line Population

PubMed Central

Jin, Hui; Wen, Weie; Liu, Jindong; Zhai, Shengnan; Zhang, Yan; Yan, Jun; Liu, Zhiyong; Xia, Xianchun; He, Zhonghu

2016-01-01

Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.). In the present study, a recombinant inbred line (RIL) population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs) for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA), and Mixolab parameters using the wheat 90 and 660 K single nucleotide polymorphism (SNP) chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90 and 660 K SNP assays spanned a total length of 4121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6596 new SNP markers were anchored to the bread wheat linkage map, with 1046 and 5550 markers from the 90 and 660 K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP) technique for improvement of processing quality in bread wheat. PMID:27486464

The effectiveness of concept mapping on development of critical thinking in nursing education: A systematic review and meta-analysis.

PubMed

Yue, Meng; Zhang, Meng; Zhang, Chunmei; Jin, Changde

2017-05-01

As an essential skill in daily clinical nursing practice, critical thinking ability has been an important objective in nursing education. Concept mapping enables nursing students connect new information to existing knowledge and integrates interdisciplinary knowledge. However, there is a lack of evidence related to critical thinking ability and concept mapping in nursing education. The purpose of this systematic review and meta-analysis was to assess the effect of concept mapping in developing critical thinking in nursing education. This systematic review was reported in line with Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). A search was conducted in PubMed, Web of science, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Cumulative Index to Nursing and Allied Health (CINAHL) and China National Knowledge Infrastructure (CNKI). Randomized controlled trials (RCT) comparing concept mapping and traditional teaching method were retrieved. Data were collected by two reviewers according to the data extraction tables. The methodological quality of included studies was assessed by other two reviewers. The results of meta-analysis were presented using mean difference (MD). Thirteen trials were summarized in the systematic review and eleven trials were included in the meta-analysis. The pooled effect size showed that, comparing with traditional methods, concept mapping could improve subjects' critical thinking ability measured by California Critical Thinking Disposition Inventory (CCTDI), California Critical Thinking Skill Test (CCTST) and Critical Thinking Scale (CTS). The subgroup analyses showed that concept mapping improved the score of all subscales. The result of this review indicated that concept mapping could affect the critical thinking affective dispositions and critical thinking cognitive skills. Further high quality research using uniform evaluation is required. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diversity arrays technology (DArT) markers in apple for genetic linkage maps.

PubMed

Schouten, Henk J; van de Weg, W Eric; Carling, Jason; Khan, Sabaz Ali; McKay, Steven J; van Kaauwen, Martijn P W; Wittenberg, Alexander H J; Koehorst-van Putten, Herma J J; Noordijk, Yolanda; Gao, Zhongshan; Rees, D Jasper G; Van Dyk, Maria M; Jaccoud, Damian; Considine, Michael J; Kilian, Andrzej

2012-03-01

Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.

Generating high-accuracy urban distribution map for short-term change monitoring based on convolutional neural network by utilizing SAR imagery

NASA Astrophysics Data System (ADS)

Iino, Shota; Ito, Riho; Doi, Kento; Imaizumi, Tomoyuki; Hikosaka, Shuhei

2017-10-01

In the developing countries, urban areas are expanding rapidly. With the rapid developments, a short term monitoring of urban changes is important. A constant observation and creation of urban distribution map of high accuracy and without noise pollution are the key issues for the short term monitoring. SAR satellites are highly suitable for day or night and regardless of atmospheric weather condition observations for this type of study. The current study highlights the methodology of generating high-accuracy urban distribution maps derived from the SAR satellite imagery based on Convolutional Neural Network (CNN), which showed the outstanding results for image classification. Several improvements on SAR polarization combinations and dataset construction were performed for increasing the accuracy. As an additional data, Digital Surface Model (DSM), which are useful to classify land cover, were added to improve the accuracy. From the obtained result, high-accuracy urban distribution map satisfying the quality for short-term monitoring was generated. For the evaluation, urban changes were extracted by taking the difference of urban distribution maps. The change analysis with time series of imageries revealed the locations of urban change areas for short-term. Comparisons with optical satellites were performed for validating the results. Finally, analysis of the urban changes combining X-band, L-band and C-band SAR satellites was attempted to increase the opportunity of acquiring satellite imageries. Further analysis will be conducted as future work of the present study

Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.).

PubMed

Ma, Yu; Coyne, Clarice J; Grusak, Michael A; Mazourek, Michael; Cheng, Peng; Main, Dorrie; McGee, Rebecca J

2017-02-13

Marker-assisted breeding is now routinely used in major crops to facilitate more efficient cultivar improvement. This has been significantly enabled by the use of next-generation sequencing technology to identify loci and markers associated with traits of interest. While rich in a range of nutritional components, such as protein, mineral nutrients, carbohydrates and several vitamins, pea (Pisum sativum L.), one of the oldest domesticated crops in the world, remains behind many other crops in the availability of genomic and genetic resources. To further improve mineral nutrient levels in pea seeds requires the development of genome-wide tools. The objectives of this research were to develop these tools by: identifying genome-wide single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS); constructing a high-density linkage map and comparative maps with other legumes, and identifying quantitative trait loci (QTL) for levels of boron, calcium, iron, potassium, magnesium, manganese, molybdenum, phosphorous, sulfur, and zinc in the seed, as well as for seed weight. In this study, 1609 high quality SNPs were found to be polymorphic between 'Kiflica' and 'Aragorn', two parents of an F 6 -derived recombinant inbred line (RIL) population. Mapping 1683 markers including 75 previously published markers and 1608 SNPs developed from the present study generated a linkage map of size 1310.1 cM. Comparative mapping with other legumes demonstrated that the highest level of synteny was observed between pea and the genome of Medicago truncatula. QTL analysis of the RIL population across two locations revealed at least one QTL for each of the mineral nutrient traits. In total, 46 seed mineral concentration QTLs, 37 seed mineral content QTLs, and 6 seed weight QTLs were discovered. The QTLs explained from 2.4% to 43.3% of the phenotypic variance. The genome-wide SNPs and the genetic linkage map developed in this study permitted QTL identification for pea seed mineral nutrients that will serve as important resources to enable marker-assisted selection (MAS) for nutritional quality traits in pea breeding programs.

Teaching Plate Tectonic Concepts using GeoMapApp Learning Activities

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.; Kluge, S.

2012-12-01

GeoMapApp Learning Activities ( http://serc.carleton.edu/geomapapp/collection.html ) can help educators to expose undergraduate students to a range of earth science concepts using high-quality data sets in an easy-to-use map-based interface called GeoMapApp. GeoMapApp Learning Activities require students to interact with and analyse research-quality geoscience data as a means to explore and enhance their understanding of underlying content and concepts. Each activity is freely available through the SERC-Carleton web site and offers step-by-step student instructions and answer sheets. Also provided are annotated educator versions of the worksheets that include teaching tips, additional content and suggestions for further work. The activities can be used "off-the-shelf". Or, since the educator may require flexibility to tailor the activities, the documents are provided in Word format for easy modification. Examples of activities include one on the concept of seafloor spreading that requires students to analyse global seafloor crustal age data to calculate spreading rates in different ocean basins. Another activity has students explore hot spots using radiometric age dating of rocks along the Hawaiian-Emperor seamount chain. A third focusses upon the interactive use of contours and profiles to help students visualise 3-D topography on 2-D computer screens. A fourth activity provides a study of mass wasting as revealed through geomorphological evidence. The step-by-step instructions and guided inquiry approach reduce the need for teacher intervention whilst boosting the time that students can spend on productive exploration and learning. The activities can be used, for example, in a classroom lab with the educator present and as self-paced assignments in an out-of-class setting. GeoMapApp Learning Activities are funded through the NSF GeoEd program and are aimed at students in the introductory undergraduate, community college and high school levels. The activities are based upon GeoMapApp (http://www.geomapapp.org), a free map-based data exploration and visualisation tool that allows students to access a wide range of geoscience data in a virtual lab-like environment.

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

PubMed Central

2013-01-01

Background The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution. Results Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere. Conclusions This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications. PMID:24359668

A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.)

PubMed Central

2013-01-01

Background Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. Results A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. Conclusion We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications. PMID:24377374

Impact of land-use on groundwater quality: GIS-based study from an alluvial aquifer in the western Ganges basin

NASA Astrophysics Data System (ADS)

Khan, Arina; Khan, Haris Hasan; Umar, Rashid

2017-12-01

In this study, groundwater quality of an alluvial aquifer in the western Ganges basin is assessed using a GIS-based groundwater quality index (GQI) concept that uses groundwater quality data from field survey and laboratory analysis. Groundwater samples were collected from 42 wells during pre-monsoon and post-monsoon periods of 2012 and analysed for pH, EC, TDS, Anions (Cl, SO4, NO3), and Cations (Ca, Mg, Na). To generate the index, several parameters were selected based on WHO recommendations. The spatially variable grids of each parameter were modified by normalizing with the WHO standards and finally integrated into a GQI grid. The mean GQI values for both the season suggest good groundwater quality. However, spatial variations exist and are represented by GQI map of both seasons. This spatial variability was compared with the existing land-use, prepared using high-resolution satellite imagery available in Google earth. The GQI grids were compared to the land-use map using an innovative GIS-based method. Results indicate that the spatial variability of groundwater quality in the region is not fully controlled by the land-use pattern. This probably reflects the diffuse nature of land-use classes, especially settlements and plantations.

An unsupervised classification method for inferring original case locations from low-resolution disease maps.

PubMed

Brownstein, John S; Cassa, Christopher A; Kohane, Isaac S; Mandl, Kenneth D

2006-12-08

Widespread availability of geographic information systems software has facilitated the use of disease mapping in academia, government and private sector. Maps that display the address of affected patients are often exchanged in public forums, and published in peer-reviewed journal articles. As previously reported, a search of figure legends in five major medical journals found 19 articles from 1994-2004 that identify over 19,000 patient addresses. In this report, a method is presented to evaluate whether patient privacy is being breached in the publication of low-resolution disease maps. To demonstrate the effect, a hypothetical low-resolution map of geocoded patient addresses was created and the accuracy with which patient addresses can be resolved is described. Through georeferencing and unsupervised classification of the original image, the method precisely re-identified 26% (144/550) of the patient addresses from a presentation quality map and 79% (432/550) from a publication quality map. For the presentation quality map, 99.8% of the addresses were within 70 meters (approximately one city block length) of the predicted patient location, 51.6% of addresses were identified within five buildings, 70.7% within ten buildings and 93% within twenty buildings. For the publication quality map, all addresses were within 14 meters and 11 buildings of the predicted patient location. This study demonstrates that lowering the resolution of a map displaying geocoded patient addresses does not sufficiently protect patient addresses from re-identification. Guidelines to protect patient privacy, including those of medical journals, should reflect policies that ensure privacy protection when spatial data are displayed or published.

Updated symbol catalogue for geologic and geomorphologic mapping in Planetary Scinces

NASA Astrophysics Data System (ADS)

Nass, Andrea; Fortezzo, Corey; Skinner, James, Jr.; Hunter, Marc; Hare, Trent

2017-04-01

Maps are one of the most powerful communication tools for spatial data. This is true for terrestrial data, as well as the many types of planetary data. Geologic and/or geomorphologic maps of planetary surfaces, in particular those of the Moon, Mars, and Venus, are standardized products and often prepared as a part of hypothesis-driven science investigations. The NASA-funded Planetary Geologic Mapping program, coordinated by the USGS Astrogeology Science Center (ASC), produces high-quality, standardized, and refereed geologic maps and digital databases of planetary bodies. In this context, 242 geologic, geomorphologic, and thematic map sheets and map series have been published since the 1962. However, outside of this program, numerous non-USGS published maps are created as result of scientific investigations and published, e.g. as figures or supplemental materials within a peer-reviewed journal article. Due to the complexity of planetary surfaces, diversity between different planet surfaces, and the varied resolution of the data, geomorphologic and geologic mapping is a challenging task. Because of these limiting conditions, the mapping process is a highly interpretative work and is mostly limited to remotely sensed satellite data - with a few expetions from rover data. Uniform and an unambiguous data are fundamental to make quality observations that lead to unbiased and supported interpretations, especially when there is no current groundtruthing. To allow for correlation between different map products (digital or analog), the most commonly used spatial objects are predefined cartographic symbols. The Federal Geographic Data Committee (FGDC) Digital Cartographic Standard for Geologic Map Symbolization (DCSGMS) defines the most commonly used symbols, colors, and hatch patterns in one comprehensive document. Chapter 25 of the DCSGMS defines the Planetary Geology Features based on the symbols defined in the Venus Mapper's Handbook. After reviewing the 242 planetary geological maps, we propose to 1) review standardized symbols for planetary maps, and 2) recommend an updated symbol collection for adoption by the planetary mapping community. Within these points, the focus is on the changing of symbology with respect to time and how it effects communication within and between the maps. Two key questions to address are 1) does chapter 25 provides enough variability within the subcategories (e.g., faults) to represent the data within the maps? 2) How recommendations to the mapping community and their steering committees could be delivered to enhance a map's communicability, and convey information succinctly but thoroughly. For determining the most representative symbol collection of existing maps to support future map results (within or outside of USGS mapping program) we defined a stepwise task list: 1) Statistical review of existing symbol sets and collections, 2) Establish a representative symbol set for planetary mapping, 3) Update cartographic symbols, 4) Implementation into GIS-based mapping software (this implementation will mimic the 2010 application of the planetary symbol set into ArcGIS (more information https://planetarymapping.wr.usgs.gov/Project). 6) Platform to provide the symbol set to the mapping community. This project was initiated within an ongoing cooperation work between the USGS ASC and the German Aerospace Center (DLR), Dept. of Planetary Geology.

Air Data - Concentration Map

EPA Pesticide Factsheets

Make a map of daily concentrations over several days. The daily air quality can be displayed in terms of the Air Quality Index or in concentration ranges for certain PM species like organic carbon, nitrates, and sulfates.

US EPA Nonattainment Areas and Designations-Annual PM2.5 (1997 NAAQS)

EPA Pesticide Factsheets

This web service contains the following layers: PM2.5 Annual 1997 NAAQS State Level and PM2.5 Annual 1997 NAAQS National . It also contains the following tables: maps99.FRED_MAP_VIEWER.%fred_area_map_data and maps99.FRED_MAP_VIEWER.%fred_area_map_view. Full FGDC metadata records for each layer may be found by clicking the layer name at the web service endpoint (https://gispub.epa.gov/arcgis/rest/services/OAR_OAQPS/NAA1997PM25Annual/MapServer) and viewing the layer description.These layers identify areas in the U.S. where air pollution levels have not met the National Ambient Air Quality Standards (NAAQS) for criteria air pollutants and have been designated nonattainment?? areas (NAA). The data are updated weekly from an OAQPS internal database. However, that does not necessarily mean the data have changed. The EPA Office of Air Quality Planning and Standards (OAQPS) has set National Ambient Air Quality Standards for six principal pollutants, which are called criteria pollutants. Under provisions of the Clean Air Act, which is intended to improve the quality of the air we breathe, EPA is required to set National Ambient Air Quality Standards for six common air pollutants. These commonly found air pollutants (also known as criteria pollutants) are found all over the United States. They are particle pollution (often referred to as particulate matter), ground-level ozone, carbon monoxide, sulfur oxides, nitrogen oxides, and lead. For each criteria pollutant, there

Use of Genome Sequence Information for Meat Quality Trait QTL Mining for Causal Genes and Mutations on Pig Chromosome 17

PubMed Central

Hu, Zhi-Liang; Ramos, Antonio M.; Humphray, Sean J.; Rogers, Jane; Reecy, James M.; Rothschild, Max F.

2011-01-01

The newly available pig genome sequence has provided new information to fine map quantitative trait loci (QTL) in order to eventually identify causal variants. With targeted genomic sequencing efforts, we were able to obtain high quality BAC sequences that cover a region on pig chromosome 17 where a number of meat quality QTL have been previously discovered. Sequences from 70 BAC clones were assembled to form an 8-Mbp contig. Subsequently, we successfully mapped five previously identified QTL, three for meat color and two for lactate related traits, to the contig. With an additional 25 genetic markers that were identified by sequence comparison, we were able to carry out further linkage disequilibrium analysis to narrow down the genomic locations of these QTL, which allowed identification of the chromosomal regions that likely contain the causative variants. This research has provided one practical approach to combine genetic and molecular information for QTL mining. PMID:22303339

Monolayer-crystal streptavidin support films provide an internal standard of cryo-EM image quality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Bong-Gyoon; Watson, Zoe; Cate, Jamie H. D.

Analysis of images of biotinylated Escherichia coli 70S ribosome particles, bound to streptavidin affinity grids, demonstrates that the image-quality of particles can be predicted by the image-quality of the monolayer crystalline support film. Also, the quality of the Thon rings is a good predictor of the image-quality of particles, but only when images of the streptavidin crystals extend to relatively high resolution. When the estimated resolution of streptavidin was 5 Å or worse, for example, the ribosomal density map obtained from 22,697 particles went to only 9.5 Å, while the resolution of the map reached 4.0 Å for the samemore » number of particles, when the estimated resolution of streptavidin crystal was 4 Å or better. It thus is easy to tell which images in a data set ought to be retained for further work, based on the highest resolution seen for Bragg peaks in the computed Fourier transforms of the streptavidin component. The refined density map obtained from 57,826 particles obtained in this way extended to 3.6 Å, a marked improvement over the value of 3.9 Å obtained previously from a subset of 52,433 particles obtained from the same initial data set of 101,213 particles after 3-D classification. These results are consistent with the hypothesis that interaction with the air-water interface can damage particles when the sample becomes too thin. Finally, streptavidin monolayer crystals appear to provide a good indication of when that is the case.« less

Pansharpening in coastal ecosystems using Worldview-2 imagery

NASA Astrophysics Data System (ADS)

Ibarrola-Ulzurrun, Edurne; Marcello-Ruiz, Javier; Gonzalo-Martin, Consuelo

2016-10-01

Both climate change and anthropogenic pressure impacts are producing a declining in ecosystem natural resources. In this work, a vulnerable coastal ecosystem, Maspalomas Natural Reserve (Canary Islands, Spain), is analyzed. The development of advanced image processing techniques, applied to new satellites with very high resolution sensors (VHR), are essential to obtain accurate and systematic information about such natural areas. Thus, remote sensing offers a practical and cost-effective means for a good environmental management although some improvements are needed by the application of pansharpening techniques. A preliminary assessment was performed selecting classical and new algorithms that could achieve good performance with WorldView-2 imagery. Moreover, different quality indices were used in order to asses which pansharpening technique gives a better fused image. A total of 7 pansharpening algorithms were analyzed using 6 spectral and spatial quality indices. The quality assessment was implemented for the whole set of multispectral bands and for those bands covered by the wavelength range of the panchromatic image and outside of it. After an extensive evaluation, the most suitable algorithm was the Weighted Wavelet `à trous' through Fractal Dimension Maps technique which provided the best compromise between the spectral and spatial quality for the image. Finally, Quality Map Analysis was performed in order to study the fusion in each band at local level. As conclusion, novel analysis has been conducted covering the evaluation of fusion methods in shallow water areas. Hence, the excellent results provided by this study have been applied to the generation of challenging thematic maps of coastal and dunes protected areas.

The INIA19 Template and NeuroMaps Atlas for Primate Brain Image Parcellation and Spatial Normalization

PubMed Central

Rohlfing, Torsten; Kroenke, Christopher D.; Sullivan, Edith V.; Dubach, Mark F.; Bowden, Douglas M.; Grant, Kathleen A.; Pfefferbaum, Adolf

2012-01-01

The INIA19 is a new, high-quality template for imaging-based studies of non-human primate brains, created from high-resolution, T1-weighted magnetic resonance (MR) images of 19 rhesus macaque (Macaca mulatta) animals. Combined with the comprehensive cortical and sub-cortical label map of the NeuroMaps atlas, the INIA19 is equally suitable for studies requiring both spatial normalization and atlas label propagation. Population-averaged template images are provided for both the brain and the whole head, to allow alignment of the atlas with both skull-stripped and unstripped data, and thus to facilitate its use for skull stripping of new images. This article describes the construction of the template using freely available software tools, as well as the template itself, which is being made available to the scientific community (http://nitrc.org/projects/inia19/). PMID:23230398

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.

PubMed

Wright, Imogen A; Travers, Simon A

2014-07-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mapping the Collaborative Research Process

ERIC Educational Resources Information Center

Kochanek, Julie Reed; Scholz, Carrie; Garcia, Alicia N.

2015-01-01

Despite significant federal investments in the production of high-quality education research, the direct use of that research in policy and practice is not evident. Some education researchers are increasingly employing collaborative research models that use structures and processes to integrate practitioners into the research process in an effort…

A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.).

PubMed

Topdar, N; Kundu, A; Sinha, M K; Sarkar, D; Das, M; Banerjee, S; Kar, C S; Satya, P; Balyan, H S; Mahapatra, B S; Gupta, P K

2013-01-01

We report the first complete microsatellite genetic map of jute (Corchorus olitorius L.; 2n = 2x = 14) using an F6 recombinant inbred population. Of the 403 microsatellite markers screened, 82 were mapped on the seven linkage groups (LGs) that covered a total genetic distance of 799.9 cM, with an average marker interval of 10.7 cM. LG5 had the longest and LG7 the shortest genetic lengths, whereas LG1 had the maximum and LG7 the minimum number of markers. Segregation distortion of microsatellite loci was high (61%), with the majority of them (76%) skewed towards the female parent. Genomewide non-parametric single-marker analysis in combination with multiple quantitative trait loci (QTL)-models (MQM) mapping detected 26 definitive QTLs for bast fibre quality, yield and yield-related traits. These were unevenly distributed on six LGs, as colocalized clusters, at genomic sectors marked by 15 microsatellite loci. LG1 was the QTL-richest map sector, with the densest colocalized clusters of QTLs governing fibre yield, yield-related traits and tensile strength. Expectedly, favorable QTLs were derived from the desirable parents, except for nearly all of those of fibre fineness, which might be due to the creation of new gene combinations. Our results will be a good starting point for further genome analyses in jute.

Risk of nitrate in groundwaters of the United States - A national perspective

USGS Publications Warehouse

Nolan, B.T.; Ruddy, B.C.; Hitt, K.J.; Helsel, D.R.

1997-01-01

Nitrate contamination of groundwater occurs in predictable patterns, based on findings of the U.S. Geological Survey's (USGS) National Water Quality Assessment (NAWQA) Program. The NAWQA Program was begun in 1991 to describe the quality of the Nation's water resources, using nationally consistent methods. Variables affecting nitrate concentration in groundwater were grouped as 'input' factors (population density end the amount of nitrogen contributed by fertilizer, manure, and atmospheric sources) and 'aquifer vulnerability' factors (soil drainage characteristic and the ratio of woodland acres to cropland acres in agricultural areas) and compiled in a national map that shows patterns of risk for nitrate contamination of groundwater. Areas with high nitrogen input, well-drained soils, and low woodland to cropland ratio have the highest potential for contamination of shallow groundwater by nitrate. Groundwater nitrate data collected through 1992 from wells less than 100 ft deep generally verified the risk patterns shown on the national map. Median nitrate concentration was 0.2 mg/L in wells representing the low-risk group, and the maximum contaminant level (MCL) was exceeded in 3% of the wells. In contrast, median nitrate concentration was 4.8 mg/L in wells representing the high-risk group, and the MCL was exceeded in 25% of the wells.Nitrate contamination of groundwater occurs in predictable patterns, based on findings of the U.S. Geological Survey's (USGS) National Water Quality Assessment (NAWQA) Program. The NAWQA Program was begun in 1991 to describe the quality of the Nation's water resources, using nationally consistent methods. Variables affecting nitrate concentration in groundwater were grouped as `input' factors (population density and the amount of nitrogen contributed by fertilizer, manure, and atmospheric sources) and `aquifer vulnerability' factors (soil drainage characteristic and the ratio of woodland acres to cropland acres in agricultural areas) and compiled in a national map that shows patterns of risk for nitrate contamination of groundwater. Areas with high nitrogen input, well-drained soils, and low woodland to cropland ratio have the highest potential for contamination of shallow groundwater by nitrate. Groundwater nitrate data collected through 1992 from wells less than 100 ft deep generally verified the risk patterns shown on the national map. Median nitrate concentration was 0.2 mg/L in wells representing the low-risk group, and the maximum contaminant level (MCL) was exceeded in 3% of the wells. In contrast, median nitrate concentration was 4.8 mg/L in wells representing the high-risk group, and the MCL was exceeded in 25% of the wells.

Global geologic mapping of Mars: The western equatorial region

USGS Publications Warehouse

Scott, D.H.

1985-01-01

Global geologic mapping of Mars was originally accomplished following acquisition of orbital spacecraft images from the Mariner 9 mission. The mapping program represented a joint enterprise by the U.S. Geological Survey and other planetary scientists from universities in the United States and Europe. Many of the Mariner photographs had low resolution or poor albedo contrast caused by atmospheric haze and high-sun angles. Some of the early geologic maps reflect these deficiencies in their poor discrimination and subdivision of rock units. New geologic maps made from higher resolution and better quality Viking images also represent a cooperative effort, by geologists from the U.S. Geological Survey, Arizona State University, and the University of London. This second series of global maps consists of three parts: 1) western equatorial region, 2) eastern equatorial region, and 3) north and south polar regions. These maps, at 1:15 million scale, show more than 60 individual rock-stratigraphic units assigned to three Martian time-stratigraphic systems. The first completed map of the series covers the western equatorial region of Mars. Accompanying the map is a description of the sequence and distribution of major tectonic, volcanic, and fluvial episodes as recorded in the stratigraphic record. ?? 1985.

Multi-channel Analysis of Passive Surface Waves (MAPS)

NASA Astrophysics Data System (ADS)

Xia, J.; Cheng, F. Mr; Xu, Z.; Wang, L.; Shen, C.; Liu, R.; Pan, Y.; Mi, B.; Hu, Y.

2017-12-01

Urbanization is an inevitable trend in modernization of human society. In the end of 2013 the Chinese Central Government launched a national urbanization plan—"Three 100 Million People", which aggressively and steadily pushes forward urbanization. Based on the plan, by 2020, approximately 100 million people from rural areas will permanently settle in towns, dwelling conditions of about 100 million people in towns and villages will be improved, and about 100 million people in the central and western China will permanently settle in towns. China's urbanization process will run at the highest speed in the urbanization history of China. Environmentally friendly, non-destructive and non-invasive geophysical assessment method has played an important role in the urbanization process in China. Because human noise and electromagnetic field due to industrial life, geophysical methods already used in urban environments (gravity, magnetics, electricity, seismic) face great challenges. But humanity activity provides an effective source of passive seismic methods. Claerbout pointed out that wavefileds that are received at one point with excitation at the other point can be reconstructed by calculating the cross-correlation of noise records at two surface points. Based on this idea (cross-correlation of two noise records) and the virtual source method, we proposed Multi-channel Analysis of Passive Surface Waves (MAPS). MAPS mainly uses traffic noise recorded with a linear receiver array. Because Multi-channel Analysis of Surface Waves can produces a shear (S) wave velocity model with high resolution in shallow part of the model, MPAS combines acquisition and processing of active source and passive source data in a same flow, which does not require to distinguish them. MAPS is also of ability of real-time quality control of noise recording that is important for near-surface applications in urban environment. The numerical and real-world examples demonstrated that MAPS can be used for accurate and fast imaging of high-frequency surface wave energy, and some examples also show that high quality imaging similar to those with active sources can be generated only by the use of a few minutes of noise. The use of cultural noise in town, MAPS can image S-wave velocity structure from the ground surface to hundreds of meters depth.

Production of a water quality map of Saginaw Bay by computer processing of LANDSAT-2 data

NASA Technical Reports Server (NTRS)

Mckeon, J. B.; Rogers, R. H.; Smith, V. E.

1977-01-01

Surface truth and LANDSAT measurements collected July 31, 1975, for Saginaw Bay were used to demonstrate a technique for producing a color coded water quality map. On this map, color was used as a code to quantify five discrete ranges in the following water quality parameters: (1) temperature, (2) Secchi depth, (3) chloride, (4) conductivity, (5) total Kjeldahl nitrogen, (6) total phosphorous, (7)chlorophyll a, (8) total solids and (9) suspended solids. The LANDSAT and water quality relationship was established through the use of a set of linear regression equations where the water quality parameters are the dependent variables and LANDSAT measurements are the independent variables. Although the procedure is scene and surface truth dependent, it provides both a basis for extrapolating water quality parameters from point samples to unsampled areas and a synoptic view of water mass boundaries over the 3000 sq. km bay area made from one day's ship data that is superior, in many ways, to the traditional machine contoured maps made from three day's ship data.

Analyzing Variability in Landscape Nutrient Loading Using Spatially-Explicit Maps in the Great Lakes Basin

NASA Astrophysics Data System (ADS)

Hamlin, Q. F.; Kendall, A. D.; Martin, S. L.; Whitenack, H. D.; Roush, J. A.; Hannah, B. A.; Hyndman, D. W.

2017-12-01

Excessive loading of nitrogen and phosphorous to the landscape has caused biologically and economically damaging eutrophication and harmful algal blooms in the Great Lakes Basin (GLB) and across the world. We mapped source-specific loads of nitrogen and phosphorous to the landscape using broadly available data across the GLB. SENSMap (Spatially Explicit Nutrient Source Map) is a 30m resolution snapshot of nutrient loads ca. 2010. We use these maps to study variable nutrient loading and provide this information to watershed managers through NOAA's GLB Tipping Points Planner. SENSMap individually maps nutrient point sources and six non-point sources: 1) atmospheric deposition, 2) septic tanks, 3) non-agricultural chemical fertilizer, 4) agricultural chemical fertilizer, 5) manure, and 6) nitrogen fixation from legumes. To model source-specific loads at high resolution, SENSMap synthesizes a wide range of remotely sensed, surveyed, and tabular data. Using these spatially explicit nutrient loading maps, we can better calibrate local land use-based water quality models and provide insight to watershed managers on how to focus nutrient reduction strategies. Here we examine differences in dominant nutrient sources across the GLB, and how those sources vary by land use. SENSMap's high resolution, source-specific approach offers a different lens to understand nutrient loading than traditional semi-distributed or land use based models.

LOD map--A visual interface for navigating multiresolution volume visualization.

PubMed

Wang, Chaoli; Shen, Han-Wei

2006-01-01

In multiresolution volume visualization, a visual representation of level-of-detail (LOD) quality is important for us to examine, compare, and validate different LOD selection algorithms. While traditional methods rely on ultimate images for quality measurement, we introduce the LOD map--an alternative representation of LOD quality and a visual interface for navigating multiresolution data exploration. Our measure for LOD quality is based on the formulation of entropy from information theory. The measure takes into account the distortion and contribution of multiresolution data blocks. A LOD map is generated through the mapping of key LOD ingredients to a treemap representation. The ordered treemap layout is used for relative stable update of the LOD map when the view or LOD changes. This visual interface not only indicates the quality of LODs in an intuitive way, but also provides immediate suggestions for possible LOD improvement through visually-striking features. It also allows us to compare different views and perform rendering budget control. A set of interactive techniques is proposed to make the LOD adjustment a simple and easy task. We demonstrate the effectiveness and efficiency of our approach on large scientific and medical data sets.

Dynamic spatial filtering using a digital micromirror device for high-speed optical diffraction tomography.

PubMed

Jin, Di; Zhou, Renjie; Yaqoob, Zahid; So, Peter T C

2018-01-08

Optical diffraction tomography (ODT) is an emerging microscopy technique for three-dimensional (3D) refractive index (RI) mapping of transparent specimens. Recently, the digital micromirror device (DMD) based scheme for angle-controlled plane wave illumination has been proposed to improve the imaging speed and stability of ODT. However, undesired diffraction noise always exists in the reported DMD-based illumination scheme, which leads to a limited contrast ratio of the measurement fringe and hence inaccurate RI mapping. Here we present a novel spatial filtering method, based on a second DMD, to dynamically remove the diffraction noise. The reported results illustrate significantly enhanced image quality of the obtained interferograms and the subsequently derived phase maps. And moreover, with this method, we demonstrate mapping of 3D RI distribution of polystyrene beads as well as biological cells with high accuracy. Importantly, with the proper hardware configuration, our method does not compromise the 3D imaging speed advantage promised by the DMD-based illumination scheme. Specifically, we have been able to successfully obtain interferograms at over 1 kHz speed, which is critical for potential high-throughput label-free 3D image cytometry applications.

Rapid 2D-to-3D conversion

NASA Astrophysics Data System (ADS)

Harman, Philip V.; Flack, Julien; Fox, Simon; Dowley, Mark

2002-05-01

The conversion of existing 2D images to 3D is proving commercially viable and fulfills the growing need for high quality stereoscopic images. This approach is particularly effective when creating content for the new generation of autostereoscopic displays that require multiple stereo images. The dominant technique for such content conversion is to develop a depth map for each frame of 2D material. The use of a depth map as part of the 2D to 3D conversion process has a number of desirable characteristics: 1. The resolution of the depth may be lower than that of the associated 2D image. 2. It can be highly compressed. 3. 2D compatibility is maintained. 4. Real time generation of stereo, or multiple stereo pairs, is possible. The main disadvantage has been the laborious nature of the manual conversion techniques used to create depth maps from existing 2D images, which results in a slow and costly process. An alternative, highly productive technique has been developed based upon the use of Machine Leaning Algorithm (MLAs). This paper describes the application of MLAs to the generation of depth maps and presents the results of the commercial application of this approach.

On-site phytoremediation applicability assessment in Alur Ilmu, Universiti Kebangsaan Malaysia based on spatial and pollution removal analyses.

PubMed

Mahmud, Mohd Hafiyyan; Lee, Khai Ern; Goh, Thian Lai

2017-10-01

The present paper aims to assess the phytoremediation performance based on pollution removal efficiency of the highly polluted region of Alur Ilmu urban river for its applicability of on-site treatment. Thirteen stations along Alur Ilmu were selected to produce thematic maps through spatial distribution analysis based on six water quality parameters of Malaysia's Water Quality Index (WQI) for dry and raining seasons. The maps generated were used to identify the highly polluted region for phytoremediation applicability assessment. Four free-floating plants were tested in treating water samples from the highly polluted region under three different conditions, namely controlled, aerated and normal treatments. The selected free-floating plants were water hyacinth (Eichhornia crassipes), water lettuce (Pistia stratiotes), rose water lettuce (Pistia sp.) and pennywort (Centella asiatica). The results showed that Alur Ilmu was more polluted during dry season compared to raining season based on the water quality analysis. During dry season, four parameters were marked as polluted along Alur Ilmu, namely dissolve oxygen (DO), 4.72 mg/L (class III); ammoniacal nitrogen (NH 3 -N), 0.85 mg/L (class IV); total suspended solid (TSS), 402 mg/L (class V) and biological oxygen demand (BOD), 3.89 mg/L (class III), whereas, two parameters were classed as polluted during raining season, namely total suspended solid (TSS), 571 mg/L (class V) and biological oxygen demand (BOD), 4.01 mg/L (class III). The thematic maps generated from spatial distribution analysis using Kriging gridding method showed that the highly polluted region was recorded at station AL 5. Hence, water samples were taken from this station for pollution removal analysis. All the free-floating plants were able to reduce TSS and COD in less than 14 days. However, water hyacinth showed the least detrimental effect from the phytoremediation process compared to other free-floating plants, thus made it a suitable free-floating plants to be used for on-site treatment.

Geophysical Data from Offshore of the Chandeleur Islands, Eastern Mississippi Delta

USGS Publications Warehouse

Baldwin, Wayne E.; Pendleton, Elizabeth A.; Twichell, David C.

2009-01-01

This report contains the geophysical and geospatial data that were collected during two cruises on the R/V Acadiana along the eastern, offshore side of the Chandeleur Islands in 2006 and 2007. Data were acquired with the following equipment: a Systems Engineering and Assessment, Ltd., SwathPlus interferometric sonar; a Klein 3000 dual-frequency sidescan sonar; and an EdgeTech 512i chirp sub-bottom profiling system. The long-term goal of this mapping effort is to produce high-quality, high-resolution geologic maps and geophysical interpretations that can be utilized to investigate the impact of Hurricane Katrina, identify sand resources within the region, and make predictions regarding the future evolution of this coastal system.

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

PubMed

Ryan, Michael; Diekhans, Mark; Lien, Stephanie; Liu, Yun; Karchin, Rachel

2009-06-01

LS-SNP/PDB is a new WWW resource for genome-wide annotation of human non-synonymous (amino acid changing) SNPs. It serves high-quality protein graphics rendered with UCSF Chimera molecular visualization software. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features. LS-SNP/PDB is available at (http://ls-snp.icm.jhu.edu/ls-snp-pdb) and via links from protein data bank (PDB) biology and chemistry tabs, UCSC Genome Browser Gene Details and SNP Details pages and PharmGKB Gene Variants Downloads/Cross-References pages.

WE-AB-209-10: Optimizing the Delivery of Sequential Fluence Maps for Efficient VMAT Delivery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Craft, D; Balvert, M

2016-06-15

Purpose: To develop an optimization model and solution approach for computing MLC leaf trajectories and dose rates for high quality matching of a set of optimized fluence maps to be delivered sequentially around a patient in a VMAT treatment. Methods: We formulate the fluence map matching problem as a nonlinear optimization problem where time is discretized but dose rates and leaf positions are continuous variables. For a given allotted time, which is allocated across the fluence maps based on the complexity of each fluence map, the optimization problem searches for the best leaf trajectories and dose rates such that themore » original fluence maps are closely recreated. Constraints include maximum leaf speed, maximum dose rate, and leaf collision avoidance, as well as the constraint that the ending leaf positions for one map are the starting leaf positions for the next map. The resulting model is non-convex but smooth, and therefore we solve it by local searches from a variety of starting positions. We improve solution time by a custom decomposition approach which allows us to decouple the rows of the fluence maps and solve each leaf pair individually. This decomposition also makes the problem easily parallelized. Results: We demonstrate method on a prostate case and a head-and-neck case and show that one can recreate fluence maps to high degree of fidelity in modest total delivery time (minutes). Conclusion: We present a VMAT sequencing method that reproduces optimal fluence maps by searching over a vast number of possible leaf trajectories. By varying the total allotted time given, this approach is the first of its kind to allow users to produce VMAT solutions that span the range of wide-field coarse VMAT deliveries to narrow-field high-MU sliding window-like approaches.« less

Partnerships - Working Together to Build The National Map

USGS Publications Warehouse

,

2004-01-01

Through The National Map, the U.S. Geological Survey (USGS) is working with partners to ensure that current, accurate, and complete base geographic information is available for the Nation. Designed as a network of online digital databases, it provides a consistent geographic data framework for the country and serves as a foundation for integrating, sharing, and using data easily and reliably. It provides public access to high quality geospatial data and information from multiple partners to help inform decisionmaking by resource managers and the public, and to support intergovernmental homeland security and emergency management requirements.

Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.).

PubMed

Zhang, Zhen; Shang, Haihong; Shi, Yuzhen; Huang, Long; Li, Junwen; Ge, Qun; Gong, Juwu; Liu, Aiying; Chen, Tingting; Wang, Dan; Wang, Yanling; Palanga, Koffi Kibalou; Muhammad, Jamshed; Li, Weijie; Lu, Quanwei; Deng, Xiaoying; Tan, Yunna; Song, Weiwu; Cai, Juan; Li, Pengtao; Rashid, Harun or; Gong, Wankui; Yuan, Youlu

2016-04-11

Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.

Factor weighting in DRASTIC modelling for assessing the groundwater vulnerability in Salatiga groundwater basin, Central Java Province, Indonesia

NASA Astrophysics Data System (ADS)

Kesuma, D. A.; Purwanto, P.; Putranto, T. T.; Rahmani, T. P. D.

2017-06-01

The increase in human population as well as area development in Salatiga Groundwater Basin, Central Java Province, will increase the potency of groundwater contamination in that area. Groundwater quality, especially the shallow groundwater, is very vulnerable to the contamination from industrial waste, fertilizer/agricultural waste, and domestic waste. The first step in the conservation of groundwater quality is by conducting the mapping of the groundwater vulnerability zonation against the contamination. The result of this research was groundwater vulnerability map which showed the areas vulnerable to the groundwater contamination. In this study, groundwater vulnerability map was assessed based on the DRASTIC Method and was processed spatially using Geographic Information System. The DRASTIC method is used to assess the level of groundwater vulnerability based on weighting on seven parameters, which are: depth to the water table (D), recharge (R), aquifer material (A), soil media (S), topography (T), impact of vadose zone (I), and hydraulic conductivity (C). The higher the DRASTIC Index will result in the higher vulnerability level of groundwater contamination in that area. The DRASTIC Indexes in the researched area were 85 - 100 (low vulnerability level), 101 -120 (low to moderate vulnerability level), 121 - 140 (moderate vulnerability level), 141 - 150, (moderate to high vulnerability level), and 151 - 159 (high vulnerability level). The output of this study can be used by local authority as a tool for consideration to arrange the policy for sustainable area development, especially the development in an area affecting the quality of Salatiga Groundwater Basin.

An effective XML based name mapping mechanism within StoRM

NASA Astrophysics Data System (ADS)

Corso, E.; Forti, A.; Ghiselli, A.; Magnoni, L.; Zappi, R.

2008-07-01

In a Grid environment the naming capability allows users to refer to specific data resources in a physical storage system using a high level logical identifier. This logical identifier is typically organized in a file system like structure, a hierarchical tree of names. Storage Resource Manager (SRM) services map the logical identifier to the physical location of data evaluating a set of parameters as the desired quality of services and the VOMS attributes specified in the requests. StoRM is a SRM service developed by INFN and ICTP-EGRID to manage file and space on standard POSIX and high performing parallel and cluster file systems. An upcoming requirement in the Grid data scenario is the orthogonality of the logical name and the physical location of data, in order to refer, with the same identifier, to different copies of data archived in various storage areas with different quality of service. The mapping mechanism proposed in StoRM is based on a XML document that represents the different storage components managed by the service, the storage areas defined by the site administrator, the quality of service they provide and the Virtual Organization that want to use the storage area. An appropriate directory tree is realized in each storage component reflecting the XML schema. In this scenario StoRM is able to identify the physical location of a requested data evaluating the logical identifier and the specified attributes following the XML schema, without querying any database service. This paper presents the namespace schema defined, the different entities represented and the technical details of the StoRM implementation.

Efficient high-throughput sequencing of a laser microdissected chromosome arm

PubMed Central

2013-01-01

Background Genomic sequence assemblies are key tools for a broad range of gene function and evolutionary studies. The diploid amphibian Xenopus tropicalis plays a pivotal role in these fields due to its combination of experimental flexibility, diploid genome, and early-branching tetrapod taxonomic position, having diverged from the amniote lineage ~360 million years ago. A genome assembly and a genetic linkage map have recently been made available. Unfortunately, large gaps in the linkage map attenuate long-range integrity of the genome assembly. Results We laser dissected the short arm of X. tropicalis chromosome 7 for next generation sequencing and computational mapping to the reference genome. This arm is of particular interest as it encodes the sex determination locus, but its genetic map contains large gaps which undermine available genome assemblies. Whole genome amplification of 15 laser-microdissected 7p arms followed by next generation sequencing yielded ~35 million reads, over four million of which uniquely mapped to the X. tropicalis genome. Our analysis placed more than 200 previously unmapped scaffolds on the analyzed chromosome arm, providing valuable low-resolution physical map information for de novo genome assembly. Conclusion We present a new approach for improving and validating genetic maps and sequence assemblies. Whole genome amplification of 15 microdissected chromosome arms provided sufficient high-quality material for localizing previously unmapped scaffolds and genes as well as recognizing mislocalized scaffolds. PMID:23714049

The use of Sentinel-2 imagery for seagrass mapping: Kalloni Gulf (Lesvos Island, Greece) case study

NASA Astrophysics Data System (ADS)

Topouzelis, Konstantinos; Charalampis Spondylidis, Spyridon; Papakonstantinou, Apostolos; Soulakellis, Nikolaos

2016-08-01

Seagrass meadows play a significant role in ecosystems by stabilizing sediment and improving water clarity, which enhances seagrass growing conditions. It is high on the priority of EU legislation to map and protect them. The traditional use of medium spatial resolution satellite imagery e.g. Landsat-8 (30m) is very useful for mapping seagrass meadows on a regional scale. However, the availability of Sentinel-2 data, the recent ESA's satellite with its payload Multi-Spectral Instrument (MSI) is expected to improve the mapping accuracy. MSI designed to improve coastline studies due to its enhanced spatial and spectral capabilities e.g. optical bands with 10m spatial resolution. The present work examines the quality of Sentinel-2 images for seagrass mapping, the ability of each band in detection and discrimination of different habitats and estimates the accuracy of seagrass mapping. After pre-processing steps, e.g. radiometric calibration and atmospheric correction, image classified into four classes. Classification classes included sub-bottom composition e.g. seagrass, soft bottom, and hard bottom. Concrete vectors describing the areas covered by seagrass extracted from the high-resolution satellite image and used as in situ measurements. The developed methodology applied in the Gulf of Kalloni, (Lesvos Island - Greece). Results showed that Sentinel-2 images can be robustly used for seagrass mapping due to their spatial resolution, band availability and radiometric accuracy.

Optimal and fast E/B separation with a dual messenger field

NASA Astrophysics Data System (ADS)

Kodi Ramanah, Doogesh; Lavaux, Guilhem; Wandelt, Benjamin D.

2018-05-01

We adapt our recently proposed dual messenger algorithm for spin field reconstruction and showcase its efficiency and effectiveness in Wiener filtering polarized cosmic microwave background (CMB) maps. Unlike conventional preconditioned conjugate gradient (PCG) solvers, our preconditioner-free technique can deal with high-resolution joint temperature and polarization maps with inhomogeneous noise distributions and arbitrary mask geometries with relative ease. Various convergence diagnostics illustrate the high quality of the dual messenger reconstruction. In contrast, the PCG implementation fails to converge to a reasonable solution for the specific problem considered. The implementation of the dual messenger method is straightforward and guarantees numerical stability and convergence. We show how the algorithm can be modified to generate fluctuation maps, which, combined with the Wiener filter solution, yield unbiased constrained signal realizations, consistent with observed data. This algorithm presents a pathway to exact global analyses of high-resolution and high-sensitivity CMB data for a statistically optimal separation of E and B modes. It is therefore relevant for current and next-generation CMB experiments, in the quest for the elusive primordial B-mode signal.

High-throughput physical mapping of chromosomes using automated in situ hybridization.

PubMed

George, Phillip; Sharakhova, Maria V; Sharakhov, Igor V

2012-06-28

Projects to obtain whole-genome sequences for 10,000 vertebrate species and for 5,000 insect and related arthropod species are expected to take place over the next 5 years. For example, the sequencing of the genomes for 15 malaria mosquitospecies is currently being done using an Illumina platform. This Anopheles species cluster includes both vectors and non-vectors of malaria. When the genome assemblies become available, researchers will have the unique opportunity to perform comparative analysis for inferring evolutionary changes relevant to vector ability. However, it has proven difficult to use next-generation sequencing reads to generate high-quality de novo genome assemblies. Moreover, the existing genome assemblies for Anopheles gambiae, although obtained using the Sanger method, are gapped or fragmented. Success of comparative genomic analyses will be limited if researchers deal with numerous sequencing contigs, rather than with chromosome-based genome assemblies. Fragmented, unmapped sequences create problems for genomic analyses because: (i) unidentified gaps cause incorrect or incomplete annotation of genomic sequences; (ii) unmapped sequences lead to confusion between paralogous genes and genes from different haplotypes; and (iii) the lack of chromosome assignment and orientation of the sequencing contigs does not allow for reconstructing rearrangement phylogeny and studying chromosome evolution. Developing high-resolution physical maps for species with newly sequenced genomes is a timely and cost-effective investment that will facilitate genome annotation, evolutionary analysis, and re-sequencing of individual genomes from natural populations. Here, we present innovative approaches to chromosome preparation, fluorescent in situ hybridization (FISH), and imaging that facilitate rapid development of physical maps. Using An. gambiae as an example, we demonstrate that the development of physical chromosome maps can potentially improve genome assemblies and, thus, the quality of genomic analyses. First, we use a high-pressure method to prepare polytene chromosome spreads. This method, originally developed for Drosophila, allows the user to visualize more details on chromosomes than the regular squashing technique. Second, a fully automated, front-end system for FISH is used for high-throughput physical genome mapping. The automated slide staining system runs multiple assays simultaneously and dramatically reduces hands-on time. Third, an automatic fluorescent imaging system, which includes a motorized slide stage, automatically scans and photographs labeled chromosomes after FISH. This system is especially useful for identifying and visualizing multiple chromosomal plates on the same slide. In addition, the scanning process captures a more uniform FISH result. Overall, the automated high-throughput physical mapping protocol is more efficient than a standard manual protocol.

Predicting "Hot" and "Warm" Spots for Fragment Binding.

PubMed

Rathi, Prakash Chandra; Ludlow, R Frederick; Hall, Richard J; Murray, Christopher W; Mortenson, Paul N; Verdonk, Marcel L

2017-05-11

Computational fragment mapping methods aim to predict hotspots on protein surfaces where small fragments will bind. Such methods are popular for druggability assessment as well as structure-based design. However, to date researchers developing or using such tools have had no clear way of assessing the performance of these methods. Here, we introduce the first diverse, high quality validation set for computational fragment mapping. The set contains 52 diverse examples of fragment binding "hot" and "warm" spots from the Protein Data Bank (PDB). Additionally, we describe PLImap, a novel protocol for fragment mapping based on the Protein-Ligand Informatics force field (PLIff). We evaluate PLImap against the new fragment mapping test set, and compare its performance to that of simple shape-based algorithms and fragment docking using GOLD. PLImap is made publicly available from https://bitbucket.org/AstexUK/pli .

On the influence of zero-padding on the nonlinear operations in Quantitative Susceptibility Mapping

PubMed Central

Eskreis-Winkler, Sarah; Zhou, Dong; Liu, Tian; Gupta, Ajay; Gauthier, Susan A.; Wang, Yi; Spincemaille, Pascal

2016-01-01

Purpose Zero padding is a well-studied interpolation technique that improves image visualization without increasing image resolution. This interpolation is often performed as a last step before images are displayed on clinical workstations. Here, we seek to demonstrate the importance of zero padding before rather than after performing non-linear post-processing algorithms, such as Quantitative Susceptibility Mapping (QSM). To do so, we evaluate apparent spatial resolution, relative error and depiction of multiple sclerosis (MS) lesions on images that were zero padded prior to, in the middle of, and after the application of the QSM algorithm. Materials and Methods High resolution gradient echo (GRE) data were acquired on twenty MS patients, from which low resolution data were derived using k-space cropping. Pre-, mid-, and post-zero padded QSM images were reconstructed from these low resolution data by zero padding prior to field mapping, after field mapping, and after susceptibility mapping, respectively. Using high resolution QSM as the gold standard, apparent spatial resolution, relative error, and image quality of the pre-, mid-, and post-zero padded QSM images were measured and compared. Results Both the accuracy and apparent spatial resolution of the pre-zero padded QSM was higher than that of mid-zero padded QSM (p < 0.001; p < 0.001), which was higher than that of post-zero padded QSM (p < 0.001; p < 0.001). The image quality of pre-zero padded reconstructions was higher than that of mid- and post-zero padded reconstructions (p = 0.004; p < 0.001). Conclusion Zero padding of the complex GRE data prior to nonlinear susceptibility mapping improves image accuracy and apparent resolution compared to zero padding afterwards. It also provides better delineation of MS lesion geometry, which may improve lesion subclassification and disease monitoring in MS patients. PMID:27587225

New Tool Quantitatively Maps Minority-Carrier Lifetime of Multicrystalline Silicon Bricks (Fact Sheet)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2011-11-01

NREL's new imaging tool could provide manufacturers with insight on their processes. Scientists at the National Renewable Energy Laboratory (NREL) have used capabilities within the Process Development and Integration Laboratory (PDIL) to generate quantitative minority-carrier lifetime maps of multicrystalline silicon (mc-Si) bricks. This feat has been accomplished by using the PDIL's photoluminescence (PL) imaging system in conjunction with transient lifetime measurements obtained using a custom NREL-designed resonance-coupled photoconductive decay (RCPCD) system. PL imaging can obtain rapid high-resolution images that provide a qualitative assessment of the material lifetime-with the lifetime proportional to the pixel intensity. In contrast, the RCPCD technique providesmore » a fast quantitative measure of the lifetime with a lower resolution and penetrates millimeters into the mc-Si brick, providing information on bulk lifetimes and material quality. This technique contrasts with commercially available minority-carrier lifetime mapping systems that use microwave conductivity measurements. Such measurements are dominated by surface recombination and lack information on the material quality within the bulk of the brick. By combining these two complementary techniques, we obtain high-resolution lifetime maps at very fast data acquisition times-attributes necessary for a production-based diagnostic tool. These bulk lifetime measurements provide manufacturers with invaluable feedback on their silicon ingot casting processes. NREL has been applying the PL images of lifetime in mc-Si bricks in collaboration with a U.S. photovoltaic industry partner through Recovery Act Funded Project ARRA T24. NREL developed a new tool to quantitatively map minority-carrier lifetime of multicrystalline silicon bricks by using photoluminescence imaging in conjunction with resonance-coupled photoconductive decay measurements. Researchers are not hindered by surface recombination and can look deeper into the material to map bulk lifetimes. The tool is being applied to silicon bricks in a project collaborating with a U.S. photovoltaic industry partner. Photovoltaic manufacturers can use the NREL tool to obtain valuable feedback on their silicon ingot casting processes.« less

On the influence of zero-padding on the nonlinear operations in Quantitative Susceptibility Mapping.

PubMed

Eskreis-Winkler, Sarah; Zhou, Dong; Liu, Tian; Gupta, Ajay; Gauthier, Susan A; Wang, Yi; Spincemaille, Pascal

2017-01-01

Zero padding is a well-studied interpolation technique that improves image visualization without increasing image resolution. This interpolation is often performed as a last step before images are displayed on clinical workstations. Here, we seek to demonstrate the importance of zero padding before rather than after performing non-linear post-processing algorithms, such as Quantitative Susceptibility Mapping (QSM). To do so, we evaluate apparent spatial resolution, relative error and depiction of multiple sclerosis (MS) lesions on images that were zero padded prior to, in the middle of, and after the application of the QSM algorithm. High resolution gradient echo (GRE) data were acquired on twenty MS patients, from which low resolution data were derived using k-space cropping. Pre-, mid-, and post-zero padded QSM images were reconstructed from these low resolution data by zero padding prior to field mapping, after field mapping, and after susceptibility mapping, respectively. Using high resolution QSM as the gold standard, apparent spatial resolution, relative error, and image quality of the pre-, mid-, and post-zero padded QSM images were measured and compared. Both the accuracy and apparent spatial resolution of the pre-zero padded QSM was higher than that of mid-zero padded QSM (p<0.001; p<0.001), which was higher than that of post-zero padded QSM (p<0.001; p<0.001). The image quality of pre-zero padded reconstructions was higher than that of mid- and post-zero padded reconstructions (p=0.004; p<0.001). Zero padding of the complex GRE data prior to nonlinear susceptibility mapping improves image accuracy and apparent resolution compared to zero padding afterwards. It also provides better delineation of MS lesion geometry, which may improve lesion subclassification and disease monitoring in MS patients. Copyright © 2016 Elsevier Inc. All rights reserved.

Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean.

PubMed

Wang, Xianzhi; Jiang, Guo-Liang; Green, Marci; Scott, Roy A; Song, Qijian; Hyten, David L; Cregan, Perry B

2014-10-01

Soybean seeds contain high levels of oil and protein, and are the important sources of vegetable oil and plant protein for human consumption and livestock feed. Increased seed yield, oil and protein contents are the main objectives of soybean breeding. The objectives of this study were to identify and validate quantitative trait loci (QTLs) associated with seed yield, oil and protein contents in two recombinant inbred line populations, and to evaluate the consistency of QTLs across different environments, studies and genetic backgrounds. Both the mapping population (SD02-4-59 × A02-381100) and validation population (SD02-911 × SD00-1501) were phenotyped for the three traits in multiple environments. Genetic analysis indicated that oil and protein contents showed high heritabilities while yield exhibited a lower heritability in both populations. Based on a linkage map constructed previously with the mapping population and using composite interval mapping and/or interval mapping analysis, 12 QTLs for seed yield, 16 QTLs for oil content and 11 QTLs for protein content were consistently detected in multiple environments and/or the average data over all environments. Of the QTLs detected in the mapping population, five QTLs for seed yield, eight QTLs for oil content and five QTLs for protein content were confirmed in the validation population by single marker analysis in at least one environment and the average data and by ANOVA over all environments. Eight of these validated QTLs were newly identified. Compared with the other studies, seven QTLs for seed yield, eight QTLs for oil content and nine QTLs for protein content further verified the previously reported QTLs. These QTLs will be useful for breeding higher yield and better quality cultivars, and help effectively and efficiently improve yield potential and nutritional quality in soybean.

Enabling Science Integration through the Marine Geoscience Data System Media Bank

NASA Astrophysics Data System (ADS)

Leung, A.; Ferrini, V.; Arko, R.; Carbotte, S. M.; Goehring, L.; Simms, E.

2008-12-01

The Marine Geoscience Data System Media Bank (http://media.marine-geo.org) was constructed to enable the sharing of high quality images, illustrations and animations among members of the science community and to provide a new forum for education and public outreach (EPO). The initial focus of Media Bank was to serve Ridge 2000 research and EPO efforts, but it was constructed as a flexible system that could accommodate media from other multidisciplinary marine geoscience research initiatives. Media Bank currently contains digital photographs, maps, 3-D visualizations, and video clips from the Ridge 2000 and MARGINS focus sites as well as the Antarctic and Southern Ocean. We actively seek contributions of other high quality marine geoscience media for inclusion in Media Bank. Media Bank is driven by a relational database backend, enabling image browsing, sorting by category, keyword search functionality, and the creation of media galleries. All media are accompanied by a descriptive figure caption that provides easy access to expert knowledge to help foster data integration across disciplines as well as EPO efforts. In addition to access to high quality media, Media Bank also provides basic metadata including geographic position, investigator name and affiliation, as well as copyright information, and links to references and relevant data sets. Since media are tied to geospatial coordinates, a map-based interface is also provided for access to media.

Improving Operational Readiness through Total Quality Management

DTIC Science & Technology

1991-06-21

DTIC AD-A236 611 EL CT F NAVAL WAR COLL GE C Newport, R. I. IMPROVING OPERATIONAL READINESS THROUGH TOTAL QUALITY MANAGEMENT by Herb Westphal Defense...IMPROVING OPERATIONAL READINESS THROUGH TOTAL QUALITY MANAGEMENT (TQM) A Case Study: The Defense Mapping Agency Combat Support Center (DMACSC) initiated a...of the Defense Mapping Agency Combat Support Center’s (DMACSC) Total Quality Management (TQM) improvement methodology. This allows the reader to

Enhanced video indirect ophthalmoscopy (VIO) via robust mosaicing.

PubMed

Estrada, Rolando; Tomasi, Carlo; Cabrera, Michelle T; Wallace, David K; Freedman, Sharon F; Farsiu, Sina

2011-10-01

Indirect ophthalmoscopy (IO) is the standard of care for evaluation of the neonatal retina. When recorded on video from a head-mounted camera, IO images have low quality and narrow Field of View (FOV). We present an image fusion methodology for converting a video IO recording into a single, high quality, wide-FOV mosaic that seamlessly blends the best frames in the video. To this end, we have developed fast and robust algorithms for automatic evaluation of video quality, artifact detection and removal, vessel mapping, registration, and multi-frame image fusion. Our experiments show the effectiveness of the proposed methods.

Universities Becoming the Outsourcing Solution

ERIC Educational Resources Information Center

Bohley, Katharine A.

2010-01-01

This paper provides a road map for universities to follow in responding to corporations that are in need of a solution to the dilemma of building an executive development program and simultaneously providing their executives with a high quality MBA degree. Difficulties experienced by many corporations are complicated by the fact that MBA programs…

Candidate gene association mapping for winter survival and spring regrowth in perennial ryegrass

USDA-ARS?s Scientific Manuscript database

Perennial ryegrass (Lolium perenne L.) is a widely cultivated cool-season grass species because of its high quality for forage and turf. Susceptibility to freezing damage limits its further use in temperate zones. The objective of this study was to identify candidate genes significantly associated w...

Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize

USDA-ARS?s Scientific Manuscript database

A genome-wide association study (GWAS) is the foremost strategy used for finding genes that control human diseases and agriculturally important traits, but it often reports false positives. In contrast, its complementary method, linkage analysis, provides direct genetic confirmation, but with limite...

Brain-Wide Maps of "Fos" Expression during Fear Learning and Recall

ERIC Educational Resources Information Center

Cho, Jin-Hyung; Rendall, Sam D.; Gray, Jesse M.

2017-01-01

"Fos" induction during learning labels neuronal ensembles in the hippocampus that encode a specific physical environment, revealing a memory trace. In the cortex and other regions, the extent to which "Fos" induction during learning reveals specific sensory representations is unknown. Here we generate high-quality brain-wide…

The Aeroflex: A Bicycle for Mobile Air Quality Measurements

PubMed Central

Elen, Bart; Peters, Jan; Van Poppel, Martine; Bleux, Nico; Theunis, Jan; Reggente, Matteo; Standaert, Arnout

2013-01-01

Fixed air quality stations have limitations when used to assess people's real life exposure to air pollutants. Their spatial coverage is too limited to capture the spatial variability in, e.g., an urban or industrial environment. Complementary mobile air quality measurements can be used as an additional tool to fill this void. In this publication we present the Aeroflex, a bicycle for mobile air quality monitoring. The Aeroflex is equipped with compact air quality measurement devices to monitor ultrafine particle number counts, particulate mass and black carbon concentrations at a high resolution (up to 1 second). Each measurement is automatically linked to its geographical location and time of acquisition using GPS and Internet time. Furthermore, the Aeroflex is equipped with automated data transmission, data pre-processing and data visualization. The Aeroflex is designed with adaptability, reliability and user friendliness in mind. Over the past years, the Aeroflex has been successfully used for high resolution air quality mapping, exposure assessment and hot spot identification. PMID:23262484

The Aeroflex: a bicycle for mobile air quality measurements.

PubMed

Elen, Bart; Peters, Jan; Poppel, Martine Van; Bleux, Nico; Theunis, Jan; Reggente, Matteo; Standaert, Arnout

2012-12-24

Fixed air quality stations have limitations when used to assess people's real life exposure to air pollutants. Their spatial coverage is too limited to capture the spatial variability in, e.g., an urban or industrial environment. Complementary mobile air quality measurements can be used as an additional tool to fill this void. In this publication we present the Aeroflex, a bicycle for mobile air quality monitoring. The Aeroflex is equipped with compact air quality measurement devices to monitor ultrafine particle number counts, particulate mass and black carbon concentrations at a high resolution (up to 1 second). Each measurement is automatically linked to its geographical location and time of acquisition using GPS and Internet time. Furthermore, the Aeroflex is equipped with automated data transmission, data pre-processing and data visualization. The Aeroflex is designed with adaptability, reliability and user friendliness in mind. Over the past years, the Aeroflex has been successfully used for high resolution air quality mapping, exposure assessment and hot spot identification. 

Using genotyping-by-sequencing to develop broccoli markers for construction of a high-density linkage map and to identify quantitative trait loci associated with heat tolerance

USDA-ARS?s Scientific Manuscript database

Heat stress reduces the yield and quality of broccoli heads imposing seasonal and geographic limits to broccoli production. For the most part, the risk of producing broccoli with head defects (uneven beads, bracts in heads, etc.) induced by high temperatures has restricted commercial production in t...

A Map of Kilometer-Scale Topographic Roughness of Mercury

NASA Astrophysics Data System (ADS)

Kreslavsky, M. A.; Head, J. W., III; Kokhanov, A. A.; Neumann, G. A.; Smith, D. E.; Zuber, M. T.; Kozlova, N. A.

2014-12-01

We present a new map of the multiscale topographic roughness of the northern circumpolar area of Mercury. The map utilizes high internal vertical precision surface ranging by the laser altimeter MLA onboard MESSENGER mission to Mercury. This map is analogous to global roughness maps that had been created by M.A.K. with collaborators for Mars (MOLA data) and the Moon (LOLA data). As measures of roughness, we used the interquartile range of along-track profile curvature at three baselines: 0.7 km, 2.8 km, and 11 km. Unlike in the cases of LOLA data for the Moon, and MOLA data for Mars, the MLA data allow high-quality roughness mapping only for a small part of the surface of the planet: the map covers 65N - 84N latitude zone, where the density of MLA data is the highest. The map captures the regional variations of the typical background topographic texture of the surface. The map shows the clear dichotomy between smooth northern plains and rougher cratered terrains. The lowered contrast of this dichotomy at the shortest (0.7 km) baseline indicates that regolith on Mercury is thicker and/or gardening processes are more intensive in comparison to the Moon, approximately by a factor of three. The map reveals sharp roughness contrasts within northern plains of Mercury that we interpret as geologic boundaries of volcanic plains of different age. In particular, the map suggests a younger volcanic plains unit inside Goethe basin and inside another unnamed stealth basin. -- Acknowledgement: Work on data processing was carried out at MIIGAiK by MAK, AAK, NAK and supported by Russian Science Foundation project 14-22-00197.

Quality and physiological responses of two late-season sweet cherry cultivars 'Lapins' and 'Skeena' to modified atmosphere packaging (MAP) during simulated long distance ocean shipping

USDA-ARS?s Scientific Manuscript database

Flavor loss, skin darkening, pitting, splitting, pedicel browning, and decay are the major quality deteriorations in sweet cherries during storage/shipping. In this research, three modified atmosphere packaging (MAP) liners with varied gas permeability were evaluated for the effect on quality deteri...

Effect of modified atmosphere packaging on quality and shelf life of 'Robusta' banana (Musa sp.) stored at low temperature.

PubMed

Kudachikar, V B; Kulkarni, S G; Prakash, M N Keshava

2011-06-01

Banana (Musa sp var. 'Robusta') stored under active and passive modified atmosphere packaging (MAP) at 12 ± 1°C and 85-90% RH for 2 seasons were evaluated for fruit quality and shelf-life. A steady state of about 8.6 and 8.2% of CO2 and 2.8 and 2.6% of O2 in passive MAP and MAP+GK (Green Keeper) packages, respectively, were established after 3 weeks of storage. Passive MAP and MAP+GK treatments of banana resulted in reduction in physiological loss in weight (PLW) of 0.7 and 0.8% after 5 and 7 weeks of storage, respectively as against 5% PLW in openly kept green banana after 3 weeks. Both MAP and MAP+GK treatments delayed colour, texture, pulp to peel ratio and total soluble solids (TSS) content as compared to openly kept control banana. Results indicated that the shelf life of fruits packed under MAP and MAP+GK could be extended up to 5 and 7 weeks, respectively as compared to 3 weeks for openly kept control fruits. Sensory quality of fully ripe fruits of both passive MAP and MAP+GK treatments, 5 days after ethrel dip was very good. Thus, MAP+GK at 12 ± 1°C and 85-90% RH could be commercially used for long term storage and long distance transportation of banana with maximum shelf-life of 7 weeks.

High quality transmission Kikuchi diffraction analysis of deformed alloys - Case study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tokarski, Tomasz, E-mail: tokarski@agh.edu.pl

Modern scanning electron microscopes (SEM) equipped with thermally assisted field emission guns (Schottky FEG) are capable of imaging with a resolution in the range of several nanometers or better. Simultaneously, the high electron beam current can be used, which enables fast chemical and crystallographic analysis with a higher resolution than is normally offered by SEM with a tungsten cathode. The current resolution that limits the EDS and EBSD analysis is related to materials' physics, particularly to the electron-specimen interaction volume. The application of thin, electron-transparent specimens, instead of bulk samples, improves the resolution and allows for the detailed analysis ofmore » very fine microstructural features. Beside the typical imaging mode, it is possible to use a standard EBSD camera in such a configuration that only transmitted and scattered electrons are detected. This modern approach was successfully applied to various materials giving rise to significant resolution improvement, especially for the light element magnesium based alloys. This paper presents an insight into the application of the transmission Kikuchi diffraction (TKD) technique applied to the most troublesome, heavily-deformed materials. In particular, the values of the highest possible acquisition rates for high resolution and high quality mapping were estimated within typical imaging conditions of stainless steel and magnesium-yttrium alloy. - Highlights: •Monte Carlo simulations were used to simulate EBSD camera intensity for various measuring conditions. •Transmission Kikuchi diffraction parameters were evaluated for highly deformed, light and heavy elements based alloys. •High quality maps with 20 nm spatial resolution were acquired for Mg and Fe based alloys. •High speed TKD measurements were performed at acquisition rates comparable to the reflection EBSD.« less

Some Comments on Mapping from Disease-Specific to Generic Health-Related Quality-of-Life Scales

PubMed Central

Palta, Mari

2013-01-01

An article by Lu et al. in this issue of Value in Health addresses the mapping of treatment or group differences in disease-specific measures (DSMs) of health-related quality of life onto differences in generic health-related quality-of-life scores, with special emphasis on how the mapping is affected by the reliability of the DSM. In the proposed mapping, a factor analytic model defines a conversion factor between the scores as the ratio of factor loadings. Hence, the mapping applies to convert true underlying scales and has desirable properties facilitating the alignment of instruments and understanding their relationship in a coherent manner. It is important to note, however, that when DSM means or differences in mean DSMs are estimated, their mapping is still of a measurement error–prone predictor, and the correct conversion coefficient is the true mapping multiplied by the reliability of the DSM in the relevant sample. In addition, the proposed strategy for estimating the factor analytic mapping in practice requires assumptions that may not hold. We discuss these assumptions and how they may be the reason we obtain disparate estimates of the mapping factor in an application of the proposed methods to groups of patients. PMID:23337233

Improving the quality of mass produced maps

USGS Publications Warehouse

Simley, J.

2001-01-01

Quality is critical in cartography because key decisions are often made based on the information the map communicates. The mass production of digital cartographic information to support geographic information science has now added a new dimension to the problem of cartographic quality, as problems once limited to small volumes can now proliferate in mass production programs. These problems can also affect the economics of map production by diverting a sizeable portion of production cost to pay for rework on maps with poor quality. Such problems are common to general industry-in response, the quality engineering profession has developed a number of successful methods to overcome these problems. Two important methods are the reduction of error through statistical analysis and addressing the quality environment in which people work. Once initial and obvious quality problems have been solved, outside influences periodically appear that cause adverse variations in quality and consequently increase production costs. Such errors can be difficult to detect before the customer is affected. However, a number of statistical techniques can be employed to detect variation so that the problem is eliminated before significant damage is caused. Additionally, the environment in which the workforce operates must be conductive to quality. Managers have a powerful responsibility to create this environment. Two sets of guidelines, known as Deming's Fourteen Points and ISO-9000, provide models for this environment.

A multi-part matching strategy for mapping LOINC with laboratory terminologies

PubMed Central

Lee, Li-Hui; Groß, Anika; Hartung, Michael; Liou, Der-Ming; Rahm, Erhard

2014-01-01

Objective To address the problem of mapping local laboratory terminologies to Logical Observation Identifiers Names and Codes (LOINC). To study different ontology matching algorithms and investigate how the probability of term combinations in LOINC helps to increase match quality and reduce manual effort. Materials and methods We proposed two matching strategies: full name and multi-part. The multi-part approach also considers the occurrence probability of combined concept parts. It can further recommend possible combinations of concept parts to allow more local terms to be mapped. Three real-world laboratory databases from Taiwanese hospitals were used to validate the proposed strategies with respect to different quality measures and execution run time. A comparison with the commonly used tool, Regenstrief LOINC Mapping Assistant (RELMA) Lab Auto Mapper (LAM), was also carried out. Results The new multi-part strategy yields the best match quality, with F-measure values between 89% and 96%. It can automatically match 70–85% of the laboratory terminologies to LOINC. The recommendation step can further propose mapping to (proposed) LOINC concepts for 9–20% of the local terminology concepts. On average, 91% of the local terminology concepts can be correctly mapped to existing or newly proposed LOINC concepts. Conclusions The mapping quality of the multi-part strategy is significantly better than that of LAM. It enables domain experts to perform LOINC matching with little manual work. The probability of term combinations proved to be a valuable strategy for increasing the quality of match results, providing recommendations for proposed LOINC conepts, and decreasing the run time for match processing. PMID:24363318

Integrationof Remote Sensing and Geographic information system in Ground Water Quality Assessment and Management

NASA Astrophysics Data System (ADS)

Shakak, N.

2015-04-01

Spatial variations in ground water quality in the Khartoum state, Sudan, have been studied using geographic information system (GIS) and remote sensing technique. Gegraphical informtion system a tool which is used for storing, analyzing and displaying spatial data is also used for investigating ground water quality information. Khartoum landsat mosac image aquired in 2013was used, Arc/Gis software applied to extract the boundary of the study area, the image was classified to create land use/land cover map. The land use map,geological and soil map are used for correlation between land use , geological formations, and soil types to understand the source of natural pollution that can lower the ground water quality. For this study, the global positioning system (GPS), used in the field to identify the borehole location in a three dimentional coordinate (Latitude, longitude, and altitude), water samples were collected from 156 borehole wells, and analyzed for physico-chemical parameters like electrical conductivity, Total dissolved solid,Chloride, Nitrate, Sodium, Magnisium, Calcium,and Flouride, using standard techniques in the laboratory and compared with the standards.The ground water quality maps of the entire study area have been prepared using spatial interpolation technique for all the above parameters.then the created maps used to visualize, analyze, and understand the relationship among the measured points. Mapping was coded for potable zones, non-potable zones in the study area, in terms of water quality sutability for drinking water and sutability for irrigation. In general satellite remote sensing in conjunction with geographical information system (GIS) offers great potential for water resource development and management.

Super-chilling (-0.7°C) with high-CO2 packaging inhibits biochemical changes of microbial origin in catfish (Clarias gariepinus) muscle during storage.

PubMed

Zhu, Yingchun; Ma, Lizhen; Yang, Hua; Xiao, Yan; Xiong, Youling L

2016-09-01

Controlled freezing-point storage (CFPS) is an emerging preservative technique desirable for fish. In the present study, catfish fillets were stored at -0.7°C under different packaging atmospheres: air (AP), vacuum (VP), and 60% CO2/40% N2 (MAP). Chemical, microbiological, and sensory analyses were performed during storage. Results showed the following descending order of chemical changes (degradation of nucleotides, conversion of protein to volatile-based nitrogen and biogenic amines, and production of trimethylamine nitrogen), as well as loss of sensory properties: 4°C AP>-0.7°C AP≈4°C VP>-0.7°C VP≈4°C MAP>-0.7°C MAP. The chemical changes were well-correlated with microbial growth suggesting the microbiological pathways. Hence, CFPS at -0.7°C in combination with high-CO2 MAP can effectively maintain the quality of fresh catfish meat compared to traditional preservation methods. Copyright © 2016 Elsevier Ltd. All rights reserved.

Global motion compensated visual attention-based video watermarking

NASA Astrophysics Data System (ADS)

Oakes, Matthew; Bhowmik, Deepayan; Abhayaratne, Charith

2016-11-01

Imperceptibility and robustness are two key but complementary requirements of any watermarking algorithm. Low-strength watermarking yields high imperceptibility but exhibits poor robustness. High-strength watermarking schemes achieve good robustness but often suffer from embedding distortions resulting in poor visual quality in host media. This paper proposes a unique video watermarking algorithm that offers a fine balance between imperceptibility and robustness using motion compensated wavelet-based visual attention model (VAM). The proposed VAM includes spatial cues for visual saliency as well as temporal cues. The spatial modeling uses the spatial wavelet coefficients while the temporal modeling accounts for both local and global motion to arrive at the spatiotemporal VAM for video. The model is then used to develop a video watermarking algorithm, where a two-level watermarking weighting parameter map is generated from the VAM saliency maps using the saliency model and data are embedded into the host image according to the visual attentiveness of each region. By avoiding higher strength watermarking in the visually attentive region, the resulting watermarked video achieves high perceived visual quality while preserving high robustness. The proposed VAM outperforms the state-of-the-art video visual attention methods in joint saliency detection and low computational complexity performance. For the same embedding distortion, the proposed visual attention-based watermarking achieves up to 39% (nonblind) and 22% (blind) improvement in robustness against H.264/AVC compression, compared to existing watermarking methodology that does not use the VAM. The proposed visual attention-based video watermarking results in visual quality similar to that of low-strength watermarking and a robustness similar to those of high-strength watermarking.

Understanding critical factors for the quality and shelf-life of MAP fresh meat: a review.

PubMed

Singh, Preeti; Wani, Ali Abas; Saengerlaub, Sven; Langowski, Horst-Christian

2011-02-01

Due to increased demands for greater stringency in relation to hygiene and safety issues associated with fresh food products, coupled with ever-increasing demands by retailers for cost-effective extensions to product shelf-lives and the requirement to meet consumer expectations in relation to convenience and quality, the food packaging industry has rapidly developed to meet and satisfy expectations. One of the areas of research that has shown promise, and had success, is modified atmosphere packaging (MAP). The success of MAP-fresh meat depends on many factors including good initial product quality, good hygiene from the source plants, correct packaging material selection, the appropriate gas mix for the product, reliable packaging equipment, and maintenance of controlled temperatures and humidity levels. Advances in plastic materials and equipment have propelled advances in MAP, but other technological and logistical considerations are needed for successful MAP systems for raw chilled meat. Although several parameters critical for the quality of MA packed meat have been studied and each found to be crucial, understanding of the interactions between the parameters is needed. This review was undertaken to present the most comprehensive and current overview of the widely available, scattered information about the various integrated critical factors responsible for the quality and shelf life of MA packed meat with an interest to stimulate further research to optimize different quality parameters.

Galactic reddening in 3D from stellar photometry - an improved map

NASA Astrophysics Data System (ADS)

Green, Gregory M.; Schlafly, Edward F.; Finkbeiner, Douglas; Rix, Hans-Walter; Martin, Nicolas; Burgett, William; Draper, Peter W.; Flewelling, Heather; Hodapp, Klaus; Kaiser, Nicholas; Kudritzki, Rolf-Peter; Magnier, Eugene A.; Metcalfe, Nigel; Tonry, John L.; Wainscoat, Richard; Waters, Christopher

2018-07-01

We present a new 3D map of interstellar dust reddening, covering three quarters of the sky (declinations of δ ≳ -30°) out to a distance of several kiloparsecs. The map is based on high-quality stellar photometry of 800 million stars from Pan-STARRS 1 and 2MASS. We divide the sky into sightlines containing a few hundred stars each, and then infer stellar distances and types, along with the line-of-sight dust distribution. Our new map incorporates a more accurate average extinction law and an additional 1.5 yr of Pan-STARRS 1 data, tracing dust to greater extinctions and at higher angular resolutions than our previous map. Out of the plane of the Galaxy, our map agrees well with 2D reddening maps derived from far-infrared dust emission. After accounting for a 25 per cent difference in scale, we find a mean scatter of ˜10 per cent between our map and the Planck far-infrared emission-based dust map, out to a depth of 0.8 mag in E(gP1 - rP1), with the level of agreement varying over the sky. Our map can be downloaded at http://argonaut.skymaps.info, or from the Harvard Dataverse (Green 2017).

Performance of 3DOSEM and MAP algorithms for reconstructing low count SPECT acquisitions.

PubMed

Grootjans, Willem; Meeuwis, Antoi P W; Slump, Cornelis H; de Geus-Oei, Lioe-Fee; Gotthardt, Martin; Visser, Eric P

2016-12-01

Low count single photon emission computed tomography (SPECT) is becoming more important in view of whole body SPECT and reduction of radiation dose. In this study, we investigated the performance of several 3D ordered subset expectation maximization (3DOSEM) and maximum a posteriori (MAP) algorithms for reconstructing low count SPECT images. Phantom experiments were conducted using the National Electrical Manufacturers Association (NEMA) NU2 image quality (IQ) phantom. The background compartment of the phantom was filled with varying concentrations of pertechnetate and indiumchloride, simulating various clinical imaging conditions. Images were acquired using a hybrid SPECT/CT scanner and reconstructed with 3DOSEM and MAP reconstruction algorithms implemented in Siemens Syngo MI.SPECT (Flash3D) and Hermes Hybrid Recon Oncology (Hyrid Recon 3DOSEM and MAP). Image analysis was performed by calculating the contrast recovery coefficient (CRC),percentage background variability (N%), and contrast-to-noise ratio (CNR), defined as the ratio between CRC and N%. Furthermore, image distortion is characterized by calculating the aspect ratio (AR) of ellipses fitted to the hot spheres. Additionally, the performance of these algorithms to reconstruct clinical images was investigated. Images reconstructed with 3DOSEM algorithms demonstrated superior image quality in terms of contrast and resolution recovery when compared to images reconstructed with filtered-back-projection (FBP), OSEM and 2DOSEM. However, occurrence of correlated noise patterns and image distortions significantly deteriorated the quality of 3DOSEM reconstructed images. The mean AR for the 37, 28, 22, and 17mm spheres was 1.3, 1.3, 1.6, and 1.7 respectively. The mean N% increase in high and low count Flash3D and Hybrid Recon 3DOSEM from 5.9% and 4.0% to 11.1% and 9.0%, respectively. Similarly, the mean CNR decreased in high and low count Flash3D and Hybrid Recon 3DOSEM from 8.7 and 8.8 to 3.6 and 4.2, respectively. Regularization with smoothing priors could suppress these noise patterns at the cost of reduced image contrast. The mean N% was 6.4% and 6.8% for low count QSP and MRP MAP reconstructed images. Alternatively, regularization with an anatomical Bowhser prior resulted in sharp images with high contrast, limited image distortion, and low N% of 8.3% in low count images, although some image artifacts did occur. Analysis of clinical images suggested that the same effects occur in clinical imaging. Image quality of low count SPECT acquisitions reconstructed with modern 3DOSEM algorithms is deteriorated by the occurrence of correlated noise patterns and image distortions. The artifacts observed in the phantom experiments can also occur in clinical imaging. Copyright © 2015. Published by Elsevier GmbH.

Cartographic quality of ERTS-1 images

NASA Technical Reports Server (NTRS)

Welch, R. I.

1973-01-01

Analyses of simulated and operational ERTS images have provided initial estimates of resolution, ground resolution, detectability thresholds and other measures of image quality of interest to earth scientists and cartographers. Based on these values, including an approximate ground resolution of 250 meters for both RBV and MSS systems, the ERTS-1 images appear suited to the production and/or revision of planimetric and photo maps of 1:500,000 scale and smaller for which map accuracy standards are compatible with the imaged detail. Thematic mapping, although less constrained by map accuracy standards, will be influenced by measurement thresholds and errors which have yet to be accurately determined for ERTS images. This study also indicates the desirability of establishing a quantitative relationship between image quality values and map products which will permit both engineers and cartographers/earth scientists to contribute to the design requirements of future satellite imaging systems.

High-speed atomic force microscopy and peak force tapping control

NASA Astrophysics Data System (ADS)

Hu, Shuiqing; Mininni, Lars; Hu, Yan; Erina, Natalia; Kindt, Johannes; Su, Chanmin

2012-03-01

ITRS Roadmap requires defect size measurement below 10 nanometers and challenging classifications for both blank and patterned wafers and masks. Atomic force microscope (AFM) is capable of providing metrology measurement in 3D at sub-nanometer accuracy but has long suffered from drawbacks in throughput and limitation of slow topography imaging without chemical information. This presentation focus on two disruptive technology developments, namely high speed AFM and quantitative nanomechanical mapping, which enables high throughput measurement with capability of identifying components through concurrent physical property imaging. The high speed AFM technology has allowed the imaging speed increase by 10-100 times without loss of the data quality. Such improvement enables the speed of defect review on a wafer to increase from a few defects per hour to nearly 100 defects an hour, approaching the requirements of ITRS Roadmap. Another technology development, Peak Force Tapping, substantially simplified the close loop system response, leading to self-optimization of most challenging samples groups to generate expert quality data. More importantly, AFM also simultaneously provides a series of mechanical property maps with a nanometer spatial resolution during defect review. These nanomechanical maps (including elastic modulus, hardness, and surface adhesion) provide complementary information for elemental analysis, differentiate defect materials by their physical properties, and assist defect classification beyond topographic measurements. This paper will explain the key enabling technologies, namely high speed tip-scanning AFM using innovative flexure design and control algorithm. Another critical element is AFM control using Peak Force Tapping, in which the instantaneous tip-sample interaction force is measured and used to derive a full suite of physical properties at each imaging pixel. We will provide examples of defect review data on different wafers and media disks. The similar AFM-based defect review capacity was also applied to EUV masks.

Macromolecule mapping of the brain using ultrashort-TE acquisition and reference-based metabolite removal.

PubMed

Lam, Fan; Li, Yudu; Clifford, Bryan; Liang, Zhi-Pei

2018-05-01

To develop a practical method for mapping macromolecule distribution in the brain using ultrashort-TE MRSI data. An FID-based chemical shift imaging acquisition without metabolite-nulling pulses was used to acquire ultrashort-TE MRSI data that capture the macromolecule signals with high signal-to-noise-ratio (SNR) efficiency. To remove the metabolite signals from the ultrashort-TE data, single voxel spectroscopy data were obtained to determine a set of high-quality metabolite reference spectra. These spectra were then incorporated into a generalized series (GS) model to represent general metabolite spatiospectral distributions. A time-segmented algorithm was developed to back-extrapolate the GS model-based metabolite distribution from truncated FIDs and remove it from the MRSI data. Numerical simulations and in vivo experiments have been performed to evaluate the proposed method. Simulation results demonstrate accurate metabolite signal extrapolation by the proposed method given a high-quality reference. For in vivo experiments, the proposed method is able to produce spatiospectral distributions of macromolecules in the brain with high SNR from data acquired in about 10 minutes. We further demonstrate that the high-dimensional macromolecule spatiospectral distribution resides in a low-dimensional subspace. This finding provides a new opportunity to use subspace models for quantification and accelerated macromolecule mapping. Robustness of the proposed method is also demonstrated using multiple data sets from the same and different subjects. The proposed method is able to obtain macromolecule distributions in the brain from ultrashort-TE acquisitions. It can also be used for acquiring training data to determine a low-dimensional subspace to represent the macromolecule signals for subspace-based MRSI. Magn Reson Med 79:2460-2469, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Spatial Quality Evaluation of Resampled Unmanned Aerial Vehicle-Imagery for Weed Mapping.

PubMed

Borra-Serrano, Irene; Peña, José Manuel; Torres-Sánchez, Jorge; Mesas-Carrascosa, Francisco Javier; López-Granados, Francisca

2015-08-12

Unmanned aerial vehicles (UAVs) combined with different spectral range sensors are an emerging technology for providing early weed maps for optimizing herbicide applications. Considering that weeds, at very early phenological stages, are similar spectrally and in appearance, three major components are relevant: spatial resolution, type of sensor and classification algorithm. Resampling is a technique to create a new version of an image with a different width and/or height in pixels, and it has been used in satellite imagery with different spatial and temporal resolutions. In this paper, the efficiency of resampled-images (RS-images) created from real UAV-images (UAV-images; the UAVs were equipped with two types of sensors, i.e., visible and visible plus near-infrared spectra) captured at different altitudes is examined to test the quality of the RS-image output. The performance of the object-based-image-analysis (OBIA) implemented for the early weed mapping using different weed thresholds was also evaluated. Our results showed that resampling accurately extracted the spectral values from high spatial resolution UAV-images at an altitude of 30 m and the RS-image data at altitudes of 60 and 100 m, was able to provide accurate weed cover and herbicide application maps compared with UAV-images from real flights.

Spatial Quality Evaluation of Resampled Unmanned Aerial Vehicle-Imagery for Weed Mapping

PubMed Central

Borra-Serrano, Irene; Peña, José Manuel; Torres-Sánchez, Jorge; Mesas-Carrascosa, Francisco Javier; López-Granados, Francisca

2015-01-01

Unmanned aerial vehicles (UAVs) combined with different spectral range sensors are an emerging technology for providing early weed maps for optimizing herbicide applications. Considering that weeds, at very early phenological stages, are similar spectrally and in appearance, three major components are relevant: spatial resolution, type of sensor and classification algorithm. Resampling is a technique to create a new version of an image with a different width and/or height in pixels, and it has been used in satellite imagery with different spatial and temporal resolutions. In this paper, the efficiency of resampled-images (RS-images) created from real UAV-images (UAV-images; the UAVs were equipped with two types of sensors, i.e., visible and visible plus near-infrared spectra) captured at different altitudes is examined to test the quality of the RS-image output. The performance of the object-based-image-analysis (OBIA) implemented for the early weed mapping using different weed thresholds was also evaluated. Our results showed that resampling accurately extracted the spectral values from high spatial resolution UAV-images at an altitude of 30 m and the RS-image data at altitudes of 60 and 100 m, was able to provide accurate weed cover and herbicide application maps compared with UAV-images from real flights. PMID:26274960

Texturing of continuous LOD meshes with the hierarchical texture atlas

NASA Astrophysics Data System (ADS)

Birkholz, Hermann

2006-02-01

For the rendering of detailed virtual environments, trade-offs have to be made between image quality and rendering time. An immersive experience of virtual reality always demands high frame-rates with the best reachable image qual-ity. Continuous Level of Detail (cLoD) triangle-meshes provide an continuous spectrum of detail for a triangle mesh that can be used to create view-dependent approximations of the environment in real-time. This enables the rendering with a constant number of triangles and thus with constant frame-rates. Normally the construction of such cLoD mesh representations leads to the loss of all texture information of the original mesh. To overcome this problem, a parameter domain can be created, in order to map the surface properties (colour, texture, normal) to it. This parameter domain can be used to map the surface properties back to arbitrary approximations of the original mesh. The parameter domain is often a simplified version of the mesh to be parameterised. This limits the reachable simplification to the domain mesh which has to map the surface of the original mesh with the least possible stretch. In this paper, a hierarchical domain mesh is presented, that scales between very coarse domain meshes and good property-mapping.

Agricultural Land Use mapping by multi-sensor approach for hydrological water quality monitoring

NASA Astrophysics Data System (ADS)

Brodsky, Lukas; Kodesova, Radka; Kodes, Vit

2010-05-01

The main objective of this study is to demonstrate potential of operational use of the high and medium resolution remote sensing data for hydrological water quality monitoring by mapping agriculture intensity and crop structures. In particular use of remote sensing mapping for optimization of pesticide monitoring. The agricultural mapping task is tackled by means of medium spatial and high temporal resolution ESA Envisat MERIS FR images together with single high spatial resolution IRS AWiFS image covering the whole area of interest (the Czech Republic). High resolution data (e.g. SPOT, ALOS, Landsat) are often used for agricultural land use classification, but usually only at regional or local level due to data availability and financial constraints. AWiFS data (nominal spatial resolution 56 m) due to the wide satellite swath seems to be more suitable for use at national level. Nevertheless, one of the critical issues for such a classification is to have sufficient image acquisitions over the whole vegetation period to describe crop development in appropriate way. ESA MERIS middle-resolution data were used in several studies for crop classification. The high temporal and also spectral resolution of MERIS data has indisputable advantage for crop classification. However, spatial resolution of 300 m results in mixture signal in a single pixel. AWiFS-MERIS data synergy brings new perspectives in agricultural Land Use mapping. Also, the developed methodology procedure is fully compatible with future use of ESA (GMES) Sentinel satellite images. The applied methodology of hybrid multi-sensor approach consists of these main stages: a/ parcel segmentation and spectral pre-classification of high resolution image (AWiFS); b/ ingestion of middle resolution (MERIS) vegetation spectro-temporal features; c/ vegetation signatures unmixing; and d/ semantic object-oriented classification of vegetation classes into final classification scheme. These crop groups were selected to be classified: winter crops, spring crops, oilseed rape, legumes, summer and other crops. This study highlights operational potentials of high temporal full resolution MERIS images in agricultural land use monitoring. Practical application of this methodology is foreseen, among others, in the water quality monitoring. Effective pesticide monitoring relies also on spatial distribution of applied pesticides, which can be derived from crop - plant protection product relationship. Knowledge of areas with predominant occurrence of specific crop based on remote sensing data described above can be used for a forecast of probable plant protection product application, thus cost-effective pesticide monitoring. The remote sensing data used on a continuous basis can be used in other long-term water management issues and provide valuable data for decision makers. Acknowledgement: Authors acknowledge the financial support of the Ministry of Education, Youth and Sports of the Czech Republic (grants No. 2B06095 and No. MSM 6046070901). The study was also supported by ESA CAT-1 (ref. 4358) and SOSI projects (Spatial Observation Services and Infrastructure; ref. GSTP-RTDA-EOPG-SW-08-0004).

Linking Air Quality and Human Health Effects Models: An Application to the Los Angeles Air Basin

PubMed Central

Stewart, Devoun R; Saunders, Emily; Perea, Roberto A; Fitzgerald, Rosa; Campbell, David E; Stockwell, William R

2017-01-01

Proposed emission control strategies for reducing ozone and particulate matter are evaluated better when air quality and health effects models are used together. The Community Multiscale Air Quality (CMAQ) model is the US Environmental Protection Agency’s model for determining public policy and forecasting air quality. CMAQ was used to forecast air quality changes due to several emission control strategies that could be implemented between 2008 and 2030 for the South Coast Air Basin that includes Los Angeles. The Environmental Benefits Mapping and Analysis Program—Community Edition (BenMAP-CE) was used to estimate health and economic impacts of the different emission control strategies based on CMAQ simulations. BenMAP-CE is a computer program based on epidemiologic studies that link human health and air quality. This modeling approach is better for determining optimum public policy than approaches that only examine concentration changes. PMID:29162976

Linking Air Quality and Human Health Effects Models: An Application to the Los Angeles Air Basin.

PubMed

Stewart, Devoun R; Saunders, Emily; Perea, Roberto A; Fitzgerald, Rosa; Campbell, David E; Stockwell, William R

2017-01-01

Proposed emission control strategies for reducing ozone and particulate matter are evaluated better when air quality and health effects models are used together. The Community Multiscale Air Quality (CMAQ) model is the US Environmental Protection Agency's model for determining public policy and forecasting air quality. CMAQ was used to forecast air quality changes due to several emission control strategies that could be implemented between 2008 and 2030 for the South Coast Air Basin that includes Los Angeles. The Environmental Benefits Mapping and Analysis Program-Community Edition (BenMAP-CE) was used to estimate health and economic impacts of the different emission control strategies based on CMAQ simulations. BenMAP-CE is a computer program based on epidemiologic studies that link human health and air quality. This modeling approach is better for determining optimum public policy than approaches that only examine concentration changes.

The State-of-the-art HST Astro-photometric Analysis of the Core of ω Centauri. II. Differential-reddening Map

NASA Astrophysics Data System (ADS)

Bellini, A.; Anderson, J.; van der Marel, R. P.; King, I. R.; Piotto, G.; Bedin, L. R.

2017-06-01

We take advantage of the exquisite quality of the Hubble Space Telescope astro-photometric catalog of the core of ωCen presented in the first paper of this series to derive a high-resolution, high-precision, high-accuracy differential-reddening map of the field. The map has a spatial resolution of 2 × 2 arcsec2 over a total field of view of about 4.‧3 × 4.‧3. The differential reddening itself is estimated via an iterative procedure using five distinct color-magnitude diagrams, which provided consistent results to within the 0.1% level. Assuming an average reddening value E(B - V) = 0.12, the differential reddening within the cluster’s core can vary by up to ±10%, with a typical standard deviation of about 4%. Our differential-reddening map is made available to the astronomical community in the form of a multi-extension FITS file. This differential-reddening map is essential for a detailed understanding of the multiple stellar populations of ωCen, as presented in the next paper in this series. Moreover, it provides unique insight into the level of small spatial-scale extinction variations in the Galactic foreground. Based on archival observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS 5-26555.

A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea

PubMed Central

Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D.; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C.L.L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23–47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea. PMID:26058368

High-resolution tree canopy mapping for New York City using LIDAR and object-based image analysis

NASA Astrophysics Data System (ADS)

MacFaden, Sean W.; O'Neil-Dunne, Jarlath P. M.; Royar, Anna R.; Lu, Jacqueline W. T.; Rundle, Andrew G.

2012-01-01

Urban tree canopy is widely believed to have myriad environmental, social, and human-health benefits, but a lack of precise canopy estimates has hindered quantification of these benefits in many municipalities. This problem was addressed for New York City using object-based image analysis (OBIA) to develop a comprehensive land-cover map, including tree canopy to the scale of individual trees. Mapping was performed using a rule-based expert system that relied primarily on high-resolution LIDAR, specifically its capacity for evaluating the height and texture of aboveground features. Multispectral imagery was also used, but shadowing and varying temporal conditions limited its utility. Contextual analysis was a key part of classification, distinguishing trees according to their physical and spectral properties as well as their relationships to adjacent, nonvegetated features. The automated product was extensively reviewed and edited via manual interpretation, and overall per-pixel accuracy of the final map was 96%. Although manual editing had only a marginal effect on accuracy despite requiring a majority of project effort, it maximized aesthetic quality and ensured the capture of small, isolated trees. Converting high-resolution LIDAR and imagery into usable information is a nontrivial exercise, requiring significant processing time and labor, but an expert system-based combination of OBIA and manual review was an effective method for fine-scale canopy mapping in a complex urban environment.

Review and critical appraisal of studies mapping from quality of life or clinical measures to EQ-5D: an online database and application of the MAPS statement.

PubMed

Dakin, Helen; Abel, Lucy; Burns, Richéal; Yang, Yaling

2018-02-12

The Health Economics Research Centre (HERC) Database of Mapping Studies was established in 2013, based on a systematic review of studies developing mapping algorithms predicting EQ-5D. The Mapping onto Preference-based measures reporting Standards (MAPS) statement was published in 2015 to improve reporting of mapping studies. We aimed to update the systematic review and assess the extent to which recently-published studies mapping condition-specific quality of life or clinical measures to the EQ-5D follow the guidelines published in the MAPS Reporting Statement. A published systematic review was updated using the original inclusion criteria to include studies published by December 2016. We included studies reporting novel algorithms mapping from any clinical measure or patient-reported quality of life measure to either the EQ-5D-3L or EQ-5D-5L. Titles and abstracts of all identified studies and the full text of papers published in 2016 were assessed against the MAPS checklist. The systematic review identified 144 mapping studies reporting 190 algorithms mapping from 110 different source instruments to EQ-5D. Of the 17 studies published in 2016, nine (53%) had titles that followed the MAPS statement guidance, although only two (12%) had abstracts that fully addressed all MAPS items. When the full text of these papers was assessed against the complete MAPS checklist, only two studies (12%) were found to fulfil or partly fulfil all criteria. Of the 141 papers (across all years) that included abstracts, the items on the MAPS statement checklist that were fulfilled by the largest number of studies comprised having a structured abstract (95%) and describing target instruments (91%) and source instruments (88%). The number of published mapping studies continues to increase. Our updated database provides a convenient way to identify mapping studies for use in cost-utility analysis. Most recent studies do not fully address all items on the MAPS checklist.

Evaluating HDR photos using Web 2.0 technology

NASA Astrophysics Data System (ADS)

Qiu, Guoping; Mei, Yujie; Duan, Jiang

2011-01-01

High dynamic range (HDR) photography is an emerging technology that has the potential to dramatically enhance the visual quality and realism of digital photos. One of the key technical challenges of HDR photography is displaying HDR photos on conventional devices through tone mapping or dynamic range compression. Although many different tone mapping techniques have been developed in recent years, evaluating tone mapping operators prove to be extremely difficult. Web2.0, social media and crowd-sourcing are emerging Internet technologies which can be harnessed to harvest the brain power of the mass to solve difficult problems in science, engineering and businesses. Paired comparison is used in the scientific study of preferences and attitudes and has been shown to be capable of obtaining an interval-scale ordering of items along a psychometric dimension such as preference or importance. In this paper, we exploit these technologies for evaluating HDR tone mapping algorithms. We have developed a Web2.0 style system that enables Internet users from anywhere to evaluate tone mapped HDR photos at any time. We adopt a simple paired comparison protocol, Internet users are presented a pair of tone mapped images and are simply asked to select the one that they think is better or click a "no difference" button. These user inputs are collected in the web server and analyzed by a rank aggregation algorithm which ranks the tone mapped photos according to the votes they received. We present experimental results which demonstrate that the emerging Internet technologies can be exploited as a new paradigm for evaluating HDR tone mapping algorithms. The advantages of this approach include the potential of collecting large user inputs under a variety of viewing environments rather than limited user participation under controlled laboratory environments thus enabling more robust and reliable quality assessment. We also present data analysis to correlate user generated qualitative indices with quantitative image statistics which may provide useful guidance for developing better tone mapping operators.

Modelling Soil Erosion in the Densu River Basin Using RUSLE and GIS Tools.

PubMed

Ashiagbori, G; Forkuo, E K; Laari, P; Aabeyir, R

2014-07-01

Soil erosion involves detachment and transport of soil particles from top soil layers, degrading soil quality and reducing the productivity of affected lands. Soil eroded from the upland catchment causes depletion of fertile agricultural land and the resulting sediment deposited at the river networks creates river morphological change and reservoir sedimentation problems. However, land managers and policy makers are more interested in the spatial distribution of soil erosion risk than in absolute values of soil erosion loss. The aim of this paper is to model the spatial distribution of soil erosion in Densu River Basin of Ghana using RUSLE and GIS tools and to use the model to explore the relationship between erosion susceptibility, slope and land use/land cover (LULC) in the Basin. The rainfall map, digital elevation model, soil type map, and land cover map, were input data in the soil erosion model developed. This model was then categorized into four different erosion risk classes. The developed soil erosion map was then overlaid with the slope and LULC maps of the study area to explore their effects on erosion susceptibility of the soil in the Densu River Basin. The Model, predicted 88% of the basin as low erosion risk and 6% as moderate erosion risk, 3% as high erosion risk and 3% as severe risk. The high and severe erosion areas were distributed mainly within the areas of high slope gradient and also sections of the moderate forest LULC class. Also, the areas within the moderate forest LULC class found to have high erosion risk, had an intersecting high erodibility soil group.

QTL detection for forage quality and stem histology in four connected mapping populations of the model legume Medicago truncatula.

PubMed

Lagunes Espinoza, Luz Del Carmen; Julier, Bernadette

2013-02-01

Forage quality combines traits related to protein content and energy value. High-quality forages contribute to increase farm autonomy by reducing the use of energy or protein-rich supplements. Genetic analyses in forage legume species are complex because of their tetraploidy and allogamy. Indeed, no genetic studies of quality have been published at the molecular level on these species. Nonetheless, mapping populations of the model species M. truncatula can be used to detect QTL for forage quality. Here, we studied a crossing design involving four connected populations of M. truncatula. Each population was composed of ca. 200 recombinant inbred lines (RIL). We sought population-specific QTL and QTL explaining the whole design variation. We grew parents and RIL in a greenhouse for 2 or 3 seasons and analysed plants for chemical composition of vegetative organs (protein content, digestibility, leaf-to-stem ratio) and stem histology (stem cross-section area, tissue proportions). Over the four populations and all the traits, QTL were found on all chromosomes. Among these QTL, only four genomic regions, on chromosomes 1, 3, 7 and 8, contributed to explaining the variations in the whole crossing design. Surprisingly, we found that quality QTL were located in the same genomic regions as morphological QTL. We thus confirmed the quantitative inheritance of quality traits and tight relationships between quality and morphology. Our findings could be explained by a co-location of genes involved in quality and morphology. This study will help to detect candidate genes involved in quantitative variation for quality in forage legume species.

Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome

PubMed Central

Petroli, César D.; Sansaloni, Carolina P.; Carling, Jason; Steane, Dorothy A.; Vaillancourt, René E.; Myburg, Alexander A.; da Silva, Orzenil Bonfim; Pappas, Georgios Joannis; Kilian, Andrzej; Grattapaglia, Dario

2012-01-01

Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization. PMID:22984541

High energy near- and far-field ptychographic tomography at the ESRF

NASA Astrophysics Data System (ADS)

da Silva, Julio C.; Haubrich, Jan; Requena, Guillermo; Hubert, Maxime; Pacureanu, Alexandra; Bloch, Leonid; Yang, Yang; Cloetens, Peter

2017-09-01

In high-resolution tomography, one needs high-resolved projections in order to reconstruct a high-quality 3D map of a sample. X-ray ptychography is a robust technique which can provide such high-resolution 2D projections taking advantage of coherent X-rays. This technique was used in the far-field regime for a fair amount of time, but it can now also be implemented in the near-field regime. In both regimes, the technique enables not only high-resolution imaging, but also high sensitivity to the electron density of the sample. The combination with tomography makes 3D imaging possible via ptychographic X-ray computed tomography (PXCT), which can provide a 3D map of the complex-valued refractive index of the sample. The extension of PXCT to X-ray energies above 15 keV is challenging, but it can allow the imaging of object opaque to lower energy. We present here the implementation and developments of high-energy near- and far-field PXCT at the ESRF.

Mapping by sequencing in cotton (Gossypium hirsutum) line MD52ne identified candidate genes for fiber strength and its related quality attributes

USDA-ARS?s Scientific Manuscript database

Fiber strength, length, maturity and fineness determine the market value of cotton fibers and the quality of spun yarn. Cotton fiber strength has been recognized as a critical quality attribute in the modern textile industry. Fine mapping along with quantitative trait loci (QTL) validation and candi...

Geographic information systems (GIS) spatial data compilation of geodynamic, tectonic, metallogenic, mineral deposit, and geophysical maps and associated descriptive data for northeast Asia

USGS Publications Warehouse

Naumova, Vera V.; Patuk, Mikhail I.; Kapitanchuk, Marina Yu.; Nokleberg, Warren J.; Khanchuk, Alexander I.; Parfenov, Leonid M.; Rodionov, Sergey M.; Miller, Robert J.; Diggles, Michael F.

2006-01-01

This is the online version of a CD-ROM publication. It contains all of the data that are on the disc but extra files have been removed: index files, software installers, and Windows autolaunch files. The purpose of this publication is to provide a high-quality spatial data compilation (Geographical Information System or GIS) of geodynamic, mineral deposit, and metallogenic belt maps, and descriptive data for Northeast Asia for customers and users. This area consists of Eastern Siberia, Russian Far East, Mongolia, northern China, South Korea, and Japan. The GIS compilation contains integrated spatial data for: (1) a geodynamics map at a scale of 1:5,000,000; (2) a mineral deposit location map; (3) metallogenic belt maps; (4) detailed descriptions of geologic units, including tectonostratigraphic terranes, cratons, major melange zones, and overlap assemblages, with references; (5) detailed descriptions of metallogenic belts with references; (6) detailed mineral deposit descriptions with references; and (7) page-size stratigraphic columns for major terranes.

A review of catalytic microwave pyrolysis of lignocellulosic biomass for value-added fuel and chemicals.

PubMed

Morgan, Hervan Marion; Bu, Quan; Liang, Jianghui; Liu, Yujing; Mao, Hanping; Shi, Aiping; Lei, Hanwu; Ruan, Roger

2017-04-01

Lignocellulosic biomass is an abundant renewable resource and can be efficiently converted into bio-energy by a bio-refinery. From the various techniques available for biomass thermo-chemical conversion; microwave assisted pyrolysis (MAP) seems to be the very promising. The principles of microwave technology were reviewed and the parameters for the efficient production of bio-oil using microwave technology were summarized. Microwave technology by itself cannot efficiently produce high quality bio-oil products, catalysts are used to improve the reaction conditions and selectivity for valued products during MAP. The catalysts used to optimize MAP are revised in the development of this article. The origins for bio-oils that are phenol rich or hydrocarbon rich are reviewed and their experimental results were summarized. The kinetics of MAP is discussed briefly in the development of the article. Future prospects and scientific development of MAP are also considered in the development of this article. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fully Convolutional Architecture for Low-Dose CT Image Noise Reduction

NASA Astrophysics Data System (ADS)

Badretale, S.; Shaker, F.; Babyn, P.; Alirezaie, J.

2017-10-01

One of the critical topics in medical low-dose Computed Tomography (CT) imaging is how best to maintain image quality. As the quality of images decreases with lowering the X-ray radiation dose, improving image quality is extremely important and challenging. We have proposed a novel approach to denoise low-dose CT images. Our algorithm learns directly from an end-to-end mapping from the low-dose Computed Tomography images for denoising the normal-dose CT images. Our method is based on a deep convolutional neural network with rectified linear units. By learning various low-level to high-level features from a low-dose image the proposed algorithm is capable of creating a high-quality denoised image. We demonstrate the superiority of our technique by comparing the results with two other state-of-the-art methods in terms of the peak signal to noise ratio, root mean square error, and a structural similarity index.

Multi-dimensional water quality assessment of an urban drinking water source elucidated by high resolution underwater towed vehicle mapping.

PubMed

Lock, Alan; Spiers, Graeme; Hostetler, Blair; Ray, James; Wallschläger, Dirk

2016-04-15

Spatial surveys of Ramsey Lake, Sudbury, Ontario water quality were conducted using an innovative underwater towed vehicle (UTV) equipped with a multi-parameter probe providing real-time water quality data. The UTV revealed underwater vent sites through high resolution monitoring of different spatial chemical characteristics using common sensors (turbidity, chloride, dissolved oxygen, and oxidation/reduction sensors) that would not be feasible with traditional water sampling methods. Multi-parameter probe vent site identification is supported by elevated alkalinity and silica concentrations at these sites. The identified groundwater vent sites appear to be controlled by bedrock fractures that transport water from different sources with different contaminants of concern. Elevated contaminants, such as, arsenic and nickel and/or nutrient concentrations are evident at the vent sites, illustrating the potential of these sources to degrade water quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mapping Skills and Activities with Children's Literature

ERIC Educational Resources Information Center

Gandy, S. Kay

2006-01-01

In the primary grades, maps are useful tools to help the young reader put stories into perspective. This article presents 18 quality children's books that contain maps or lessons about maps, as well as activities to use in the classroom to teach map skills. A table is included with ratings of the usability of the maps.

Identifier mapping performance for integrating transcriptomics and proteomics experimental results

PubMed Central

2011-01-01

Background Studies integrating transcriptomic data with proteomic data can illuminate the proteome more clearly than either separately. Integromic studies can deepen understanding of the dynamic complex regulatory relationship between the transcriptome and the proteome. Integrating these data dictates a reliable mapping between the identifier nomenclature resultant from the two high-throughput platforms. However, this kind of analysis is well known to be hampered by lack of standardization of identifier nomenclature among proteins, genes, and microarray probe sets. Therefore data integration may also play a role in critiquing the fallible gene identifications that both platforms emit. Results We compared three freely available internet-based identifier mapping resources for mapping UniProt accessions (ACCs) to Affymetrix probesets identifications (IDs): DAVID, EnVision, and NetAffx. Liquid chromatography-tandem mass spectrometry analyses of 91 endometrial cancer and 7 noncancer samples generated 11,879 distinct ACCs. For each ACC, we compared the retrieval sets of probeset IDs from each mapping resource. We confirmed a high level of discrepancy among the mapping resources. On the same samples, mRNA expression was available. Therefore, to evaluate the quality of each ACC-to-probeset match, we calculated proteome-transcriptome correlations, and compared the resources presuming that better mapping of identifiers should generate a higher proportion of mapped pairs with strong inter-platform correlations. A mixture model for the correlations fitted well and supported regression analysis, providing a window into the performance of the mapping resources. The resources have added and dropped matches over two years, but their overall performance has not changed. Conclusions The methods presented here serve to achieve concrete context-specific insight, to support well-informed decisions in choosing an ID mapping strategy for "omic" data merging. PMID:21619611

Using self-organizing maps to develop ambient air quality classifications: a time series example

PubMed Central

2014-01-01

Background Development of exposure metrics that capture features of the multipollutant environment are needed to investigate health effects of pollutant mixtures. This is a complex problem that requires development of new methodologies. Objective Present a self-organizing map (SOM) framework for creating ambient air quality classifications that group days with similar multipollutant profiles. Methods Eight years of day-level data from Atlanta, GA, for ten ambient air pollutants collected at a central monitor location were classified using SOM into a set of day types based on their day-level multipollutant profiles. We present strategies for using SOM to develop a multipollutant metric of air quality and compare results with more traditional techniques. Results Our analysis found that 16 types of days reasonably describe the day-level multipollutant combinations that appear most frequently in our data. Multipollutant day types ranged from conditions when all pollutants measured low to days exhibiting relatively high concentrations for either primary or secondary pollutants or both. The temporal nature of class assignments indicated substantial heterogeneity in day type frequency distributions (~1%-14%), relatively short-term durations (<2 day persistence), and long-term and seasonal trends. Meteorological summaries revealed strong day type weather dependencies and pollutant concentration summaries provided interesting scenarios for further investigation. Comparison with traditional methods found SOM produced similar classifications with added insight regarding between-class relationships. Conclusion We find SOM to be an attractive framework for developing ambient air quality classification because the approach eases interpretation of results by allowing users to visualize classifications on an organized map. The presented approach provides an appealing tool for developing multipollutant metrics of air quality that can be used to support multipollutant health studies. PMID:24990361

Association mapping analysis of fiber yield and quality traits in Upland cotton (Gossypium hirsutum L.).

PubMed

Ademe, Mulugeta Seyoum; He, Shoupu; Pan, Zhaoe; Sun, Junling; Wang, Qinglian; Qin, Hongde; Liu, Jinhai; Liu, Hui; Yang, Jun; Xu, Dongyong; Yang, Jinlong; Ma, Zhiying; Zhang, Jinbiao; Li, Zhikun; Cai, Zhongmin; Zhang, Xuelin; Zhang, Xin; Huang, Aifen; Yi, Xianda; Zhou, Guanyin; Li, Lin; Zhu, Haiyong; Pang, Baoyin; Wang, Liru; Jia, Yinhua; Du, Xiongming

2017-12-01

Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China. Three subpopulations were found after the estimation of population structure. The pair-wise kinship values varied from 0 to 0.867. Only 1.59% of the total marker locus pairs showed significant linkage disequilibrium (LD, p < 0.001). The genome-wide LD decayed within the genetic distance of ~30 to 32 cM at r 2  = 0.1, and decreased to ~1 to 2 cM at r 2  = 0.2, indicating the potential for association mapping. Analysis based on a mixed linear model detected 57 significant (p < 0.01) marker-trait associations, including seven associations for fiber length, ten for fiber micronaire, nine for fiber strength, eight for fiber elongation, five for fiber uniformity index, five for fiber uniformity ratio, six for boll weight and seven for lint percent, for a total of 35 SSR markers, of which 11 markers were associated with more than one trait. Among marker-trait associations, 24 associations coincided with the previously reported quantitative trait loci (QTLs), the remainder were newly identified QTLs/genes. The QTLs identified in this study will potentially facilitate improvement of fiber yield and quality in the future cotton molecular breeding programs.

New ShakeMaps for Georgia Resulting from Collaboration with EMME

NASA Astrophysics Data System (ADS)

Kvavadze, N.; Tsereteli, N. S.; Varazanashvili, O.; Alania, V.

2015-12-01

Correct assessment of probabilistic seismic hazard and risks maps are first step for advance planning and action to reduce seismic risk. Seismic hazard maps for Georgia were calculated based on modern approach that was developed in the frame of EMME (Earthquake Modl for Middle east region) project. EMME was one of GEM's successful endeavors at regional level. With EMME and GEM assistance, regional models were analyzed to identify the information and additional work needed for the preparation national hazard models. Probabilistic seismic hazard map (PSH) provides the critical bases for improved building code and construction. The most serious deficiency in PSH assessment for the territory of Georgia is the lack of high-quality ground motion data. Due to this an initial hybrid empirical ground motion model is developed for PGA and SA at selected periods. An application of these coefficients for ground motion models have been used in probabilistic seismic hazard assessment. Obtained results of seismic hazard maps show evidence that there were gaps in seismic hazard assessment and the present normative seismic hazard map needed a careful recalculation.

Geomatics for Mapping of Groundwater Potential Zones in Northern Part of the United Arab Emiratis - Sharjah City

NASA Astrophysics Data System (ADS)

Al-Ruzouq, R.; Shanableh, A.; Merabtene, T.

2015-04-01

In United Arab Emirates (UAE) domestic water consumption has increased rapidly over the last decade. The increased demand for high-quality water, create an urgent need to evaluate the groundwater production of aquifers. The development of a reasonable model for groundwater potential is therefore crucial for future systematic developments, efficient management, and sustainable use of groundwater resources. The objective of this study is to map the groundwater potential zones in northern part of UAE and assess the contributing factors for exploration of potential groundwater resources. Remote sensing data and geographic information system will be used to locate potential zones for groundwater. Various maps (i.e., base, soil, geological, Hydro-geological, Geomorphologic Map, structural, drainage, slope, land use/land cover and average annual rainfall map) will be prepared based on geospatial techniques. The groundwater availability of the basin will qualitatively classified into different classes based on its hydro-geo-morphological conditions. The land use/land cover map will be also prepared for the different seasons using a digital classification technique with a ground truth based on field investigation.

Fusion of Remote Sensing Methods, UAV Photogrammetry and LiDAR Scanning products for monitoring fluvial dynamics

NASA Astrophysics Data System (ADS)

Lendzioch, Theodora; Langhammer, Jakub; Hartvich, Filip

2015-04-01

Fusion of remote sensing data is a common and rapidly developing discipline, which combines data from multiple sources with different spatial and spectral resolution, from satellite sensors, aircraft and ground platforms. Fusion data contains more detailed information than each of the source and enhances the interpretation performance and accuracy of the source data and produces a high-quality visualisation of the final data. Especially, in fluvial geomorphology it is essential to get valuable images in sub-meter resolution to obtain high quality 2D and 3D information for a detailed identification, extraction and description of channel features of different river regimes and to perform a rapid mapping of changes in river topography. In order to design, test and evaluate a new approach for detection of river morphology, we combine different research techniques from remote sensing products to drone-based photogrammetry and LiDAR products (aerial LiDAR Scanner and TLS). Topographic information (e.g. changes in river channel morphology, surface roughness, evaluation of floodplain inundation, mapping gravel bars and slope characteristics) will be extracted either from one single layer or from combined layers in accordance to detect fluvial topographic changes before and after flood events. Besides statistical approaches for predictive geomorphological mapping and the determination of errors and uncertainties of the data, we will also provide 3D modelling of small fluvial features.

Evidence mapping based on systematic reviews of therapeutic interventions for gastrointestinal stromal tumors (GIST).

PubMed

Ballesteros, Mónica; Montero, Nadia; López-Pousa, Antonio; Urrútia, Gerard; Solà, Ivan; Rada, Gabriel; Pardo-Hernandez, Hector; Bonfill, Xavier

2017-09-07

Gastrointestinal Stromal Tumours (GISTs) are the most common mesenchymal tumours. Currently, different pharmacological and surgical options are used to treat localised and metastatic GISTs, although this research field is broad and the body of evidence is scattered and expanding. Our objectives are to identify, describe and organise the current available evidence for GIST through an evidence mapping approach. We followed the methodology of Global Evidence Mapping (GEM). We searched Pubmed, EMBASE, The Cochrane Library and Epistemonikos in order to identify systematic reviews (SRs) with or without meta-analyses published between 1990 and March 2016. Two authors assessed eligibility and extracted data. Methodological quality of the included systematic reviews was assessed using AMSTAR. We organised the results according to identified PICO questions and presented the evidence map in tables and a bubble plot. A total of 17 SRs met eligibility criteria. These reviews included 66 individual studies, of which three quarters were either observational or uncontrolled clinical trials. Overall, the quality of the included SRs was moderate or high. In total, we extracted 14 PICO questions from them and the corresponding results mostly favoured the intervention arm. The most common type of study used to evaluate therapeutic interventions in GIST sarcomas has been non-experimental studies. However, the majority of the interventions are reported as beneficial or probably beneficial by the respective authors of SRs. The evidence mapping is a useful and reliable methodology to identify and present the existing evidence about therapeutic interventions.

Crop biometric maps: the key to prediction.

PubMed

Rovira-Más, Francisco; Sáiz-Rubio, Verónica

2013-09-23

The sustainability of agricultural production in the twenty-first century, both in industrialized and developing countries, benefits from the integration of farm management with information technology such that individual plants, rows, or subfields may be endowed with a singular "identity." This approach approximates the nature of agricultural processes to the engineering of industrial processes. In order to cope with the vast variability of nature and the uncertainties of agricultural production, the concept of crop biometrics is defined as the scientific analysis of agricultural observations confined to spaces of reduced dimensions and known position with the purpose of building prediction models. This article develops the idea of crop biometrics by setting its principles, discussing the selection and quantization of biometric traits, and analyzing the mathematical relationships among measured and predicted traits. Crop biometric maps were applied to the case of a wine-production vineyard, in which vegetation amount, relative altitude in the field, soil compaction, berry size, grape yield, juice pH, and grape sugar content were selected as biometric traits. The enological potential of grapes was assessed with a quality-index map defined as a combination of titratable acidity, sugar content, and must pH. Prediction models for yield and quality were developed for high and low resolution maps, showing the great potential of crop biometric maps as a strategic tool for vineyard growers as well as for crop managers in general, due to the wide versatility of the methodology proposed.

Crop Biometric Maps: The Key to Prediction

PubMed Central

Rovira-Más, Francisco; Sáiz-Rubio, Verónica

2013-01-01

The sustainability of agricultural production in the twenty-first century, both in industrialized and developing countries, benefits from the integration of farm management with information technology such that individual plants, rows, or subfields may be endowed with a singular “identity.” This approach approximates the nature of agricultural processes to the engineering of industrial processes. In order to cope with the vast variability of nature and the uncertainties of agricultural production, the concept of crop biometrics is defined as the scientific analysis of agricultural observations confined to spaces of reduced dimensions and known position with the purpose of building prediction models. This article develops the idea of crop biometrics by setting its principles, discussing the selection and quantization of biometric traits, and analyzing the mathematical relationships among measured and predicted traits. Crop biometric maps were applied to the case of a wine-production vineyard, in which vegetation amount, relative altitude in the field, soil compaction, berry size, grape yield, juice pH, and grape sugar content were selected as biometric traits. The enological potential of grapes was assessed with a quality-index map defined as a combination of titratable acidity, sugar content, and must pH. Prediction models for yield and quality were developed for high and low resolution maps, showing the great potential of crop biometric maps as a strategic tool for vineyard growers as well as for crop managers in general, due to the wide versatility of the methodology proposed. PMID:24064605

Digital files for northeast Asia geodynamics, mineral deposit location, and metallogenic belt maps, stratigraphic columns, descriptions of map units, and descriptions of metallogenic belts

USGS Publications Warehouse

Nokleberg, Warren J.; Badarch, Gombosuren; Berzin, Nikolai A.; Diggles, Michael F.; Hwang, Duk-Hwan; Khanchuk, Alexander I.; Miller, Robert J.; Naumova, Vera V.; Obolensky, Alexander A.; Ogasawara, Masatsugu; Parfenov, Leonid M.; Prokopiev, Andrei V.; Rodionov, Sergey M.; Yan, Hongquan

2004-01-01

This is the online version of a CD-ROM publication. It contains all of the data that are on the disc but extra files have been removed: index files, software installers, and Windows autolaunch files. This publication contains a a series of files for Northeast Asia geodynamics, mineral deposit location, and metallogenic belt maps descriptions of map units and metallogenic belts, and stratigraphic columns. This region includes Eastern Siberia, Russian Far East, Mongolia, Northeast China, South Korea, and Japan. The files include: (1) a geodynamics map at a scale of 1:5,000,000; (2) page-size stratigraphic columns for major terranes; (3) a generalized geodynamics map at a scale of 1:15,000,000; (4) a mineral deposit location map at a scale of 1:7,500,000; (5) metallogenic belt maps at a scale of 1:15,000,000; (6) detailed descriptions of geologic units with references; (7) detailed descriptions of metallogenic belts with references; and (8) summary mineral deposit and metallogenic belt tables. The purpose of this publication is to provide high-quality, digital graphic files for maps and figures, and Word files for explanations, descriptions, and references to customers and users.

[The primary research and development of software oversampling mapping system for electrocardiogram].

PubMed

Zhou, Yu; Ren, Jie

2011-04-01

We put forward a new concept of software oversampling mapping system for electrocardiogram (ECG) to assist the research of the ECG inverse problem to improve the generality of mapping system and the quality of mapping signals. We then developed a conceptual system based on the traditional ECG detecting circuit, Labview and DAQ card produced by National Instruments, and at the same time combined the newly-developed oversampling method into the system. The results indicated that the system could map ECG signals accurately and the quality of the signals was good. The improvement of hardware and enhancement of software made the system suitable for mapping in different situations. So the primary development of the software for oversampling mapping system was successful and further research and development can make the system a powerful tool for researching ECG inverse problem.

High Dynamic Range Imaging Using Multiple Exposures

NASA Astrophysics Data System (ADS)

Hou, Xinglin; Luo, Haibo; Zhou, Peipei; Zhou, Wei

2017-06-01

It is challenging to capture a high-dynamic range (HDR) scene using a low-dynamic range (LDR) camera. This paper presents an approach for improving the dynamic range of cameras by using multiple exposure images of same scene taken under different exposure times. First, the camera response function (CRF) is recovered by solving a high-order polynomial in which only the ratios of the exposures are used. Then, the HDR radiance image is reconstructed by weighted summation of the each radiance maps. After that, a novel local tone mapping (TM) operator is proposed for the display of the HDR radiance image. By solving the high-order polynomial, the CRF can be recovered quickly and easily. Taken the local image feature and characteristic of histogram statics into consideration, the proposed TM operator could preserve the local details efficiently. Experimental result demonstrates the effectiveness of our method. By comparison, the method outperforms other methods in terms of imaging quality.

Application of chlorophyll fluorescence imaging and hyperspectral imaging in evaluation of decay in fresh-cut lettuce

USDA-ARS?s Scientific Manuscript database

Lettuce (Lactuca sativa L.) is commercially the most popular leafy vegetable whose leaves are usually consumed raw. Cleaned, cored, and chopped (fresh-cut) lettuce is a desirable, but highly perishable product. Modified atmosphere packaging (MAP) has been introduced to maintain quality of fresh-cut ...

Ecosystem processes at the watershed scale: mapping and modeling ecohydrological controls

Treesearch

Lawrence E. Band; T. Hwang; T.C. Hales; James Vose; Chelcy Ford

2012-01-01

Mountain watersheds are sources of a set of valuable ecosystem services as well as potential hazards. The former include high quality freshwater, carbon sequestration, nutrient retention, and biodiversity, whereas the latter include flash floods, landslides and forest fires. Each of these ecosystem services and hazards represents different elements of the integrated...

Modeling streams and hydrogeomorphic attributes in Oregon from digital and field data

Treesearch

Sharon E. Clarke; Kelly M. Burnett; Daniel J. Miller

2008-01-01

Managers, regulators, and researchers of aquatic ecosystems are increasingly pressed to consider large areas. However, accurate stream maps with geo-referenced attributes are uncommon over relevant spatial extents. Field inventories provide high-quality data, particularly for habitat characteristics at fine spatial resolutions (e.g., large wood), but are costly and so...

Race, Choice and Richmond Public Schools: New Possibilities and Ongoing Challenges for Diversity in Urban Districts

ERIC Educational Resources Information Center

Siegel-Hawley, Genevieve

2014-01-01

Several contemporary demographic trends suggest that school systems in America's central cities, typically characterized by high levels of racial and economic isolation, are being presented with new opportunities to create quality, diverse schools. Still, numerous obstacles linger. Using multiple sources of data and innovative mapping tools, this…

Exploring the Use of Participatory Information to Improve Monitoring, Mapping and Assessment of Aquatic Ecosystem Services at Landascape Scales

EPA Science Inventory

Traditionally, the EPA has monitored aquatic ecosystems using statistically rigorous sample designs and intensive field efforts which provide high quality datasets. But by their nature they leave many aquatic systems unsampled, follow a top down approach, have a long lag between ...

Smart Phone Application Development and Demonstration in Support of EPA HICO Imagery for Coastal and Ocean Protection

EPA Science Inventory

High resolution spectral data from the ISS Hyperspectral Imager of the Coastal Ocean (HICO) system has been used to map the spatial distribution of selected water quality indicators for four Florida Gulf Coast estuaries from 2010-2012. HICO is the first hyperspectral imager speci...

Estimating Douglas-fir site quality from aerial photographs.

Treesearch

Grover A. Choate

1961-01-01

This study investigated the feasibility of developing a technique for estimating site index of Douglas-fir in the Pacific Northwest, using aerial photos and topographic maps. Physiographic features were used as indicators of site index. Analysis showed that although most of the features were highly significant as criteria for predicting site index, they explained less...

Pharmacophore-Map-Pick: A Method to Generate Pharmacophore Models for All Human GPCRs.

PubMed

Dai, Shao-Xing; Li, Gong-Hua; Gao, Yue-Dong; Huang, Jing-Fei

2016-02-01

GPCR-based drug discovery is hindered by a lack of effective screening methods for most GPCRs that have neither ligands nor high-quality structures. With the aim to identify lead molecules for these GPCRs, we developed a new method called Pharmacophore-Map-Pick to generate pharmacophore models for all human GPCRs. The model of ADRB2 generated using this method not only predicts the binding mode of ADRB2-ligands correctly but also performs well in virtual screening. Findings also demonstrate that this method is powerful for generating high-quality pharmacophore models. The average enrichment for the pharmacophore models of the 15 targets in different GPCR families reached 15-fold at 0.5 % false-positive rate. Therefore, the pharmacophore models can be applied in virtual screening directly with no requirement for any ligand information or shape constraints. A total of 2386 pharmacophore models for 819 different GPCRs (99 % coverage (819/825)) were generated and are available at http://bsb.kiz.ac.cn/GPCRPMD. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Effect of Modified Atmosphere Packaging and Addition of Rosemary Extract, Sodium Acetate and Calcium Lactate Mixture on the Quality of Pre-cooked Hamburger Patties during Refrigerated Storage

PubMed Central

Muhlisin; Kang, Sun Moon; Choi, Won Hee; Lee, Keun Taik; Cheong, Sung Hee; Lee, Sung Ki

2013-01-01

The effect of modified atmosphere packaging (MAP; 30% CO2+70% N2 or 100% N2) and an additive mixture (500 ppm rosemary extract, 3,000 ppm sodium acetate and 1,500 ppm calcium lactate) on the quality of pre-cooked hamburger patties during storage at 5°C for 14 d was evaluated. The addition of the additive mixture reduced aerobic and anaerobic bacteria counts in both 30% CO2-MAP (30% CO2+70% N2) and 100% N2-MAP (p<0.05). The 30% CO2-MAP was more effective to suppress the microbial growth than 100% N2-MAP, moreover the 30% CO2-MAP combined with additive mixture resulted in the lowest bacterial counts. The hamburger patties with additive mixture showed lower CIE L* and CIE a*, and higher CIE b* than those with no additive mixture. The 30% CO2-MAP tended to decrease the TBARS during storage regardless of the addition of additives. The use of 30% CO2-MAP in combination with additives mixture was effective for maintaining the quality and extending the shelf-life of pre-cooked hamburger patties. PMID:25049716

MO-E-9A-01: Risk Based Quality Management: TG100 In Action

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huq, M; Palta, J; Dunscombe, P

2014-06-15

One of the goals of quality management in radiation therapy is to gain high confidence that patients will receive the prescribed treatment correctly. To accomplish these goals professional societies such as the American Association of Physicists in Medicine (AAPM) has published many quality assurance (QA), quality control (QC), and quality management (QM) guidance documents. In general, the recommendations provided in these documents have emphasized on performing device-specific QA at the expense of process flow and protection of the patient against catastrophic errors. Analyses of radiation therapy incidents find that they are most often caused by flaws in the overall therapymore » process, from initial consult through final treatment, than by isolated hardware or computer failures detectable by traditional physics QA. This challenge is shared by many intrinsically hazardous industries. Risk assessment tools and analysis techniques have been developed to define, identify, and eliminate known and/or potential failures, problems, or errors, from a system, process and/or service before they reach the customer. These include, but are not limited to, process mapping, failure modes and effects analysis (FMEA), fault tree analysis (FTA), and establishment of a quality management program that best avoids the faults and risks that have been identified in the overall process. These tools can be easily adapted to radiation therapy practices because of their simplicity and effectiveness to provide efficient ways to enhance the safety and quality of treatment processes. Task group 100 (TG100) of AAPM has developed a risk-based quality management program that uses these tools. This session will be devoted to a discussion of these tools and how these tools can be used in a given radiotherapy clinic to develop a risk based QM program. Learning Objectives: Learn how to design a process map for a radiotherapy process. Learn how to perform a FMEA analysis for a given process. Learn what Fault tree analysis is all about. Learn how to design a quality management program based upon the information obtained from process mapping, FMEA and FTA.« less

Some comments on mapping from disease-specific to generic health-related quality-of-life scales.

PubMed

Palta, Mari

2013-01-01

An article by Lu et al. in this issue of Value in Health addresses the mapping of treatment or group differences in disease-specific measures (DSMs) of health-related quality of life onto differences in generic health-related quality-of-life scores, with special emphasis on how the mapping is affected by the reliability of the DSM. In the proposed mapping, a factor analytic model defines a conversion factor between the scores as the ratio of factor loadings. Hence, the mapping applies to convert true underlying scales and has desirable properties facilitating the alignment of instruments and understanding their relationship in a coherent manner. It is important to note, however, that when DSM means or differences in mean DSMs are estimated, their mapping is still of a measurement error-prone predictor, and the correct conversion coefficient is the true mapping multiplied by the reliability of the DSM in the relevant sample. In addition, the proposed strategy for estimating the factor analytic mapping in practice requires assumptions that may not hold. We discuss these assumptions and how they may be the reason we obtain disparate estimates of the mapping factor in an application of the proposed methods to groups of patients. Copyright © 2013 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Monitoring-well network and sampling design for ground-water quality, Wind River Indian Reservation, Wyoming

USGS Publications Warehouse

Mason, Jon P.; Sebree, Sonja K.; Quinn, Thomas L.

2005-01-01

The Wind River Indian Reservation, located in parts of Fremont and Hot Springs Counties, Wyoming, has a total land area of more than 3,500 square miles. Ground water on the Wind River Indian Reservation is a valuable resource for Shoshone and Northern Arapahoe tribal members and others who live on the Reservation. There are many types of land uses on the Reservation that have the potential to affect the quality of ground-water resources. Urban areas, rural housing developments, agricultural lands, landfills, oil and natural gas fields, mining, and pipeline utility corridors all have the potential to affect ground-water quality. A cooperative study was developed between the U.S. Geological Survey and the Wind River Environmental Quality Commission to identify areas of the Reservation that have the highest potential for ground-water contamination and develop a comprehensive plan to monitor these areas. An arithmetic overlay model for the Wind River Indian Reservation was created using seven geographic information system data layers representing factors with varying potential to affect ground-water quality. The data layers used were: the National Land Cover Dataset, water well density, aquifer sensitivity, oil and natural gas fields and petroleum pipelines, sites with potential contaminant sources, sites that are known to have ground-water contamination, and National Pollutant Discharge Elimination System sites. A prioritization map for monitoring ground-water quality on the Reservation was created using the model. The prioritization map ranks the priority for monitoring ground-water quality in different areas of the Reservation as low, medium, or high. To help minimize bias in selecting sites for a monitoring well network, an automated stratified random site-selection approach was used to select 30 sites for ground-water quality monitoring within the high priority areas. In addition, the study also provided a sampling design for constituents to be monitored, sampling frequency, and a simple water-table level observation well network.

India Solar Resource Data: Enhanced Data for Accelerated Deployment (Fact Sheet)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

Identifying potential locations for solar photovoltaic (PV) and concentrating solar power (CSP) projects requires an understanding of the underlying solar resource. Under a bilateral partnership between the United States and India - the U.S.-India Energy Dialogue - the National Renewable Energy Laboratory has updated Indian solar data and maps using data provided by the Ministry of New and Renewable Energy (MNRE) and the National Institute for Solar Energy (NISE). This fact sheet overviews the updated maps and data, which help identify high-quality solar energy projects. This can help accelerate the deployment of solar energy in India.

India Solar Resource Data: Enhanced Data for Accelerated Deployment

DOE Office of Scientific and Technical Information (OSTI.GOV)

None, None

Identifying potential locations for solar photovoltaic (PV) and concentrating solar power (CSP) projects requires an understanding of the underlying solar resource. Under a bilateral partnership between the United States and India - the U.S.-India Energy Dialogue - the National Renewable Energy Laboratory has updated Indian solar data and maps using data provided by the Ministry of New and Renewable Energy (MNRE) and the National Institute for Solar Energy (NISE). This fact sheet overviews the updated maps and data, which help identify high-quality solar energy projects. This can help accelerate the deployment of solar energy in India.

Morphology, geology and water quality assessment of former tin mining catchment.

PubMed

Ashraf, Muhammad Aqeel; Maah, Mohd Jamil; Yusoff, Ismail

2012-01-01

Bestari Jaya, former tin mining catchment covers an area of 2656.31 hectares comprised of four hundred and forty-two different-size lakes and ponds. The present study area comprise of 92 hectares of the catchment that include four large size lakes. Arc GIS version 9.2 used to develop bathymetric map, Global Positioning System (GPS) for hydrographical survey and flow meter was utilized for water discharge analysis (flow routing) of the catchment. The water quality parameters (pH, temperature, electric conductivity, dissolved oxygen DO, total dissolved solids TDS, chlorides, ammonium, nitrates) were analyzed by using Hydrolab. Quality assurance (QA) and quality control (QC) procedures were strictly followed throughout the field work and data analysis. Different procedures were employed to evaluate the analytical data and to check for possible transcription or dilution errors, changes during analysis, or unusual or unlikely values. The results obtained are compared with interim national water quality standards for Malaysia indicates that water quality of area is highly degraded. It is concluded that Bestri Jaya ex-mining catchment has a high pollution potential due to mining activities and River Ayer Hitam, recipient of catchment water, is a highly polluted river.

Morphology, Geology and Water Quality Assessment of Former Tin Mining Catchment

PubMed Central

Ashraf, Muhammad Aqeel; Maah, Mohd. Jamil; Yusoff, Ismail

2012-01-01

Bestari Jaya, former tin mining catchment covers an area of 2656.31 hectares comprised of four hundred and forty-two different-size lakes and ponds. The present study area comprise of 92 hectares of the catchment that include four large size lakes. Arc GIS version 9.2 used to develop bathymetric map, Global Positioning System (GPS) for hydrographical survey and flow meter was utilized for water discharge analysis (flow routing) of the catchment. The water quality parameters (pH, temperature, electric conductivity, dissolved oxygen DO, total dissolved solids TDS, chlorides, ammonium, nitrates) were analyzed by using Hydrolab. Quality assurance (QA) and quality control (QC) procedures were strictly followed throughout the field work and data analysis. Different procedures were employed to evaluate the analytical data and to check for possible transcription or dilution errors, changes during analysis, or unusual or unlikely values. The results obtained are compared with interim national water quality standards for Malaysia indicates that water quality of area is highly degraded. It is concluded that Bestri Jaya ex-mining catchment has a high pollution potential due to mining activities and River Ayer Hitam, recipient of catchment water, is a highly polluted river. PMID:22761549

Probability-based nitrate contamination map of groundwater in Kinmen.

PubMed

Liu, Chen-Wuing; Wang, Yeuh-Bin; Jang, Cheng-Shin

2013-12-01

Groundwater supplies over 50% of drinking water in Kinmen. Approximately 16.8% of groundwater samples in Kinmen exceed the drinking water quality standard (DWQS) of NO3 (-)-N (10 mg/L). The residents drinking high nitrate-polluted groundwater pose a potential risk to health. To formulate effective water quality management plan and assure a safe drinking water in Kinmen, the detailed spatial distribution of nitrate-N in groundwater is a prerequisite. The aim of this study is to develop an efficient scheme for evaluating spatial distribution of nitrate-N in residential well water using logistic regression (LR) model. A probability-based nitrate-N contamination map in Kinmen is constructed. The LR model predicted the binary occurrence probability of groundwater nitrate-N concentrations exceeding DWQS by simple measurement variables as independent variables, including sampling season, soil type, water table depth, pH, EC, DO, and Eh. The analyzed results reveal that three statistically significant explanatory variables, soil type, pH, and EC, are selected for the forward stepwise LR analysis. The total ratio of correct classification reaches 92.7%. The highest probability of nitrate-N contamination map presents in the central zone, indicating that groundwater in the central zone should not be used for drinking purposes. Furthermore, a handy EC-pH-probability curve of nitrate-N exceeding the threshold of DWQS was developed. This curve can be used for preliminary screening of nitrate-N contamination in Kinmen groundwater. This study recommended that the local agency should implement the best management practice strategies to control nonpoint nitrogen sources and carry out a systematic monitoring of groundwater quality in residential wells of the high nitrate-N contamination zones.

Evaluating Sentinel-2 for Lakeshore Habitat Mapping Based on Airborne Hyperspectral Data.

PubMed

Stratoulias, Dimitris; Balzter, Heiko; Sykioti, Olga; Zlinszky, András; Tóth, Viktor R

2015-09-11

Monitoring of lakeshore ecosystems requires fine-scale information to account for the high biodiversity typically encountered in the land-water ecotone. Sentinel-2 is a satellite with high spatial and spectral resolution and improved revisiting frequency and is expected to have significant potential for habitat mapping and classification of complex lakeshore ecosystems. In this context, investigations of the capabilities of Sentinel-2 in regard to the spatial and spectral dimensions are needed to assess its potential and the quality of the expected output. This study presents the first simulation of the high spatial resolution (i.e., 10 m and 20 m) bands of Sentinel-2 for lakeshore mapping, based on the satellite's Spectral Response Function and hyperspectral airborne data collected over Lake Balaton, Hungary in August 2010. A comparison of supervised classifications of the simulated products is presented and the information loss from spectral aggregation and spatial upscaling in the context of lakeshore vegetation classification is discussed. We conclude that Sentinel-2 imagery has a strong potential for monitoring fine-scale habitats, such as reed beds.

Automated detection of ice cliffs within supraglacial debris cover

NASA Astrophysics Data System (ADS)

Herreid, Sam; Pellicciotti, Francesca

2018-05-01

Ice cliffs within a supraglacial debris cover have been identified as a source for high ablation relative to the surrounding debris-covered area. Due to their small relative size and steep orientation, ice cliffs are difficult to detect using nadir-looking space borne sensors. The method presented here uses surface slopes calculated from digital elevation model (DEM) data to map ice cliff geometry and produce an ice cliff probability map. Surface slope thresholds, which can be sensitive to geographic location and/or data quality, are selected automatically. The method also attempts to include area at the (often narrowing) ends of ice cliffs which could otherwise be neglected due to signal saturation in surface slope data. The method was calibrated in the eastern Alaska Range, Alaska, USA, against a control ice cliff dataset derived from high-resolution visible and thermal data. Using the same input parameter set that performed best in Alaska, the method was tested against ice cliffs manually mapped in the Khumbu Himal, Nepal. Our results suggest the method can accommodate different glaciological settings and different DEM data sources without a data intensive (high-resolution, multi-data source) recalibration.

Geography literacy can develop Geography skills for high school students: is it true?

NASA Astrophysics Data System (ADS)

Utami, W. S.; Zain, I. M.; Sumarmi

2018-01-01

The most important issue related to education in Indonesia is the low quality of student learning and competence. The basic thing that is important to be studied is the demands of 21st-century skills that are difficult to fulfil with the low competence of student learning. Low competence of student learning demonstrated by low capacity of scientific literacy includes geography literacy. Geography skills of Indonesian students are also low. It is shown from the students’ ability to use maps to describe and to analyze is low. The purpose of this study is to determine the correlation between the literacy skills of geography to develop geography skills of high school students in Surabaya. Written and performance tests were given to the sample of 29 high school students. The results of the tests we analyzed based on Geography literacy and its correlation to Geography skills in terms of the ability to use the media, map, and analyze the phenomenon of the geosphere. The results showed that the students who have low literacy geography have difficulty in using map.

Hi-fidelity multi-scale local processing for visually optimized far-infrared Herschel images

NASA Astrophysics Data System (ADS)

Li Causi, G.; Schisano, E.; Liu, S. J.; Molinari, S.; Di Giorgio, A.

2016-07-01

In the context of the "Hi-Gal" multi-band full-plane mapping program for the Galactic Plane, as imaged by the Herschel far-infrared satellite, we have developed a semi-automatic tool which produces high definition, high quality color maps optimized for visual perception of extended features, like bubbles and filaments, against the high background variations. We project the map tiles of three selected bands onto a 3-channel panorama, which spans the central 130 degrees of galactic longitude times 2.8 degrees of galactic latitude, at the pixel scale of 3.2", in cartesian galactic coordinates. Then we process this image piecewise, applying a custom multi-scale local stretching algorithm, enforced by a local multi-scale color balance. Finally, we apply an edge-preserving contrast enhancement to perform an artifact-free details sharpening. Thanks to this tool, we have thus produced a stunning giga-pixel color image of the far-infrared Galactic Plane that we made publicly available with the recent release of the Hi-Gal mosaics and compact source catalog.

Evaluating Sentinel-2 for Lakeshore Habitat Mapping Based on Airborne Hyperspectral Data

PubMed Central

Stratoulias, Dimitris; Balzter, Heiko; Sykioti, Olga; Zlinszky, András; Tóth, Viktor R.

2015-01-01

Monitoring of lakeshore ecosystems requires fine-scale information to account for the high biodiversity typically encountered in the land-water ecotone. Sentinel-2 is a satellite with high spatial and spectral resolution and improved revisiting frequency and is expected to have significant potential for habitat mapping and classification of complex lakeshore ecosystems. In this context, investigations of the capabilities of Sentinel-2 in regard to the spatial and spectral dimensions are needed to assess its potential and the quality of the expected output. This study presents the first simulation of the high spatial resolution (i.e., 10 m and 20 m) bands of Sentinel-2 for lakeshore mapping, based on the satellite’s Spectral Response Function and hyperspectral airborne data collected over Lake Balaton, Hungary in August 2010. A comparison of supervised classifications of the simulated products is presented and the information loss from spectral aggregation and spatial upscaling in the context of lakeshore vegetation classification is discussed. We conclude that Sentinel-2 imagery has a strong potential for monitoring fine-scale habitats, such as reed beds. PMID:26378538

An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population.

PubMed

Chen, Zongliang; Wang, Baobao; Dong, Xiaomei; Liu, Han; Ren, Longhui; Chen, Jian; Hauck, Andrew; Song, Weibin; Lai, Jinsheng

2014-06-04

Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the underlying molecular basis of phenotypic variation. Advanced populations, such as recombinant inbred lines, have been broadly adopted for QTL mapping; however, construction of large advanced generation crop populations is time-consuming and costly. The rapidly declining cost of genotyping due to recent advances in next-generation sequencing technologies has generated new possibilities for QTL mapping using large early generation populations. A set of 708 F2 progeny derived from inbreds Chang7-2 and 787 were generated and genotyped by whole genome low-coverage genotyping-by-sequencing method (average 0.04×). A genetic map containing 6,533 bin-markers was constructed based on the parental SNPs and a sliding-window method, spanning a total genetic distance of 1,396 cM. The high quality and accuracy of this map was validated by the identification of two well-studied genes, r1, a qualitative trait locus for color of silk (chromosome 10) and ba1 for tassel branch number (chromosome 3). Three traits of tassel and ear architecture were evaluated in this population, a total of 10 QTL were detected using a permutation-based-significance threshold, seven of which overlapped with reported QTL. Three genes (GRMZM2G316366, GRMZM2G492156 and GRMZM5G805008) encoding MADS-box domain proteins and a BTB/POZ domain protein were located in the small intervals of qTBN5 and qTBN7 (~800 Kb and 1.6 Mb in length, respectively) and may be involved in patterning of tassel architecture. The small physical intervals of most QTL indicate high-resolution mapping is obtainable with this method. We constructed an ultra-high-dentisy linkage map for the large early generation population in maize. Our study provides an efficient approach for fast detection of quantitative loci responsible for complex trait variation with high accuracy, thus helping to dissect the underlying molecular basis of phenotypic variation and accelerate improvement of crop breeding in a cost-effective fashion.

larvalign: Aligning Gene Expression Patterns from the Larval Brain of Drosophila melanogaster.

PubMed

Muenzing, Sascha E A; Strauch, Martin; Truman, James W; Bühler, Katja; Thum, Andreas S; Merhof, Dorit

2018-01-01

The larval brain of the fruit fly Drosophila melanogaster is a small, tractable model system for neuroscience. Genes for fluorescent marker proteins can be expressed in defined, spatially restricted neuron populations. Here, we introduce the methods for 1) generating a standard template of the larval central nervous system (CNS), 2) spatial mapping of expression patterns from different larvae into a reference space defined by the standard template. We provide a manually annotated gold standard that serves for evaluation of the registration framework involved in template generation and mapping. A method for registration quality assessment enables the automatic detection of registration errors, and a semi-automatic registration method allows one to correct registrations, which is a prerequisite for a high-quality, curated database of expression patterns. All computational methods are available within the larvalign software package: https://github.com/larvalign/larvalign/releases/tag/v1.0.

Preferred reporting items for studies mapping onto preference-based outcome measures: The MAPS statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-08-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. The primary audiences for the MAPS statement are researchers reporting mapping studies, the funders of the research, and peer reviewers and editors involved in assessing mapping studies for publication.A de novo list of 29 candidate reporting items and accompanying explanations was created by a working group comprised of six health economists and one Delphi methodologist. Following a two-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community, a final set of 23 items deemed essential for transparent reporting, and accompanying explanations, was developed. The items are contained in a user friendly 23 item checklist. They are presented numerically and categorised within six sections, namely: (i) title and abstract; (ii) introduction; (iii) methods; (iv) results; (v) discussion; and (vi) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document.It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by eight health economics and quality of life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in five years' time.This statement was published jointly in Applied Health Economics and Health Policy, Health and Quality of Life Outcomes, International Journal of Technology Assessment in Health Care, Journal of Medical Economics, Medical Decision Making, PharmacoEconomics, and Quality of Life Research.

Single Image Super-Resolution Using Global Regression Based on Multiple Local Linear Mappings.

PubMed

Choi, Jae-Seok; Kim, Munchurl

2017-03-01

Super-resolution (SR) has become more vital, because of its capability to generate high-quality ultra-high definition (UHD) high-resolution (HR) images from low-resolution (LR) input images. Conventional SR methods entail high computational complexity, which makes them difficult to be implemented for up-scaling of full-high-definition input images into UHD-resolution images. Nevertheless, our previous super-interpolation (SI) method showed a good compromise between Peak-Signal-to-Noise Ratio (PSNR) performances and computational complexity. However, since SI only utilizes simple linear mappings, it may fail to precisely reconstruct HR patches with complex texture. In this paper, we present a novel SR method, which inherits the large-to-small patch conversion scheme from SI but uses global regression based on local linear mappings (GLM). Thus, our new SR method is called GLM-SI. In GLM-SI, each LR input patch is divided into 25 overlapped subpatches. Next, based on the local properties of these subpatches, 25 different local linear mappings are applied to the current LR input patch to generate 25 HR patch candidates, which are then regressed into one final HR patch using a global regressor. The local linear mappings are learned cluster-wise in our off-line training phase. The main contribution of this paper is as follows: Previously, linear-mapping-based conventional SR methods, including SI only used one simple yet coarse linear mapping to each patch to reconstruct its HR version. On the contrary, for each LR input patch, our GLM-SI is the first to apply a combination of multiple local linear mappings, where each local linear mapping is found according to local properties of the current LR patch. Therefore, it can better approximate nonlinear LR-to-HR mappings for HR patches with complex texture. Experiment results show that the proposed GLM-SI method outperforms most of the state-of-the-art methods, and shows comparable PSNR performance with much lower computational complexity when compared with a super-resolution method based on convolutional neural nets (SRCNN15). Compared with the previous SI method that is limited with a scale factor of 2, GLM-SI shows superior performance with average 0.79 dB higher in PSNR, and can be used for scale factors of 3 or higher.

Marine Air Penetration: The Effect of Synoptic-scale Change on Regional Climate

NASA Astrophysics Data System (ADS)

Wang, M.; Ullrich, P. A.

2016-12-01

Marine air penetration (MAP) around the California San Francisco Bay Delta region has a pronounced impact on local temperature and air quality, and is highly correlated with inland wind penetration and hence wind power generation. Observational MAP criteria are defined based on the 900hPa across-shore wind speed greater than or equal to 3m/s at the Oakland radiosonde station, and a surface temperature difference greater than or equal to 7 degrees Celsius between two California Irrigation Management Information System (CIMIS) stations at Fresno, CA and Lodi, CA. This choice reflects marine cooling of Lodi, and was found to be highly correlated with inland specific humidity and breeze front activity. The observational MAP criteria were tuned based on small biases from Climate Forecast System Reanalysis (CFSR) to selected MAP days from CFSR, to identify synoptic-scale indicators associated with MAP events. A multivariate logistic regression model was constructed based on the selected five synoptic indicators from CFSR and demonstrated good model performance. Two synoptic-scale patterns were identified and analyzed out of the 32 categories from the regression model, suggesting a strong influence from the off-shore trough and the inland thermal ridge on MAP events. Future projection of MAP events included the 21st century Coupled Model Intercomparison Project Phase 5 (CMIP5), and Variable resolution in the Community Earth System Model (VR-CESM). Both showed no statistically significant trend associated with MAP events through the end of this century under both Representative Concentration Pathways (RCP) 2.6 and RCP 8.5.

A unified approach for debugging is-a structure and mappings in networked taxonomies

PubMed Central

2013-01-01

Background With the increased use of ontologies and ontology mappings in semantically-enabled applications such as ontology-based search and data integration, the issue of detecting and repairing defects in ontologies and ontology mappings has become increasingly important. These defects can lead to wrong or incomplete results for the applications. Results We propose a unified framework for debugging the is-a structure of and mappings between taxonomies, the most used kind of ontologies. We present theory and algorithms as well as an implemented system RepOSE, that supports a domain expert in detecting and repairing missing and wrong is-a relations and mappings. We also discuss two experiments performed by domain experts: an experiment on the Anatomy ontologies from the Ontology Alignment Evaluation Initiative, and a debugging session for the Swedish National Food Agency. Conclusions Semantically-enabled applications need high quality ontologies and ontology mappings. One key aspect is the detection and removal of defects in the ontologies and ontology mappings. Our system RepOSE provides an environment that supports domain experts to deal with this issue. We have shown the usefulness of the approach in two experiments by detecting and repairing circa 200 and 30 defects, respectively. PMID:23548155

System Considerations and Challendes in 3d Mapping and Modeling Using Low-Cost Uav Systems

NASA Astrophysics Data System (ADS)

Lari, Z.; El-Sheimy, N.

2015-08-01

In the last few years, low-cost UAV systems have been acknowledged as an affordable technology for geospatial data acquisition that can meet the needs of a variety of traditional and non-traditional mapping applications. In spite of its proven potential, UAV-based mapping is still lacking in terms of what is needed for it to become an acceptable mapping tool. In other words, a well-designed system architecture that considers payload restrictions as well as the specifications of the utilized direct geo-referencing component and the imaging systems in light of the required mapping accuracy and intended application is still required. Moreover, efficient data processing workflows, which are capable of delivering the mapping products with the specified quality while considering the synergistic characteristics of the sensors onboard, the wide range of potential users who might lack deep knowledge in mapping activities, and time constraints of emerging applications, are still needed to be adopted. Therefore, the introduced challenges by having low-cost imaging and georeferencing sensors onboard UAVs with limited payload capability, the necessity of efficient data processing techniques for delivering required products for intended applications, and the diversity of potential users with insufficient mapping-related expertise needs to be fully investigated and addressed by UAV-based mapping research efforts. This paper addresses these challenges and reviews system considerations, adaptive processing techniques, and quality assurance/quality control procedures for achievement of accurate mapping products from these systems.

Planetary Geologic Mapping Python Toolbox: A Suite of Tools to Support Mapping Workflows

NASA Astrophysics Data System (ADS)

Hunter, M. A.; Skinner, J. A.; Hare, T. M.; Fortezzo, C. M.

2017-06-01

The collective focus of the Planetary Geologic Mapping Python Toolbox is to provide researchers with additional means to migrate legacy GIS data, assess the quality of data and analysis results, and simplify common mapping tasks.

A global reference database of crowdsourced cropland data collected using the Geo-Wiki platform.

PubMed

Laso Bayas, Juan Carlos; Lesiv, Myroslava; Waldner, François; Schucknecht, Anne; Duerauer, Martina; See, Linda; Fritz, Steffen; Fraisl, Dilek; Moorthy, Inian; McCallum, Ian; Perger, Christoph; Danylo, Olha; Defourny, Pierre; Gallego, Javier; Gilliams, Sven; Akhtar, Ibrar Ul Hassan; Baishya, Swarup Jyoti; Baruah, Mrinal; Bungnamei, Khangsembou; Campos, Alfredo; Changkakati, Trishna; Cipriani, Anna; Das, Krishna; Das, Keemee; Das, Inamani; Davis, Kyle Frankel; Hazarika, Purabi; Johnson, Brian Alan; Malek, Ziga; Molinari, Monia Elisa; Panging, Kripal; Pawe, Chandra Kant; Pérez-Hoyos, Ana; Sahariah, Parag Kumar; Sahariah, Dhrubajyoti; Saikia, Anup; Saikia, Meghna; Schlesinger, Peter; Seidacaru, Elena; Singha, Kuleswar; Wilson, John W

2017-09-26

A global reference data set on cropland was collected through a crowdsourcing campaign using the Geo-Wiki crowdsourcing tool. The campaign lasted three weeks, with over 80 participants from around the world reviewing almost 36,000 sample units, focussing on cropland identification. For quality assessment purposes, two additional data sets are provided. The first is a control set of 1,793 sample locations validated by students trained in satellite image interpretation. This data set was used to assess the quality of the crowd as the campaign progressed. The second data set contains 60 expert validations for additional evaluation of the quality of the contributions. All data sets are split into two parts: the first part shows all areas classified as cropland and the second part shows cropland average per location and user. After further processing, the data presented here might be suitable to validate and compare medium and high resolution cropland maps generated using remote sensing. These could also be used to train classification algorithms for developing new maps of land cover and cropland extent.

A global reference database of crowdsourced cropland data collected using the Geo-Wiki platform

PubMed Central

Laso Bayas, Juan Carlos; Lesiv, Myroslava; Waldner, François; Schucknecht, Anne; Duerauer, Martina; See, Linda; Fritz, Steffen; Fraisl, Dilek; Moorthy, Inian; McCallum, Ian; Perger, Christoph; Danylo, Olha; Defourny, Pierre; Gallego, Javier; Gilliams, Sven; Akhtar, Ibrar ul Hassan; Baishya, Swarup Jyoti; Baruah, Mrinal; Bungnamei, Khangsembou; Campos, Alfredo; Changkakati, Trishna; Cipriani, Anna; Das, Krishna; Das, Keemee; Das, Inamani; Davis, Kyle Frankel; Hazarika, Purabi; Johnson, Brian Alan; Malek, Ziga; Molinari, Monia Elisa; Panging, Kripal; Pawe, Chandra Kant; Pérez-Hoyos, Ana; Sahariah, Parag Kumar; Sahariah, Dhrubajyoti; Saikia, Anup; Saikia, Meghna; Schlesinger, Peter; Seidacaru, Elena; Singha, Kuleswar; Wilson, John W

2017-01-01

A global reference data set on cropland was collected through a crowdsourcing campaign using the Geo-Wiki crowdsourcing tool. The campaign lasted three weeks, with over 80 participants from around the world reviewing almost 36,000 sample units, focussing on cropland identification. For quality assessment purposes, two additional data sets are provided. The first is a control set of 1,793 sample locations validated by students trained in satellite image interpretation. This data set was used to assess the quality of the crowd as the campaign progressed. The second data set contains 60 expert validations for additional evaluation of the quality of the contributions. All data sets are split into two parts: the first part shows all areas classified as cropland and the second part shows cropland average per location and user. After further processing, the data presented here might be suitable to validate and compare medium and high resolution cropland maps generated using remote sensing. These could also be used to train classification algorithms for developing new maps of land cover and cropland extent. PMID:28949323

A global reference database of crowdsourced cropland data collected using the Geo-Wiki platform

NASA Astrophysics Data System (ADS)

Laso Bayas, Juan Carlos; Lesiv, Myroslava; Waldner, François; Schucknecht, Anne; Duerauer, Martina; See, Linda; Fritz, Steffen; Fraisl, Dilek; Moorthy, Inian; McCallum, Ian; Perger, Christoph; Danylo, Olha; Defourny, Pierre; Gallego, Javier; Gilliams, Sven; Akhtar, Ibrar Ul Hassan; Baishya, Swarup Jyoti; Baruah, Mrinal; Bungnamei, Khangsembou; Campos, Alfredo; Changkakati, Trishna; Cipriani, Anna; Das, Krishna; Das, Keemee; Das, Inamani; Davis, Kyle Frankel; Hazarika, Purabi; Johnson, Brian Alan; Malek, Ziga; Molinari, Monia Elisa; Panging, Kripal; Pawe, Chandra Kant; Pérez-Hoyos, Ana; Sahariah, Parag Kumar; Sahariah, Dhrubajyoti; Saikia, Anup; Saikia, Meghna; Schlesinger, Peter; Seidacaru, Elena; Singha, Kuleswar; Wilson, John W.

2017-09-01

A global reference data set on cropland was collected through a crowdsourcing campaign using the Geo-Wiki crowdsourcing tool. The campaign lasted three weeks, with over 80 participants from around the world reviewing almost 36,000 sample units, focussing on cropland identification. For quality assessment purposes, two additional data sets are provided. The first is a control set of 1,793 sample locations validated by students trained in satellite image interpretation. This data set was used to assess the quality of the crowd as the campaign progressed. The second data set contains 60 expert validations for additional evaluation of the quality of the contributions. All data sets are split into two parts: the first part shows all areas classified as cropland and the second part shows cropland average per location and user. After further processing, the data presented here might be suitable to validate and compare medium and high resolution cropland maps generated using remote sensing. These could also be used to train classification algorithms for developing new maps of land cover and cropland extent.

High-resolution mapping of vehicle emissions in China in 2008

NASA Astrophysics Data System (ADS)

Zheng, B.; Huo, H.; Zhang, Q.; Yao, Z. L.; Wang, X. T.; Yang, X. F.; Liu, H.; He, K. B.

2014-09-01

This study is the first in a series of papers that aim to develop high-resolution emission databases for different anthropogenic sources in China. Here we focus on on-road transportation. Because of the increasing impact of on-road transportation on regional air quality, developing an accurate and high-resolution vehicle emission inventory is important for both the research community and air quality management. This work proposes a new inventory methodology to improve the spatial and temporal accuracy and resolution of vehicle emissions in China. We calculate, for the first time, the monthly vehicle emissions for 2008 in 2364 counties (an administrative unit one level lower than city) by developing a set of approaches to estimate vehicle stock and monthly emission factors at county-level, and technology distribution at provincial level. We then introduce allocation weights for the vehicle kilometers traveled to assign the county-level emissions onto 0.05° × 0.05° grids based on the China Digital Road-network Map (CDRM). The new methodology overcomes the common shortcomings of previous inventory methods, including neglecting the geographical differences between key parameters and using surrogates that are weakly related to vehicle activities to allocate vehicle emissions. The new method has great advantages over previous methods in depicting the spatial distribution characteristics of vehicle activities and emissions. This work provides a better understanding of the spatial representation of vehicle emissions in China and can benefit both air quality modeling and management with improved spatial accuracy.

Integrated change detection and temporal trajectory analysis of coastal wetlands using high spatial resolution Korean Multi-Purpose Satellite series imagery

NASA Astrophysics Data System (ADS)

Nguyen, Hoang Hai; Tran, Hien; Sunwoo, Wooyeon; Yi, Jong-hyuk; Kim, Dongkyun; Choi, Minha

2017-04-01

A series of multispectral high-resolution Korean Multi-Purpose Satellite (KOMPSAT) images was used to detect the geographical changes in four different tidal flats between the Yellow Sea and the west coast of South Korea. The method of unsupervised classification was used to generate a series of land use/land cover (LULC) maps from satellite images, which were then used as input for temporal trajectory analysis to detect the temporal change of coastal wetlands and its association with natural and anthropogenic activities. The accurately classified LULC maps of KOMPSAT images, with overall accuracy ranging from 83.34% to 95.43%, indicate that these multispectral high-resolution satellite data are highly applicable to the generation of high-quality thematic maps for extracting wetlands. The result of the trajectory analysis showed that, while the variation of the tidal flats in the Gyeonggi and Jeollabuk provinces was well correlated with the regular tidal regimes, the reductive trajectory of the wetland areas belonging to the Saemangeum province was caused by a high degree of human-induced activities including large reclamation and urbanization. The conservation of the Jeungdo Wetland Protected Area in the Jeollanam province revealed that effective social and environmental policies could help in protecting coastal wetlands from degradation.

Digital mapping techniques '06 - Workshop proceedings

USGS Publications Warehouse

Soller, David R.

2007-01-01

The Digital Mapping Techniques `06 (DMT`06) workshop was attended by more than 110 technical experts from 51 agencies, universities, and private companies, including representatives from 27 state geological surveys (see Appendix A of these Proceedings). This workshop was similar in nature to the previous nine meetings, which were held in Lawrence, Kansas (Soller, 1997), Champaign, Illinois (Soller, 1998), Madison, Wisconsin (Soller, 1999), Lexington, Kentucky (Soller, 2000), Tuscaloosa, Alabama (Soller, 2001), Salt Lake City, Utah (Soller, 2002), Millersville, Pennsylvania (Soller, 2003), Portland, Oregon (Soller, 2004), and Baton Rouge, Louisiana (Soller, 2005). This year?s meeting was hosted by the Ohio Geological Survey, from June 11-14, 2006, on the Ohio State University campus in Columbus, Ohio. As in the previous meetings, the objective was to foster informal discussion and exchange of technical information. It is with great pleasure that I note that the objective was successfully met, as attendees continued to share and exchange knowledge and information, and renew friendships and collegial work begun at past DMT workshops.Each DMT workshop has been coordinated by the Association of American State Geologists (AASG) and U.S. Geological Survey (USGS) Data Capture Working Group, the latter of which was formed in August 1996 to support the AASG and the USGS in their effort to build a National Geologic Map Database (see Soller, this volume, and http://ngmdb.usgs.gov/info/standards/datacapt/). The Working Group was formed because increased production efficiencies, standardization, and quality of digital map products were needed for the database - and for the State and Federal geological surveys - to provide more high-quality digital maps to the public.At the 2006 meeting, oral and poster presentations and special discussion sessions emphasized: 1) methods for creating and publishing map products (here, "publishing" includes Web-based release); 2) field data capture software and techniques, including the use of LIDAR; 3) digital cartographic techniques; 4) migration of digital maps into ArcGIS Geodatabase format; 5) analytical GIS techniques; and 6) continued development of the National Geologic Map Database.

No-reference image quality assessment based on statistics of convolution feature maps

NASA Astrophysics Data System (ADS)

Lv, Xiaoxin; Qin, Min; Chen, Xiaohui; Wei, Guo

2018-04-01

We propose a Convolutional Feature Maps (CFM) driven approach to accurately predict image quality. Our motivation bases on the finding that the Nature Scene Statistic (NSS) features on convolution feature maps are significantly sensitive to distortion degree of an image. In our method, a Convolutional Neural Network (CNN) is trained to obtain kernels for generating CFM. We design a forward NSS layer which performs on CFM to better extract NSS features. The quality aware features derived from the output of NSS layer is effective to describe the distortion type and degree an image suffered. Finally, a Support Vector Regression (SVR) is employed in our No-Reference Image Quality Assessment (NR-IQA) model to predict a subjective quality score of a distorted image. Experiments conducted on two public databases demonstrate the promising performance of the proposed method is competitive to state of the art NR-IQA methods.

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues.

PubMed

Ernst, Jason; Kellis, Manolis

2015-04-01

With hundreds of epigenomic maps, the opportunity arises to exploit the correlated nature of epigenetic signals, across both marks and samples, for large-scale prediction of additional datasets. Here, we undertake epigenome imputation by leveraging such correlations through an ensemble of regression trees. We impute 4,315 high-resolution signal maps, of which 26% are also experimentally observed. Imputed signal tracks show overall similarity to observed signals and surpass experimental datasets in consistency, recovery of gene annotations and enrichment for disease-associated variants. We use the imputed data to detect low-quality experimental datasets, to find genomic sites with unexpected epigenomic signals, to define high-priority marks for new experiments and to delineate chromatin states in 127 reference epigenomes spanning diverse tissues and cell types. Our imputed datasets provide the most comprehensive human regulatory region annotation to date, and our approach and the ChromImpute software constitute a useful complement to large-scale experimental mapping of epigenomic information.

Distribution, richness, quality, and thermal maturity of source rock units on the North Slope of Alaska

USGS Publications Warehouse

Peters, K.E.; Bird, K.J.; Keller, M.A.; Lillis, P.G.; Magoon, L.B.

2003-01-01

Four source rock units on the North Slope were identified, characterized, and mapped to better understand the origin of petroleum in the area: Hue-gamma ray zone (Hue-GRZ), pebble shale unit, Kingak Shale, and Shublik Formation. Rock-Eval pyrolysis, total organic carbon analysis, and well logs were used to map the present-day thickness, organic quantity (TOC), quality (hydrogen index, HI), and thermal maturity (Tmax) of each unit. To map these units, we screened all available geochemical data for wells in the study area and assumed that the top and bottom of the oil window occur at Tmax of ~440° and 470°C, respectively. Based on several assumptions related to carbon mass balance and regional distributions of TOC, the present-day source rock quantity and quality maps were used to determine the extent of fractional conversion of the kerogen to petroleum and to map the original organic richness prior to thermal maturation.

Application of principal component analysis to ecodiversity assessment of postglacial landscape (on the example of Debnica Kaszubska commune, Middle Pomerania)

NASA Astrophysics Data System (ADS)

Wojciechowski, Adam

2017-04-01

In order to assess ecodiversity understood as a comprehensive natural landscape factor (Jedicke 2001), it is necessary to apply research methods which recognize the environment in a holistic way. Principal component analysis may be considered as one of such methods as it allows to distinguish the main factors determining landscape diversity on the one hand, and enables to discover regularities shaping the relationships between various elements of the environment under study on the other hand. The procedure adopted to assess ecodiversity with the use of principal component analysis involves: a) determining and selecting appropriate factors of the assessed environment qualities (hypsometric, geological, hydrographic, plant, and others); b) calculating the absolute value of individual qualities for the basic areas under analysis (e.g. river length, forest area, altitude differences, etc.); c) principal components analysis and obtaining factor maps (maps of selected components); d) generating a resultant, detailed map and isolating several classes of ecodiversity. An assessment of ecodiversity with the use of principal component analysis was conducted in the test area of 299,67 km2 in Debnica Kaszubska commune. The whole commune is situated in the Weichselian glaciation area of high hypsometric and morphological diversity as well as high geo- and biodiversity. The analysis was based on topographical maps of the commune area in scale 1:25000 and maps of forest habitats. Consequently, nine factors reflecting basic environment elements were calculated: maximum height (m), minimum height (m), average height (m), the length of watercourses (km), the area of water reservoirs (m2), total forest area (ha), coniferous forests habitats area (ha), deciduous forest habitats area (ha), alder habitats area (ha). The values for individual factors were analysed for 358 grid cells of 1 km2. Based on the principal components analysis, four major factors affecting commune ecodiversity were distinguished: hypsometric component (PC1), deciduous forest habitats component (PC2), river valleys and alder habitats component (PC3), and lakes component (PC4). The distinguished factors characterise natural qualities of postglacial area and reflect well the role of the four most important groups of environment components in shaping ecodiversity of the area under study. The map of ecodiversity of Debnica Kaszubska commune was created on the basis of the first four principal component scores and then five classes of diversity were isolated: very low, low, average, high and very high. As a result of the assessment, five commune regions of very high ecodiversity were separated. These regions are also very attractive for tourists and valuable in terms of their rich nature which include protected areas such as Slupia Valley Landscape Park. The suggested method of ecodiversity assessment with the use of principal component analysis may constitute an alternative methodological proposition to other research methods used so far. Literature Jedicke E., 2001. Biodiversität, Geodiversität, Ökodiversität. Kriterien zur Analyse der Landschaftsstruktur - ein konzeptioneller Diskussionsbeitrag. Naturschutz und Landschaftsplanung, 33(2/3), 59-68.

Characterization of polysaccharides from Ganoderma spp. using saccharide mapping.

PubMed

Wu, Ding-Tao; Xie, Jing; Hu, De-Jun; Zhao, Jing; Li, Shao-Ping

2013-09-12

Polysaccharides from Ganoderma spp. and their adulterants were firstly investigated and compared using saccharide mapping, enzymatic (endo-1,3-β-D-glucanase and pectinase) digestion followed by polysaccharide analysis using carbohydrate gel electrophoresis analysis. The results showed that both 1,3-β-D-glucosidic and 1,4-α-D-galactosiduronic linkages were existed in Lingzhi (Ganoderma lucidum and Ganoderma sinense), and the similarity of polysaccharides from G. lucidum and G. sinense was high, which may contribute to rational use of Lingzhi. Different species of Ganoderma and their adulterants can be differentiated based on the saccharide mapping, which is helpful to well understand the structural characters of polysaccharides from different species of Ganoderma and to improve the quality control of polysaccharides in Lingzhi. Copyright © 2013 Elsevier Ltd. All rights reserved.

Lithofacies control of lignite distribution and ground-water quality, Wilcox group (Eocene), east-central Texas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ayers, W.B. Jr.; Lewis, A.H.

1984-04-01

Deep lignite resources (200-2000 ft; 61-610 m) were evaluated regionally using 1470 geophysical well logs to interpret lithofacies, lignite occurrence, and resistivity (water quality). The regional distribution of lithofacies indicates that in the region, the Wilcox Group is a fluvial-deltaic system. The primary fluvial system entered the Wilcox coastal plain west of Waco, Texas, trended southeast, and supplied a 75-mi (120-km) wide fluvial-deltaic system comparable in size to the Mississippi system. Lignites are most abundant in the Calvert Bluff Formation (upper Wilcox). Lower Calvert Bluff lignites are thickest and most extensive southwest of the Navasota River, whereas those of themore » upper Calvert Bluff are thickest northeast of the Brazos River. In the shallow subsurface, Calvert Bluff lignites are found in dip-elongate low-sand areas (flood plains) between channel-sand belts. Basinward, laterally continuous lignites coincide with high net sand areas comprise of distributary channel sands indicative of a delta-plain setting. The wilcox Group is a major aquifer. Maps of resistivity values show that Wilcox channel sands are conduits for ground-water flow. High values of formation resistivity (low total dissolved solids) exist in recharge areas at outcrop and around salt domes. Elongate trends of high resistivity values extend tens of miles basinward and coincide with axes of major sands. Resistivity values decrease basinward and the 20 ohm-m contour delineates the downdip limit of fresh water. Lithofacies and lignite occurrence maps are guides to exploration for deep lignite. Resistivity maps can be used to explore for ground-water resources.« less

Fast Updating National Geo-Spatial Databases with High Resolution Imagery: China's Methodology and Experience

NASA Astrophysics Data System (ADS)

Chen, J.; Wang, D.; Zhao, R. L.; Zhang, H.; Liao, A.; Jiu, J.

2014-04-01

Geospatial databases are irreplaceable national treasure of immense importance. Their up-to-dateness referring to its consistency with respect to the real world plays a critical role in its value and applications. The continuous updating of map databases at 1:50,000 scales is a massive and difficult task for larger countries of the size of more than several million's kilometer squares. This paper presents the research and technological development to support the national map updating at 1:50,000 scales in China, including the development of updating models and methods, production tools and systems for large-scale and rapid updating, as well as the design and implementation of the continuous updating workflow. The use of many data sources and the integration of these data to form a high accuracy, quality checked product were required. It had in turn required up to date techniques of image matching, semantic integration, generalization, data base management and conflict resolution. Design and develop specific software tools and packages to support the large-scale updating production with high resolution imagery and large-scale data generalization, such as map generalization, GIS-supported change interpretation from imagery, DEM interpolation, image matching-based orthophoto generation, data control at different levels. A national 1:50,000 databases updating strategy and its production workflow were designed, including a full coverage updating pattern characterized by all element topographic data modeling, change detection in all related areas, and whole process data quality controlling, a series of technical production specifications, and a network of updating production units in different geographic places in the country.

Electricity Consumption Risk Map - The use of Urban Climate Mapping for smarter analysis: Case study for Birmingham, UK.

NASA Astrophysics Data System (ADS)

Antunes Azevedo, Juliana; Burghardt, René; Chapman, Lee; Katzchner, Lutz; Muller, Catherine L.

2015-04-01

Climate is a key driving factor in energy consumption. However, income, vegetation, building mass structure, topography also impact on the amount of energy consumption. In a changing climate, increased temperatures are likely to lead to increased electricity consumption, affecting demand, distribution and generation. Furthermore, as the world population becomes more urbanized, increasing numbers of people will need to deal with not only increased temperatures from climate change, but also from the unintentional modification of the urban climate in the form of urban heat islands. Hence, climate and climate change needs to be taken into account for future urban planning aspects to increase the climate and energy resilience of the community and decrease the future social and economic costs. Geographical Information Systems provide a means to create urban climate maps as part of the urban planning process. Geostatistical analyses linking these maps with demographic and social data, enables a geo-statistical analysis to identify linkages to high-risk groups of the community and vulnerable areas of town and cities. Presently, the climatope classification is oriented towards thermal aspects and the ventilation quality (roughness) of the urban areas but can also be adapted to take into account other structural "environmental factors". This study aims to use the climatope approach to predict areas of potential high electricity consumption in Birmingham, UK. Several datasets were used to produce an average surface temperature map, vegetation map, land use map, topography map, building height map, built-up area roughness calculations, an average air temperature map and a domestic electricity consumption map. From the correlations obtained between the layers it is possible to average the importance of each factor and create a map for domestic electricity consumption to understand the influence of environmental aspects on spatial energy consumption. Based on these results city planners and local authorities can guide their directives and policies towards electricity consumption, demand, generation and distribution.

Enabling high-quality observations of surface imperviousness for water runoff modelling from unmanned aerial vehicles

NASA Astrophysics Data System (ADS)

Tokarczyk, Piotr; Leitao, Joao Paulo; Rieckermann, Jörg; Schindler, Konrad; Blumensaat, Frank

2015-04-01

Modelling rainfall-runoff in urban areas is increasingly applied to support flood risk assessment particularly against the background of a changing climate and an increasing urbanization. These models typically rely on high-quality data for rainfall and surface characteristics of the area. While recent research in urban drainage has been focusing on providing spatially detailed rainfall data, the technological advances in remote sensing that ease the acquisition of detailed land-use information are less prominently discussed within the community. The relevance of such methods increase as in many parts of the globe, accurate land-use information is generally lacking, because detailed image data is unavailable. Modern unmanned air vehicles (UAVs) allow acquiring high-resolution images on a local level at comparably lower cost, performing on-demand repetitive measurements, and obtaining a degree of detail tailored for the purpose of the study. In this study, we investigate for the first time the possibility to derive high-resolution imperviousness maps for urban areas from UAV imagery and to use this information as input for urban drainage models. To do so, an automatic processing pipeline with a modern classification method is tested and applied in a state-of-the-art urban drainage modelling exercise. In a real-life case study in the area of Lucerne, Switzerland, we compare imperviousness maps generated from a consumer micro-UAV and standard large-format aerial images acquired by the Swiss national mapping agency (swisstopo). After assessing their correctness, we perform an end-to-end comparison, in which they are used as an input for an urban drainage model. Then, we evaluate the influence which different image data sources and their processing methods have on hydrological and hydraulic model performance. We analyze the surface runoff of the 307 individual sub-catchments regarding relevant attributes, such as peak runoff and volume. Finally, we evaluate the model's channel flow prediction performance through a cross-comparison with reference flow measured at the catchment outlet. We show that imperviousness maps generated using UAV imagery processed with modern classification methods achieve accuracy comparable with standard, off-the-shelf aerial imagery. In the examined case study, we find that the different imperviousness maps only have a limited influence on modelled surface runoff and pipe flows. We conclude that UAV imagery represents a valuable alternative data source for urban drainage model applications due to the possibility to flexibly acquire up-to-date aerial images at a superior quality and a competitive price. Our analyses furthermore suggest that spatially more detailed urban drainage models can even better benefit from the full detail of UAV imagery.

High-quality observation of surface imperviousness for urban runoff modelling using UAV imagery

NASA Astrophysics Data System (ADS)

Tokarczyk, P.; Leitao, J. P.; Rieckermann, J.; Schindler, K.; Blumensaat, F.

2015-01-01

Modelling rainfall-runoff in urban areas is increasingly applied to support flood risk assessment particularly against the background of a changing climate and an increasing urbanization. These models typically rely on high-quality data for rainfall and surface characteristics of the area. While recent research in urban drainage has been focusing on providing spatially detailed rainfall data, the technological advances in remote sensing that ease the acquisition of detailed land-use information are less prominently discussed within the community. The relevance of such methods increase as in many parts of the globe, accurate land-use information is generally lacking, because detailed image data is unavailable. Modern unmanned air vehicles (UAVs) allow acquiring high-resolution images on a local level at comparably lower cost, performing on-demand repetitive measurements, and obtaining a degree of detail tailored for the purpose of the study. In this study, we investigate for the first time the possibility to derive high-resolution imperviousness maps for urban areas from UAV imagery and to use this information as input for urban drainage models. To do so, an automatic processing pipeline with a modern classification method is tested and applied in a state-of-the-art urban drainage modelling exercise. In a real-life case study in the area of Lucerne, Switzerland, we compare imperviousness maps generated from a consumer micro-UAV and standard large-format aerial images acquired by the Swiss national mapping agency (swisstopo). After assessing their correctness, we perform an end-to-end comparison, in which they are used as an input for an urban drainage model. Then, we evaluate the influence which different image data sources and their processing methods have on hydrological and hydraulic model performance. We analyze the surface runoff of the 307 individual subcatchments regarding relevant attributes, such as peak runoff and volume. Finally, we evaluate the model's channel flow prediction performance through a cross-comparison with reference flow measured at the catchment outlet. We show that imperviousness maps generated using UAV imagery processed with modern classification methods achieve accuracy comparable with standard, off-the-shelf aerial imagery. In the examined case study, we find that the different imperviousness maps only have a limited influence on modelled surface runoff and pipe flows. We conclude that UAV imagery represents a valuable alternative data source for urban drainage model applications due to the possibility to flexibly acquire up-to-date aerial images at a superior quality and a competitive price. Our analyses furthermore suggest that spatially more detailed urban drainage models can even better benefit from the full detail of UAV imagery.

Important Value of Economic Potency Mangrove Using NDVI Satellite High Resolution Image To Support Eco Tourism Of Pamurbaya Area (Case Study: East Cost of Surabaya)

NASA Astrophysics Data System (ADS)

Sukojo, B. M.; Hidayat, H.; Ratnasari, D.

2017-12-01

Indonesia is a vast maritime country; many mangrove conservations is found around coastal areas of Indonesia. Mangroves support the life of a large number of animal species by providing breeding, spawning and feeding. Mangrove forests as one of the unique ecosystems are potential natural resources, supporting the diversity of flora and fauna of terrestrial aquatic communities that directly or indirectly play an important role for human life in economic, social and environmental terms. East Coast Surabaya is an area with the most extensive and diverse mangrove ecosystems along the coast of Surabaya. Currently Pamurbaya used as a recreational object or nature tourism called eco tours. Utilization of mangrove ecosystem as a place of this eco tour bring positive impact on economic potency around pamurbaya area. So, to know the value of the economic potential of mangrove ecosystems for support of nature tourism Pamurbaya region needs to study mapping mangrove ecosystem conditions in the East Coast area of Surabaya. Mapping of mangrove conditions can use remote sensing technology by utilizing satellite image data with high resolution. Data used for mapping mangrove ecosystem conditions on the east coast of Surabaya are high resolution satellite image data of Pleiades 1A and field observation data such as Ground Control Point, soil spectral parameters and water quality. From satellite image data will be classification of mangrove vegetation canopy classification using NDVI vegetation index method using algorithm formula which then will be tested correlation with field observation data on reflectant value of field and water quality parameter. The purpose of this research is to know the condition of mangrove ecosystem to know the economic potential of mangrove ecosystem in supporting Pamurbaya nature tourism. The expected result of this research is the existence of basic geospatial information in the form of mangrove ecosystem condition map. So that can be used as decision makers to find out how big economic potential of mangrove ecosystem in supporting nature tourism Pamurbaya beside that can be used as reference research related mapping, conservation and development of mangrove ecosystem.

Digital mapping techniques '00, workshop proceedings - May 17-20, 2000, Lexington, Kentucky

USGS Publications Warehouse

Soller, David R.

2000-01-01

Introduction: The Digital Mapping Techniques '00 (DMT'00) workshop was attended by 99 technical experts from 42 agencies, universities, and private companies, including representatives from 28 state geological surveys (see Appendix A). This workshop was similar in nature to the first three meetings, held in June, 1997, in Lawrence, Kansas (Soller, 1997), in May, 1998, in Champaign, Illinois (Soller, 1998a), and in May, 1999, in Madison, Wisconsin (Soller, 1999). This year's meeting was hosted by the Kentucky Geological Survey, from May 17 to 20, 2000, on the University of Kentucky campus in Lexington. As in the previous meetings, the objective was to foster informal discussion and exchange of technical information. When, based on discussions at the workshop, an attendee adopts or modifies a newly learned technique, the workshop clearly has met that objective. Evidence of learning and cooperation among participating agencies continued to be a highlight of the DMT workshops (see example in Soller, 1998b, and various papers in this volume). The meeting's general goal was to help move the state geological surveys and the USGS toward development of more cost-effective, flexible, and useful systems for digital mapping and geographic information systems (GIS) analysis. Through oral and poster presentations and special discussion sessions, emphasis was given to: 1) methods for creating and publishing map products (here, 'publishing' includes Web-based release); 2) continued development of the National Geologic Map Database; 3) progress toward building a standard geologic map data model; 4) field data-collection systems; and 5) map citation and authorship guidelines. Four representatives of the GIS hardware and software vendor community were invited to participate. The four annual DMT workshops were coordinated by the AASG/USGS Data Capture Working Group, which was formed in August, 1996, to support the Association of American State Geologists and the USGS in their effort to build a National Geologic Map Database (see Soller and Berg, this volume, and http://ncgmp.usgs.gov/ngmdbproject/standards/datacapt/). The Working Group was formed because increased production efficiencies, standardization, and quality of digital map products were needed to help the Database, and the State and Federal geological surveys, provide more high-quality digital maps to the public.

An early warning system for groundwater pollution based on the assessment of groundwater pollution risks.

NASA Astrophysics Data System (ADS)

Zhang, Weihong.; Zhao, Yongsheng; Hong, Mei; Guo, Xiaodong

2009-04-01

Groundwater pollution usually is complex and concealed, remediation of which is difficult, high cost, time-consuming, and ineffective. An early warning system for groundwater pollution is needed that detects groundwater quality problems and gets the information necessary to make sound decisions before massive groundwater quality degradation occurs. Groundwater pollution early warning were performed by considering comprehensively the current groundwater quality, groundwater quality varying trend and groundwater pollution risk . The map of the basic quality of the groundwater was obtained by fuzzy comprehensive evaluation or BP neural network evaluation. Based on multi-annual groundwater monitoring datasets, Water quality state in sometime of the future was forecasted using time-sequenced analyzing methods. Water quality varying trend was analyzed by Spearman's rank correlative coefficient.The relative risk map of groundwater pollution was estimated through a procedure that identifies, cell by cell,the values of three factors, that is inherent vulnerability, load risk of pollution source and contamination hazard. DRASTIC method was used to assess inherent vulnerability of aquifer. Load risk of pollution source was analyzed based on the potential of contamination and pollution degree. Assessment index of load risk of pollution source which involves the variety of pollution source, quantity of contaminants, releasing potential of pollutants, and distance were determined. The load risks of all sources considered by GIS overlay technology. Early warning model of groundwater pollution combined with ComGIS technology organically, the regional groundwater pollution early-warning information system was developed, and applied it into Qiqiha'er groundwater early warning. It can be used to evaluate current water quality, to forecast water quality changing trend, and to analyze space-time influencing range of groundwater quality by natural process and human activities. Keywords: groundwater pollution, early warning, aquifer vulnerability, pollution load, pollution risk, ComGIS

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images.

PubMed

Ameisen, David; Deroulers, Christophe; Perrier, Valérie; Bouhidel, Fatiha; Battistella, Maxime; Legrès, Luc; Janin, Anne; Bertheau, Philippe; Yunès, Jean-Baptiste

2014-01-01

Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow.

Quality assessment of color images based on the measure of just noticeable color difference

NASA Astrophysics Data System (ADS)

Chou, Chun-Hsien; Hsu, Yun-Hsiang

2014-01-01

Accurate assessment on the quality of color images is an important step to many image processing systems that convey visual information of the reproduced images. An accurate objective image quality assessment (IQA) method is expected to give the assessment result highly agreeing with the subjective assessment. To assess the quality of color images, many approaches simply apply the metric for assessing the quality of gray scale images to each of three color channels of the color image, neglecting the correlation among three color channels. In this paper, a metric for assessing color images' quality is proposed, in which the model of variable just-noticeable color difference (VJNCD) is employed to estimate the visibility thresholds of distortion inherent in each color pixel. With the estimated visibility thresholds of distortion, the proposed metric measures the average perceptible distortion in terms of the quantized distortion according to the perceptual error map similar to that defined by National Bureau of Standards (NBS) for converting the color difference enumerated by CIEDE2000 to the objective score of perceptual quality assessment. The perceptual error map in this case is designed for each pixel according to the visibility threshold estimated by the VJNCD model. The performance of the proposed metric is verified by assessing the test images in the LIVE database, and is compared with those of many well-know IQA metrics. Experimental results indicate that the proposed metric is an effective IQA method that can accurately predict the image quality of color images in terms of the correlation between objective scores and subjective evaluation.

Characterization of Three Maize Bacterial Artificial Chromosome Libraries toward Anchoring of the Physical Map to the Genetic Map Using High-Density Bacterial Artificial Chromosome Filter Hybridization1

PubMed Central

Yim, Young-Sun; Davis, Georgia L.; Duru, Ngozi A.; Musket, Theresa A.; Linton, Eric W.; Messing, Joachim W.; McMullen, Michael D.; Soderlund, Carol A.; Polacco, Mary L.; Gardiner, Jack M.; Coe, Edward H.

2002-01-01

Three maize (Zea mays) bacterial artificial chromosome (BAC) libraries were constructed from inbred line B73. High-density filter sets from all three libraries, made using different restriction enzymes (HindIII, EcoRI, and MboI, respectively), were evaluated with a set of complex probes including the185-bp knob repeat, ribosomal DNA, two telomere-associated repeat sequences, four centromere repeats, the mitochondrial genome, a multifragment chloroplast DNA probe, and bacteriophage λ. The results indicate that the libraries are of high quality with low contamination by organellar and λ-sequences. The use of libraries from multiple enzymes increased the chance of recovering each region of the genome. Ninety maize restriction fragment-length polymorphism core markers were hybridized to filters of the HindIII library, representing 6× coverage of the genome, to initiate development of a framework for anchoring BAC contigs to the intermated B73 × Mo17 genetic map and to mark the bin boundaries on the physical map. All of the clones used as hybridization probes detected at least three BACs. Twenty-two single-copy number core markers identified an average of 7.4 ± 3.3 positive clones, consistent with the expectation of six clones. This information is integrated into fingerprinting data generated by the Arizona Genomics Institute to assemble the BAC contigs using fingerprint contig and contributed to the process of physical map construction. PMID:12481051

WE-H-BRC-04: Implement Lean Methodology to Make Our Current Process of CT Simulation to Treatment More Efficient

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boddu, S; Morrow, A; Krishnamurthy, N

Purpose: Our goal is to implement lean methodology to make our current process of CT simulation to treatment more efficient. Methods: In this study, we implemented lean methodology and tools and employed flowchart in excel for process-mapping. We formed a group of physicians, physicists, dosimetrists, therapists and a clinical physics assistant and huddled bi-weekly to map current value streams. We performed GEMBA walks and observed current processes from scheduling patient CT Simulations to treatment plan approval. From this, the entire workflow was categorized into processes, sub-processes, and tasks. For each process we gathered data on touch time, first time quality,more » undesirable effects (UDEs), and wait-times from relevant members of each task. UDEs were binned per frequency of their occurrence. We huddled to map future state and to find solutions to high frequency UDEs. We implemented visual controls, hard stops, and documented issues found during chart checks prior to treatment plan approval. Results: We have identified approximately 64 UDEs in our current workflow that could cause delays, re-work, compromise the quality and safety of patient treatments, or cause wait times between 1 – 6 days. While some UDEs are unavoidable, such as re-planning due to patient weight loss, eliminating avoidable UDEs is our goal. In 2015, we found 399 issues with patient treatment plans, of which 261, 95 and 43 were low, medium and high severity, respectively. We also mapped patient-specific QA processes for IMRT/Rapid Arc and SRS/SBRT, involving 10 and 18 steps, respectively. From these, 13 UDEs were found and 5 were addressed that solved 20% of issues. Conclusion: We have successfully implemented lean methodology and tools. We are further mapping treatment site specific workflows to identify bottlenecks, potential breakdowns and personnel allocation and employ tools like failure mode effects analysis to mitigate risk factors to make this process efficient.« less

Wilderness quality mapping - the Australian experiences

Treesearch

Nick Sawyer

2015-01-01

By 1995 wilderness quality maps developed under the Australian Government's National Wilderness Inventory (NWI) program had been published for most of Australia, but few traces of the NWI now remain and the word "wilderness" has become almost unmentionable in government and professional land management circles. Yet its popular appeal is demonstrated by...

A globally complete map of supraglacial debris cover and a new toolkit for debris cover research

NASA Astrophysics Data System (ADS)

Herreid, Sam; Pellicciotti, Francesca

2017-04-01

A growing canon of literature is focused on resolving the processes and implications of debris cover on glaciers. However, this work is often confined to a handful of glaciers that were likely selected based on criteria optimizing their suitability to test a specific hypothesis or logistical ease. The role of debris cover in a glacier system is likely to not go overlooked in forthcoming research, yet the magnitude of this role at a global scale has not yet been fully described. Here, we present a map of debris cover for all glacierized regions on Earth including the Greenland Ice Sheet using 30 m Landsat data. This dataset will begin to open a wider context to the high quality, localized findings from the debris-covered glacier research community and help inform large-scale modeling efforts. A global map of debris cover also facilitates analysis attempting to isolate first order geomorphological and climate controls of supraglacial debris production. Furthering the objective of expanding the inclusion of debris cover in forthcoming research, we also present an under development suite of open-source, Python based tools. Requiring minimal and often freely available input data, we have automated the mapping of: i) debris cover, ii) ice cliffs, iii) debris cover evolution over the Landsat era and iv) glacier flow instabilities from altered debris structures. At the present time, debris extent is the only globally complete quantity but with the expanding repository of high quality global datasets and further tool development minimizing manual tasks and computational cost, we foresee all of these tools being applied globally in the near future.

The 3D Elevation Program—Flood risk management

USGS Publications Warehouse

Carswell, William J.; Lukas, Vicki

2018-01-25

Flood-damage reduction in the United States has been a longstanding but elusive societal goal. The national strategy for reducing flood damage has shifted over recent decades from a focus on construction of flood-control dams and levee systems to a three-pronged strategy to (1) improve the design and operation of such structures, (2) provide more accurate and accessible flood forecasting, and (3) shift the Federal Emergency Management Agency (FEMA) National Flood Insurance Program to a more balanced, less costly flood-insurance paradigm. Expanding the availability and use of high-quality, three-dimensional (3D) elevation information derived from modern light detection and ranging (lidar) technologies to provide essential terrain data poses a singular opportunity to dramatically enhance the effectiveness of all three components of this strategy. Additionally, FEMA, the National Weather Service, and the U.S. Geological Survey (USGS) have developed tools and joint program activities to support the national strategy.The USGS 3D Elevation Program (3DEP) has the programmatic infrastructure to produce and provide essential terrain data. This infrastructure includes (1) data acquisition partnerships that leverage funding and reduce duplicative efforts, (2) contracts with experienced private mapping firms that ensure acquisition of consistent, low-cost 3D elevation data, and (3) the technical expertise, standards, and specifications required for consistent, edge-to-edge utility across multiple collection platforms and public access unfettered by individual database designs and limitations.High-quality elevation data, like that collected through 3DEP, are invaluable for assessing and documenting flood risk and communicating detailed information to both responders and planners alike. Multiple flood-mapping programs make use of USGS streamflow and 3DEP data. Flood insurance rate maps, flood documentation studies, and flood-inundation map libraries are products of these programs.

A mapping review of international guidance on the management and care of amyotrophic lateral sclerosis (ALS).

PubMed

Janssens, Astrid I W A; Ruytings, Marijke; Al-Chalabi, Ammar; Chio, Adriano; Hardiman, Orla; Mcdermott, Christopher J; Meyer, Thomas; Mora, Gabriele; Van Damme, Philip; Van Den Berg, Leonard H; Vanhaecht, Kris; Winkler, Andrea S; Sermeus, Walter

2016-01-01

Management of ALS is suboptimal. Consequently, quality improvement interventions are needed to improve ALS care. An evidence-based insight into how patients should be managed is essential when developing quality improvement interventions. Therefore, this study aimed to map, categorize and summarize international guidance on the management and care of ALS and to identify gaps in this guidance by means of a mapping review. Literature was searched for clinical practice guidelines, quality indicators and evidence-based clinical summaries. A content analysis and meta-synthesis of the included literature was performed. Interventions and outcomes used in the management and care of ALS were identified and categorized. Furthermore, the amount of guidance underpinning these interventions and outcomes was analysed. Six clinical practice guidelines, one set of quality indicators and three evidence-based clinical summaries were identified. The results demonstrated that certain domains in ALS care, mainly disease-specific domains such as breathing and swallowing, are extensively addressed in the literature whereas other subjects, such as care coordination, receive little attention. In conclusion, this mapping review provides a scientific basis for targeting and developing the clinical content of a quality improvement intervention for the management of ALS.

24 CFR 200.1545 - Appeals of MAP Lender Review Board decisions.

Code of Federal Regulations, 2011 CFR

2011-04-01

...): MAP Lender Quality Assurance Enforcement § 200.1545 Appeals of MAP Lender Review Board decisions. (a... information included in the administrative record and any new information presented at the appeal conference... to overturn will be posted on HUD's MAP Web site. ...

24 CFR 200.1545 - Appeals of MAP Lender Review Board decisions.

Code of Federal Regulations, 2012 CFR

2012-04-01

...): MAP Lender Quality Assurance Enforcement § 200.1545 Appeals of MAP Lender Review Board decisions. (a... information included in the administrative record and any new information presented at the appeal conference... to overturn will be posted on HUD's MAP Web site. ...

24 CFR 200.1545 - Appeals of MAP Lender Review Board decisions.

Code of Federal Regulations, 2014 CFR

2014-04-01

...): MAP Lender Quality Assurance Enforcement § 200.1545 Appeals of MAP Lender Review Board decisions. (a... information included in the administrative record and any new information presented at the appeal conference... to overturn will be posted on HUD's MAP Web site. ...

24 CFR 200.1545 - Appeals of MAP Lender Review Board decisions.

Code of Federal Regulations, 2013 CFR

2013-04-01

...): MAP Lender Quality Assurance Enforcement § 200.1545 Appeals of MAP Lender Review Board decisions. (a... information included in the administrative record and any new information presented at the appeal conference... to overturn will be posted on HUD's MAP Web site. ...

Reliable Radiation Hybrid Maps: An Efficient Scalable Clustering-based Approach

USDA-ARS?s Scientific Manuscript database

The process of mapping markers from radiation hybrid mapping (RHM) experiments is equivalent to the traveling salesman problem and, thereby, has combinatorial complexity. As an additional problem, experiments typically result in some unreliable markers that reduce the overall quality of the map. We ...

Candidate gene association mapping for winter survival and spring regrowth in perennial ryegrass

Treesearch

Xiaoqing Yu; Paula M. Pijut; Stephen Byrne; Torben Asp; Guihua Bai; Yiwei Jiang

2015-01-01

Perennial ryegrass (Lolium perenne L.) is a widely cultivated cool-season grass species because of its high quality for forage and turf. Susceptibility to freezing damage limits its further use in temperate zones. The objective of this study was to identify candidate genes significantly associated with winter survival and spring regrowth in a global...

Dating the Moon: Teaching Lunar Stratigraphy and the Nature of Science

ERIC Educational Resources Information Center

Murphy, Edward; Bell, Randy

2013-01-01

As our closest celestial neighbor, the Moon is a familiar and inspiring object to investigate using a small telescope, binoculars, or even photographs or one of the many high quality maps available online. The wondrously varied surface of the Moon--filled with craters, mountains, volcanic flows, scarps, and rilles--makes the Moon an excellent…

a Free and Open Source Tool to Assess the Accuracy of Land Cover Maps: Implementation and Application to Lombardy Region (italy)

NASA Astrophysics Data System (ADS)

Bratic, G.; Brovelli, M. A.; Molinari, M. E.

2018-04-01

The availability of thematic maps has significantly increased over the last few years. Validation of these maps is a key factor in assessing their suitability for different applications. The evaluation of the accuracy of classified data is carried out through a comparison with a reference dataset and the generation of a confusion matrix from which many quality indexes can be derived. In this work, an ad hoc free and open source Python tool was implemented to automatically compute all the matrix confusion-derived accuracy indexes proposed by literature. The tool was integrated into GRASS GIS environment and successfully applied to evaluate the quality of three high-resolution global datasets (GlobeLand30, Global Urban Footprint, Global Human Settlement Layer Built-Up Grid) in the Lombardy Region area (Italy). In addition to the most commonly used accuracy measures, e.g. overall accuracy and Kappa, the tool allowed to compute and investigate less known indexes such as the Ground Truth and the Classification Success Index. The promising tool will be further extended with spatial autocorrelation analysis functions and made available to researcher and user community.

Supervised classification of continental shelf sediment off western Donegal, Ireland

NASA Astrophysics Data System (ADS)

Monteys, X.; Craven, K.; McCarron, S. G.

2017-12-01

Managing human impacts on marine ecosystems requires natural regions to be identified and mapped over a range of hierarchically nested scales. In recent years (2000-present) the Irish National Seabed Survey (INSS) and Integrated Mapping for the Sustainable Development of Ireland's Marine Resources programme (INFOMAR) (Geological Survey Ireland and Marine Institute collaborations) has provided unprecedented quantities of high quality data on Ireland's offshore territories. The increasing availability of large, detailed digital representations of these environments requires the application of objective and quantitative analyses. This study presents results of a new approach for sea floor sediment mapping based on an integrated analysis of INFOMAR multibeam bathymetric data (including the derivatives of slope and relative position), backscatter data (including derivatives of angular response analysis) and sediment groundtruthing over the continental shelf, west of Donegal. It applies a Geographic-Object-Based Image Analysis software package to provide a supervised classification of the surface sediment. This approach can provide a statistically robust, high resolution classification of the seafloor. Initial results display a differentiation of sediment classes and a reduction in artefacts from previously applied methodologies. These results indicate a methodology that could be used during physical habitat mapping and classification of marine environments.

Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana.

PubMed

Wittenberg, Alexander H J; van der Lee, Theo; Cayla, Cyril; Kilian, Andrzej; Visser, Richard G F; Schouten, Henk J

2005-08-01

Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds of restriction site based polymorphisms between genotypes and does not require DNA sequence information or site-specific oligonucleotides. This paper demonstrates the potential of DArT for genetic mapping by validating the quality and molecular basis of the markers, using the model plant Arabidopsis thaliana. Restriction fragments from a genomic representation of the ecotype Landsberg erecta (Ler) were amplified by PCR, individualized by cloning and spotted onto glass slides. The arrays were then hybridized with labeled genomic representations of the ecotypes Columbia (Col) and Ler and of individuals from an F(2) population obtained from a Col x Ler cross. The scoring of markers with specialized software was highly reproducible and 107 markers could unambiguously be ordered on a genetic linkage map. The marker order on the genetic linkage map coincided with the order on the DNA sequence map. Sequencing of the Ler markers and alignment with the available Col genome sequence confirmed that the polymorphism in DArT markers is largely a result of restriction site polymorphisms.

Very High Resolution Bathymetric Mapping at the Ridge 2000 Integrated Study Sites: Acquisition and Processing Protocols Developed During Recent Alvin Field Programs to the East Pacific Rise and Juan de Fuca Ridge

NASA Astrophysics Data System (ADS)

Ferrini, V.; Fornari, D. J.; Shank, T.; Tivey, M.; Kelley, D. S.; Glickson, D.; Carbotte, S. M.; Howland, J.; Whitcomb, L. L.; Yoerger, D.

2004-12-01

Recent field programs at the East Pacific Rise and Juan de Fuca Ridge have resulted in the refinement of data processing protocols that enable the rapid creation of high-resolution (meter-scale) bathymetric maps from pencil-beam altimetric sonar data that are routinely collected during DSV Alvin dives. With the development of the appropriate processing tools, the Imagenex sonar, a permanent sensor on Alvin, can be used by a broad range of scientists permitting the analysis of various data sets within the context of high-quality bathymetric maps. The data processing protocol integrates depth data recorded with Alvin's Paroscientific pressure sensor with bathymetric soundings collected with an Imagenex 675 kHz articulating (scanning) sonar system, and high-resolution navigational data acquired with DVLNAV, which includes bottom lock Doppler sonar and long baseline (LBL) navigation. Together these data allow us, for the first time, to visualize portions of Ridge 2000 Integrated Study Sites (ISS) at 1-m vertical and horizontal resolution. These maps resolve morphological details of structures within the summit trough at scales that are relevant to biological communities (e.g. hydrothermal vents, lava pillars, trough walls), thus providing the important geologic context necessary to better understand spatial patterns associated with integrated biological-hydrothermal-geological processes. The Imagenex sonar is also a permanent sensor on the Jason2 ROV, which is also equipped with an SM2000 (200 kHz) near-bottom multibeam sonar. In the future, it is envisioned that near-bottom multibeam sonars will be standard sensors on all National Deep Submergence Facility (NDSF) vehicles. Streamlining data processing protocols makes these datasets more accessible to NDSF users and ensures broad compatibility between data formats among NDSF vehicle systems and allied vehicles (e.g. ABE). Establishing data processing protocols and software suites, routinely calibrating sensors (e.g. Paroscientific depth sensors), and ensuring good navigational benchmarks between various cruises to the Ridge 2000 ISS improves the capability and quality of rapidly produced high-resolution bathymetric maps enabling users to optimize their diving programs. This is especially important within the context of augmenting high-resolution bathymetric data collection in ISS areas (several cruises to the same area over multiple years) and investigating possible changes in seafloor topography, hydrothermal vent features and/or biological communities that are related to tectonic or volcanic events.

Comparing the Potential of Multispectral and Hyperspectral Data for Monitoring Oil Spill Impact.

PubMed

Khanna, Shruti; Santos, Maria J; Ustin, Susan L; Shapiro, Kristen; Haverkamp, Paul J; Lay, Mui

2018-02-12

Oil spills from offshore drilling and coastal refineries often cause significant degradation of coastal environments. Early oil detection may prevent losses and speed up recovery if monitoring of the initial oil extent, oil impact, and recovery are in place. Satellite imagery data can provide a cost-effective alternative to expensive airborne imagery or labor intensive field campaigns for monitoring effects of oil spills on wetlands. However, these satellite data may be restricted in their ability to detect and map ecosystem recovery post-spill given their spectral measurement properties and temporal frequency. In this study, we assessed whether spatial and spectral resolution, and other sensor characteristics influence the ability to detect and map vegetation stress and mortality due to oil. We compared how well three satellite multispectral sensors: WorldView2, RapidEye and Landsat EMT+, match the ability of the airborne hyperspectral AVIRIS sensor to map oil-induced vegetation stress, recovery, and mortality after the DeepWater Horizon oil spill in the Gulf of Mexico in 2010. We found that finer spatial resolution (3.5 m) provided better delineation of the oil-impacted wetlands and better detection of vegetation stress along oiled shorelines in saltmarsh wetland ecosystems. As spatial resolution become coarser (3.5 m to 30 m) the ability to accurately detect and map stressed vegetation decreased. Spectral resolution did improve the detection and mapping of oil-impacted wetlands but less strongly than spatial resolution, suggesting that broad-band data may be sufficient to detect and map oil-impacted wetlands. AVIRIS narrow-band data performs better detecting vegetation stress, followed by WorldView2, RapidEye and then Landsat 15 m (pan sharpened) data. Higher quality sensor optics and higher signal-to-noise ratio (SNR) may also improve detection and mapping of oil-impacted wetlands; we found that resampled coarser resolution AVIRIS data with higher SNR performed better than either of the three satellite sensors. The ability to acquire imagery during certain times (midday, low tide, etc.) or a certain date (cloud-free, etc.) is also important in these tidal wetlands; WorldView2 imagery captured at high-tide detected a narrower band of shoreline affected by oil likely because some of the impacted wetland was below the tideline. These results suggest that while multispectral data may be sufficient for detecting the extent of oil-impacted wetlands, high spectral and spatial resolution, high-quality sensor characteristics, and the ability to control time of image acquisition may improve assessment and monitoring of vegetation stress and recovery post oil spills.

Comparing the Potential of Multispectral and Hyperspectral Data for Monitoring Oil Spill Impact

PubMed Central

Santos, Maria J.; Ustin, Susan L.; Haverkamp, Paul J.; Lay, Mui

2018-01-01

Oil spills from offshore drilling and coastal refineries often cause significant degradation of coastal environments. Early oil detection may prevent losses and speed up recovery if monitoring of the initial oil extent, oil impact, and recovery are in place. Satellite imagery data can provide a cost-effective alternative to expensive airborne imagery or labor intensive field campaigns for monitoring effects of oil spills on wetlands. However, these satellite data may be restricted in their ability to detect and map ecosystem recovery post-spill given their spectral measurement properties and temporal frequency. In this study, we assessed whether spatial and spectral resolution, and other sensor characteristics influence the ability to detect and map vegetation stress and mortality due to oil. We compared how well three satellite multispectral sensors: WorldView2, RapidEye and Landsat EMT+, match the ability of the airborne hyperspectral AVIRIS sensor to map oil-induced vegetation stress, recovery, and mortality after the DeepWater Horizon oil spill in the Gulf of Mexico in 2010. We found that finer spatial resolution (3.5 m) provided better delineation of the oil-impacted wetlands and better detection of vegetation stress along oiled shorelines in saltmarsh wetland ecosystems. As spatial resolution become coarser (3.5 m to 30 m) the ability to accurately detect and map stressed vegetation decreased. Spectral resolution did improve the detection and mapping of oil-impacted wetlands but less strongly than spatial resolution, suggesting that broad-band data may be sufficient to detect and map oil-impacted wetlands. AVIRIS narrow-band data performs better detecting vegetation stress, followed by WorldView2, RapidEye and then Landsat 15 m (pan sharpened) data. Higher quality sensor optics and higher signal-to-noise ratio (SNR) may also improve detection and mapping of oil-impacted wetlands; we found that resampled coarser resolution AVIRIS data with higher SNR performed better than either of the three satellite sensors. The ability to acquire imagery during certain times (midday, low tide, etc.) or a certain date (cloud-free, etc.) is also important in these tidal wetlands; WorldView2 imagery captured at high-tide detected a narrower band of shoreline affected by oil likely because some of the impacted wetland was below the tideline. These results suggest that while multispectral data may be sufficient for detecting the extent of oil-impacted wetlands, high spectral and spatial resolution, high-quality sensor characteristics, and the ability to control time of image acquisition may improve assessment and monitoring of vegetation stress and recovery post oil spills. PMID:29439504

Models of regional habitat quality and connectivity for pumas (Puma concolor) in the southwestern United States.

PubMed

Dickson, Brett G; Roemer, Gary W; McRae, Brad H; Rundall, Jill M

2013-01-01

The impact of landscape changes on the quality and connectivity of habitats for multiple wildlife species is of global conservation concern. In the southwestern United States, pumas (Puma concolor) are a well distributed and wide-ranging large carnivore that are sensitive to loss of habitat and to the disruption of pathways that connect their populations. We used an expert-based approach to define and derive variables hypothesized to influence the quality, location, and permeability of habitat for pumas within an area encompassing the entire states of Arizona and New Mexico. Survey results indicated that the presence of woodland and forest cover types, rugged terrain, and canyon bottom and ridgeline topography were expected to be important predictors of both high quality habitat and heightened permeability. As road density, distance to water, or human population density increased, the quality and permeability of habitats were predicted to decline. Using these results, we identified 67 high quality patches across the study area, and applied concepts from electronic circuit theory to estimate regional patterns of connectivity among these patches. Maps of current flow among individual pairs of patches highlighted possible pinch points along two major interstate highways. Current flow summed across all pairs of patches highlighted areas important for keeping the entire network connected, regardless of patch size. Cumulative current flow was highest in Arizona north of the Colorado River and around Grand Canyon National Park, and in the Sky Islands region owing to the many small habitat patches present. Our outputs present a first approximation of habitat quality and connectivity for dispersing pumas in the southwestern United States. Map results can be used to help target finer-scaled analyses in support of planning efforts concerned with the maintenance of puma metapopulation structure, as well as the protection of landscape features that facilitate the dispersal process.

Models of Regional Habitat Quality and Connectivity for Pumas (Puma concolor) in the Southwestern United States

PubMed Central

Dickson, Brett G.; Roemer, Gary W.; McRae, Brad H.; Rundall, Jill M.

2013-01-01

The impact of landscape changes on the quality and connectivity of habitats for multiple wildlife species is of global conservation concern. In the southwestern United States, pumas (Puma concolor) are a well distributed and wide-ranging large carnivore that are sensitive to loss of habitat and to the disruption of pathways that connect their populations. We used an expert-based approach to define and derive variables hypothesized to influence the quality, location, and permeability of habitat for pumas within an area encompassing the entire states of Arizona and New Mexico. Survey results indicated that the presence of woodland and forest cover types, rugged terrain, and canyon bottom and ridgeline topography were expected to be important predictors of both high quality habitat and heightened permeability. As road density, distance to water, or human population density increased, the quality and permeability of habitats were predicted to decline. Using these results, we identified 67 high quality patches across the study area, and applied concepts from electronic circuit theory to estimate regional patterns of connectivity among these patches. Maps of current flow among individual pairs of patches highlighted possible pinch points along two major interstate highways. Current flow summed across all pairs of patches highlighted areas important for keeping the entire network connected, regardless of patch size. Cumulative current flow was highest in Arizona north of the Colorado River and around Grand Canyon National Park, and in the Sky Islands region owing to the many small habitat patches present. Our outputs present a first approximation of habitat quality and connectivity for dispersing pumas in the southwestern United States. Map results can be used to help target finer-scaled analyses in support of planning efforts concerned with the maintenance of puma metapopulation structure, as well as the protection of landscape features that facilitate the dispersal process. PMID:24367495

An application of MC-SDSS for water supply management during a drought crisis.

PubMed

Jeihouni, Mehrdad; Toomanian, Ara; Alavipanah, Seyed Kazem; Shahabi, Mahmoud; Bazdar, Saba

2015-07-01

Climate change influences many countries' rainfall patterns and temperatures. In Iran, population growth has increased water demands. Tabriz is the capital of East Azerbaijan province, in northwestern Iran. A large proportion of the water required for this city is supplied from dams; thus, it is important to find alternatives to supply water for this city, which is the largest industrial city in northwestern Iran. In this paper, the groundwater quality was assessed using 70 wells in Tabriz Township. This work seeks to define the spatial distribution of groundwater quality parameters such as chloride, electrical conductivity (EC), pH, hardness, and sulfate using Geographic Information Systems (GIS) and geostatistics; map groundwater quality for drinking purposes employing multiple-criteria decision-making (MCDM), such as the Analytical Hierarchy Process (AHP) and fuzzy logic, in the study area; and develop an Spatial Decision Support System (SDSS) for managing a water crisis in the region. The map produced by the AHP is more accurate than the map produced using fuzzy logic because in the AHP, priorities were assigned to each parameter based on the weights given by water quality experts. The final map indicates that the groundwater quality increases from the north to the south and from the west to the east within the study area. During critical conditions, the groundwater quality maps and the presented SDSS core can be utilized by East Azerbaijan Regional Water Company to develop an SDSS to drill new wells or to select existing wells to supply drinking water to Tabriz City.

Measurable realistic image-based 3D mapping

NASA Astrophysics Data System (ADS)

Liu, W.; Wang, J.; Wang, J. J.; Ding, W.; Almagbile, A.

2011-12-01

Maps with 3D visual models are becoming a remarkable feature of 3D map services. High-resolution image data is obtained for the construction of 3D visualized models.The3D map not only provides the capabilities of 3D measurements and knowledge mining, but also provides the virtual experienceof places of interest, such as demonstrated in the Google Earth. Applications of 3D maps are expanding into the areas of architecture, property management, and urban environment monitoring. However, the reconstruction of high quality 3D models is time consuming, and requires robust hardware and powerful software to handle the enormous amount of data. This is especially for automatic implementation of 3D models and the representation of complicated surfacesthat still need improvements with in the visualisation techniques. The shortcoming of 3D model-based maps is the limitation of detailed coverage since a user can only view and measure objects that are already modelled in the virtual environment. This paper proposes and demonstrates a 3D map concept that is realistic and image-based, that enables geometric measurements and geo-location services. Additionally, image-based 3D maps provide more detailed information of the real world than 3D model-based maps. The image-based 3D maps use geo-referenced stereo images or panoramic images. The geometric relationships between objects in the images can be resolved from the geometric model of stereo images. The panoramic function makes 3D maps more interactive with users but also creates an interesting immersive circumstance. Actually, unmeasurable image-based 3D maps already exist, such as Google street view, but only provide virtual experiences in terms of photos. The topographic and terrain attributes, such as shapes and heights though are omitted. This paper also discusses the potential for using a low cost land Mobile Mapping System (MMS) to implement realistic image 3D mapping, and evaluates the positioning accuracy that a measureable realistic image-based (MRI) system can produce. The major contribution here is the implementation of measurable images on 3D maps to obtain various measurements from real scenes.

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

PubMed

Holt, Kathryn E; Teo, Yik Y; Li, Heng; Nair, Satheesh; Dougan, Gordon; Wain, John; Parkhill, Julian

2009-08-15

Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal parameters, which afforded > or =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40x, declining only slightly at read depths 20-40x. The method was implemented in Perl and relies on the opensource software Maq for read mapping and SNP calling. The Perl script is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/pools/.

Lake water quality mapping from Landsat

NASA Technical Reports Server (NTRS)

Scherz, J. P.

1977-01-01

In the project described remote sensing was used to check the quality of lake waters. The lakes of three Landsat scenes were mapped with the Bendix MDAS multispectral analysis system. From the MDAS color coded maps, the lake with the worst algae problem was easily located. The lake was closely checked, and the presence of 100 cows in the springs which fed the lake could be identified as the pollution source. The laboratory and field work involved in the lake classification project is described.

Maps & minds : mapping through the ages

USGS Publications Warehouse

,

1984-01-01

Throughout time, maps have expressed our understanding of our world. Human affairs have been influenced strongly by the quality of maps available to us at the major turning points in our history. "Maps & Minds" traces the ebb and flow of a few central ideas in the mainstream of mapping. Our expanding knowledge of our cosmic neighborhood stems largely from a small number of simple but grand ideas, vigorously pursued.

Detailed geomorphological mapping from high resolution DEM data (LiDAR, TanDEM-X): two case studies from Germany and SE Tibet

NASA Astrophysics Data System (ADS)

Loibl, D.

2012-04-01

Two major obstacles are hampering the production of high resolution geomorphological maps: the complexity of the subject that should be depicted and the enormous efforts necessary to obtain data by field work. The first factor prevented the establishment of a generally accepted map legend; the second hampered efforts to collect comprehensive sets of geomorphological data. This left geomorphologists to produce applied maps, focusing on very few layers of information and often not sticking to any of the numerous standards proposed in the second half of the 20th century. Technological progress of the recent years, especially in the fields of digital elevation models, GIS environments, and computational hardware, today offers promising opportunities to overcome the obstacles and to produce detailed geomorphological maps even for remote or inhospitable regions. The feasibility of detailed geomorphological mapping from two new sets of digital elevation data, the 1 m LiDAR DTM provided by Germany's State Surveying Authority and the upcoming TanDEM-X DEM, has been evaluated in two case studies from a low mountain range in Germany and a high mountain range in SE Tibet. The results indicate that most layers of information of classical geomorphological maps (e.g. the German GMK) can be extracted from this data at appropriate scales but that significant differences occur concerning the quality and the grades of certainty of key contents. Generally, an enhancement of the geomorphographical, especially the geomorphometrical, and a weakening of geomorphogenetical contents was observed. From these findings, theoretical, methodological, and cartographical remarks on detailed geomorphological mapping from DEM data in GIS environments were educed. As GIS environments decouple data and design and enable the geomorphologist to choose information layer combinations freely to fit research topics, a general purpose legend becomes obsolete. Yet, a unified data structure is demanded to ensure that data collected by different scientists or in different studies can be exchanged and reused.

Modeling microbial spoilage and quality of gilthead seabream fillets: combined effect of osmotic pretreatment, modified atmosphere packaging, and nisin on shelf life.

PubMed

Tsironi, Theofania N; Taoukis, Petros S

2010-05-01

The objective of the study was the kinetic modeling of the effect of storage temperature on the quality and shelf life of chilled fish, modified atmosphere-packed (MAP), and osmotically pretreated with the addition of nisin as antimicrobial agent. Fresh gilthead seabream (Sparus aurata) fillets were osmotically treated with 50% high dextrose equivalent maltodextrin (DE 47) plus 5% NaCl. Water loss, solid gain, salt content, and water activity were monitored throughout treatment and treatment conditions were selected for the shelf life study. Untreated and osmotically pretreated slices with and without nisin (2 x 10(4) IU/100 g osmotic solution), packed in air or modified atmosphere (50% CO(2)-50% air), and stored at controlled isothermal conditions (0, 5, 10, and 15 degrees C) were studied. Quality assessment and modeling were based on growth of several microbial indices, total volatile nitrogen, trimethylamine nitrogen, lipid oxidation (TBARS), and sensory scoring. Temperature dependence of quality loss rates was modeled by the Arrhenius equation, validated under dynamic conditions. Pretreated samples showed improved quality stability during subsequent refrigerated storage, in terms of microbial growth, chemical changes, and organoleptic degradation. Osmotic pretreatment with the addition of nisin in combination with MAP was the most effective treatment resulting in significant shelf life extension of gilthead seabream fillets (48 days compared to 10 days for the control at 0 degrees C).

Spatial distribution of intrinsic and scattering seismic attenuation in active volcanic islands - I: model and the case of Tenerife Island

NASA Astrophysics Data System (ADS)

Prudencio, Janire; Del Pezzo, Edoardo; García-Yeguas, Araceli; Ibáñez, Jesús M.

2013-12-01

The complex volcanic system of Tenerife Island is known to have a highly heterogeneous character, as recently confirmed by velocity tomography. We present new information derived from intrinsic quality factor inverse maps (Qi-1), scattering quality factor inverse maps (Qs-1) and total quality factor inverse maps (Qt-1) obtained for the same region. The data set used in this work is the result of the analysis of an active seismic experiment carried out, using offshore shots (air guns) recorded at over 85 onshore seismic stations. The estimates of the attenuation parameters are based on the assumption that the seismogram energy envelopes are determined by seismic energy diffusion processes occurring inside the island. Diffusion model parameters, proportional to Qi-1 and to Qs-1, are estimated from the inversion of the energy envelopes for any source-receiver couple. They are then weighted with a new graphical approach based on a Gaussian space probability function, which allowed us to create `2-D probabilistic maps' representing the space distribution of the attenuation parameters. The 2-D images obtained reveal the existence of a zone in the centre of the island characterized by the lowest attenuation effects. This effect is interpreted as highly rigid and cooled rocks. This low-attenuation region is bordered by zones of high attenuation, associated with the recent historical volcanic activity. We calculate the transport mean free path obtaining a value of around 4 km for the frequency range 6-12 Hz. This result is two orders of magnitude smaller than values calculated for the crust of the Earth. An absorption length between 10 and 14 km is associated with the average intrinsic attenuation parameter. These values, while small in the context of tectonic regions, are greater than those obtained in volcanic regions such as Vesuvius or Merapi. Such differences may be explained by the magnitude of the region of study, over three times larger than the aforementioned study areas. This also implies deeper sampling of the crust, which is evidenced by a change in the values of seismic attenuation. One important observation is that scattering attenuation dominates over the intrinsic effects, Qi being at least twice the value of Qs.

Single-crystal-like, c-axis oriented BaTiO3 thin films with high-performance on flexible metal templates for ferroelectric applications

NASA Astrophysics Data System (ADS)

Shin, Junsoo; Goyal, Amit; Jesse, Stephen; Kim, Dae Ho

2009-06-01

Epitaxial, c-axis oriented BaTiO3 thin films were deposited using pulsed laser ablation on flexible, polycrystalline Ni alloy tape with biaxially textured oxide buffer multilayers. The high quality of epitaxial BaTiO3 thin films with P4mm group symmetry was confirmed by x-ray diffraction. The microscopic ferroelectric domain structure and the piezoelectric domain switching in these films were confirmed via spatially resolved piezoresponse mapping and local hysteresis loops. Macroscopic measurements demonstrate that the films have well-saturated hysteresis loops with a high remanent polarization of ˜11.5 μC/cm2. Such high-quality, single-crystal-like BaTiO3 films on low-cost, polycrystalline, flexible Ni alloy substrates are attractive for applications in flexible lead-free ferroelectric devices.

Preliminary Assessment of the Impact of Culture on Understanding Cartographic Representations

NASA Astrophysics Data System (ADS)

Reolon Schmidt, Marcio Augusto; de Alencar Mendonça, André Luiz; Wieczorek, Małgorzata

2018-05-01

When users read a topographic map, they have to decode the represented information. This decoding passes through various processes in order to perceive, interpret, and understand the reported information. This set of processes is intrinsically a question that is influenced by culture. In particular, when one thinks of maps distributed across the internet or representations of audiences from different origins, the chance of efficient communication is reduced or at least influenced. Therefore, there should be some degree of common visual communication, which the symbology of maps can be applied in order to assure the adequate communication of phenomenon being represented on it. In this context, the present work aims at testing which evaluation factors influence the reading of maps, the understanding of space and reasoning of the map user, in particular national topographic maps. The assessment was through internet considering official map representation from Brazil and Poland and questionnaires. The results shown that conventional topographic maps on the same scale are not capable of producing the correct interpretation of the user from another culture. This means that formal training has a direct influence on the quality of the interpretation and spatial reasoning. Those results indicate that high levels of formal training positively influence the reading and interpretation results of the map and that there is no evidence that the specialists with the symbology of their own country have significantly positive results, when compared to those used maps with systematic mapping from another country.

Implementation science for ambulatory care safety: a novel method to develop context-sensitive interventions to reduce quality gaps in monitoring high-risk patients.

PubMed

McDonald, Kathryn M; Su, George; Lisker, Sarah; Patterson, Emily S; Sarkar, Urmimala

2017-06-24

Missed evidence-based monitoring in high-risk conditions (e.g., cancer) leads to delayed diagnosis. Current technological solutions fail to close this safety gap. In response, we aim to demonstrate a novel method to identify common vulnerabilities across clinics and generate attributes for context-flexible population-level monitoring solutions for widespread implementation to improve quality. Based on interviews with staff in otolaryngology, pulmonary, urology, breast, and gastroenterology clinics at a large urban publicly funded health system, we applied journey mapping to co-develop a visual representation of how patients are monitored for high-risk conditions. Using a National Academies framework and context-sensitivity theory, we identified common systems vulnerabilities and developed preliminary concepts for improving the robustness for monitoring patients with high-risk conditions ("design seeds" for potential solutions). Finally, we conducted a face validity and prioritization assessment of the design seeds with the original interviewees. We identified five high-risk situations for potentially consequential diagnostic delays arising from suboptimal patient monitoring. All situations related to detection of cancer (head and neck, lung, prostate, breast, and colorectal). With clinic participants we created 5 journey maps, each representing specialty clinic workflow directed at evidence-based monitoring. System vulnerabilities common to the different clinics included challenges with: data systems, communications handoffs, population-level tracking, and patient activities. Clinic staff ranked 13 design seeds (e.g., keep patient list up to date, use triggered notifications) addressing these vulnerabilities. Each design seed has unique evaluation criteria for the usefulness of potential solutions developed from the seed. We identified and ranked 13 design seeds that characterize situations that clinicians described 'wake them up at night', and thus could reduce their anxiety, save time, and improve monitoring of high-risk patients. We anticipate that the design seed approach promotes robust and context-sensitive solutions to safety and quality problems because it provides a human-centered link between the experienced problem and various solutions that can be tested for viability. The study also demonstrates a novel integration of industrial and human factors methods (journey mapping, process tracing and design seeds) linked to implementation theory for use in designing interventions that anticipate and reduce implementation challenges.

The use of LANDSAT-1 imagery in mapping and managing soil and range resources in the Sand Hills region of Nebraska

NASA Technical Reports Server (NTRS)

Seevers, P. M. (Principal Investigator); Drew, J. V.

1976-01-01

The author has identified the following significant results. Evaluation of ERTS-1 imagery for the Sand Hills region of Nebraska has shown that the data can be used to effectively measure several parameters of inventory needs. (1) Vegetative biomass can be estimated with a high degree of confidence using computer compatable tape data. (2) Soils can be mapped to the subgroup level with high altitude aircraft color infrared photography and to the association level with multitemporal ERTS-1 imagery. (3) Water quality in Sand Hills lakes can be estimated utilizing computer compatable tape data. (4) Center pivot irrigation can be inventoried from satellite data and can be monitored regarding site selection and relative success of establishment from high altitude aircraft color infrared photography. (5) ERTS-1 data is of exceptional value in wide-area inventory of natural resource data in the Sand Hills region of Nebraska.