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Sample records for automatically extracting molecular

  1. Automatic River Network Extraction from LIDAR Data

    Science.gov (United States)

    Maderal, E. N.; Valcarcel, N.; Delgado, J.; Sevilla, C.; Ojeda, J. C.

    2016-06-01

    National Geographic Institute of Spain (IGN-ES) has launched a new production system for automatic river network extraction for the Geospatial Reference Information (GRI) within hydrography theme. The goal is to get an accurate and updated river network, automatically extracted as possible. For this, IGN-ES has full LiDAR coverage for the whole Spanish territory with a density of 0.5 points per square meter. To implement this work, it has been validated the technical feasibility, developed a methodology to automate each production phase: hydrological terrain models generation with 2 meter grid size and river network extraction combining hydrographic criteria (topographic network) and hydrological criteria (flow accumulation river network), and finally the production was launched. The key points of this work has been managing a big data environment, more than 160,000 Lidar data files, the infrastructure to store (up to 40 Tb between results and intermediate files), and process; using local virtualization and the Amazon Web Service (AWS), which allowed to obtain this automatic production within 6 months, it also has been important the software stability (TerraScan-TerraSolid, GlobalMapper-Blue Marble , FME-Safe, ArcGIS-Esri) and finally, the human resources managing. The results of this production has been an accurate automatic river network extraction for the whole country with a significant improvement for the altimetric component of the 3D linear vector. This article presents the technical feasibility, the production methodology, the automatic river network extraction production and its advantages over traditional vector extraction systems.

  2. AUTOMATIC RIVER NETWORK EXTRACTION FROM LIDAR DATA

    Directory of Open Access Journals (Sweden)

    E. N. Maderal

    2016-06-01

    Full Text Available National Geographic Institute of Spain (IGN-ES has launched a new production system for automatic river network extraction for the Geospatial Reference Information (GRI within hydrography theme. The goal is to get an accurate and updated river network, automatically extracted as possible. For this, IGN-ES has full LiDAR coverage for the whole Spanish territory with a density of 0.5 points per square meter. To implement this work, it has been validated the technical feasibility, developed a methodology to automate each production phase: hydrological terrain models generation with 2 meter grid size and river network extraction combining hydrographic criteria (topographic network and hydrological criteria (flow accumulation river network, and finally the production was launched. The key points of this work has been managing a big data environment, more than 160,000 Lidar data files, the infrastructure to store (up to 40 Tb between results and intermediate files, and process; using local virtualization and the Amazon Web Service (AWS, which allowed to obtain this automatic production within 6 months, it also has been important the software stability (TerraScan-TerraSolid, GlobalMapper-Blue Marble , FME-Safe, ArcGIS-Esri and finally, the human resources managing. The results of this production has been an accurate automatic river network extraction for the whole country with a significant improvement for the altimetric component of the 3D linear vector. This article presents the technical feasibility, the production methodology, the automatic river network extraction production and its advantages over traditional vector extraction systems.

  3. Automatic extraction of legal concepts and definitions

    NARCIS (Netherlands)

    Winkels, R.; Hoekstra, R.

    2012-01-01

    In this paper we present the results of an experiment in automatic concept and definition extraction from written sources of law using relatively simple natural language and standard semantic web technology. The software was tested on six laws from the tax domain.

  4. Automatically extracting class diagrams from spreadsheets

    NARCIS (Netherlands)

    Hermans, F.; Pinzger, M.; Van Deursen, A.

    2010-01-01

    The use of spreadsheets to capture information is widespread in industry. Spreadsheets can thus be a wealthy source of domain information. We propose to automatically extract this information and transform it into class diagrams. The resulting class diagram can be used by software engineers to

  5. Automatic Contour Extraction from 2D Image

    Directory of Open Access Journals (Sweden)

    Panagiotis GIOANNIS

    2011-03-01

    Full Text Available Aim: To develop a method for automatic contour extraction from a 2D image. Material and Method: The method is divided in two basic parts where the user initially chooses the starting point and the threshold. Finally the method is applied to computed tomography of bone images. Results: An interesting method is developed which can lead to a successful boundary extraction of 2D images. Specifically data extracted from a computed tomography images can be used for 2D bone reconstruction. Conclusions: We believe that such an algorithm or part of it can be applied on several other applications for shape feature extraction in medical image analysis and generally at computer graphics.

  6. Automatic Feature Extraction from Planetary Images

    Science.gov (United States)

    Troglio, Giulia; Le Moigne, Jacqueline; Benediktsson, Jon A.; Moser, Gabriele; Serpico, Sebastiano B.

    2010-01-01

    With the launch of several planetary missions in the last decade, a large amount of planetary images has already been acquired and much more will be available for analysis in the coming years. The image data need to be analyzed, preferably by automatic processing techniques because of the huge amount of data. Although many automatic feature extraction methods have been proposed and utilized for Earth remote sensing images, these methods are not always applicable to planetary data that often present low contrast and uneven illumination characteristics. Different methods have already been presented for crater extraction from planetary images, but the detection of other types of planetary features has not been addressed yet. Here, we propose a new unsupervised method for the extraction of different features from the surface of the analyzed planet, based on the combination of several image processing techniques, including a watershed segmentation and the generalized Hough Transform. The method has many applications, among which image registration and can be applied to arbitrary planetary images.

  7. Refining Automatically Extracted Knowledge Bases Using Crowdsourcing.

    Science.gov (United States)

    Li, Chunhua; Zhao, Pengpeng; Sheng, Victor S; Xian, Xuefeng; Wu, Jian; Cui, Zhiming

    2017-01-01

    Machine-constructed knowledge bases often contain noisy and inaccurate facts. There exists significant work in developing automated algorithms for knowledge base refinement. Automated approaches improve the quality of knowledge bases but are far from perfect. In this paper, we leverage crowdsourcing to improve the quality of automatically extracted knowledge bases. As human labelling is costly, an important research challenge is how we can use limited human resources to maximize the quality improvement for a knowledge base. To address this problem, we first introduce a concept of semantic constraints that can be used to detect potential errors and do inference among candidate facts. Then, based on semantic constraints, we propose rank-based and graph-based algorithms for crowdsourced knowledge refining, which judiciously select the most beneficial candidate facts to conduct crowdsourcing and prune unnecessary questions. Our experiments show that our method improves the quality of knowledge bases significantly and outperforms state-of-the-art automatic methods under a reasonable crowdsourcing cost.

  8. An automatic molecular dispenser of chloride.

    Science.gov (United States)

    Alibrandi, Giuseppe; Amendola, Valeria; Bergamaschi, Greta; Dollenz, Riccardo; Fabbrizzi, Luigi; Licchelli, Maurizio; Lo Vecchio, Carmelo

    2013-03-11

    The combined activity of the 1.1.1-cryptand and of a dicopper(II) bistren cryptate complex including chloride makes the Cl(-) ion be continuously and slowly delivered to the solution, without any external intervention. The 1.1.1-cryptand slowly releases OH(-) ions, according to a defined kinetics, and each OH(-) ion displaces a Cl(-) ion from the cryptate. Chloride displacement induces a sharp colour change from bright yellow to aquamarine and can be conveniently monitored spectrophotometrically, even in diluted solutions. The 1.1.1-cryptand is the motor of a molecular dispenser (the dicopper(II) cryptate) delivering chloride ion automatically, from the inside of the solution. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Automatically Extracting Typical Syntactic Differences from Corpora

    NARCIS (Netherlands)

    Wiersma, Wybo; Nerbonne, John; Lauttamus, Timo

    We develop an aggregate measure of syntactic difference for automatically finding common syntactic differences between collections of text. With the use of this measure, it is possible to mine for differences between, for example, the English of learners and natives, or between related dialects. If

  10. Automatic fault extraction using a modified ant-colony algorithm

    International Nuclear Information System (INIS)

    Zhao, Junsheng; Sun, Sam Zandong

    2013-01-01

    The basis of automatic fault extraction is seismic attributes, such as the coherence cube which is always used to identify a fault by the minimum value. The biggest challenge in automatic fault extraction is noise, including that of seismic data. However, a fault has a better spatial continuity in certain direction, which makes it quite different from noise. Considering this characteristic, a modified ant-colony algorithm is introduced into automatic fault identification and tracking, where the gradient direction and direction consistency are used as constraints. Numerical model test results show that this method is feasible and effective in automatic fault extraction and noise suppression. The application of field data further illustrates its validity and superiority. (paper)

  11. Automatic extraction of planetary image features

    Science.gov (United States)

    LeMoigne-Stewart, Jacqueline J. (Inventor); Troglio, Giulia (Inventor); Benediktsson, Jon A. (Inventor); Serpico, Sebastiano B. (Inventor); Moser, Gabriele (Inventor)

    2013-01-01

    A method for the extraction of Lunar data and/or planetary features is provided. The feature extraction method can include one or more image processing techniques, including, but not limited to, a watershed segmentation and/or the generalized Hough Transform. According to some embodiments, the feature extraction method can include extracting features, such as, small rocks. According to some embodiments, small rocks can be extracted by applying a watershed segmentation algorithm to the Canny gradient. According to some embodiments, applying a watershed segmentation algorithm to the Canny gradient can allow regions that appear as close contours in the gradient to be segmented.

  12. Automatic target extraction in complicated background for camera calibration

    Science.gov (United States)

    Guo, Xichao; Wang, Cheng; Wen, Chenglu; Cheng, Ming

    2016-03-01

    In order to perform high precise calibration of camera in complex background, a novel design of planar composite target and the corresponding automatic extraction algorithm are presented. Unlike other commonly used target designs, the proposed target contains the information of feature point coordinate and feature point serial number simultaneously. Then based on the original target, templates are prepared by three geometric transformations and used as the input of template matching based on shape context. Finally, parity check and region growing methods are used to extract the target as final result. The experimental results show that the proposed method for automatic extraction and recognition of the proposed target is effective, accurate and reliable.

  13. Automatic Statistics Extraction for Amateur Soccer Videos

    NARCIS (Netherlands)

    Gemert, J.C. van; Schavemaker, J.G.M.; Bonenkamp, C.W.B.

    2014-01-01

    Amateur soccer statistics have interesting applications such as providing insights to improve team performance, individual coaching, monitoring team progress and personal or team entertainment. Professional soccer statistics are extracted with labor intensive expensive manual effort which is not

  14. Automatic extraction of left ventricle in SPECT myocardial perfusion imaging

    International Nuclear Information System (INIS)

    Liu Li; Zhao Shujun; Yao Zhiming; Wang Daoyu

    1999-01-01

    An automatic method of extracting left ventricle from SPECT myocardial perfusion data was introduced. This method was based on the least square analysis of the positions of all short-axis slices pixels from the half sphere-cylinder myocardial model, and used a iterative reconstruction technique to automatically cut off the non-left ventricular tissue from the perfusion images. Thereby, this technique provided the bases for further quantitative analysis

  15. A Risk Assessment System with Automatic Extraction of Event Types

    Science.gov (United States)

    Capet, Philippe; Delavallade, Thomas; Nakamura, Takuya; Sandor, Agnes; Tarsitano, Cedric; Voyatzi, Stavroula

    In this article we describe the joint effort of experts in linguistics, information extraction and risk assessment to integrate EventSpotter, an automatic event extraction engine, into ADAC, an automated early warning system. By detecting as early as possible weak signals of emerging risks ADAC provides a dynamic synthetic picture of situations involving risk. The ADAC system calculates risk on the basis of fuzzy logic rules operated on a template graph whose leaves are event types. EventSpotter is based on a general purpose natural language dependency parser, XIP, enhanced with domain-specific lexical resources (Lexicon-Grammar). Its role is to automatically feed the leaves with input data.

  16. Automatic Definition Extraction and Crossword Generation From Spanish News Text

    Directory of Open Access Journals (Sweden)

    Jennifer Esteche

    2017-08-01

    Full Text Available This paper describes the design and implementation of a system that takes Spanish texts and generates crosswords (board and definitions in a fully automatic way using definitions extracted from those texts. Our solution divides the problem in two parts: a definition extraction module that applies pattern matching implemented in Python, and a crossword generation module that uses a greedy strategy implemented in Prolog. The system achieves 73% precision and builds crosswords similar to those built by humans.

  17. An enhanced model for automatically extracting topic phrase from ...

    African Journals Online (AJOL)

    The key benefit foreseen from this automatic document classification is not only related to search engines, but also to many other fields like, document organization, text filtering and semantic index managing. Key words: Keyphrase extraction, machine learning, search engine snippet, document classification, topic tracking ...

  18. Temporally rendered automatic cloud extraction (TRACE) system

    Science.gov (United States)

    Bodrero, Dennis M.; Yale, James G.; Davis, Roger E.; Rollins, John M.

    1999-10-01

    Smoke/obscurant testing requires that 2D cloud extent be extracted from visible and thermal imagery. These data are used alone or in combination with 2D data from other aspects to make 3D calculations of cloud properties, including dimensions, volume, centroid, travel, and uniformity. Determining cloud extent from imagery has historically been a time-consuming manual process. To reduce time and cost associated with smoke/obscurant data processing, automated methods to extract cloud extent from imagery were investigated. The TRACE system described in this paper was developed and implemented at U.S. Army Dugway Proving Ground, UT by the Science and Technology Corporation--Acuity Imaging Incorporated team with Small Business Innovation Research funding. TRACE uses dynamic background subtraction and 3D fast Fourier transform as primary methods to discriminate the smoke/obscurant cloud from the background. TRACE has been designed to run on a PC-based platform using Windows. The PC-Windows environment was chosen for portability, to give TRACE the maximum flexibility in terms of its interaction with peripheral hardware devices such as video capture boards, removable media drives, network cards, and digital video interfaces. Video for Windows provides all of the necessary tools for the development of the video capture utility in TRACE and allows for interchangeability of video capture boards without any software changes. TRACE is designed to take advantage of future upgrades in all aspects of its component hardware. A comparison of cloud extent determined by TRACE with manual method is included in this paper.

  19. Automatically extracting information needs from complex clinical questions.

    Science.gov (United States)

    Cao, Yong-gang; Cimino, James J; Ely, John; Yu, Hong

    2010-12-01

    Clinicians pose complex clinical questions when seeing patients, and identifying the answers to those questions in a timely manner helps improve the quality of patient care. We report here on two natural language processing models, namely, automatic topic assignment and keyword identification, that together automatically and effectively extract information needs from ad hoc clinical questions. Our study is motivated in the context of developing the larger clinical question answering system AskHERMES (Help clinicians to Extract and aRrticulate Multimedia information for answering clinical quEstionS). We developed supervised machine-learning systems to automatically assign predefined general categories (e.g. etiology, procedure, and diagnosis) to a question. We also explored both supervised and unsupervised systems to automatically identify keywords that capture the main content of the question. We evaluated our systems on 4654 annotated clinical questions that were collected in practice. We achieved an F1 score of 76.0% for the task of general topic classification and 58.0% for keyword extraction. Our systems have been implemented into the larger question answering system AskHERMES. Our error analyses suggested that inconsistent annotation in our training data have hurt both question analysis tasks. Our systems, available at http://www.askhermes.org, can automatically extract information needs from both short (the number of word tokens 20), and from both well-structured and ill-formed questions. We speculate that the performance of general topic classification and keyword extraction can be further improved if consistently annotated data are made available. Copyright © 2010 Elsevier Inc. All rights reserved.

  20. Automatic building extraction using LiDAR and aerial photographs

    Directory of Open Access Journals (Sweden)

    Melis Uzar

    Full Text Available This paper presents an automatic building extraction approach using LiDAR data and aerial photographs from a multi-sensor system positioned at the same platform. The automatic building extraction approach consists of segmentation, analysis and classification steps based on object-based image analysis. The chessboard, contrast split and multi-resolution segmentation methods were used in the segmentation step. The determined object primitives in segmentation, such as scale parameter, shape, completeness, brightness, and statistical parameters, were used to determine threshold values for classification in the analysis step. The rule-based classification was carried out with defined decision rules based on determined object primitives and fuzzy rules. In this study, hierarchical classification was preferred. First, the vegetation and ground classes were generated; the building class was then extracted. The NDVI, slope and Hough images were generated and used to avoid confusing the building class with other classes. The intensity images generated from the LiDAR data and morphological operations were utilized to improve the accuracy of the building class. The proposed approach achieved an overall accuracy of approximately 93% for the target class in a suburban neighborhood, which was the study area. Moreover, completeness (96.73% and correctness (95.02% analyses were performed by comparing the automatically extracted buildings and reference data.

  1. Design of Automatic Extraction Algorithm of Knowledge Points for MOOCs

    Directory of Open Access Journals (Sweden)

    Haijian Chen

    2015-01-01

    Full Text Available In recent years, Massive Open Online Courses (MOOCs are very popular among college students and have a powerful impact on academic institutions. In the MOOCs environment, knowledge discovery and knowledge sharing are very important, which currently are often achieved by ontology techniques. In building ontology, automatic extraction technology is crucial. Because the general methods of text mining algorithm do not have obvious effect on online course, we designed automatic extracting course knowledge points (AECKP algorithm for online course. It includes document classification, Chinese word segmentation, and POS tagging for each document. Vector Space Model (VSM is used to calculate similarity and design the weight to optimize the TF-IDF algorithm output values, and the higher scores will be selected as knowledge points. Course documents of “C programming language” are selected for the experiment in this study. The results show that the proposed approach can achieve satisfactory accuracy rate and recall rate.

  2. Rapid automatic keyword extraction for information retrieval and analysis

    Science.gov (United States)

    Rose, Stuart J [Richland, WA; Cowley,; E, Wendy [Richland, WA; Crow, Vernon L [Richland, WA; Cramer, Nicholas O [Richland, WA

    2012-03-06

    Methods and systems for rapid automatic keyword extraction for information retrieval and analysis. Embodiments can include parsing words in an individual document by delimiters, stop words, or both in order to identify candidate keywords. Word scores for each word within the candidate keywords are then calculated based on a function of co-occurrence degree, co-occurrence frequency, or both. Based on a function of the word scores for words within the candidate keyword, a keyword score is calculated for each of the candidate keywords. A portion of the candidate keywords are then extracted as keywords based, at least in part, on the candidate keywords having the highest keyword scores.

  3. Automatic sentence extraction for the detection of scientific paper relations

    Science.gov (United States)

    Sibaroni, Y.; Prasetiyowati, S. S.; Miftachudin, M.

    2018-03-01

    The relations between scientific papers are very useful for researchers to see the interconnection between scientific papers quickly. By observing the inter-article relationships, researchers can identify, among others, the weaknesses of existing research, performance improvements achieved to date, and tools or data typically used in research in specific fields. So far, methods that have been developed to detect paper relations include machine learning and rule-based methods. However, a problem still arises in the process of sentence extraction from scientific paper documents, which is still done manually. This manual process causes the detection of scientific paper relations longer and inefficient. To overcome this problem, this study performs an automatic sentences extraction while the paper relations are identified based on the citation sentence. The performance of the built system is then compared with that of the manual extraction system. The analysis results suggested that the automatic sentence extraction indicates a very high level of performance in the detection of paper relations, which is close to that of manual sentence extraction.

  4. Automatic extraction of drug indications from FDA drug labels.

    Science.gov (United States)

    Khare, Ritu; Wei, Chih-Hsuan; Lu, Zhiyong

    2014-01-01

    Extracting computable indications, i.e. drug-disease treatment relationships, from narrative drug resources is the key for building a gold standard drug indication repository. The two steps to the extraction problem are disease named-entity recognition (NER) to identify disease mentions from a free-text description and disease classification to distinguish indications from other disease mentions in the description. While there exist many tools for disease NER, disease classification is mostly achieved through human annotations. For example, we recently resorted to human annotations to prepare a corpus, LabeledIn, capturing structured indications from the drug labels submitted to FDA by pharmaceutical companies. In this study, we present an automatic end-to-end framework to extract structured and normalized indications from FDA drug labels. In addition to automatic disease NER, a key component of our framework is a machine learning method that is trained on the LabeledIn corpus to classify the NER-computed disease mentions as "indication vs. non-indication." Through experiments with 500 drug labels, our end-to-end system delivered 86.3% F1-measure in drug indication extraction, with 17% improvement over baseline. Further analysis shows that the indication classifier delivers a performance comparable to human experts and that the remaining errors are mostly due to disease NER (more than 50%). Given its performance, we conclude that our end-to-end approach has the potential to significantly reduce human annotation costs.

  5. AUTOMATIC EXTRACTION OF BUILDING OUTLINE FROM HIGH RESOLUTION AERIAL IMAGERY

    Directory of Open Access Journals (Sweden)

    Y. Wang

    2016-06-01

    Full Text Available In this paper, a new approach for automated extraction of building boundary from high resolution imagery is proposed. The proposed approach uses both geometric and spectral properties of a building to detect and locate buildings accurately. It consists of automatic generation of high quality point cloud from the imagery, building detection from point cloud, classification of building roof and generation of building outline. Point cloud is generated from the imagery automatically using semi-global image matching technology. Buildings are detected from the differential surface generated from the point cloud. Further classification of building roof is performed in order to generate accurate building outline. Finally classified building roof is converted into vector format. Numerous tests have been done on images in different locations and results are presented in the paper.

  6. Automatic information extraction from unstructured mammography reports using distributed semantics.

    Science.gov (United States)

    Gupta, Anupama; Banerjee, Imon; Rubin, Daniel L

    2018-02-01

    To date, the methods developed for automated extraction of information from radiology reports are mainly rule-based or dictionary-based, and, therefore, require substantial manual effort to build these systems. Recent efforts to develop automated systems for entity detection have been undertaken, but little work has been done to automatically extract relations and their associated named entities in narrative radiology reports that have comparable accuracy to rule-based methods. Our goal is to extract relations in a unsupervised way from radiology reports without specifying prior domain knowledge. We propose a hybrid approach for information extraction that combines dependency-based parse tree with distributed semantics for generating structured information frames about particular findings/abnormalities from the free-text mammography reports. The proposed IE system obtains a F 1 -score of 0.94 in terms of completeness of the content in the information frames, which outperforms a state-of-the-art rule-based system in this domain by a significant margin. The proposed system can be leveraged in a variety of applications, such as decision support and information retrieval, and may also easily scale to other radiology domains, since there is no need to tune the system with hand-crafted information extraction rules. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Morphological Feature Extraction for Automatic Registration of Multispectral Images

    Science.gov (United States)

    Plaza, Antonio; LeMoigne, Jacqueline; Netanyahu, Nathan S.

    2007-01-01

    The task of image registration can be divided into two major components, i.e., the extraction of control points or features from images, and the search among the extracted features for the matching pairs that represent the same feature in the images to be matched. Manual extraction of control features can be subjective and extremely time consuming, and often results in few usable points. On the other hand, automated feature extraction allows using invariant target features such as edges, corners, and line intersections as relevant landmarks for registration purposes. In this paper, we present an extension of a recently developed morphological approach for automatic extraction of landmark chips and corresponding windows in a fully unsupervised manner for the registration of multispectral images. Once a set of chip-window pairs is obtained, a (hierarchical) robust feature matching procedure, based on a multiresolution overcomplete wavelet decomposition scheme, is used for registration purposes. The proposed method is validated on a pair of remotely sensed scenes acquired by the Advanced Land Imager (ALI) multispectral instrument and the Hyperion hyperspectral instrument aboard NASA's Earth Observing-1 satellite.

  8. Reference region automatic extraction in dynamic [(11)C]PIB.

    Science.gov (United States)

    Ikoma, Yoko; Edison, Paul; Ramlackhansingh, Anil; Brooks, David J; Turkheimer, Federico E

    2013-11-01

    The positron emission tomography (PET) radiotracer [(11)C]Pittsburgh Compound B (PIB) is a marker of amyloid plaque deposition in brain, and binding potential is usually quantified using the cerebellum as a reference where the specific binding is negligible. The use of the cerebellum as a reference, however, has been questioned by the reported cerebellar [(11)C]PIB retention in familial Alzheimer's disease (AD) subjects. In this work, we developed a supervised clustering procedure for the automatic extraction of a reference region in [(11)C]PIB studies. Supervised clustering models each gray matter voxel as the linear combination of three predefined kinetic classes, normal and lesion gray matter, and blood pool, and extract reference voxels in which the contribution of the normal gray matter class is high. In the validation with idiopathic AD subjects, supervised clustering extracted reference voxels mostly in the cerebellum that indicated little specific [(11)C]PIB binding, and total distribution volumes of the extracted region were lower than those of the cerebellum. Next, the methodology was applied to the familial AD cohort where the cerebellar amyloid load had been demonstrated previously, resulting in higher binding potential compared with that obtained with the cerebellar reference. The supervised clustering method is a useful tool for the accurate quantification of [(11)C]PIB studies.

  9. Automatically extracting functionally equivalent proteins from SwissProt

    Directory of Open Access Journals (Sweden)

    Martin Andrew CR

    2008-10-01

    Full Text Available Abstract Background There is a frequent need to obtain sets of functionally equivalent homologous proteins (FEPs from different species. While it is usually the case that orthology implies functional equivalence, this is not always true; therefore datasets of orthologous proteins are not appropriate. The information relevant to extracting FEPs is contained in databanks such as UniProtKB/Swiss-Prot and a manual analysis of these data allow FEPs to be extracted on a one-off basis. However there has been no resource allowing the easy, automatic extraction of groups of FEPs – for example, all instances of protein C. We have developed FOSTA, an automatically generated database of FEPs annotated as having the same function in UniProtKB/Swiss-Prot which can be used for large-scale analysis. The method builds a candidate list of homologues and filters out functionally diverged proteins on the basis of functional annotations using a simple text mining approach. Results Large scale evaluation of our FEP extraction method is difficult as there is no gold-standard dataset against which the method can be benchmarked. However, a manual analysis of five protein families confirmed a high level of performance. A more extensive comparison with two manually verified functional equivalence datasets also demonstrated very good performance. Conclusion In summary, FOSTA provides an automated analysis of annotations in UniProtKB/Swiss-Prot to enable groups of proteins already annotated as functionally equivalent, to be extracted. Our results demonstrate that the vast majority of UniProtKB/Swiss-Prot functional annotations are of high quality, and that FOSTA can interpret annotations successfully. Where FOSTA is not successful, we are able to highlight inconsistencies in UniProtKB/Swiss-Prot annotation. Most of these would have presented equal difficulties for manual interpretation of annotations. We discuss limitations and possible future extensions to FOSTA, and

  10. Automatic Metadata Extraction - The High Energy Physics Use Case

    CERN Document Server

    Boyd, Joseph; Rajman, Martin

    Automatic metadata extraction (AME) of scientific papers has been described as one of the hardest problems in document engineering. Heterogeneous content, varying style, and unpredictable placement of article components render the problem inherently indeterministic. Conditional random fields (CRF), a machine learning technique, can be used to classify document metadata amidst this uncertainty, annotating document contents with semantic labels. High energy physics (HEP) papers, such as those written at CERN, have unique content and structural characteristics, with scientific collaborations of thousands of authors altering article layouts dramatically. The distinctive qualities of these papers necessitate the creation of specialised datasets and model features. In this work we build an unprecedented training set of HEP papers and propose and evaluate a set of innovative features for CRF models. We build upon state-of-the-art AME software, GROBID, a tool coordinating a hierarchy of CRF models in a full document ...

  11. Image-based mobile service: automatic text extraction and translation

    Science.gov (United States)

    Berclaz, Jérôme; Bhatti, Nina; Simske, Steven J.; Schettino, John C.

    2010-01-01

    We present a new mobile service for the translation of text from images taken by consumer-grade cell-phone cameras. Such capability represents a new paradigm for users where a simple image provides the basis for a service. The ubiquity and ease of use of cell-phone cameras enables acquisition and transmission of images anywhere and at any time a user wishes, delivering rapid and accurate translation over the phone's MMS and SMS facilities. Target text is extracted completely automatically, requiring no bounding box delineation or related user intervention. The service uses localization, binarization, text deskewing, and optical character recognition (OCR) in its analysis. Once the text is translated, an SMS message is sent to the user with the result. Further novelties include that no software installation is required on the handset, any service provider or camera phone can be used, and the entire service is implemented on the server side.

  12. EXIF Custom: Automatic image metadata extraction for Scratchpads and Drupal

    Directory of Open Access Journals (Sweden)

    Ed Baker

    2013-09-01

    Full Text Available Many institutions and individuals use embedded metadata to aid in the management of their image collections. Many deskop image management solutions such as Adobe Bridge and online tools such as Flickr also make use of embedded metadata to describe, categorise and license images. Until now Scratchpads (a data management system and virtual research environment for biodiversity  have not made use of these metadata, and users have had to manually re-enter this information if they have wanted to display it on their Scratchpad site. The Drupal described here allows users to map metadata embedded in their images to the associated field in the Scratchpads image form using one or more customised mappings. The module works seamlessly with the bulk image uploader used on Scratchpads and it is therefore possible to upload hundreds of images easily with automatic metadata (EXIF, XMP and IPTC extraction and mapping.

  13. Automatic Extraction of Road Markings from Mobile Laser Scanning Data

    Science.gov (United States)

    Ma, H.; Pei, Z.; Wei, Z.; Zhong, R.

    2017-09-01

    Road markings as critical feature in high-defination maps, which are Advanced Driver Assistance System (ADAS) and self-driving technology required, have important functions in providing guidance and information to moving cars. Mobile laser scanning (MLS) system is an effective way to obtain the 3D information of the road surface, including road markings, at highway speeds and at less than traditional survey costs. This paper presents a novel method to automatically extract road markings from MLS point clouds. Ground points are first filtered from raw input point clouds using neighborhood elevation consistency method. The basic assumption of the method is that the road surface is smooth. Points with small elevation-difference between neighborhood are considered to be ground points. Then ground points are partitioned into a set of profiles according to trajectory data. The intensity histogram of points in each profile is generated to find intensity jumps in certain threshold which inversely to laser distance. The separated points are used as seed points to region grow based on intensity so as to obtain road mark of integrity. We use the point cloud template-matching method to refine the road marking candidates via removing the noise clusters with low correlation coefficient. During experiment with a MLS point set of about 2 kilometres in a city center, our method provides a promising solution to the road markings extraction from MLS data.

  14. AUTOMATIC EXTRACTION OF ROAD MARKINGS FROM MOBILE LASER SCANNING DATA

    Directory of Open Access Journals (Sweden)

    H. Ma

    2017-09-01

    Full Text Available Road markings as critical feature in high-defination maps, which are Advanced Driver Assistance System (ADAS and self-driving technology required, have important functions in providing guidance and information to moving cars. Mobile laser scanning (MLS system is an effective way to obtain the 3D information of the road surface, including road markings, at highway speeds and at less than traditional survey costs. This paper presents a novel method to automatically extract road markings from MLS point clouds. Ground points are first filtered from raw input point clouds using neighborhood elevation consistency method. The basic assumption of the method is that the road surface is smooth. Points with small elevation-difference between neighborhood are considered to be ground points. Then ground points are partitioned into a set of profiles according to trajectory data. The intensity histogram of points in each profile is generated to find intensity jumps in certain threshold which inversely to laser distance. The separated points are used as seed points to region grow based on intensity so as to obtain road mark of integrity. We use the point cloud template-matching method to refine the road marking candidates via removing the noise clusters with low correlation coefficient. During experiment with a MLS point set of about 2 kilometres in a city center, our method provides a promising solution to the road markings extraction from MLS data.

  15. Automatic and unsupervised snore sound extraction from respiratory sound signals.

    Science.gov (United States)

    Azarbarzin, Ali; Moussavi, Zahra M K

    2011-05-01

    In this paper, an automatic and unsupervised snore detection algorithm is proposed. The respiratory sound signals of 30 patients with different levels of airway obstruction were recorded by two microphones: one placed over the trachea (the tracheal microphone), and the other was a freestanding microphone (the ambient microphone). All the recordings were done simultaneously with full-night polysomnography during sleep. The sound activity episodes were identified using the vertical box (V-Box) algorithm. The 500-Hz subband energy distribution and principal component analysis were used to extract discriminative features from sound episodes. An unsupervised fuzzy C-means clustering algorithm was then deployed to label the sound episodes as either snore or no-snore class, which could be breath sound, swallowing sound, or any other noise. The algorithm was evaluated using manual annotation of the sound signals. The overall accuracy of the proposed algorithm was found to be 98.6% for tracheal sounds recordings, and 93.1% for the sounds recorded by the ambient microphone. © 2011 IEEE

  16. Automatic Knowledge Extraction and Knowledge Structuring for a National Term Bank

    DEFF Research Database (Denmark)

    Lassen, Tine; Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2011-01-01

    This paper gives an introduction to the plans and ongoing work in a project, the aim of which is to develop methods for automatic knowledge extraction and automatic construction and updating of ontologies. The project also aims at developing methods for automatic merging of terminological data fr...... various existing sources, as well as methods for target group oriented knowledge dissemination. In this paper, we mainly focus on the plans for automatic knowledge extraction and knowledge structuring that will result in ontologies for a national term bank....

  17. A method for automatically extracting infectious disease-related primers and probes from the literature

    Directory of Open Access Journals (Sweden)

    Pérez-Rey David

    2010-08-01

    Full Text Available Abstract Background Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is becoming increasingly important for researchers to navigate this important information. In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature. These phases are: (1 convert each document into a tree of paper sections, (2 detect the candidate sequences using a set of finite state machine-based recognizers, (3 refine problem sequences using a rule-based expert system, and (4 annotate the extracted sequences with their related organism/gene information. Results We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organism/gene annotations were manually evaluated by a panel of molecular biologists. The results of the evaluation show that our approach is suitable for automatically extracting DNA sequences, achieving precision/recall rates of 97.98% and 95.77%, respectively. In addition, 76.66% of the detected sequences were correctly annotated with their organism name. The system also provided correct gene-related information for 46.18% of the sequences assigned a correct organism name. Conclusions We believe that the proposed method can facilitate routine tasks for biomedical researchers using molecular methods to diagnose and prescribe different infectious diseases. In addition, the proposed method can be expanded to detect and extract other biological sequences from the literature. The extracted information can also be used to readily update available primer/probe databases or to create new databases from scratch.

  18. Automatic archaeological feature extraction from satellite VHR images

    Science.gov (United States)

    Jahjah, Munzer; Ulivieri, Carlo

    2010-05-01

    Archaeological applications need a methodological approach on a variable scale able to satisfy the intra-site (excavation) and the inter-site (survey, environmental research). The increased availability of high resolution and micro-scale data has substantially favoured archaeological applications and the consequent use of GIS platforms for reconstruction of archaeological landscapes based on remotely sensed data. Feature extraction of multispectral remotely sensing image is an important task before any further processing. High resolution remote sensing data, especially panchromatic, is an important input for the analysis of various types of image characteristics; it plays an important role in the visual systems for recognition and interpretation of given data. The methods proposed rely on an object-oriented approach based on a theory for the analysis of spatial structures called mathematical morphology. The term "morphology" stems from the fact that it aims at analysing object shapes and forms. It is mathematical in the sense that the analysis is based on the set theory, integral geometry, and lattice algebra. Mathematical morphology has proven to be a powerful image analysis technique; two-dimensional grey tone images are seen as three-dimensional sets by associating each image pixel with an elevation proportional to its intensity level. An object of known shape and size, called the structuring element, is then used to investigate the morphology of the input set. This is achieved by positioning the origin of the structuring element to every possible position of the space and testing, for each position, whether the structuring element either is included or has a nonempty intersection with the studied set. The shape and size of the structuring element must be selected according to the morphology of the searched image structures. Other two feature extraction techniques were used, eCognition and ENVI module SW, in order to compare the results. These techniques were

  19. Automatic extraction of syntactic patterns for dependency parsing in noun phrase chunks

    Directory of Open Access Journals (Sweden)

    Mihaela Colhon

    2014-05-01

    Full Text Available In this article we present a method for automatic extraction of syntactic patterns that are used to develop a dependency parsing method. The patterns have been extracted from a corpus automatically annotated for tokens, sentences’ borders, parts of speech and noun phrases, and manually annotated for dependency relations between words. The evaluation shows promising results in the case of an order-free language.

  20. ARSENAL: Automatic Requirements Specification Extraction from Natural Language

    OpenAIRE

    Ghosh, Shalini; Elenius, Daniel; Li, Wenchao; Lincoln, Patrick; Shankar, Natarajan; Steiner, Wilfried

    2014-01-01

    Requirements are informal and semi-formal descriptions of the expected behavior of a complex system from the viewpoints of its stakeholders (customers, users, operators, designers, and engineers). However, for the purpose of design, testing, and verification for critical systems, we can transform requirements into formal models that can be analyzed automatically. ARSENAL is a framework and methodology for systematically transforming natural language (NL) requirements into analyzable formal mo...

  1. Development of automatic extraction method of left ventricular contours on long axis view MR cine images

    International Nuclear Information System (INIS)

    Utsunomiya, Shinichi; Iijima, Naoto; Yamasaki, Kazunari; Fujita, Akinori

    1995-01-01

    In the MRI cardiac function analysis, left ventricular volume curves and diagnosis parameters are obtained by extracting the left ventricular cavities as regions of interest (ROI) from long axis view MR cine images. The ROI extractions had to be done by manual operations, because automatization of the extraction is difficult. A long axis view left ventricular contour consists of a cardiac wall part and an aortic valve part. The above mentioned difficulty is due to the decline of contrast on the cardiac wall part, and the disappearance of edge on the aortic valve part. In this paper, we report a new automatic extraction method for long axis view MR cine images, which needs only 3 manually indicated points on the 1st image to extract all the contours from the total sequence of images. At first, candidate points of a contour are detected by edge detection. Then, selecting the best matched combination of candidate points by Dynamic Programming, the cardiac wall part is automatically extracted. The aortic valve part is manually extracted for the 1st image by indicating both the end points, and is automatically extracted for the rest of the images, by utilizing the aortic valve motion characteristics throughout a cardiac cycle. (author)

  2. Semi-automatic Term Extraction for the African Languages, with ...

    African Journals Online (AJOL)

    rbr

    and extract potential terms from electronic corpora, is known as (semi-)auto- matic term extraction. In the great majority of the current approaches, character- istics of a special-language corpus are compared to those of a general-language corpus. In all approaches, humans remain the final arbiters, and must decide whether ...

  3. Accurate and Automatic Building Roof Extraction Using Neighborhood Information of Point Clouds

    Directory of Open Access Journals (Sweden)

    ZHAO Chuan

    2017-09-01

    Full Text Available High accuracy building roof extraction from LiDAR data is the key to build topological relationship of building roofs and reconstruct buildings. Aiming at the poor adaptation and low extraction precision of existing roof extraction methods for complex building, an accurate and automatic building roof extraction method using neighborhood information of point clouds is proposed. Point clouds features are calculated by principle component analysis, and reliable seed points are selected after feature histogram construction. Initial roof surfaces are extracted quickly and precisely by the proposed local normal vector distribution density-based spatial clustering of applications with noise (LNVD-DBSCAN. Roof competition problem is solved effectively by the poll model based on neighborhood information. Experimental results show that the proposed method can extract building roofs automatically and precisely, and has preferable adaptation to buildings with different complexity, which is able to provide reliable roof information for building reconstruction.

  4. Automatization of laboratory extraction installation intended for investigations in the field of reprocessing of spenf fuels

    International Nuclear Information System (INIS)

    Vznuzdaev, E.A.; Galkin, B.Ya.; Gofman, F.Eh.

    1981-01-01

    Automatized stand for solving the problem of optimum control on technological extraction process in the spent fuel reprocessing by means of an automatized control system which is based on the means of computation technick is described in the paper. Preliminary experiments which had been conducted on the stand with spent fuel from WWER-440 reactor have shown high efficiency of automatization and possibility to conduct technological investigations in a short period of time and to have much of information which can not be obtained by ordinary organisation of work [ru

  5. An automatic rat brain extraction method based on a deformable surface model.

    Science.gov (United States)

    Li, Jiehua; Liu, Xiaofeng; Zhuo, Jiachen; Gullapalli, Rao P; Zara, Jason M

    2013-08-15

    The extraction of the brain from the skull in medical images is a necessary first step before image registration or segmentation. While pre-clinical MR imaging studies on small animals, such as rats, are increasing, fully automatic imaging processing techniques specific to small animal studies remain lacking. In this paper, we present an automatic rat brain extraction method, the Rat Brain Deformable model method (RBD), which adapts the popular human brain extraction tool (BET) through the incorporation of information on the brain geometry and MR image characteristics of the rat brain. The robustness of the method was demonstrated on T2-weighted MR images of 64 rats and compared with other brain extraction methods (BET, PCNN, PCNN-3D). The results demonstrate that RBD reliably extracts the rat brain with high accuracy (>92% volume overlap) and is robust against signal inhomogeneity in the images. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Automatic content extraction of filled-form images based on clustering component block projection vectors

    Science.gov (United States)

    Peng, Hanchuan; He, Xiaofeng; Long, Fuhui

    2003-12-01

    Automatic understanding of document images is a hard problem. Here we consider a sub-problem, automatically extracting content from filled form images. Without pre-selected templates or sophisticated structural/semantic analysis, we propose a novel approach based on clustering the component-block-projection-vectors. By combining spectral clustering and minimal spanning tree clustering, we generate highly accurate clusters, from which the adaptive templates are constructed to extract the filled-in content. Our experiments show this approach is effective for a set of 1040 US IRS tax form images belonging to 208 types.

  7. Automatic extraction of forward stroke volume using dynamic 11C-acetate PET/CT

    DEFF Research Database (Denmark)

    Harms, Hans; Tolbod, Lars Poulsen; Hansson, Nils Henrik

    , potentially introducing bias if measured with a separate modality. The aim of this study was to develop and validate methods for automatically extracting FSV directly from the dynamic PET used for measuring oxidative metabolism. Methods: 16 subjects underwent a dynamic 27 min PET scan on a Siemens Biograph...... TruePoint 64 PET/CT scanner after bolus injection of 399±27 MBq of 11C-acetate. The LV-aortic time-activity curve (TAC) was extracted automatically from dynamic PET data using cluster analysis. The first-pass peak was derived by automatic extrapolation of the down-slope of the TAC. FSV...... was then calculated as the injected dose divided by the product of heart rate and the area under the curve of the first-pass peak. Gold standard FSV was measured in the left ventricular outflow tract by cardiovascular magnetic resonance using phase-contrast velocity mapping within two weeks of PET imaging. Results...

  8. 2D automatic body-fitted structured mesh generation using advancing extraction method

    Science.gov (United States)

    This paper presents an automatic mesh generation algorithm for body-fitted structured meshes in Computational Fluids Dynamics (CFD) analysis using the Advancing Extraction Method (AEM). The method is applicable to two-dimensional domains with complex geometries, which have the hierarchical tree-like...

  9. Automatic extraction of ontological relations from Arabic text

    Directory of Open Access Journals (Sweden)

    Mohammed G.H. Al Zamil

    2014-12-01

    The proposed methodology has been designed to analyze Arabic text using lexical semantic patterns of the Arabic language according to a set of features. Next, the features have been abstracted and enriched with formal descriptions for the purpose of generalizing the resulted rules. The rules, then, have formulated a classifier that accepts Arabic text, analyzes it, and then displays related concepts labeled with its designated relationship. Moreover, to resolve the ambiguity of homonyms, a set of machine translation, text mining, and part of speech tagging algorithms have been reused. We performed extensive experiments to measure the effectiveness of our proposed tools. The results indicate that our proposed methodology is promising for automating the process of extracting ontological relations.

  10. Automatic Pole and Q-Value Extraction for RF Structures

    Energy Technology Data Exchange (ETDEWEB)

    C. Potratz, H.-W. Glock, U. van Rienen, F. Marhauser

    2011-09-01

    The experimental characterization of RF structures like accelerating cavities often demands for measuring resonant frequencies of Eigenmodes and corresponding (loaded) Q-values over a wide spectral range. A common procedure to determine the Q-values is the -3dB method, which works well for isolated poles, but may not be applicable directly in case of multiple poles residing in close proximity (e.g. for adjacent transverse modes differing by polarization). Although alternative methods may be used in such cases, this often comes at the expense of inherent systematic errors. We have developed an automation algorithm, which not only speeds up the measurement time significantly, but is also able to extract Eigenfrequencies and Q-values both for well isolated and overlapping poles. At the same time the measurement accuracy may be improved as a major benefit. To utilize this procedure merely complex scattering parameters have to be recorded for the spectral range of interest. In this paper we present the proposed algorithm applied to experimental data recorded for superconducting higher-order-mode damped multi-cell cavities as an application of high importance.

  11. Automatic Web Data Extraction Based on Genetic Algorithms and Regular Expressions

    Science.gov (United States)

    Barrero, David F.; Camacho, David; R-Moreno, María D.

    Data Extraction from the World Wide Web is a well known, unsolved, and critical problem when complex information systems are designed. These problems are related to the extraction, management and reuse of the huge amount ofWeb data available. These data usually has a high heterogeneity, volatility and low quality (i.e. format and content mistakes), so it is quite hard to build reliable systems. This chapter proposes an Evolutionary Computation approach to the problem of automatically learn software entities based on Genetic Algorithms and regular expressions. These entities, also called wrappers, will be able to extract some kind of Web data structures from examples.

  12. Automatic Glaucoma Detection Based on Optic Disc Segmentation and Texture Feature Extraction

    Directory of Open Access Journals (Sweden)

    Maíla de Lima Claro

    2016-08-01

    Full Text Available The use of digital image processing techniques is prominent in medical settings for the automatic diagnosis of diseases. Glaucoma is the second leading cause of blindness in the world and it has no cure. Currently, there are treatments to prevent vision loss, but the disease must be detected in the early stages. Thus, the objective of this work is to develop an automatic detection method of Glaucoma in retinal images. The methodology used in the study were: acquisition of image database, Optic Disc segmentation, texture feature extraction in different color models and classiffication of images in glaucomatous or not. We obtained results of 93% accuracy.

  13. Automatic Centerline Extraction of Coverd Roads by Surrounding Objects from High Resolution Satellite Images

    Science.gov (United States)

    Kamangir, H.; Momeni, M.; Satari, M.

    2017-09-01

    This paper presents an automatic method to extract road centerline networks from high and very high resolution satellite images. The present paper addresses the automated extraction roads covered with multiple natural and artificial objects such as trees, vehicles and either shadows of buildings or trees. In order to have a precise road extraction, this method implements three stages including: classification of images based on maximum likelihood algorithm to categorize images into interested classes, modification process on classified images by connected component and morphological operators to extract pixels of desired objects by removing undesirable pixels of each class, and finally line extraction based on RANSAC algorithm. In order to evaluate performance of the proposed method, the generated results are compared with ground truth road map as a reference. The evaluation performance of the proposed method using representative test images show completeness values ranging between 77% and 93%.

  14. Study of Burn Scar Extraction Automatically Based on Level Set Method using Remote Sensing Data

    Science.gov (United States)

    Liu, Yang; Dai, Qin; Liu, JianBo; Liu, ShiBin; Yang, Jin

    2014-01-01

    Burn scar extraction using remote sensing data is an efficient way to precisely evaluate burn area and measure vegetation recovery. Traditional burn scar extraction methodologies have no well effect on burn scar image with blurred and irregular edges. To address these issues, this paper proposes an automatic method to extract burn scar based on Level Set Method (LSM). This method utilizes the advantages of the different features in remote sensing images, as well as considers the practical needs of extracting the burn scar rapidly and automatically. This approach integrates Change Vector Analysis (CVA), Normalized Difference Vegetation Index (NDVI) and the Normalized Burn Ratio (NBR) to obtain difference image and modifies conventional Level Set Method Chan-Vese (C-V) model with a new initial curve which results from a binary image applying K-means method on fitting errors of two near-infrared band images. Landsat 5 TM and Landsat 8 OLI data sets are used to validate the proposed method. Comparison with conventional C-V model, OSTU algorithm, Fuzzy C-mean (FCM) algorithm are made to show that the proposed approach can extract the outline curve of fire burn scar effectively and exactly. The method has higher extraction accuracy and less algorithm complexity than that of the conventional C-V model. PMID:24503563

  15. Role of Artificial Intelligence Techniques (Automatic Classifiers) in Molecular Imaging Modalities in Neurodegenerative Diseases.

    Science.gov (United States)

    Cascianelli, Silvia; Scialpi, Michele; Amici, Serena; Forini, Nevio; Minestrini, Matteo; Fravolini, Mario Luca; Sinzinger, Helmut; Schillaci, Orazio; Palumbo, Barbara

    2017-01-01

    Artificial Intelligence (AI) is a very active Computer Science research field aiming to develop systems that mimic human intelligence and is helpful in many human activities, including Medicine. In this review we presented some examples of the exploiting of AI techniques, in particular automatic classifiers such as Artificial Neural Network (ANN), Support Vector Machine (SVM), Classification Tree (ClT) and ensemble methods like Random Forest (RF), able to analyze findings obtained by positron emission tomography (PET) or single-photon emission tomography (SPECT) scans of patients with Neurodegenerative Diseases, in particular Alzheimer's Disease. We also focused our attention on techniques applied in order to preprocess data and reduce their dimensionality via feature selection or projection in a more representative domain (Principal Component Analysis - PCA - or Partial Least Squares - PLS - are examples of such methods); this is a crucial step while dealing with medical data, since it is necessary to compress patient information and retain only the most useful in order to discriminate subjects into normal and pathological classes. Main literature papers on the application of these techniques to classify patients with neurodegenerative disease extracting data from molecular imaging modalities are reported, showing that the increasing development of computer aided diagnosis systems is very promising to contribute to the diagnostic process.

  16. Automatic extraction of forward stroke volume using dynamic PET/CT

    DEFF Research Database (Denmark)

    Harms, Hans; Tolbod, Lars Poulsen; Hansson, Nils Henrik Stubkjær

    2015-01-01

    Background The aim of this study was to develop and validate an automated method for extracting forward stroke volume (FSV) using indicator dilution theory directly from dynamic positron emission tomography (PET) studies for two different tracers and scanners. Methods 35 subjects underwent...... a dynamic 11 C-acetate PET scan on a Siemens Biograph TruePoint-64 PET/CT (scanner I). In addition, 10 subjects underwent both dynamic 15 O-water PET and 11 C-acetate PET scans on a GE Discovery-ST PET/CT (scanner II). The left ventricular (LV)-aortic time-activity curve (TAC) was extracted automatically...... from PET data using cluster analysis. The first-pass peak was isolated by automatic extrapolation of the downslope of the TAC. FSV was calculated as the injected dose divided by the product of heart rate and the area under the curve of the first-pass peak. Gold standard FSV was measured using phase...

  17. 2D automatic body-fitted structured mesh generation using advancing extraction method

    Science.gov (United States)

    Zhang, Yaoxin; Jia, Yafei

    2018-01-01

    This paper presents an automatic mesh generation algorithm for body-fitted structured meshes in Computational Fluids Dynamics (CFD) analysis using the Advancing Extraction Method (AEM). The method is applicable to two-dimensional domains with complex geometries, which have the hierarchical tree-like topography with extrusion-like structures (i.e., branches or tributaries) and intrusion-like structures (i.e., peninsula or dikes). With the AEM, the hierarchical levels of sub-domains can be identified, and the block boundary of each sub-domain in convex polygon shape in each level can be extracted in an advancing scheme. In this paper, several examples were used to illustrate the effectiveness and applicability of the proposed algorithm for automatic structured mesh generation, and the implementation of the method.

  18. Automatic extraction of road features in urban environments using dense ALS data

    Science.gov (United States)

    Soilán, Mario; Truong-Hong, Linh; Riveiro, Belén; Laefer, Debra

    2018-02-01

    This paper describes a methodology that automatically extracts semantic information from urban ALS data for urban parameterization and road network definition. First, building façades are segmented from the ground surface by combining knowledge-based information with both voxel and raster data. Next, heuristic rules and unsupervised learning are applied to the ground surface data to distinguish sidewalk and pavement points as a means for curb detection. Then radiometric information was employed for road marking extraction. Using high-density ALS data from Dublin, Ireland, this fully automatic workflow was able to generate a F-score close to 95% for pavement and sidewalk identification with a resolution of 20 cm and better than 80% for road marking detection.

  19. A dual growing method for the automatic extraction of individual trees from mobile laser scanning data

    Science.gov (United States)

    Li, Lin; Li, Dalin; Zhu, Haihong; Li, You

    2016-10-01

    Street trees interlaced with other objects in cluttered point clouds of urban scenes inhibit the automatic extraction of individual trees. This paper proposes a method for the automatic extraction of individual trees from mobile laser scanning data, according to the general constitution of trees. Two components of each individual tree - a trunk and a crown can be extracted by the dual growing method. This method consists of coarse classification, through which most of artifacts are removed; the automatic selection of appropriate seeds for individual trees, by which the common manual initial setting is avoided; a dual growing process that separates one tree from others by circumscribing a trunk in an adaptive growing radius and segmenting a crown in constrained growing regions; and a refining process that draws a singular trunk from the interlaced other objects. The method is verified by two datasets with over 98% completeness and over 96% correctness. The low mean absolute percentage errors in capturing the morphological parameters of individual trees indicate that this method can output individual trees with high precision.

  20. An automatic glioma grading method based on multi-feature extraction and fusion.

    Science.gov (United States)

    Zhan, Tianming; Feng, Piaopiao; Hong, Xunning; Lu, Zhenyu; Xiao, Liang; Zhang, Yudong

    2017-07-20

    An accurate assessment of tumor malignancy grade in the preoperative situation is important for clinical management. However, the manual grading of gliomas from MRIs is both a tiresome and time consuming task for radiologists. Thus, it is a priority to design an automatic and effective computer-aided diagnosis (CAD) tool to assist radiologists in grading gliomas. To design an automatic computer-aided diagnosis for grading gliomas using multi-sequence magnetic resonance imaging. The proposed method consists of two steps: (1) the features of high and low grade gliomas are extracted from multi-sequence magnetic resonance images, and (2) then, a KNN classifier is trained to grade the gliomas. In the feature extraction step, the intensity, volume, and local binary patterns (LBP) of the gliomas are extracted, and PCA is used to reduce the data dimension. The proposed "Intensity-Volume-LBP-PCA-KNN" method is validated on the MICCAI 2015 BraTS challenge dataset, and an average grade accuracy of 87.59% is obtained. The proposed method is an effective method for automatically grading gliomas and can be applied to real situations.

  1. Automatic extraction of forward stroke volume using dynamic PET/CT

    DEFF Research Database (Denmark)

    Harms, Hans; Tolbod, Lars Poulsen; Hansson, Nils Henrik

    Background: Dynamic PET can be used to extract forward stroke volume (FSV) by the indicator dilution principle. The technique employed can be automated and is in theory independent on the tracer used and may therefore be added to any dynamic cardiac PET protocol. The aim of this study was to vali......Background: Dynamic PET can be used to extract forward stroke volume (FSV) by the indicator dilution principle. The technique employed can be automated and is in theory independent on the tracer used and may therefore be added to any dynamic cardiac PET protocol. The aim of this study...... was to validate automated methods for extracting FSV directly from dynamic PET studies for two different tracers and to examine potential scanner hardware bias. Methods: 21 subjects underwent a dynamic 27 min 11C-acetate PET scan on a Siemens Biograph TruePoint 64 PET/CT scanner (scanner I). In addition, 8...... subjects underwent a dynamic 6 min 15O-water PET scan followed by a 27 min 11C-acetate PET scan on a GE Discovery ST PET/CT scanner (scanner II). The LV-aortic time-activity curve (TAC) was extracted automatically from dynamic PET data using cluster analysis. The first-pass peak was isolated by automatic...

  2. Developing an Intelligent Automatic Appendix Extraction Method from Ultrasonography Based on Fuzzy ART and Image Processing

    Directory of Open Access Journals (Sweden)

    Kwang Baek Kim

    2015-01-01

    Full Text Available Ultrasound examination (US does a key role in the diagnosis and management of the patients with clinically suspected appendicitis which is the most common abdominal surgical emergency. Among the various sonographic findings of appendicitis, outer diameter of the appendix is most important. Therefore, clear delineation of the appendix on US images is essential. In this paper, we propose a new intelligent method to extract appendix automatically from abdominal sonographic images as a basic building block of developing such an intelligent tool for medical practitioners. Knowing that the appendix is located at the lower organ area below the bottom fascia line, we conduct a series of image processing techniques to find the fascia line correctly. And then we apply fuzzy ART learning algorithm to the organ area in order to extract appendix accurately. The experiment verifies that the proposed method is highly accurate (successful in 38 out of 40 cases in extracting appendix.

  3. Four-Channel Biosignal Analysis and Feature Extraction for Automatic Emotion Recognition

    Science.gov (United States)

    Kim, Jonghwa; André, Elisabeth

    This paper investigates the potential of physiological signals as a reliable channel for automatic recognition of user's emotial state. For the emotion recognition, little attention has been paid so far to physiological signals compared to audio-visual emotion channels such as facial expression or speech. All essential stages of automatic recognition system using biosignals are discussed, from recording physiological dataset up to feature-based multiclass classification. Four-channel biosensors are used to measure electromyogram, electrocardiogram, skin conductivity and respiration changes. A wide range of physiological features from various analysis domains, including time/frequency, entropy, geometric analysis, subband spectra, multiscale entropy, etc., is proposed in order to search the best emotion-relevant features and to correlate them with emotional states. The best features extracted are specified in detail and their effectiveness is proven by emotion recognition results.

  4. Automatic extraction of forward stroke volume using dynamic PET/CT

    DEFF Research Database (Denmark)

    Harms, Hans; Tolbod, Lars Poulsen; Hansson, Nils Henrik

    subjects underwent a dynamic 6 min 15O-water PET scan followed by a 27 min 11C-acetate PET scan on a GE Discovery ST PET/CT scanner (scanner II). The LV-aortic time-activity curve (TAC) was extracted automatically from dynamic PET data using cluster analysis. The first-pass peak was isolated by automatic......Background: Dynamic PET can be used to extract forward stroke volume (FSV) by the indicator dilution principle. The technique employed can be automated and is in theory independent on the tracer used and may therefore be added to any dynamic cardiac PET protocol. The aim of this study...... was to validate automated methods for extracting FSV directly from dynamic PET studies for two different tracers and to examine potential scanner hardware bias. Methods: 21 subjects underwent a dynamic 27 min 11C-acetate PET scan on a Siemens Biograph TruePoint 64 PET/CT scanner (scanner I). In addition, 8...

  5. Realtime automatic metal extraction of medical x-ray images for contrast improvement

    Science.gov (United States)

    Prangl, Martin; Hellwagner, Hermann; Spielvogel, Christian; Bischof, Horst; Szkaliczki, Tibor

    2006-03-01

    This paper focuses on an approach for real-time metal extraction of x-ray images taken from modern x-ray machines like C-arms. Such machines are used for vessel diagnostics, surgical interventions, as well as cardiology, neurology and orthopedic examinations. They are very fast in taking images from different angles. For this reason, manual adjustment of contrast is infeasible and automatic adjustment algorithms have been applied to try to select the optimal radiation dose for contrast adjustment. Problems occur when metallic objects, e.g., a prosthesis or a screw, are in the absorption area of interest. In this case, the automatic adjustment mostly fails because the dark, metallic objects lead the algorithm to overdose the x-ray tube. This outshining effect results in overexposed images and bad contrast. To overcome this limitation, metallic objects have to be detected and extracted from images that are taken as input for the adjustment algorithm. In this paper, we present a real-time solution for extracting metallic objects of x-ray images. We will explore the characteristic features of metallic objects in x-ray images and their distinction from bone fragments which form the basis to find a successful way for object segmentation and classification. Subsequently, we will present our edge based real-time approach for successful and fast automatic segmentation and classification of metallic objects. Finally, experimental results on the effectiveness and performance of our approach based on a vast amount of input image data sets will be presented.

  6. Automatic feature extraction in large fusion databases by using deep learning approach

    International Nuclear Information System (INIS)

    Farias, Gonzalo; Dormido-Canto, Sebastián; Vega, Jesús; Rattá, Giuseppe; Vargas, Héctor; Hermosilla, Gabriel; Alfaro, Luis; Valencia, Agustín

    2016-01-01

    Highlights: • Feature extraction is a very critical stage in any machine learning algorithm. • The problem dimensionality can be reduced enormously when selecting suitable attributes. • Despite the importance of feature extraction, the process is commonly done manually by trial and error. • Fortunately, recent advances in deep learning approach have proposed an encouraging way to find a good feature representation automatically. • In this article, deep learning is applied to the TJ-II fusion database to get more robust and accurate classifiers in comparison to previous work. - Abstract: Feature extraction is one of the most important machine learning issues. Finding suitable attributes of datasets can enormously reduce the dimensionality of the input space, and from a computational point of view can help all of the following steps of pattern recognition problems, such as classification or information retrieval. However, the feature extraction step is usually performed manually. Moreover, depending on the type of data, we can face a wide range of methods to extract features. In this sense, the process to select appropriate techniques normally takes a long time. This work describes the use of recent advances in deep learning approach in order to find a good feature representation automatically. The implementation of a special neural network called sparse autoencoder and its application to two classification problems of the TJ-II fusion database is shown in detail. Results have shown that it is possible to get robust classifiers with a high successful rate, in spite of the fact that the feature space is reduced to less than 0.02% from the original one.

  7. Automatic feature extraction in large fusion databases by using deep learning approach

    Energy Technology Data Exchange (ETDEWEB)

    Farias, Gonzalo, E-mail: gonzalo.farias@ucv.cl [Pontificia Universidad Católica de Valparaíso, Valparaíso (Chile); Dormido-Canto, Sebastián [Departamento de Informática y Automática, UNED, Madrid (Spain); Vega, Jesús; Rattá, Giuseppe [Asociación EURATOM/CIEMAT Para Fusión, CIEMAT, Madrid (Spain); Vargas, Héctor; Hermosilla, Gabriel; Alfaro, Luis; Valencia, Agustín [Pontificia Universidad Católica de Valparaíso, Valparaíso (Chile)

    2016-11-15

    Highlights: • Feature extraction is a very critical stage in any machine learning algorithm. • The problem dimensionality can be reduced enormously when selecting suitable attributes. • Despite the importance of feature extraction, the process is commonly done manually by trial and error. • Fortunately, recent advances in deep learning approach have proposed an encouraging way to find a good feature representation automatically. • In this article, deep learning is applied to the TJ-II fusion database to get more robust and accurate classifiers in comparison to previous work. - Abstract: Feature extraction is one of the most important machine learning issues. Finding suitable attributes of datasets can enormously reduce the dimensionality of the input space, and from a computational point of view can help all of the following steps of pattern recognition problems, such as classification or information retrieval. However, the feature extraction step is usually performed manually. Moreover, depending on the type of data, we can face a wide range of methods to extract features. In this sense, the process to select appropriate techniques normally takes a long time. This work describes the use of recent advances in deep learning approach in order to find a good feature representation automatically. The implementation of a special neural network called sparse autoencoder and its application to two classification problems of the TJ-II fusion database is shown in detail. Results have shown that it is possible to get robust classifiers with a high successful rate, in spite of the fact that the feature space is reduced to less than 0.02% from the original one.

  8. AN EFFICIENT METHOD FOR AUTOMATIC ROAD EXTRACTION BASED ON MULTIPLE FEATURES FROM LiDAR DATA

    Directory of Open Access Journals (Sweden)

    Y. Li

    2016-06-01

    Full Text Available The road extraction in urban areas is difficult task due to the complicated patterns and many contextual objects. LiDAR data directly provides three dimensional (3D points with less occlusions and smaller shadows. The elevation information and surface roughness are distinguishing features to separate roads. However, LiDAR data has some disadvantages are not beneficial to object extraction, such as the irregular distribution of point clouds and lack of clear edges of roads. For these problems, this paper proposes an automatic road centerlines extraction method which has three major steps: (1 road center point detection based on multiple feature spatial clustering for separating road points from ground points, (2 local principal component analysis with least squares fitting for extracting the primitives of road centerlines, and (3 hierarchical grouping for connecting primitives into complete roads network. Compared with MTH (consist of Mean shift algorithm, Tensor voting, and Hough transform proposed in our previous article, this method greatly reduced the computational cost. To evaluate the proposed method, the Vaihingen data set, a benchmark testing data provided by ISPRS for “Urban Classification and 3D Building Reconstruction” project, was selected. The experimental results show that our method achieve the same performance by less time in road extraction using LiDAR data.

  9. Automatic Extraction of Contours of Buildings on Oblique View Maps Based on 3D City Models

    Directory of Open Access Journals (Sweden)

    ZHU Yuanyuan

    2015-09-01

    Full Text Available Aiming to deal with the problem that manual extraction of contours of buildings on oblique view maps are expensive and ineffective with low accuracy and coarse detail, we present a method of automatic extraction of contours buildings on oblique view maps which based on 3D city models. We employ depth-buffers to obtain a building object's color-buffers concerning the occlusion blocked by other buildings and the existence of groups of buildings, and then we trace building contours based on color-buffers. And in order to keep the occlusion consistency and match the traced contours with the map, we propose loading 3D city models by block on projection plane. Finally, the validity and feasibility of this method are proved through the experiments on 3D city models of Wuhan.

  10. The Fractal Patterns of Words in a Text: A Method for Automatic Keyword Extraction.

    Science.gov (United States)

    Najafi, Elham; Darooneh, Amir H

    2015-01-01

    A text can be considered as a one dimensional array of words. The locations of each word type in this array form a fractal pattern with certain fractal dimension. We observe that important words responsible for conveying the meaning of a text have dimensions considerably different from one, while the fractal dimensions of unimportant words are close to one. We introduce an index quantifying the importance of the words in a given text using their fractal dimensions and then ranking them according to their importance. This index measures the difference between the fractal pattern of a word in the original text relative to a shuffled version. Because the shuffled text is meaningless (i.e., words have no importance), the difference between the original and shuffled text can be used to ascertain degree of fractality. The degree of fractality may be used for automatic keyword detection. Words with the degree of fractality higher than a threshold value are assumed to be the retrieved keywords of the text. We measure the efficiency of our method for keywords extraction, making a comparison between our proposed method and two other well-known methods of automatic keyword extraction.

  11. Automatic Extraction of High-Resolution Rainfall Series from Rainfall Strip Charts

    Science.gov (United States)

    Saa-Requejo, Antonio; Valencia, Jose Luis; Garrido, Alberto; Tarquis, Ana M.

    2015-04-01

    Soil erosion is a complex phenomenon involving the detachment and transport of soil particles, storage and runoff of rainwater, and infiltration. The relative magnitude and importance of these processes depends on a host of factors, including climate, soil, topography, cropping and land management practices among others. Most models for soil erosion or hydrological processes need an accurate storm characterization. However, this data are not always available and in some cases indirect models are generated to fill this gap. In Spain, the rain intensity data known for time periods less than 24 hours back to 1924 and many studies are limited by it. In many cases this data is stored in rainfall strip charts in the meteorological stations but haven't been transfer in a numerical form. To overcome this deficiency in the raw data a process of information extraction from large amounts of rainfall strip charts is implemented by means of computer software. The method has been developed that largely automates the intensive-labour extraction work based on van Piggelen et al. (2011). The method consists of the following five basic steps: 1) scanning the charts to high-resolution digital images, 2) manually and visually registering relevant meta information from charts and pre-processing, 3) applying automatic curve extraction software in a batch process to determine the coordinates of cumulative rainfall lines on the images (main step), 4) post processing the curves that were not correctly determined in step 3, and 5) aggregating the cumulative rainfall in pixel coordinates to the desired time resolution. A colour detection procedure is introduced that automatically separates the background of the charts and rolls from the grid and subsequently the rainfall curve. The rainfall curve is detected by minimization of a cost function. Some utilities have been added to improve the previous work and automates some auxiliary processes: readjust the bands properly, merge bands when

  12. Automatic extraction of property norm-like data from large text corpora.

    Science.gov (United States)

    Kelly, Colin; Devereux, Barry; Korhonen, Anna

    2014-01-01

    Traditional methods for deriving property-based representations of concepts from text have focused on either extracting only a subset of possible relation types, such as hyponymy/hypernymy (e.g., car is-a vehicle) or meronymy/metonymy (e.g., car has wheels), or unspecified relations (e.g., car--petrol). We propose a system for the challenging task of automatic, large-scale acquisition of unconstrained, human-like property norms from large text corpora, and discuss the theoretical implications of such a system. We employ syntactic, semantic, and encyclopedic information to guide our extraction, yielding concept-relation-feature triples (e.g., car be fast, car require petrol, car cause pollution), which approximate property-based conceptual representations. Our novel method extracts candidate triples from parsed corpora (Wikipedia and the British National Corpus) using syntactically and grammatically motivated rules, then reweights triples with a linear combination of their frequency and four statistical metrics. We assess our system output in three ways: lexical comparison with norms derived from human-generated property norm data, direct evaluation by four human judges, and a semantic distance comparison with both WordNet similarity data and human-judged concept similarity ratings. Our system offers a viable and performant method of plausible triple extraction: Our lexical comparison shows comparable performance to the current state-of-the-art, while subsequent evaluations exhibit the human-like character of our generated properties.

  13. Semi-automatic road extraction from very high resolution remote sensing imagery by RoadModeler

    Science.gov (United States)

    Lu, Yao

    Accurate and up-to-date road information is essential for both effective urban planning and disaster management. Today, very high resolution (VHR) imagery acquired by airborne and spaceborne imaging sensors is the primary source for the acquisition of spatial information of increasingly growing road networks. Given the increased availability of the aerial and satellite images, it is necessary to develop computer-aided techniques to improve the efficiency and reduce the cost of road extraction tasks. Therefore, automation of image-based road extraction is a very active research topic. This thesis deals with the development and implementation aspects of a semi-automatic road extraction strategy, which includes two key approaches: multidirectional and single-direction road extraction. It requires a human operator to initialize a seed circle on a road and specify a extraction approach before the road is extracted by automatic algorithms using multiple vision cues. The multidirectional approach is used to detect roads with different materials, widths, intersection shapes, and degrees of noise, but sometimes it also interprets parking lots as road areas. Different from the multidirectional approach, the single-direction approach can detect roads with few mistakes, but each seed circle can only be used to detect one road. In accordance with this strategy, a RoadModeler prototype was developed. Both aerial and GeoEye-1 satellite images of seven different types of scenes with various road shapes in rural, downtown, and residential areas were used to evaluate the performance of the RoadModeler. The experimental results demonstrated that the RoadModeler is reliable and easy-to-use by a non-expert operator. Therefore, the RoadModeler is much better than the object-oriented classification. Its average road completeness, correctness, and quality achieved 94%, 97%, and 94%, respectively. These results are higher than those of Hu et al. (2007), which are 91%, 90%, and 85

  14. Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks

    Directory of Open Access Journals (Sweden)

    Mazo Ilya

    2007-07-01

    Full Text Available Abstract Background Uncovering cellular roles of a protein is a task of tremendous importance and complexity that requires dedicated experimental work as well as often sophisticated data mining and processing tools. Protein functions, often referred to as its annotations, are believed to manifest themselves through topology of the networks of inter-proteins interactions. In particular, there is a growing body of evidence that proteins performing the same function are more likely to interact with each other than with proteins with other functions. However, since functional annotation and protein network topology are often studied separately, the direct relationship between them has not been comprehensively demonstrated. In addition to having the general biological significance, such demonstration would further validate the data extraction and processing methods used to compose protein annotation and protein-protein interactions datasets. Results We developed a method for automatic extraction of protein functional annotation from scientific text based on the Natural Language Processing (NLP technology. For the protein annotation extracted from the entire PubMed, we evaluated the precision and recall rates, and compared the performance of the automatic extraction technology to that of manual curation used in public Gene Ontology (GO annotation. In the second part of our presentation, we reported a large-scale investigation into the correspondence between communities in the literature-based protein networks and GO annotation groups of functionally related proteins. We found a comprehensive two-way match: proteins within biological annotation groups form significantly denser linked network clusters than expected by chance and, conversely, densely linked network communities exhibit a pronounced non-random overlap with GO groups. We also expanded the publicly available GO biological process annotation using the relations extracted by our NLP technology

  15. Automatic Parameter Extraction Technique for MOS Structures by C-V Characterization Including the Effects of Interface States

    Science.gov (United States)

    Ryazantsev, D. V.; Grudtsov, V. P.

    2016-10-01

    An automatic MOS structure parameter extraction algorithm accounting for quantum effects has been developed and applied in the semiconductor device analyzer Agilent B1500A. Parameter extraction is based on matching the experimental C-V data with numerical modeling results. The algorithm is used to extract the parameters of test MOS structures with ultrathin gate dielectrics. The applicability of the algorithm for the determination of distribution function of DOS and finding the donor defect level in silicon is shown.

  16. Automatic Parameter Extraction Technique for MOS Structures by C-V Characterization Including the Effects of Interface States

    Directory of Open Access Journals (Sweden)

    Ryazantsev D. V.

    2016-10-01

    Full Text Available An automatic MOS structure parameter extraction algorithm accounting for quantum effects has been developed and applied in the semiconductor device analyzer Agilent B1500A. Parameter extraction is based on matching the experimental C-V data with numerical modeling results. The algorithm is used to extract the parameters of test MOS structures with ultrathin gate dielectrics. The applicability of the algorithm for the determination of distribution function of DOS and finding the donor defect level in silicon is shown.

  17. Automatic cell object extraction of red tide algae in microscopic images

    Science.gov (United States)

    Yu, Kun; Ji, Guangrong; Zheng, Haiyong

    2017-03-01

    Extracting the cell objects of red tide algae is the most important step in the construction of an automatic microscopic image recognition system for harmful algal blooms. This paper describes a set of composite methods for the automatic segmentation of cells of red tide algae from microscopic images. Depending on the existence of setae, we classify the common marine red tide algae into non-setae algae species and Chaetoceros, and design segmentation strategies for these two categories according to their morphological characteristics. In view of the varied forms and fuzzy edges of non-setae algae, we propose a new multi-scale detection algorithm for algal cell regions based on border- correlation, and further combine this with morphological operations and an improved GrabCut algorithm to segment single-cell and multicell objects. In this process, similarity detection is introduced to eliminate the pseudo cellular regions. For Chaetoceros, owing to the weak grayscale information of their setae and the low contrast between the setae and background, we propose a cell extraction method based on a gray surface orientation angle model. This method constructs a gray surface vector model, and executes the gray mapping of the orientation angles. The obtained gray values are then reconstructed and linearly stretched. Finally, appropriate morphological processing is conducted to preserve the orientation information and tiny features of the setae. Experimental results demonstrate that the proposed methods can effectively remove noise and accurately extract both categories of algae cell objects possessing a complete shape, regular contour, and clear edge. Compared with other advanced segmentation techniques, our methods are more robust when considering images with different appearances and achieve more satisfactory segmentation effects.

  18. Automatic extraction and identification of users' responses in Facebook medical quizzes.

    Science.gov (United States)

    Rodríguez-González, Alejandro; Menasalvas Ruiz, Ernestina; Mayer Pujadas, Miguel A

    2016-04-01

    In the last few years the use of social media in medicine has grown exponentially, providing a new area of research based on the analysis and use of Web 2.0 capabilities. In addition, the use of social media in medical education is a subject of particular interest which has been addressed in several studies. One example of this application is the medical quizzes of The New England Journal of Medicine (NEJM) that regularly publishes a set of questions through their Facebook timeline. We present an approach for the automatic extraction of medical quizzes and their associated answers on a Facebook platform by means of a set of computer-based methods and algorithms. We have developed a tool for the extraction and analysis of medical quizzes stored on Facebook timeline at the NEJM Facebook page, based on a set of computer-based methods and algorithms using Java. The system is divided into two main modules: Crawler and Data retrieval. The system was launched on December 31, 2014 and crawled through a total of 3004 valid posts and 200,081 valid comments. The first post was dated on July 23, 2009 and the last one on December 30, 2014. 285 quizzes were analyzed with 32,780 different users providing answers to the aforementioned quizzes. Of the 285 quizzes, patterns were found in 261 (91.58%). From these 261 quizzes where trends were found, we saw that users follow trends of incorrect answers in 13 quizzes and trends of correct answers in 248. This tool is capable of automatically identifying the correct and wrong answers to a quiz provided on Facebook posts in a text format to a quiz, with a small rate of false negative cases and this approach could be applicable to the extraction and analysis of other sources after including some adaptations of the information on the Internet. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Automatic 3D Extraction of Buildings, Vegetation and Roads from LIDAR Data

    Directory of Open Access Journals (Sweden)

    A. Bellakaout

    2016-06-01

    Full Text Available Aerial topographic surveys using Light Detection and Ranging (LiDAR technology collect dense and accurate information from the surface or terrain; it is becoming one of the important tools in the geosciences for studying objects and earth surface. Classification of Lidar data for extracting ground, vegetation, and buildings is a very important step needed in numerous applications such as 3D city modelling, extraction of different derived data for geographical information systems (GIS, mapping, navigation, etc... Regardless of what the scan data will be used for, an automatic process is greatly required to handle the large amount of data collected because the manual process is time consuming and very expensive. This paper is presenting an approach for automatic classification of aerial Lidar data into five groups of items: buildings, trees, roads, linear object and soil using single return Lidar and processing the point cloud without generating DEM. Topological relationship and height variation analysis is adopted to segment, preliminary, the entire point cloud preliminarily into upper and lower contours, uniform and non-uniform surface, non-uniform surfaces, linear objects, and others. This primary classification is used on the one hand to know the upper and lower part of each building in an urban scene, needed to model buildings façades; and on the other hand to extract point cloud of uniform surfaces which contain roofs, roads and ground used in the second phase of classification. A second algorithm is developed to segment the uniform surface into buildings roofs, roads and ground, the second phase of classification based on the topological relationship and height variation analysis, The proposed approach has been tested using two areas : the first is a housing complex and the second is a primary school. The proposed approach led to successful classification results of buildings, vegetation and road classes.

  20. Automatic 3D Extraction of Buildings, Vegetation and Roads from LIDAR Data

    Science.gov (United States)

    Bellakaout, A.; Cherkaoui, M.; Ettarid, M.; Touzani, A.

    2016-06-01

    Aerial topographic surveys using Light Detection and Ranging (LiDAR) technology collect dense and accurate information from the surface or terrain; it is becoming one of the important tools in the geosciences for studying objects and earth surface. Classification of Lidar data for extracting ground, vegetation, and buildings is a very important step needed in numerous applications such as 3D city modelling, extraction of different derived data for geographical information systems (GIS), mapping, navigation, etc... Regardless of what the scan data will be used for, an automatic process is greatly required to handle the large amount of data collected because the manual process is time consuming and very expensive. This paper is presenting an approach for automatic classification of aerial Lidar data into five groups of items: buildings, trees, roads, linear object and soil using single return Lidar and processing the point cloud without generating DEM. Topological relationship and height variation analysis is adopted to segment, preliminary, the entire point cloud preliminarily into upper and lower contours, uniform and non-uniform surface, non-uniform surfaces, linear objects, and others. This primary classification is used on the one hand to know the upper and lower part of each building in an urban scene, needed to model buildings façades; and on the other hand to extract point cloud of uniform surfaces which contain roofs, roads and ground used in the second phase of classification. A second algorithm is developed to segment the uniform surface into buildings roofs, roads and ground, the second phase of classification based on the topological relationship and height variation analysis, The proposed approach has been tested using two areas : the first is a housing complex and the second is a primary school. The proposed approach led to successful classification results of buildings, vegetation and road classes.

  1. Molecular and supramolecular speciation of monoamide extractant systems

    International Nuclear Information System (INIS)

    Ferru, G.

    2012-01-01

    DEHiBA (N,N-di-(ethyl-2-hexyl)isobutyramide, a monoamide, was chosen as selective extractant for the recovery of uranium in the first cycle of the GANEX process, which aims to realize the grouped extraction of actinides in the second step of the process. The aim of this work is an improved description of monoamide organic solutions in alkane diluent after solutes extraction: water, nitric acid and uranyl nitrate. A parametric study was undertaken to characterize species at molecular scale (by IR spectroscopy, UV-visible spectroscopy, time-resolved laser-induced fluorescence spectroscopy, and electro-spray ionisation mass spectrometry) and at supramolecular scale (by vapor pressure osmometry and small angle X-ray scattering coupled to molecular dynamic simulations). Extraction isotherms were modelled taking into account the molecular and supramolecular speciation. These works showed that the organization of the organic solution depends on the amide concentration, the nature and the concentration of the extracted solute. Three regimes can be distinguished. 1/For extractant concentration less than 0.5 mol/L, monomers are predominate species. 2/ For extractant concentrations between 0.5 and 1 mol/L, small aggregates are formed containing 2 to 4 molecules of monoamide. 3/ For more concentrated solutions (greater than 1 mol/L), slightly larger species can be formed after water or nitric acid extraction. Concerning uranyl nitrate extraction, an important and strong organization of the organic phase is observed, which no longer allows the formation of well spherical defined aggregates. At molecular scale, complexes are not sensitive to the organization of the solution: the same species are observed, regardless of the solute and extractant concentrations in organic phase. (author) [fr

  2. Automatic extraction of semantic relations between medical entities: a rule based approach

    Directory of Open Access Journals (Sweden)

    Ben Abacha Asma

    2011-10-01

    Full Text Available Abstract Background Information extraction is a complex task which is necessary to develop high-precision information retrieval tools. In this paper, we present the platform MeTAE (Medical Texts Annotation and Exploration. MeTAE allows (i to extract and annotate medical entities and relationships from medical texts and (ii to explore semantically the produced RDF annotations. Results Our annotation approach relies on linguistic patterns and domain knowledge and consists in two steps: (i recognition of medical entities and (ii identification of the correct semantic relation between each pair of entities. The first step is achieved by an enhanced use of MetaMap which improves the precision obtained by MetaMap by 19.59% in our evaluation. The second step relies on linguistic patterns which are built semi-automatically from a corpus selected according to semantic criteria. We evaluate our system’s ability to identify medical entities of 16 types. We also evaluate the extraction of treatment relations between a treatment (e.g. medication and a problem (e.g. disease: we obtain 75.72% precision and 60.46% recall. Conclusions According to our experiments, using an external sentence segmenter and noun phrase chunker may improve the precision of MetaMap-based medical entity recognition. Our pattern-based relation extraction method obtains good precision and recall w.r.t related works. A more precise comparison with related approaches remains difficult however given the differences in corpora and in the exact nature of the extracted relations. The selection of MEDLINE articles through queries related to known drug-disease pairs enabled us to obtain a more focused corpus of relevant examples of treatment relations than a more general MEDLINE query.

  3. Automatic extraction of pavement markings on streets from point cloud data of mobile LiDAR

    Science.gov (United States)

    Gao, Yang; Zhong, Ruofei; Tang, Tao; Wang, Liuzhao; Liu, Xianlin

    2017-08-01

    Pavement markings provide an important foundation as they help to keep roads users safe. Accurate and comprehensive information about pavement markings assists the road regulators and is useful in developing driverless technology. Mobile light detection and ranging (LiDAR) systems offer new opportunities to collect and process accurate pavement markings’ information. Mobile LiDAR systems can directly obtain the three-dimensional (3D) coordinates of an object, thus defining spatial data and the intensity of (3D) objects in a fast and efficient way. The RGB attribute information of data points can be obtained based on the panoramic camera in the system. In this paper, we present a novel method process to automatically extract pavement markings using multiple attribute information of the laser scanning point cloud from the mobile LiDAR data. This method process utilizes a differential grayscale of RGB color, laser pulse reflection intensity, and the differential intensity to identify and extract pavement markings. We utilized point cloud density to remove the noise and used morphological operations to eliminate the errors. In the application, we tested our method process on different sections of roads in Beijing, China, and Buffalo, NY, USA. The results indicated that both correctness (p) and completeness (r) were higher than 90%. The method process of this research can be applied to extract pavement markings from huge point cloud data produced by mobile LiDAR.

  4. Performance Analysis of the SIFT Operator for Automatic Feature Extraction and Matching in Photogrammetric Applications

    Directory of Open Access Journals (Sweden)

    Francesco Nex

    2009-05-01

    Full Text Available In the photogrammetry field, interest in region detectors, which are widely used in Computer Vision, is quickly increasing due to the availability of new techniques. Images acquired by Mobile Mapping Technology, Oblique Photogrammetric Cameras or Unmanned Aerial Vehicles do not observe normal acquisition conditions. Feature extraction and matching techniques, which are traditionally used in photogrammetry, are usually inefficient for these applications as they are unable to provide reliable results under extreme geometrical conditions (convergent taking geometry, strong affine transformations, etc. and for bad-textured images. A performance analysis of the SIFT technique in aerial and close-range photogrammetric applications is presented in this paper. The goal is to establish the suitability of the SIFT technique for automatic tie point extraction and approximate DSM (Digital Surface Model generation. First, the performances of the SIFT operator have been compared with those provided by feature extraction and matching techniques used in photogrammetry. All these techniques have been implemented by the authors and validated on aerial and terrestrial images. Moreover, an auto-adaptive version of the SIFT operator has been developed, in order to improve the performances of the SIFT detector in relation to the texture of the images. The Auto-Adaptive SIFT operator (A2 SIFT has been validated on several aerial images, with particular attention to large scale aerial images acquired using mini-UAV systems.

  5. A semi-automatic method for extracting thin line structures in images as rooted tree network

    Energy Technology Data Exchange (ETDEWEB)

    Brazzini, Jacopo [Los Alamos National Laboratory; Dillard, Scott [Los Alamos National Laboratory; Soille, Pierre [EC - JRC

    2010-01-01

    This paper addresses the problem of semi-automatic extraction of line networks in digital images - e.g., road or hydrographic networks in satellite images, blood vessels in medical images, robust. For that purpose, we improve a generic method derived from morphological and hydrological concepts and consisting in minimum cost path estimation and flow simulation. While this approach fully exploits the local contrast and shape of the network, as well as its arborescent nature, we further incorporate local directional information about the structures in the image. Namely, an appropriate anisotropic metric is designed by using both the characteristic features of the target network and the eigen-decomposition of the gradient structure tensor of the image. Following, the geodesic propagation from a given seed with this metric is combined with hydrological operators for overland flow simulation to extract the line network. The algorithm is demonstrated for the extraction of blood vessels in a retina image and of a river network in a satellite image.

  6. Cluster based statistical feature extraction method for automatic bleeding detection in wireless capsule endoscopy video.

    Science.gov (United States)

    Ghosh, Tonmoy; Fattah, Shaikh Anowarul; Wahid, Khan A; Zhu, Wei-Ping; Ahmad, M Omair

    2018-03-01

    Wireless capsule endoscopy (WCE) is capable of demonstrating the entire gastrointestinal tract at an expense of exhaustive reviewing process for detecting bleeding disorders. The main objective is to develop an automatic method for identifying the bleeding frames and zones from WCE video. Different statistical features are extracted from the overlapping spatial blocks of the preprocessed WCE image in a transformed color plane containing green to red pixel ratio. The unique idea of the proposed method is to first perform unsupervised clustering of different blocks for obtaining two clusters and then extract cluster based features (CBFs). Finally, a global feature consisting of the CBFs and differential CBF is used to detect bleeding frame via supervised classification. In order to handle continuous WCE video, a post-processing scheme is introduced utilizing the feature trends in neighboring frames. The CBF along with some morphological operations is employed to identify bleeding zones. Based on extensive experimentation on several WCE videos, it is found that the proposed method offers significantly better performance in comparison to some existing methods in terms of bleeding detection accuracy, sensitivity, specificity and precision in bleeding zone detection. It is found that the bleeding detection performance obtained by using the proposed CBF based global feature is better than the feature extracted from the non-clustered image. The proposed method can reduce the burden of physicians in investigating WCE video to detect bleeding frame and zone with a high level of accuracy. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. Performance Analysis of the SIFT Operator for Automatic Feature Extraction and Matching in Photogrammetric Applications.

    Science.gov (United States)

    Lingua, Andrea; Marenchino, Davide; Nex, Francesco

    2009-01-01

    In the photogrammetry field, interest in region detectors, which are widely used in Computer Vision, is quickly increasing due to the availability of new techniques. Images acquired by Mobile Mapping Technology, Oblique Photogrammetric Cameras or Unmanned Aerial Vehicles do not observe normal acquisition conditions. Feature extraction and matching techniques, which are traditionally used in photogrammetry, are usually inefficient for these applications as they are unable to provide reliable results under extreme geometrical conditions (convergent taking geometry, strong affine transformations, etc.) and for bad-textured images. A performance analysis of the SIFT technique in aerial and close-range photogrammetric applications is presented in this paper. The goal is to establish the suitability of the SIFT technique for automatic tie point extraction and approximate DSM (Digital Surface Model) generation. First, the performances of the SIFT operator have been compared with those provided by feature extraction and matching techniques used in photogrammetry. All these techniques have been implemented by the authors and validated on aerial and terrestrial images. Moreover, an auto-adaptive version of the SIFT operator has been developed, in order to improve the performances of the SIFT detector in relation to the texture of the images. The Auto-Adaptive SIFT operator (A(2) SIFT) has been validated on several aerial images, with particular attention to large scale aerial images acquired using mini-UAV systems.

  8. A method for automatic feature points extraction of human vertebrae three-dimensional model

    Science.gov (United States)

    Wu, Zhen; Wu, Junsheng

    2017-05-01

    A method for automatic extraction of the feature points of the human vertebrae three-dimensional model is presented. Firstly, the statistical model of vertebrae feature points is established based on the results of manual vertebrae feature points extraction. Then anatomical axial analysis of the vertebrae model is performed according to the physiological and morphological characteristics of the vertebrae. Using the axial information obtained from the analysis, a projection relationship between the statistical model and the vertebrae model to be extracted is established. According to the projection relationship, the statistical model is matched with the vertebrae model to get the estimated position of the feature point. Finally, by analyzing the curvature in the spherical neighborhood with the estimated position of feature points, the final position of the feature points is obtained. According to the benchmark result on multiple test models, the mean relative errors of feature point positions are less than 5.98%. At more than half of the positions, the error rate is less than 3% and the minimum mean relative error is 0.19%, which verifies the effectiveness of the method.

  9. Chemical name extraction based on automatic training data generation and rich feature set.

    Science.gov (United States)

    Yan, Su; Spangler, W Scott; Chen, Ying

    2013-01-01

    The automation of extracting chemical names from text has significant value to biomedical and life science research. A major barrier in this task is the difficulty of getting a sizable and good quality data to train a reliable entity extraction model. Another difficulty is the selection of informative features of chemical names, since comprehensive domain knowledge on chemistry nomenclature is required. Leveraging random text generation techniques, we explore the idea of automatically creating training sets for the task of chemical name extraction. Assuming the availability of an incomplete list of chemical names, called a dictionary, we are able to generate well-controlled, random, yet realistic chemical-like training documents. We statistically analyze the construction of chemical names based on the incomplete dictionary, and propose a series of new features, without relying on any domain knowledge. Compared to state-of-the-art models learned from manually labeled data and domain knowledge, our solution shows better or comparable results in annotating real-world data with less human effort. Moreover, we report an interesting observation about the language for chemical names. That is, both the structural and semantic components of chemical names follow a Zipfian distribution, which resembles many natural languages.

  10. AUTOMATIC ROOFTOP EXTRACTION IN STEREO IMAGERY USING DISTANCE AND BUILDING SHAPE REGULARIZED LEVEL SET EVOLUTION

    Directory of Open Access Journals (Sweden)

    J. Tian

    2017-05-01

    Full Text Available Automatic rooftop extraction is one of the most challenging problems in remote sensing image analysis. Classical 2D image processing techniques are expensive due to the high amount of features required to locate buildings. This problem can be avoided when 3D information is available. In this paper, we show how to fuse the spectral and height information of stereo imagery to achieve an efficient and robust rooftop extraction. In the first step, the digital terrain model (DTM and in turn the normalized digital surface model (nDSM is generated by using a newly step-edge approach. In the second step, the initial building locations and rooftop boundaries are derived by removing the low-level pixels and high-level pixels with higher probability to be trees and shadows. This boundary is then served as the initial level set function, which is further refined to fit the best possible boundaries through distance regularized level-set curve evolution. During the fitting procedure, the edge-based active contour model is adopted and implemented by using the edges indicators extracted from panchromatic image. The performance of the proposed approach is tested by using the WorldView-2 satellite data captured over Munich.

  11. Statistical Analysis of Automatic Seed Word Acquisition to Improve Harmful Expression Extraction in Cyberbullying Detection

    Directory of Open Access Journals (Sweden)

    Suzuha Hatakeyama

    2016-04-01

    Full Text Available We study the social problem of cyberbullying, defined as a new form of bullying that takes place in the Internet space. This paper proposes a method for automatic acquisition of seed words to improve performance of the original method for the cyberbullying detection by Nitta et al. [1]. We conduct an experiment exactly in the same settings to find out that the method based on a Web mining technique, lost over 30% points of its performance since being proposed in 2013. Thus, we hypothesize on the reasons for the decrease in the performance and propose a number of improvements, from which we experimentally choose the best one. Furthermore, we collect several seed word sets using different approaches, evaluate and their precision. We found out that the influential factor in extraction of harmful expressions is not the number of seed words, but the way the seed words were collected and filtered.

  12. A New Dataset of Automatically Extracted Structure of Arms and Bars in Spiral Galaxies

    Science.gov (United States)

    Hayes, Wayne B.; Davis, D.

    2012-05-01

    We present an algorithm capable of automatically extracting quantitative structure (bars and arms) from images of spiral galaxies. We have run the algorithm on 30,000 galaxies and compared the results to human classifications generously provided pre-publication by the Galaxy Zoo 2 team. In all available measures, our algorithm agrees with the humans about as well as they agree with each other. In addition we provide objective, quantitative measures not available in human classifications. We provide a preliminary analysis of this dataset to see how the properties of arms and bars vary as a function of basic variables such as environment, redshift, absolute magnitude, and color. We also show how structure can vary across wavebands as well as along and across individual arms and bars. Finally, we present preliminary results of a measurement of the total angular momentum present in our observed set of galaxies with an eye towards determining if there is a preferred "handedness" in the universe.

  13. DEVELOPMENT OF AUTOMATIC EXTRACTION METHOD FOR ROAD UPDATE INFORMATION BASED ON PUBLIC WORK ORDER OUTLOOK

    Science.gov (United States)

    Sekimoto, Yoshihide; Nakajo, Satoru; Minami, Yoshitaka; Yamaguchi, Syohei; Yamada, Harutoshi; Fuse, Takashi

    Recently, disclosure of statistic data, representing financial effects or burden for public work, through each web site of national or local government, enables us to discuss macroscopic financial trends. However, it is still difficult to grasp a basic property nationwide how each spot was changed by public work. In this research, our research purpose is to collect road update information reasonably which various road managers provide, in order to realize efficient updating of various maps such as car navigation maps. In particular, we develop the system extracting public work concerned and registering summary including position information to database automatically from public work order outlook, released by each local government, combinating some web mining technologies. Finally, we collect and register several tens of thousands from web site all over Japan, and confirm the feasibility of our method.

  14. Automatic extraction of Manhattan-World building masses from 3D laser range scans.

    Science.gov (United States)

    Vanegas, Carlos A; Aliaga, Daniel G; Benes, Bedrich

    2012-10-01

    We propose a novel approach for the reconstruction of urban structures from 3D point clouds with an assumption of Manhattan World (MW) building geometry; i.e., the predominance of three mutually orthogonal directions in the scene. Our approach works in two steps. First, the input points are classified according to the MW assumption into four local shape types: walls, edges, corners, and edge corners. The classified points are organized into a connected set of clusters from which a volume description is extracted. The MW assumption allows us to robustly identify the fundamental shape types, describe the volumes within the bounding box, and reconstruct visible and occluded parts of the sampled structure. We show results of our reconstruction that has been applied to several synthetic and real-world 3D point data sets of various densities and from multiple viewpoints. Our method automatically reconstructs 3D building models from up to 10 million points in 10 to 60 seconds.

  15. Automatic extraction of soft tissues from 3D MRI head images using model driven analysis

    International Nuclear Information System (INIS)

    Jiang, Hao; Yamamoto, Shinji; Imao, Masanao.

    1995-01-01

    This paper presents an automatic extraction system (called TOPS-3D : Top Down Parallel Pattern Recognition System for 3D Images) of soft tissues from 3D MRI head images by using model driven analysis algorithm. As the construction of system TOPS we developed, two concepts have been considered in the design of system TOPS-3D. One is the system having a hierarchical structure of reasoning using model information in higher level, and the other is a parallel image processing structure used to extract plural candidate regions for a destination entity. The new points of system TOPS-3D are as follows. (1) The TOPS-3D is a three-dimensional image analysis system including 3D model construction and 3D image processing techniques. (2) A technique is proposed to increase connectivity between knowledge processing in higher level and image processing in lower level. The technique is realized by applying opening operation of mathematical morphology, in which a structural model function defined in higher level by knowledge representation is immediately used to the filter function of opening operation as image processing in lower level. The system TOPS-3D applied to 3D MRI head images consists of three levels. First and second levels are reasoning part, and third level is image processing part. In experiments, we applied 5 samples of 3D MRI head images with size 128 x 128 x 128 pixels to the system TOPS-3D to extract the regions of soft tissues such as cerebrum, cerebellum and brain stem. From the experimental results, the system is robust for variation of input data by using model information, and the position and shape of soft tissues are extracted corresponding to anatomical structure. (author)

  16. Multiple Adaptive Neuro-Fuzzy Inference System with Automatic Features Extraction Algorithm for Cervical Cancer Recognition

    Directory of Open Access Journals (Sweden)

    Mohammad Subhi Al-batah

    2014-01-01

    Full Text Available To date, cancer of uterine cervix is still a leading cause of cancer-related deaths in women worldwide. The current methods (i.e., Pap smear and liquid-based cytology (LBC to screen for cervical cancer are time-consuming and dependent on the skill of the cytopathologist and thus are rather subjective. Therefore, this paper presents an intelligent computer vision system to assist pathologists in overcoming these problems and, consequently, produce more accurate results. The developed system consists of two stages. In the first stage, the automatic features extraction (AFE algorithm is performed. In the second stage, a neuro-fuzzy model called multiple adaptive neuro-fuzzy inference system (MANFIS is proposed for recognition process. The MANFIS contains a set of ANFIS models which are arranged in parallel combination to produce a model with multi-input-multioutput structure. The system is capable of classifying cervical cell image into three groups, namely, normal, low-grade squamous intraepithelial lesion (LSIL and high-grade squamous intraepithelial lesion (HSIL. The experimental results prove the capability of the AFE algorithm to be as effective as the manual extraction by human experts, while the proposed MANFIS produces a good classification performance with 94.2% accuracy.

  17. Automatic Extraction of Road Surface and Curbstone Edges from Mobile Laser Scanning Data

    Science.gov (United States)

    Miraliakbari, A.; Hahn, M.; Sok, S.

    2015-05-01

    We present a procedure for automatic extraction of the road surface from geo-referenced mobile laser scanning data. The basic assumption of the procedure is that the road surface is smooth and limited by curbstones. Two variants of jump detection are investigated for detecting curbstone edges, one based on height differences the other one based on histograms of the height data. Region growing algorithms are proposed which use the irregular laser point cloud. Two- and four-neighbourhood growing strategies utilize the two height criteria for examining the neighborhood. Both height criteria rely on an assumption about the minimum height of a low curbstone. Road boundaries with lower or no jumps will not stop the region growing process. In contrast to this objects on the road can terminate the process. Therefore further processing such as bridging gaps between detected road boundary points and the removal of wrongly detected curbstone edges is necessary. Road boundaries are finally approximated by splines. Experiments are carried out with a ca. 2 km network of smalls streets located in the neighbourhood of University of Applied Sciences in Stuttgart. For accuracy assessment of the extracted road surfaces, ground truth measurements are digitized manually from the laser scanner data. For completeness and correctness of the region growing result values between 92% and 95% are achieved.

  18. Multiple adaptive neuro-fuzzy inference system with automatic features extraction algorithm for cervical cancer recognition.

    Science.gov (United States)

    Al-batah, Mohammad Subhi; Isa, Nor Ashidi Mat; Klaib, Mohammad Fadel; Al-Betar, Mohammed Azmi

    2014-01-01

    To date, cancer of uterine cervix is still a leading cause of cancer-related deaths in women worldwide. The current methods (i.e., Pap smear and liquid-based cytology (LBC)) to screen for cervical cancer are time-consuming and dependent on the skill of the cytopathologist and thus are rather subjective. Therefore, this paper presents an intelligent computer vision system to assist pathologists in overcoming these problems and, consequently, produce more accurate results. The developed system consists of two stages. In the first stage, the automatic features extraction (AFE) algorithm is performed. In the second stage, a neuro-fuzzy model called multiple adaptive neuro-fuzzy inference system (MANFIS) is proposed for recognition process. The MANFIS contains a set of ANFIS models which are arranged in parallel combination to produce a model with multi-input-multioutput structure. The system is capable of classifying cervical cell image into three groups, namely, normal, low-grade squamous intraepithelial lesion (LSIL) and high-grade squamous intraepithelial lesion (HSIL). The experimental results prove the capability of the AFE algorithm to be as effective as the manual extraction by human experts, while the proposed MANFIS produces a good classification performance with 94.2% accuracy.

  19. Infrared Cephalic-Vein to Assist Blood Extraction Tasks: Automatic Projection and Recognition

    Science.gov (United States)

    Lagüela, S.; Gesto, M.; Riveiro, B.; González-Aguilera, D.

    2017-05-01

    Thermal infrared band is not commonly used in photogrammetric and computer vision algorithms, mainly due to the low spatial resolution of this type of imagery. However, this band captures sub-superficial information, increasing the capabilities of visible bands regarding applications. This fact is especially important in biomedicine and biometrics, allowing the geometric characterization of interior organs and pathologies with photogrammetric principles, as well as the automatic identification and labelling using computer vision algorithms. This paper presents advances of close-range photogrammetry and computer vision applied to thermal infrared imagery, with the final application of Augmented Reality in order to widen its application in the biomedical field. In this case, the thermal infrared image of the arm is acquired and simultaneously projected on the arm, together with the identification label of the cephalic-vein. This way, blood analysts are assisted in finding the vein for blood extraction, especially in those cases where the identification by the human eye is a complex task. Vein recognition is performed based on the Gaussian temperature distribution in the area of the vein, while the calibration between projector and thermographic camera is developed through feature extraction and pattern recognition. The method is validated through its application to a set of volunteers, with different ages and genres, in such way that different conditions of body temperature and vein depth are covered for the applicability and reproducibility of the method.

  20. A Method for Automatic Extracting Intracranial Region in MR Brain Image

    Science.gov (United States)

    Kurokawa, Keiji; Miura, Shin; Nishida, Makoto; Kageyama, Yoichi; Namura, Ikuro

    It is well known that temporal lobe in MR brain image is in use for estimating the grade of Alzheimer-type dementia. It is difficult to use only region of temporal lobe for estimating the grade of Alzheimer-type dementia. From the standpoint for supporting the medical specialists, this paper proposes a data processing approach on the automatic extraction of the intracranial region from the MR brain image. The method is able to eliminate the cranium region with the laplacian histogram method and the brainstem with the feature points which are related to the observations given by a medical specialist. In order to examine the usefulness of the proposed approach, the percentage of the temporal lobe in the intracranial region was calculated. As a result, the percentage of temporal lobe in the intracranial region on the process of the grade was in agreement with the visual sense standards of temporal lobe atrophy given by the medical specialist. It became clear that intracranial region extracted by the proposed method was good for estimating the grade of Alzheimer-type dementia.

  1. Effect of Feature Extraction on Automatic Sleep Stage Classification by Artificial Neural Network

    Directory of Open Access Journals (Sweden)

    Prucnal Monika

    2017-06-01

    Full Text Available EEG signal-based sleep stage classification facilitates an initial diagnosis of sleep disorders. The aim of this study was to compare the efficiency of three methods for feature extraction: power spectral density (PSD, discrete wavelet transform (DWT and empirical mode decomposition (EMD in the automatic classification of sleep stages by an artificial neural network (ANN. 13650 30-second EEG epochs from the PhysioNet database, representing five sleep stages (W, N1-N3 and REM, were transformed into feature vectors using the aforementioned methods and principal component analysis (PCA. Three feed-forward ANNs with the same optimal structure (12 input neurons, 23 + 22 neurons in two hidden layers and 5 output neurons were trained using three sets of features, obtained with one of the compared methods each. Calculating PSD from EEG epochs in frequency sub-bands corresponding to the brain waves (81.1% accuracy for the testing set, comparing with 74.2% for DWT and 57.6% for EMD appeared to be the most effective feature extraction method in the analysed problem.

  2. Automatically extracting sentences from Medline citations to support clinicians' information needs.

    Science.gov (United States)

    Jonnalagadda, Siddhartha Reddy; Del Fiol, Guilherme; Medlin, Richard; Weir, Charlene; Fiszman, Marcelo; Mostafa, Javed; Liu, Hongfang

    2013-01-01

    Online health knowledge resources contain answers to most of the information needs raised by clinicians in the course of care. However, significant barriers limit the use of these resources for decision-making, especially clinicians' lack of time. In this study we assessed the feasibility of automatically generating knowledge summaries for a particular clinical topic composed of relevant sentences extracted from Medline citations. The proposed approach combines information retrieval and semantic information extraction techniques to identify relevant sentences from Medline abstracts. We assessed this approach in two case studies on the treatment alternatives for depression and Alzheimer's disease. A total of 515 of 564 (91.3%) sentences retrieved in the two case studies were relevant to the topic of interest. About one-third of the relevant sentences described factual knowledge or a study conclusion that can be used for supporting information needs at the point of care. The high rate of relevant sentences is desirable, given that clinicians' lack of time is one of the main barriers to using knowledge resources at the point of care. Sentence rank was not significantly associated with relevancy, possibly due to most sentences being highly relevant. Sentences located closer to the end of the abstract and sentences with treatment and comparative predications were likely to be conclusive sentences. Our proposed technical approach to helping clinicians meet their information needs is promising. The approach can be extended for other knowledge resources and information need types.

  3. Machine learning based sample extraction for automatic speech recognition using dialectal Assamese speech.

    Science.gov (United States)

    Agarwalla, Swapna; Sarma, Kandarpa Kumar

    2016-06-01

    Automatic Speaker Recognition (ASR) and related issues are continuously evolving as inseparable elements of Human Computer Interaction (HCI). With assimilation of emerging concepts like big data and Internet of Things (IoT) as extended elements of HCI, ASR techniques are found to be passing through a paradigm shift. Oflate, learning based techniques have started to receive greater attention from research communities related to ASR owing to the fact that former possess natural ability to mimic biological behavior and that way aids ASR modeling and processing. The current learning based ASR techniques are found to be evolving further with incorporation of big data, IoT like concepts. Here, in this paper, we report certain approaches based on machine learning (ML) used for extraction of relevant samples from big data space and apply them for ASR using certain soft computing techniques for Assamese speech with dialectal variations. A class of ML techniques comprising of the basic Artificial Neural Network (ANN) in feedforward (FF) and Deep Neural Network (DNN) forms using raw speech, extracted features and frequency domain forms are considered. The Multi Layer Perceptron (MLP) is configured with inputs in several forms to learn class information obtained using clustering and manual labeling. DNNs are also used to extract specific sentence types. Initially, from a large storage, relevant samples are selected and assimilated. Next, a few conventional methods are used for feature extraction of a few selected types. The features comprise of both spectral and prosodic types. These are applied to Recurrent Neural Network (RNN) and Fully Focused Time Delay Neural Network (FFTDNN) structures to evaluate their performance in recognizing mood, dialect, speaker and gender variations in dialectal Assamese speech. The system is tested under several background noise conditions by considering the recognition rates (obtained using confusion matrices and manually) and computation time

  4. Detection of fiducial gold markers for automatic on-line megavoltage position verification using a marker extraction kernel (MEK)

    NARCIS (Netherlands)

    Nederveen, A.; Lagendijk, J.; Hofman, P.

    2000-01-01

    PURPOSE: In this study automatic detection of implanted gold markers in megavoltage portal images for on-line position verification was investigated. METHODS AND MATERIALS: A detection method for fiducial gold markers, consisting of a marker extraction kernel (MEK), was developed. The detection

  5. Extracting contextual information in digital imagery: applications to automatic target recognition and mammography

    Science.gov (United States)

    Spence, Clay D.; Sajda, Paul; Pearson, John C.

    1996-02-01

    An important problem in image analysis is finding small objects in large images. The problem is challenging because (1) searching a large image is computationally expensive, and (2) small targets (on the order of a few pixels in size) have relatively few distinctive features which enable them to be distinguished from non-targets. To overcome these challenges we have developed a hierarchical neural network (HNN) architecture which combines multi-resolution pyramid processing with neural networks. The advantages of the architecture are: (1) both neural network training and testing can be done efficiently through coarse-to-fine techniques, and (2) such a system is capable of learning low-resolution contextual information to facilitate the detection of small target objects. We have applied this neural network architecture to two problems in which contextual information appears to be important for detecting small targets. The first problem is one of automatic target recognition (ATR), specifically the problem of detecting buildings in aerial photographs. The second problem focuses on a medical application, namely searching mammograms for microcalcifications, which are cues for breast cancer. Receiver operating characteristic (ROC) analysis suggests that the hierarchical architecture improves the detection accuracy for both the ATR and microcalcification detection problems, reducing false positive rates by a significant factor. In addition, we have examined the hidden units at various levels of the processing hierarchy and found what appears to be representations of road location (for the ATR example) and ductal/vasculature location (for mammography), both of which are in agreement with the contextual information used by humans to find these classes of targets. We conclude that this hierarchical neural network architecture is able to automatically extract contextual information in imagery and utilize it for target detection.

  6. eCTG: an automatic procedure to extract digital cardiotocographic signals from digital images.

    Science.gov (United States)

    Sbrollini, Agnese; Agostinelli, Angela; Marcantoni, Ilaria; Morettini, Micaela; Burattini, Luca; Di Nardo, Francesco; Fioretti, Sandro; Burattini, Laura

    2018-03-01

    Cardiotocography (CTG), consisting in the simultaneous recording of fetal heart rate (FHR) and maternal uterine contractions (UC), is a popular clinical test to assess fetal health status. Typically, CTG machines provide paper reports that are visually interpreted by clinicians. Consequently, visual CTG interpretation depends on clinician's experience and has a poor reproducibility. The lack of databases containing digital CTG signals has limited number and importance of retrospective studies finalized to set up procedures for automatic CTG analysis that could contrast visual CTG interpretation subjectivity. In order to help overcoming this problem, this study proposes an electronic procedure, termed eCTG, to extract digital CTG signals from digital CTG images, possibly obtainable by scanning paper CTG reports. eCTG was specifically designed to extract digital CTG signals from digital CTG images. It includes four main steps: pre-processing, Otsu's global thresholding, signal extraction and signal calibration. Its validation was performed by means of the "CTU-UHB Intrapartum Cardiotocography Database" by Physionet, that contains digital signals of 552 CTG recordings. Using MATLAB, each signal was plotted and saved as a digital image that was then submitted to eCTG. Digital CTG signals extracted by eCTG were eventually compared to corresponding signals directly available in the database. Comparison occurred in terms of signal similarity (evaluated by the correlation coefficient ρ, and the mean signal error MSE) and clinical features (including FHR baseline and variability; number, amplitude and duration of tachycardia, bradycardia, acceleration and deceleration episodes; number of early, variable, late and prolonged decelerations; and UC number, amplitude, duration and period). The value of ρ between eCTG and reference signals was 0.85 (P < 10 -560 ) for FHR and 0.97 (P < 10 -560 ) for UC. On average, MSE value was 0.00 for both FHR and UC. No CTG feature

  7. Automatically extracting cancer disease characteristics from pathology reports into a Disease Knowledge Representation Model.

    Science.gov (United States)

    Coden, Anni; Savova, Guergana; Sominsky, Igor; Tanenblatt, Michael; Masanz, James; Schuler, Karin; Cooper, James; Guan, Wei; de Groen, Piet C

    2009-10-01

    We introduce an extensible and modifiable knowledge representation model to represent cancer disease characteristics in a comparable and consistent fashion. We describe a system, MedTAS/P which automatically instantiates the knowledge representation model from free-text pathology reports. MedTAS/P is based on an open-source framework and its components use natural language processing principles, machine learning and rules to discover and populate elements of the model. To validate the model and measure the accuracy of MedTAS/P, we developed a gold-standard corpus of manually annotated colon cancer pathology reports. MedTAS/P achieves F1-scores of 0.97-1.0 for instantiating classes in the knowledge representation model such as histologies or anatomical sites, and F1-scores of 0.82-0.93 for primary tumors or lymph nodes, which require the extractions of relations. An F1-score of 0.65 is reported for metastatic tumors, a lower score predominantly due to a very small number of instances in the training and test sets.

  8. Automatic Extraction of Figures from Scientific Publications in High-Energy Physics

    Directory of Open Access Journals (Sweden)

    Piotr Adam Praczyk

    2013-12-01

    Full Text Available Plots and figures play an important role in the process of understanding a scientificpublication, providing overviews of large amounts of data or ideas that are difficult to in-tuitively present using only the text. State of art in digital libraries, serving as gatewaysto knowledge encoded in scholarly writings, does not take full advantage of the graphicalcontent of documents. Enabling machines to automatically unlock the meaning of scien-tific illustrations would allow immense improvements in the way scientists work and theknowledge is being processed.    In this paper we present a novel solution for the initial problem of processing graphicalcontent, obtaining figures from scholarly publications stored in PDF format. Our methodrelies on vector properties of documents and as such, does not introduce additional errors,characteristic for methods based on raster image processing. Emphasis has been placed oncorrectly processing documents in High Energy Physics. The described approach makesdistinction between different classes of objects appearing in PDF documents and usesspatial clustering techniques to group objects into larger logical entities. A number ofheuristics allow the rejection of incorrect figure candidates and the extraction of differenttypes of metadata.

  9. Automatic extraction of faults and fractal analysis from remote sensing data

    Directory of Open Access Journals (Sweden)

    R. Gloaguen

    2007-01-01

    Full Text Available Object-based classification is a promising technique for image classification. Unlike pixel-based methods, which only use the measured radiometric values, the object-based techniques can also use shape and context information of scene textures. These extra degrees of freedom provided by the objects allow the automatic identification of geological structures. In this article, we present an evaluation of object-based classification in the context of extraction of geological faults. Digital elevation models and radar data of an area near Lake Magadi (Kenya have been processed. We then determine the statistics of the fault populations. The fractal dimensions of fault dimensions are similar to fractal dimensions directly measured on remote sensing images of the study area using power spectra (PSD and variograms. These methods allow unbiased statistics of faults and help us to understand the evolution of the fault systems in extensional domains. Furthermore, the direct analysis of image texture is a good indicator of the fault statistics and allows us to classify the intensity and type of deformation. We propose that extensional fault networks can be modeled by iterative function system (IFS.

  10. Automatic Vertebral Column Extraction by Whole-Body Bone SPECT Scan

    Directory of Open Access Journals (Sweden)

    Sheng-Fang Huang

    2013-01-01

    Full Text Available Bone extraction and division can enhance the accuracy of diagnoses based on whole-body bone SPECT data. This study developed a method for using conventional SPECT for automatic recognition of the vertebral column. A novel feature of the proposed approach is a novel “bone graph" image description method that represents the connectivity between these image regions to facilitate manipulation of morphological relationships in the skeleton before surgery. By tracking the paths shown on the bone graph, skeletal structures can be identified by performing morphological operations. The performance of the method was evaluated quantitatively and qualitatively by two experienced nuclear medicine physicians. Datasets for whole-body bone SPECT scans in 46 lung cancer patients with bone metastasis were obtained with Tc-99m MDP. The algorithm successfully segmented vertebrae in the thoracolumbar spine. The quantitative assessment shows that the segmentation method achieved an average TP, FP, and FN rates of 95.1%, 9.1%, and 4.9%. The qualitative evaluation shows an average acceptance rate of 83%, where the data for the acceptable and unacceptable groups had a Cronbach’s alpha value of 0.718, which indicated reasonable internal consistency and reliability.

  11. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.

    OpenAIRE

    Pääbo, S

    1989-01-01

    Several chemical and enzymatic properties were examined in the DNA extracted from dry remains of soft tissues that vary in age from 4 to 13,000 years and represent four species, including two extinct animals (the marsupial wolf and giant ground sloth). The DNA obtained was invariably of a low average molecular size and damaged by oxidative processes, which primarily manifest themselves as modifications of pyrimidines and sugar residues as well as baseless sites and intermolecular cross-links....

  12. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.

    Science.gov (United States)

    Pääbo, S

    1989-03-01

    Several chemical and enzymatic properties were examined in the DNA extracted from dry remains of soft tissues that vary in age from 4 to 13,000 years and represent four species, including two extinct animals (the marsupial wolf and giant ground sloth). The DNA obtained was invariably of a low average molecular size and damaged by oxidative processes, which primarily manifest themselves as modifications of pyrimidines and sugar residues as well as baseless sites and intermolecular cross-links. This renders molecular cloning difficult. However, the polymerase chain reaction can be used to amplify and study short mitochondrial DNA sequences that are of anthropological and evolutionary significance. This opens up the prospect of performing diachronical studies of molecular evolutionary genetics.

  13. ScholarLens: extracting competences from research publications for the automatic generation of semantic user profiles

    Directory of Open Access Journals (Sweden)

    Bahar Sateli

    2017-07-01

    Full Text Available Motivation Scientists increasingly rely on intelligent information systems to help them in their daily tasks, in particular for managing research objects, like publications or datasets. The relatively young research field of Semantic Publishing has been addressing the question how scientific applications can be improved through semantically rich representations of research objects, in order to facilitate their discovery and re-use. To complement the efforts in this area, we propose an automatic workflow to construct semantic user profiles of scholars, so that scholarly applications, like digital libraries or data repositories, can better understand their users’ interests, tasks, and competences, by incorporating these user profiles in their design. To make the user profiles sharable across applications, we propose to build them based on standard semantic web technologies, in particular the Resource Description Framework (RDF for representing user profiles and Linked Open Data (LOD sources for representing competence topics. To avoid the cold start problem, we suggest to automatically populate these profiles by analyzing the publications (co-authored by users, which we hypothesize reflect their research competences. Results We developed a novel approach, ScholarLens, which can automatically generate semantic user profiles for authors of scholarly literature. For modeling the competences of scholarly users and groups, we surveyed a number of existing linked open data vocabularies. In accordance with the LOD best practices, we propose an RDF Schema (RDFS based model for competence records that reuses existing vocabularies where appropriate. To automate the creation of semantic user profiles, we developed a complete, automated workflow that can generate semantic user profiles by analyzing full-text research articles through various natural language processing (NLP techniques. In our method, we start by processing a set of research articles for a

  14. Extraction: a system for automatic eddy current diagnosis of steam generator tubes in nuclear power plants

    International Nuclear Information System (INIS)

    Georgel, B.; Zorgati, R.

    1994-01-01

    Improving speed and quality of Eddy Current non-destructive testing of steam generator tubes leads to automatize all processes that contribute to diagnosis. This paper describes how we use signal processing, pattern recognition and artificial intelligence to build a software package that is able to automatically provide an efficient diagnosis. (authors). 2 figs., 5 refs

  15. Automatic Extraction System for Common Artifacts in EEG Signals Based on Evolutionary Stone’s BSS Algorithm

    Directory of Open Access Journals (Sweden)

    Ahmed Kareem Abdullah

    2014-01-01

    Full Text Available An automatic artifact extraction system is proposed based on a hybridization of Stone’s BSS and genetic algorithm. This hybridization is called evolutionary Stone’s BSS algorithm (ESBSS. Original Stone’s BSS used short- and long-term half-life parameters as constant values, and the changes in these parameters will be affecting directly the separated signals; also there is no way to determine the best parameters. The genetic algorithm is a suitable technique to overcome this problem by finding randomly the optimum half-life parameters in Stone’s BSS. The proposed system is used to extract automatically the common artifacts such as ocular and heart beat artifacts from EEG mixtures without prejudice to the data; also there is no notch filter used in the proposed system in order not to lose any useful information.

  16. Review of Automatic Feature Extraction from High-Resolution Optical Sensor Data for UAV-Based Cadastral Mapping

    OpenAIRE

    Sophie Crommelinck; Rohan Bennett; Markus Gerke; Francesco Nex; Michael Ying Yang; George Vosselman

    2016-01-01

    Unmanned Aerial Vehicles (UAVs) have emerged as a rapid, low-cost and flexible acquisition system that appears feasible for application in cadastral mapping: high-resolution imagery, acquired using UAVs, enables a new approach for defining property boundaries. However, UAV-derived data are arguably not exploited to its full potential: based on UAV data, cadastral boundaries are visually detected and manually digitized. A workflow that automatically extracts boundary features from UAV data cou...

  17. Predicting the performance of molecularly imprinted polymers: Selective extraction of caffeine by molecularly imprinted solid phase extraction

    Energy Technology Data Exchange (ETDEWEB)

    Farrington, Keith [School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9 (Ireland); Magner, Edmond [Materials and Surface Science Institute, Chemical and Environmental Sciences Department, University of Limerick, Limerick (Ireland); Regan, Fiona [School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9 (Ireland)]. E-mail: fiona.regan@dcu.ie

    2006-04-27

    A rational design approach was taken to the planning and synthesis of a molecularly imprinted polymer capable of extracting caffeine (the template molecule) from a standard solution of caffeine and further from a food sample containing caffeine. Data from NMR titration experiments in conjunction with a molecular modelling approach was used in predicting the relative ratios of template to functional monomer and furthermore determined both the choice of solvent (porogen) and the amount used for the study. In addition the molecular modelling program yielded information regarding the thermodynamic stability of the pre-polymerisation complex. Post-polymerisation analysis of the polymer itself by analysis of the pore size distribution by BET yielded significant information regarding the nature of the size and distribution of the pores within the polymer matrix. Here is proposed a stepwise procedure for the development and testing of a molecularly imprinted polymer using a well-studied compound-caffeine as a model system. It is shown that both the physical characteristics of a molecularly imprinted polymer (MIP) and the analysis of the pre-polymerisation complex can yield vital information, which can predict how well a given MIP will perform.

  18. Magnetic molecularly imprinted polymer for the selective extraction of quercetagetin from Calendula officinalis extract.

    Science.gov (United States)

    Ma, Run-Tian; Shi, Yan-Ping

    2015-03-01

    A new magnetic molecularly imprinted polymers (MMIPs) for quercetagetin was prepared by surface molecular imprinting method using super paramagnetic core-shell nanoparticle as the supporter. Acrylamide as the functional monomer, ethyleneglycol dimethacrylate as the crosslinker and acetonitrile as the porogen were applied in the preparation process. Fourier transform infrared spectrometer (FT-IR), X-ray diffraction (XRD) and Vibrating sample magnetometer (VSM) were applied to characterize the MMIPs, and High performance liquid chromatography (HPLC) was utilized to analyze the target analytes. The selectivity of quercetagetin MMIPs was evaluated according to their recognition to template and its analogues. Excellent binding for quercetagetin was observed in MMIPs adsorption experiment, and the adsorption isotherm models analysis showed that the homogeneous binding sites were distributed on the surface of the MMIPs. The MMIPs were employed as adsorbents in solid phase extraction for the determination of quercetagetin in Calendula officinalis extracts. Furthermore, this method is fast, simple and could fulfill the determination and extraction of quercetagetin from herbal extract. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Design and implementation of a control automatic module for the volume extraction of a 99mTc generator

    International Nuclear Information System (INIS)

    Lopez, Yon; Urquizo, Rafael; Gago, Javier; Mendoza, Pablo

    2014-01-01

    A module for the automatic extraction of volume from 0.05 mL to 1 mL has been developed using a 3D printer, using as base material acrylonitrile butadiene styrene (ABS). The design allows automation of the input and ejection eluate 99m Tc in the generator prototype 99 Mo/ 99m Tc processes; use in other systems is feasible due to its high degree of versatility, depending on the selection of the main components: precision syringe and multi-way solenoid valve. An accuracy equivalent to commercial equipment has been obtained, but at lower cost. This article describes the mechanical design, design calculations of the movement mechanism, electronics and automatic syringe dispenser control. (authors).

  20. Enhancing interpretability of automatically extracted machine learning features: application to a RBM-Random Forest system on brain lesion segmentation.

    Science.gov (United States)

    Pereira, Sérgio; Meier, Raphael; McKinley, Richard; Wiest, Roland; Alves, Victor; Silva, Carlos A; Reyes, Mauricio

    2018-02-01

    Machine learning systems are achieving better performances at the cost of becoming increasingly complex. However, because of that, they become less interpretable, which may cause some distrust by the end-user of the system. This is especially important as these systems are pervasively being introduced to critical domains, such as the medical field. Representation Learning techniques are general methods for automatic feature computation. Nevertheless, these techniques are regarded as uninterpretable "black boxes". In this paper, we propose a methodology to enhance the interpretability of automatically extracted machine learning features. The proposed system is composed of a Restricted Boltzmann Machine for unsupervised feature learning, and a Random Forest classifier, which are combined to jointly consider existing correlations between imaging data, features, and target variables. We define two levels of interpretation: global and local. The former is devoted to understanding if the system learned the relevant relations in the data correctly, while the later is focused on predictions performed on a voxel- and patient-level. In addition, we propose a novel feature importance strategy that considers both imaging data and target variables, and we demonstrate the ability of the approach to leverage the interpretability of the obtained representation for the task at hand. We evaluated the proposed methodology in brain tumor segmentation and penumbra estimation in ischemic stroke lesions. We show the ability of the proposed methodology to unveil information regarding relationships between imaging modalities and extracted features and their usefulness for the task at hand. In both clinical scenarios, we demonstrate that the proposed methodology enhances the interpretability of automatically learned features, highlighting specific learning patterns that resemble how an expert extracts relevant data from medical images. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Using the Echo Nest's automatically extracted music features for a musicological purpose

    DEFF Research Database (Denmark)

    Andersen, Jesper Steen

    2014-01-01

    This paper sums up the preliminary observations and challenges encountered during my first engaging with the music intelligence company Echo Nest's automatically derived data of more than 35 million songs. The overall purpose is to investigate whether musicologists can draw benefit from Echo Nest...

  2. Extraction of tributyltin by magnetic molecularly imprinted polymers

    International Nuclear Information System (INIS)

    Zhu, Shanshan; Pan, Daodong; Hu, Futao; Gan, Ning; Li, Yi; Cao, Yuting; Wu, Dazhen; Yang, Ting

    2013-01-01

    We have prepared core-shell magnetic molecularly imprinted polymer nanoparticles for recognition and extraction of tributyl tin (TBT). The use of particles strongly improves the imprinting effect and leads to fast adsorption kinetics and high adsorption capacities. The functional monomer acrylamide was grafted to the surface of Fe 3 O 4 nanospheres in two steps, and MIP layers were then formed on the surface by creating a MIP layer on the surface consisting of poly(ethyleneglycol dimethacrylate) with a TBT template. The particles were characterized in terms of morphological, magnetic, adsorption, and recognition properties. We then have developed a method for the extraction of TBT from spiked mussel (Mytilidae), and its determination by liquid chromatography-tandem mass spectrometry. The method has a limit of detection of 1.0 ng g −1 (n = 5) of TBT, with a linear response between 5.0 and 1,000 ng g −1 . The proposed method was successfully applied to the determination of trace TBT in marine food samples with recoveries in the range of 78.3–95.6 %. (author)

  3. Using Probe Vehicle Data for Automatic Extraction of Road Traffic Parameters

    Directory of Open Access Journals (Sweden)

    Roman Popescu Maria Alexandra

    2016-12-01

    Full Text Available Through this paper the author aims to study and find solutions for automatic detection of traffic light position and for automatic calculation of the waiting time at traffic light. The first objective serves mainly the road transportation field, mainly because it removes the need for collaboration with local authorities to establish a national network of traffic lights. The second objective is important not only for companies which are providing navigation solutions, but especially for authorities, institutions, companies operating in road traffic management systems. Real-time dynamic determination of traffic queue length and of waiting time at traffic lights allow the creation of dynamic systems, intelligent and flexible, adapted to actual traffic conditions, and not to generic, theoretical models. Thus, cities can approach the Smart City concept by boosting, efficienting and greening the road transport, promoted in Europe through the Horizon 2020, Smart Cities, Urban Mobility initiative.

  4. Real-Time Automatic Fetal Brain Extraction in Fetal MRI by Deep Learning

    OpenAIRE

    Salehi, Seyed Sadegh Mohseni; Hashemi, Seyed Raein; Velasco-Annis, Clemente; Ouaalam, Abdelhakim; Estroff, Judy A.; Erdogmus, Deniz; Warfield, Simon K.; Gholipour, Ali

    2017-01-01

    Brain segmentation is a fundamental first step in neuroimage analysis. In the case of fetal MRI, it is particularly challenging and important due to the arbitrary orientation of the fetus, organs that surround the fetal head, and intermittent fetal motion. Several promising methods have been proposed but are limited in their performance in challenging cases and in real-time segmentation. We aimed to develop a fully automatic segmentation method that independently segments sections of the feta...

  5. Molecular characteristics of Illicium verum extractives to activate acquired immune response

    OpenAIRE

    Peng, Wanxi; Lin, Zhi; Wang, Lansheng; Chang, Junbo; Gu, Fangliang; Zhu, Xiangwei

    2016-01-01

    Illicium verum, whose extractives can activate the demic acquired immune response, is an expensive medicinal plant. However, the rich extractives in I. verum biomass were seriously wasted for the inefficient extraction and separation processes. In order to further utilize the biomedical resources for the good acquired immune response, the four extractives were obtained by SJYB extraction, and then the immunology moleculars of SJYB extractives were identified and analyzed by GC–MS. The result ...

  6. Development of automatic blood extraction device with a micro-needle for blood-sugar level measurement

    Science.gov (United States)

    Kawanaka, Kaichiro; Uetsuji, Yasutomo; Tsuchiya, Kazuyoshi; Nakamachi, Eiji

    2008-12-01

    In this study, a portable type HMS (Health Monitoring System) device is newly developed. It has features 1) puncturing a blood vessel by using a minimally invasive micro-needle, 2) extracting and transferring human blood and 3) measuring blood glucose level. This miniature SMBG (Self-Monitoring of Blood Glucose) device employs a syringe reciprocal blood extraction system equipped with an electro-mechanical control unit for accurate and steady operations. The device consists of a) a disposable syringe unit, b) a non-disposable body unit, and c) a glucose enzyme sensor. The syringe unit consists of a syringe itself, its cover, a piston and a titanium alloy micro-needle, whose inner diameter is about 100µm. The body unit consists of a linear driven-type stepping motor, a piston jig, which connects directly to the shaft of the stepping motor, and a syringe jig, which is driven by combining with the piston jig and slider, which fixes the syringe jig. The required thrust to drive the slider is designed to be greater than the value of the blood extraction force. Because of this driving mechanism, the automatic blood extraction and discharging processes are completed by only one linear driven-type stepping motor. The experimental results using our miniature SMBG device was confirmed to output more than 90% volumetric efficiency under the driving speed of the piston, 1.0mm/s. Further, the blood sugar level was measured successfully by using the glucose enzyme sensor.

  7. Automatic Extraction of Small Spatial Plots from Geo-Registered UAS Imagery

    Science.gov (United States)

    Cherkauer, Keith; Hearst, Anthony

    2015-04-01

    Accurate extraction of spatial plots from high-resolution imagery acquired by Unmanned Aircraft Systems (UAS), is a prerequisite for accurate assessment of experimental plots in many geoscience fields. If the imagery is correctly geo-registered, then it may be possible to accurately extract plots from the imagery based on their map coordinates. To test this approach, a UAS was used to acquire visual imagery of 5 ha of soybean fields containing 6.0 m2 plots in a complex planting scheme. Sixteen artificial targets were setup in the fields before flights and different spatial configurations of 0 to 6 targets were used as Ground Control Points (GCPs) for geo-registration, resulting in a total of 175 geo-registered image mosaics with a broad range of geo-registration accuracies. Geo-registration accuracy was quantified based on the horizontal Root Mean Squared Error (RMSE) of targets used as checkpoints. Twenty test plots were extracted from the geo-registered imagery. Plot extraction accuracy was quantified based on the percentage of the desired plot area that was extracted. It was found that using 4 GCPs along the perimeter of the field minimized the horizontal RMSE and enabled a plot extraction accuracy of at least 70%, with a mean plot extraction accuracy of 92%. The methods developed are suitable for work in many fields where replicates across time and space are necessary to quantify variability.

  8. Feature extraction and descriptor calculation methods for automatic georeferencing of Philippines' first microsatellite imagery

    Science.gov (United States)

    Tupas, M. E. A.; Dasallas, J. A.; Jiao, B. J. D.; Magallon, B. J. P.; Sempio, J. N. H.; Ramos, M. K. F.; Aranas, R. K. D.; Tamondong, A. M.

    2017-10-01

    The FAST-SIFT corner detector and descriptor extractor combination was used to automatically georeference DIWATA-1 Spaceborne Multispectral Imager images. Features from the Fast Accelerated Segment Test (FAST) algorithm detects corners or keypoints in an image, and these robustly detected keypoints have well-defined positions. Descriptors were computed using Scale-Invariant Feature Transform (SIFT) extractor. FAST-SIFT method effectively SMI same-subscene images detected by the NIR sensor. The method was also tested in stitching NIR images with varying subscene swept by the camera. The slave images were matched to the master image. The keypoints served as the ground control points. Random sample consensus was used to eliminate fall-out matches and ensure accuracy of the feature points from which the transformation parameters were derived. Keypoints are matched based on their descriptor vector. Nearest-neighbor matching is employed based on a metric distance between the descriptors. The metrics include Euclidean and city block, among others. Rough matching outputs not only the correct matches but also the faulty matches. A previous work in automatic georeferencing incorporates a geometric restriction. In this work, we applied a simplified version of the learning method. RANSAC was used to eliminate fall-out matches and ensure accuracy of the feature points. This method identifies if a point fits the transformation function and returns inlier matches. The transformation matrix was solved by Affine, Projective, and Polynomial models. The accuracy of the automatic georeferencing method were determined by calculating the RMSE of interest points, selected randomly, between the master image and transformed slave image.

  9. Evaluation of needle trap micro-extraction and automatic alveolar sampling for point-of-care breath analysis.

    Science.gov (United States)

    Trefz, Phillip; Rösner, Lisa; Hein, Dietmar; Schubert, Jochen K; Miekisch, Wolfram

    2013-04-01

    Needle trap devices (NTDs) have shown many advantages such as improved detection limits, reduced sampling time and volume, improved stability, and reproducibility if compared with other techniques used in breath analysis such as solid-phase extraction and solid-phase micro-extraction. Effects of sampling flow (2-30 ml/min) and volume (10-100 ml) were investigated in dry gas standards containing hydrocarbons, aldehydes, and aromatic compounds and in humid breath samples. NTDs contained (single-bed) polymer packing and (triple-bed) combinations of divinylbenzene/Carbopack X/Carboxen 1000. Substances were desorbed from the NTDs by means of thermal expansion and analyzed by gas chromatography-mass spectrometry. An automated CO2-controlled sampling device for direct alveolar sampling at the point-of-care was developed and tested in pilot experiments. Adsorption efficiency for small volatile organic compounds decreased and breakthrough increased when sampling was done with polymer needles from a water-saturated matrix (breath) instead from dry gas. Humidity did not affect analysis with triple-bed NTDs. These NTDs showed only small dependencies on sampling flow and low breakthrough from 1-5 %. The new sampling device was able to control crucial parameters such as sampling flow and volume. With triple-bed NTDs, substance amounts increased linearly with increasing sample volume when alveolar breath was pre-concentrated automatically. When compared with manual sampling, automatic sampling showed comparable or better results. Thorough control of sampling and adequate choice of adsorption material is mandatory for application of needle trap micro-extraction in vivo. The new CO2-controlled sampling device allows direct alveolar sampling at the point-of-care without the need of any additional sampling, storage, or pre-concentration steps.

  10. Supervised non-negative tensor factorization for automatic hyperspectral feature extraction and target discrimination

    Science.gov (United States)

    Anderson, Dylan; Bapst, Aleksander; Coon, Joshua; Pung, Aaron; Kudenov, Michael

    2017-05-01

    Hyperspectral imaging provides a highly discriminative and powerful signature for target detection and discrimination. Recent literature has shown that considering additional target characteristics, such as spatial or temporal profiles, simultaneously with spectral content can greatly increase classifier performance. Considering these additional characteristics in a traditional discriminative algorithm requires a feature extraction step be performed first. An example of such a pipeline is computing a filter bank response to extract spatial features followed by a support vector machine (SVM) to discriminate between targets. This decoupling between feature extraction and target discrimination yields features that are suboptimal for discrimination, reducing performance. This performance reduction is especially pronounced when the number of features or available data is limited. In this paper, we propose the use of Supervised Nonnegative Tensor Factorization (SNTF) to jointly perform feature extraction and target discrimination over hyperspectral data products. SNTF learns a tensor factorization and a classification boundary from labeled training data simultaneously. This ensures that the features learned via tensor factorization are optimal for both summarizing the input data and separating the targets of interest. Practical considerations for applying SNTF to hyperspectral data are presented, and results from this framework are compared to decoupled feature extraction/target discrimination pipelines.

  11. Geological lineament mapping in arid area by semi-automatic extraction from satellite images: example at the El Kseïbat region (Algerian Sahara)

    Energy Technology Data Exchange (ETDEWEB)

    Hammad, N.; Djidel, M.; Maabedi, N.

    2016-07-01

    Geologists in charge of a detailed lineament mapping in arid and desert area, face the extent of the land and the abundance of eolian deposits. This study presents a semi-automatic approach of extraction of lineament, different from other methods, such as the automatic extraction and manual extraction, by being both fast and objective. It consists of a series of digital processing (textural and spatial filtering, binarization by thresholding and mathematic morphology ... etc.) applied to a Landsat 7 ETM+scene. This semi-automatic approach has produced a detailed map of lineaments, while taking account of tectonic directions recognized in the region. It helps mitigate the effect of dune deposits meet the specifications of arid environment. The visual validation of these linear structures, by geoscientists and field data, allowed the identification of the majority of structural lineaments or at least those tried geological. (Author)

  12. Automatically extracting clinically useful sentences from UpToDate to support clinicians' information needs.

    Science.gov (United States)

    Mishra, Rashmi; Del Fiol, Guilherme; Kilicoglu, Halil; Jonnalagadda, Siddhartha; Fiszman, Marcelo

    2013-01-01

    Clinicians raise several information needs in the course of care. Most of these needs can be met by online health knowledge resources such as UpToDate. However, finding relevant information in these resources often requires significant time and cognitive effort. To design and assess algorithms for extracting from UpToDate the sentences that represent the most clinically useful information for patient care decision making. We developed algorithms based on semantic predications extracted with SemRep, a semantic natural language processing parser. Two algorithms were compared against a gold standard composed of UpToDate sentences rated in terms of clinical usefulness. Clinically useful sentences were strongly correlated with predication frequency (correlation= 0.95). The two algorithms did not differ in terms of top ten precision (53% vs. 49%; p=0.06). Semantic predications may serve as the basis for extracting clinically useful sentences. Future research is needed to improve the algorithms.

  13. A semi-automatic multiple view texture mapping for the surface model extracted by laser scanning

    Science.gov (United States)

    Zhang, Zhichao; Huang, Xianfeng; Zhang, Fan; Chang, Yongmin; Li, Deren

    2008-12-01

    Laser scanning is an effective way to acquire geometry data of the cultural heritage with complex architecture. After generating the 3D model of the object, it's difficult to do the exactly texture mapping for the real object. we take effort to create seamless texture maps for a virtual heritage of arbitrary topology. Texture detail is acquired directly from the real object in a light condition as uniform as we can make. After preprocessing, images are then registered on the 3D mesh by a semi-automatic way. Then we divide the mesh into mesh patches overlapped with each other according to the valid texture area of each image. An optimal correspondence between mesh patches and sections of the acquired images is built. Then, a smoothing approach is proposed to erase the seam between different images that map on adjacent mesh patches, based on texture blending. The obtained result with a Buddha of Dunhuang Mogao Grottoes is presented and discussed.

  14. Automatic electricity markets data extraction for realistic multi-agent simulations

    DEFF Research Database (Denmark)

    Pereira, Ivo F.; Sousa, Tiago M.; Praca, Isabel

    2014-01-01

    This paper presents the development of a tool that provides a database with available information from real electricity markets, ensuring the required updating mechanisms. Some important characteristics of this tool are: capability of collecting, analyzing, processing and storing real electricity...... markets data available on-line; capability of dealing with different file formats and types, some of them inserted by the user, resulting from information obtained not on-line but based on the possible collaboration with market entities; definition and implementation of database gathering information from...... different market sources, even including different market types; machine learning approach for automatic definition of downloads periodicity of new information available on-line. This is a crucial tool to go a step forward in electricity markets simulation, since the integration of this database...

  15. Semi-automatic extraction of sectional view from point clouds - The case of Ottmarsheim's abbey-church

    Science.gov (United States)

    Landes, T.; Bidino, S.; Guild, R.

    2014-06-01

    Today, elevations or sectional views of buildings are often produced from terrestrial laser scanning. However, due to the amount of data to process and because usually 2D maps are required by customers, the 3D point cloud is often degraded into 2D slices. In a sectional view, not only the portions of the objet which are intersected by the cutting plane but also edges and contours of other parts of the object which are visible behind the cutting plane are represented. To avoid the tedious manual drawing, the aim of this work is to propose a semi-automatic approach for creating sectional views by point cloud processing. The extraction of sectional views requires in a first step the segmentation of the point cloud into planar and non-planar entities. Since in cultural heritage buildings, arches, vaults, columns can be found, the position and the direction of the sectional view must be taken into account before contours extraction. Indeed, the edges of surfaces of revolution depend on the chosen view. The developed extraction approach is detailed based on point clouds acquired inside and outside churches. The resulting sectional view has been evaluated in a qualitative and quantitative way by comparing it with a reference sectional view made by hand. A mean deviation of 3 cm between both sections proves that the proposed approach is promising. Regarding the processing time, despite a few manual corrections, it has saved 40% of the time required for manual drawing.

  16. Semi-automatic Term Extraction for an isiZulu Linguistic Terms ...

    African Journals Online (AJOL)

    Abstract. The University of KwaZulu-Natal (UKZN) is compiling a series of Language for Special Purposes (LSP) dictionaries for various specialized subject domains in line with its language policy and plan. The focus in this paper is the term extraction for words in the linguistics subject domain. This paper advances the use ...

  17. Recent developments in automatic solid-phase extraction with renewable surfaces exploiting flow-based approaches

    DEFF Research Database (Denmark)

    Miró, Manuel; Hartwell, Supaporn Kradtap; Jakmunee, Jaroon

    2008-01-01

    Solid-phase extraction (SPE) is the most versatile sample-processing method for removal of interfering species and/or analyte enrichment. Although significant advances have been made over the past two decades in automating the entire analytical protocol involving SPE via flow-injection approaches...

  18. Design and screening of extractants for Zr4+-Hf4+ separation: synergistic approach using molecular modelling and solvent extraction

    International Nuclear Information System (INIS)

    Ali, Sk. Musharaf; Boda, A.; Pandey, G.; Mukhopadhyay, S.; Shenoy, K.T.; Singh, R.; Paramanik, M.; Ghosh, S.K.

    2016-01-01

    The preferential selectivity of Zr 4+ over Hf 4+ ion towards mixed alkyl organophosphorus extractants is predicted using molecular modelling and solvent extraction studies. Density Functional theory successfully captures the higher complexation stability of mixed alkyl phosphine oxide (MAPO) over mixed alkyl substituted phosphine oxide (MSAPO) for both Zr 4+ and Hf 4+ ions as observed in the solvent extraction experiment. Further, the extraction energy for Zr 4+ ion is higher than Hf 4+ ion with MAPO over MSAPO. The calculated extraction energy follows the same order of distribution constant as predicted by the solvent extraction which shows that MAPO is the best extractant in terms of higher distribution constant and selectivity over MSAPO. (author)

  19. Automatic extraction of myocardial mass and volumes using parametric images from dynamic nongated PET

    DEFF Research Database (Denmark)

    Harms, Hendrik Johannes; Hansson, Nils Henrik Stubkjær; Tolbod, Lars Poulsen

    2016-01-01

    Dynamic cardiac positron emission tomography (PET) is used to quantify molecular processes in vivo. However, measurements of left-ventricular (LV) mass and volumes require electrocardiogram (ECG)-gated PET data. The aim of this study was to explore the feasibility of measuring LV geometry using n...

  20. Automatic extraction of protein point mutations using a graph bigram association.

    Directory of Open Access Journals (Sweden)

    Lawrence C Lee

    2007-02-01

    Full Text Available Protein point mutations are an essential component of the evolutionary and experimental analysis of protein structure and function. While many manually curated databases attempt to index point mutations, most experimentally generated point mutations and the biological impacts of the changes are described in the peer-reviewed published literature. We describe an application, Mutation GraB (Graph Bigram, that identifies, extracts, and verifies point mutations from biomedical literature. The principal problem of point mutation extraction is to link the point mutation with its associated protein and organism of origin. Our algorithm uses a graph-based bigram traversal to identify these relevant associations and exploits the Swiss-Prot protein database to verify this information. The graph bigram method is different from other models for point mutation extraction in that it incorporates frequency and positional data of all terms in an article to drive the point mutation-protein association. Our method was tested on 589 articles describing point mutations from the G protein-coupled receptor (GPCR, tyrosine kinase, and ion channel protein families. We evaluated our graph bigram metric against a word-proximity metric for term association on datasets of full-text literature in these three different protein families. Our testing shows that the graph bigram metric achieves a higher F-measure for the GPCRs (0.79 versus 0.76, protein tyrosine kinases (0.72 versus 0.69, and ion channel transporters (0.76 versus 0.74. Importantly, in situations where more than one protein can be assigned to a point mutation and disambiguation is required, the graph bigram metric achieves a precision of 0.84 compared with the word distance metric precision of 0.73. We believe the graph bigram search metric to be a significant improvement over previous search metrics for point mutation extraction and to be applicable to text-mining application requiring the association of words.

  1. Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing.

    Science.gov (United States)

    González, Roberto; Zato, Carolina; Benito, Rocío; Bajo, Javier; Hernández, Jesús M; De Paz, Juan F; Vera, Vicente; Corchado, Juan M

    2012-12-01

    Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms.

  2. Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing

    Directory of Open Access Journals (Sweden)

    González Roberto

    2012-12-01

    Full Text Available Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms.

  3. Semi-automatic Term Extraction for an isiZulu Linguistic Terms ...

    African Journals Online (AJOL)

    user

    This paper advances the use of frequency analysis and the keyword analysis as strategies to extract terms for the compilation of the dictionary of isiZulu linguistic terms. The study uses the isiZulu. National Corpus (INC) of about 1,2 million tokens as a reference corpus as well as an LSP corpus of about 100,000 tokens as a ...

  4. Automatically extracting clinically useful sentences from UpToDate to support clinicians’ information needs

    Science.gov (United States)

    Mishra, Rashmi; Fiol, Guilherme Del; Kilicoglu, Halil; Jonnalagadda, Siddhartha; Fiszman, Marcelo

    2013-01-01

    Clinicians raise several information needs in the course of care. Most of these needs can be met by online health knowledge resources such as UpToDate. However, finding relevant information in these resources often requires significant time and cognitive effort. Objective: To design and assess algorithms for extracting from UpToDate the sentences that represent the most clinically useful information for patient care decision making. Methods: We developed algorithms based on semantic predications extracted with SemRep, a semantic natural language processing parser. Two algorithms were compared against a gold standard composed of UpToDate sentences rated in terms of clinical usefulness. Results: Clinically useful sentences were strongly correlated with predication frequency (correlation= 0.95). The two algorithms did not differ in terms of top ten precision (53% vs. 49%; p=0.06). Conclusions: Semantic predications may serve as the basis for extracting clinically useful sentences. Future research is needed to improve the algorithms. PMID:24551389

  5. Localized Segment Based Processing for Automatic Building Extraction from LiDAR Data

    Science.gov (United States)

    Parida, G.; Rajan, K. S.

    2017-05-01

    The current methods of object segmentation and extraction and classification of aerial LiDAR data is manual and tedious task. This work proposes a technique for object segmentation out of LiDAR data. A bottom-up geometric rule based approach was used initially to devise a way to segment buildings out of the LiDAR datasets. For curved wall surfaces, comparison of localized surface normals was done to segment buildings. The algorithm has been applied to both synthetic datasets as well as real world dataset of Vaihingen, Germany. Preliminary results show successful segmentation of the buildings objects from a given scene in case of synthetic datasets and promissory results in case of real world data. The advantages of the proposed work is non-dependence on any other form of data required except LiDAR. It is an unsupervised method of building segmentation, thus requires no model training as seen in supervised techniques. It focuses on extracting the walls of the buildings to construct the footprint, rather than focussing on roof. The focus on extracting the wall to reconstruct the buildings from a LiDAR scene is crux of the method proposed. The current segmentation approach can be used to get 2D footprints of the buildings, with further scope to generate 3D models. Thus, the proposed method can be used as a tool to get footprints of buildings in urban landscapes, helping in urban planning and the smart cities endeavour.

  6. Comparison of sample preparation methods for reliable plutonium and neptunium urinalysis using automatic extraction chromatography

    DEFF Research Database (Denmark)

    Qiao, Jixin; Xu, Yihong; Hou, Xiaolin

    2014-01-01

    This paper describes improvement and comparison of analytical methods for simultaneous determination of trace-level plutonium and neptunium in urine samples by inductively coupled plasma mass spectrometry (ICP-MS). Four sample pre-concentration techniques, including calcium phosphate, iron...... hydroxide and manganese dioxide co-precipitation and evaporation were compared and the applicability of different techniques was discussed in order to evaluate and establish the optimal method for in vivo radioassay program. The analytical results indicate that the various sample pre......-precipitation step, yet, the occurrence of sulfur compounds in the processed sample deteriorated the analytical performance of the ensuing extraction chromatographic separation with chemical yields of...

  7. Automatic Target Recognition in Synthetic Aperture Sonar Images Based on Geometrical Feature Extraction

    Directory of Open Access Journals (Sweden)

    J. Del Rio Vera

    2009-01-01

    Full Text Available This paper presents a new supervised classification approach for automated target recognition (ATR in SAS images. The recognition procedure starts with a novel segmentation stage based on the Hilbert transform. A number of geometrical features are then extracted and used to classify observed objects against a previously compiled database of target and non-target features. The proposed approach has been tested on a set of 1528 simulated images created by the NURC SIGMAS sonar model, achieving up to 95% classification accuracy.

  8. Identifying Basketball Plays from Sensor Data; towards a Low-Cost Automatic Extraction of Advanced Statistics

    DEFF Research Database (Denmark)

    Sangüesa, Adrià Arbués; Moeslund, Thomas B.; Bahnsen, Chris Holmberg

    2017-01-01

    Advanced statistics have proved to be a crucial tool for basketball coaches in order to improve training skills. Indeed, the performance of the team can be further optimized by studying the behaviour of players under certain conditions. In the United States of America, companies such as STATS...... created and meaningful basketball features have been extracted. 97.9% accuracy is obtained using Support Vector Machines when identifying 5 different classic plays: floppy offense, pick and roll, press break, post-up situation and fast breaks. After recognizing these plays in video sequences, advanced...

  9. Automatic contour extraction for multiple objects based on Schroedinger transform of image

    Science.gov (United States)

    Lou, Liantang; Lu, Ling; Li, Liguo; Gao, Wenliang; Li, Lingling; Fu, Zhongliang

    2009-10-01

    Analytical and numerical solutions of the Schroedinger Equation which was satisfied by the propagator P(b, a) , including all the paths contribution, are discussed. The definition of Schrödinger transform of image is first proposed. Exterior and interior of objects are obtained from Schroedinger transforms of original image and its inverse image. Using the bruteforce algorithm, sets of exterior and interior points are thinned. By finding pairs of exterior and interior points with the smallest distance between them, contours of multiple objects are extracted. Some experiments with simulated and real images are given.

  10. Molecularly imprinted solid-phase extraction in the analysis of agrochemicals.

    Science.gov (United States)

    Yi, Ling-Xiao; Fang, Rou; Chen, Guan-Hua

    2013-08-01

    The molecular imprinting technique is a highly predeterminative recognition technology. Molecularly imprinted polymers (MIPs) can be applied to the cleanup and preconcentration of analytes as the selective adsorbent of solid-phase extraction (SPE). In recent years, a new type of SPE has formed, molecularly imprinted polymer solid-phase extraction (MISPE), and has been widely applied to the extraction of agrochemicals. In this review, the mechanism of the molecular imprinting technique and the methodology of MIP preparations are explained. The extraction modes of MISPE, including offline and online, are discussed, and the applications of MISPE in the analysis of agrochemicals such as herbicides, fungicides and insecticides are summarized. It is concluded that MISPE is a powerful tool to selectively isolate agrochemicals from real samples with higher extraction and cleanup efficiency than commercial SPE and that it has great potential for broad applications.

  11. How Does the Preparation of Rye Porridge Affect Molecular Weight Distribution of Extractable Dietary Fibers?

    Directory of Open Access Journals (Sweden)

    Roger Andersson

    2011-05-01

    Full Text Available Extractable dietary fiber (DF plays an important role in nutrition. This study on porridge making with whole grain rye investigated the effect of rest time of flour slurries at room temperature before cooking and amount of flour and salt in the recipe on the content of DF components and molecular weight distribution of extractable fructan, mixed linkage (1→3(1→4-β-D-glucan (β-glucan and arabinoxylan (AX in the porridge. The content of total DF was increased (from about 20% to 23% of dry matter during porridge making due to formation of insoluble resistant starch. A small but significant increase in the extractability of β-glucan (P = 0.016 and AX (P = 0.002 due to rest time was also noted. The molecular weight of extractable fructan and AX remained stable during porridge making. However, incubation of the rye flour slurries at increased temperature resulted in a significant decrease in extractable AX molecular weight. The molecular weight of extractable β-glucan decreased greatly during a rest time before cooking, most likely by the action of endogenous enzymes. The amount of salt and flour used in the recipe had small but significant effects on the molecular weight of β-glucan. These results show that whole grain rye porridge made without a rest time before cooking contains extractable DF components maintaining high molecular weights. High molecular weight is most likely of nutritional importance.

  12. Automatic building extraction from LiDAR data fusion of point and grid-based features

    Science.gov (United States)

    Du, Shouji; Zhang, Yunsheng; Zou, Zhengrong; Xu, Shenghua; He, Xue; Chen, Siyang

    2017-08-01

    This paper proposes a method for extracting buildings from LiDAR point cloud data by combining point-based and grid-based features. To accurately discriminate buildings from vegetation, a point feature based on the variance of normal vectors is proposed. For a robust building extraction, a graph cuts algorithm is employed to combine the used features and consider the neighbor contexture information. As grid feature computing and a graph cuts algorithm are performed on a grid structure, a feature-retained DSM interpolation method is proposed in this paper. The proposed method is validated by the benchmark ISPRS Test Project on Urban Classification and 3D Building Reconstruction and compared to the state-art-of-the methods. The evaluation shows that the proposed method can obtain a promising result both at area-level and at object-level. The method is further applied to the entire ISPRS dataset and to a real dataset of the Wuhan City. The results show a completeness of 94.9% and a correctness of 92.2% at the per-area level for the former dataset and a completeness of 94.4% and a correctness of 95.8% for the latter one. The proposed method has a good potential for large-size LiDAR data.

  13. Characteristics of antibacterial molecular activities in poplar wood extractives.

    Science.gov (United States)

    Peng, Wanxi; Li, Dongli; Zhang, Minglong; Ge, Shengbo; Mo, Bo; Li, Shasha; Ohkoshi, Makoto

    2017-02-01

    As one of the dominant plantations in north and central China, poplar was considered as the uppermost wood raw materials, however, the chemical constituents of poplar wood weren't effectively used by high added value. Therefore, the molecules of wood extractives in Populus lasiocarpa and Populus tomentosa were extracted and studied to further utilize the bio-resources. The results showed that the LD-010, LD-021, LD-150, LD-174 wood extractives were identified as having 3, 24, 3 27 components, respectively. P. lasiocarpa wood was fit to extract 2,4-hexadiyne, 1,3,3-trimethyl-2-hydroxymethyl-3,3-dimethyl-4-(3-methylbut-2-enyl)-cyclohexene, and P. tomentosa wood was fit to extract 1,5-hexadien-3-yne, (all-E)-2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaene. So the extractives of poplar wood contained rich and rare drug and biomedical activities.

  14. MOLECULARLY IMPRINTED SOLID PHASE EXTRACTION FOR TRACE ANALYSIS OF DIAZINON IN DRINKING WATER

    Directory of Open Access Journals (Sweden)

    M. Rahiminejad ، S. J. Shahtaheri ، M. R. Ganjali ، A. Rahimi Forushani ، F. Golbabaei

    2009-04-01

    Full Text Available Amongst organophosphate pesticides, the one most widely used and common environmental contaminant is diazinon; thus methods for its trace analysis in environmental samples must be developed. Use of diazinon imprinted polymers such as sorbents in solid phase extraction, is a prominent and novel application area of molecular imprinted polymers. For diazinon extraction, high performance liquid chromatography analysis was demonstrated in this study. During optimization of the molecular imprinted solid phase extraction procedure for efficient solid phase extraction of diazinon, Plackett-Burman design was conducted. Eight experimental factors with critical influence on molecular imprinted solid phase extraction performance were selected, and 12 different experimental runs based on Plackett-Burman design were carried out. The applicability of diazinon imprinted polymers as the sorbent in solid phase extraction, presented obtained good recoveries of diazinon from LC-grade water. An increase in pH caused an increase in the recovery on molecular imprinted solid phase extraction. From these results, the optimal molecular imprinted solid phase extraction procedure was as follows: solid phase extraction packing with 100 mg diazinon imprinted polymers; conditioning with 5 mL of methanol and 6 mL of LC-grade water; sample loading containing diazinon (pH=10; washing with 1 mL of LC-grade water, 1 mL LC- grade water containing 30% acetonitrile and 0.5 mL of acetonitrile, respectively; eluting with 1 mL of methanol containing 2% acetic acid. The percentage recoveries obtained by the optimized molecular imprinted solid phase extraction were more than 90% with drinking water spiked at different trace levels of diazinon. Generally speaking, the molecular imprinted solid phase extraction procedure and subsequent high performance liquid chromatography analysis can be a relatively fast and proper approach for qualitative and quantitative analysis of diazinon in

  15. AUTOMATIC BUILDING EXTRACTION AND ROOF RECONSTRUCTION IN 3K IMAGERY BASED ON LINE SEGMENTS

    Directory of Open Access Journals (Sweden)

    A. Köhn

    2016-06-01

    Full Text Available We propose an image processing workflow to extract rectangular building footprints using georeferenced stereo-imagery and a derivative digital surface model (DSM product. The approach applies a line segment detection procedure to the imagery and subsequently verifies identified line segments individually to create a footprint on the basis of the DSM. The footprint is further optimized by morphological filtering. Towards the realization of 3D models, we decompose the produced footprint and generate a 3D point cloud from DSM height information. By utilizing the robust RANSAC plane fitting algorithm, the roof structure can be correctly reconstructed. In an experimental part, the proposed approach has been performed on 3K aerial imagery.

  16. EnvMine: A text-mining system for the automatic extraction of contextual information

    Directory of Open Access Journals (Sweden)

    de Lorenzo Victor

    2010-06-01

    Full Text Available Abstract Background For ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles. So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations from textual sources of any kind. Results EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings. Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude, thus allowing the calculation of distance between the individual locations. Conclusion EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical

  17. Extraction of low molecular weight RNA from Citrus trifolita tissues ...

    African Journals Online (AJOL)

    Jane

    2010-12-20

    Dec 20, 2010 ... reaction (RT-PCR) and Northern blotting. Key words: Citrus, low molecular weight RNA, trizol reagent, 4 M LiCl, microRNAs. INTRODUCTION. Low molecular weight RNA (LMW RNA) consists of several components with microRNAs (miRNAs) being among the important ones. miRNAs are endogenous 19-.

  18. Simple Extraction and Molecular Weight Characterization of Fucoidan from Indonesian Sargassum sp.

    Directory of Open Access Journals (Sweden)

    Lukman Junaidi

    2013-12-01

    Full Text Available Fucoidan is a complex polysaccharide compounds found in brown algae. Fucoidan exhibits various biological properties for disease prevention. There are various methods used to extract fucoidan from brown algae, such as using ethanol, acetone, HCl and microwave. This research aims to extract and characterize fucoidan from Sargassum sp. using simple methods with the variables on extracting solutions, temperature and time of extraction. Extraction solution used were water and HCl. Ttemperature used was 50°C, 70°C and 100°C  using 1, 2 and 4 hours. The result showed that the highest extraction yield was obtained from the extraction by water with 100°C and 4 hours of extraction. Fucoidan extracted by water has molecular weight of 57.77 kDa and 2.71 kDa, while fucoidan extracted by HCl has molecular weight of 46.43 kDa and 3.38 kDa. The proportion of high molecular weight fucoidan extracted by water was 52.24% compared with HCl was 44.10%.

  19. Gas chromatographic determination of N-nitrosamines in beverages following automatic solid-phase extraction.

    Science.gov (United States)

    Jurado-Sánchez, Beatriz; Ballesteros, Evaristo; Gallego, Mercedes

    2007-11-28

    A semiautomatic method for the determination of seven N-nitrosamines in beverages by gas chromatography with nitrogen-phosphorus detection is proposed. Beverage samples are aspirated into a solid-phase extraction module for preconcentration and cleanup. The influence of the experimental conditions was examined by using various sorbents among which LiChrolut EN was found to provide quantitative elution and the highest preconcentration factors of all. The proposed method is sensitive, with limits of detection between 7 and 33 ng/kg, and precise, with relative standard deviations from 4.3% to 6.0%. The recoveries of N-nitrosamines from beverage samples spiked with 0.5 or 1 microg/kg concentrations of these compounds ranged from 95% to 102%. The method was successfully applied to the determination of residues of the studied N-nitrosamines in beverages including beer, wine, liquor, whisky, cognac, rum, vodka, grape juice, cider, tonic water, and soft drinks. The analytes were only detected in beer samples, positives being confirmed by gas chromatography coupled with impact ionization mass spectrometry.

  20. On-line dynamic fractionation and automatic determination of inorganic phosphorous in environmental solid substrates exploiting sequential injection microcolumn extraction and flow injection analysi

    DEFF Research Database (Denmark)

    Buanuam, Janya; Miró, Manuel; Hansen, Elo Harald

    2006-01-01

    associations for phosphorus, that is, exchangeable, Al- and Fe-bound and Ca-bound fractions, were elucidated by accommodation in the flow manifold of the 3 steps of the Hietjles-Litjkema (HL) scheme involving the use of 1.0 M NH4Cl, 0.1 M NaOH and 0.5 M HCl, respectively, as sequential leaching reagents....... The precise timing and versatility of SI for tailoring various operational extraction modes were utilised for investigating the extractability and extent of phosphorous re-distribution for variable partitioning times. Automatic spectrophotometric determination of soluble reactive phosphorous in soil extracts...

  1. Characteristics of antibacterial molecular activities in poplar wood extractives

    Directory of Open Access Journals (Sweden)

    Wanxi Peng

    2017-02-01

    Full Text Available As one of the dominant plantations in north and central China, poplar was considered as the uppermost wood raw materials, however, the chemical constituents of poplar wood weren’t effectively used by high added value. Therefore, the molecules of wood extractives in Populus lasiocarpa and Populus tomentosa were extracted and studied to further utilize the bio-resources. The results showed that the LD-010, LD-021, LD-150, LD-174 wood extractives were identified as having 3, 24, 3 27 components, respectively. P. lasiocarpa wood was fit to extract 2,4-hexadiyne, 1,3,3-trimethyl-2-hydroxymethyl-3,3-dimethyl-4-(3-methylbut-2-enyl-cyclohexene, and P. tomentosa wood was fit to extract 1,5-hexadien-3-yne, (all-E-2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaene. So the extractives of poplar wood contained rich and rare drug and biomedical activities.

  2. Automatic detection of wheezes by evaluation of multiple acoustic feature extraction methods and C-weighted SVM

    Science.gov (United States)

    Sosa, Germán. D.; Cruz-Roa, Angel; González, Fabio A.

    2015-01-01

    This work addresses the problem of lung sound classification, in particular, the problem of distinguishing between wheeze and normal sounds. Wheezing sound detection is an important step to associate lung sounds with an abnormal state of the respiratory system, usually associated with tuberculosis or another chronic obstructive pulmonary diseases (COPD). The paper presents an approach for automatic lung sound classification, which uses different state-of-the-art sound features in combination with a C-weighted support vector machine (SVM) classifier that works better for unbalanced data. Feature extraction methods used here are commonly applied in speech recognition and related problems thanks to the fact that they capture the most informative spectral content from the original signals. The evaluated methods were: Fourier transform (FT), wavelet decomposition using Wavelet Packet Transform bank of filters (WPT) and Mel Frequency Cepstral Coefficients (MFCC). For comparison, we evaluated and contrasted the proposed approach against previous works using different combination of features and/or classifiers. The different methods were evaluated on a set of lung sounds including normal and wheezing sounds. A leave-two-out per-case cross-validation approach was used, which, in each fold, chooses as validation set a couple of cases, one including normal sounds and the other including wheezing sounds. Experimental results were reported in terms of traditional classification performance measures: sensitivity, specificity and balanced accuracy. Our best results using the suggested approach, C-weighted SVM and MFCC, achieve a 82.1% of balanced accuracy obtaining the best result for this problem until now. These results suggest that supervised classifiers based on kernel methods are able to learn better models for this challenging classification problem even using the same feature extraction methods.

  3. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model

    Science.gov (United States)

    Zhao, Song-Feng; Huang, Fang; Wang, Guo-Li; Zhou, Xiao-Xin

    2016-03-01

    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov–Popov–Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  4. Automatic spot preparation and image processing of paper microzone-based assays for analysis of bioactive compounds in plant extracts.

    Science.gov (United States)

    Vaher, M; Borissova, M; Seiman, A; Aid, T; Kolde, H; Kazarjan, J; Kaljurand, M

    2014-01-15

    The colorimetric determination of the concentration of phytochemicals in plant extract samples using a spotting automatic system, mobile phone camera and a computer with developed software for quantification is described. Method automation was achieved by using a robotic system for spotting. The instrument was set to disperse the appropriate aliquots of the reagents and sample on a Whatman paper sheet. Spots were photographed and analysed by ImageJ software or by applying the developed MatLab based algorithm. The developed assay was found to be effective, with a linear response at the concentration range of 0.03-0.25g/L for polyphenols. The detection limit of the proposed method is sub 0.03g/L. The paper microzone-based assays for flavonoids and amino acids/peptides were also developed and evaluated as applicable. Comparing the results with conventional PμZP methods demonstrates that both methods yield similar results. At the same time, the proposed method has an attractive advantage in analysis time and repeatability/reproducibility. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Comparison of manual and semi-automatic DNA extraction protocols for the barcoding characterization of hematophagous louse flies (Diptera: Hippoboscidae).

    Science.gov (United States)

    Gutiérrez-López, Rafael; Martínez-de la Puente, Josué; Gangoso, Laura; Soriguer, Ramón C; Figuerola, Jordi

    2015-06-01

    The barcoding of life initiative provides a universal molecular tool to distinguish animal species based on the amplification and sequencing of a fragment of the subunit 1 of the cytochrome oxidase (COI) gene. Obtaining good quality DNA for barcoding purposes is a limiting factor, especially in studies conducted on small-sized samples or those requiring the maintenance of the organism as a voucher. In this study, we compared the number of positive amplifications and the quality of the sequences obtained using DNA extraction methods that also differ in their economic costs and time requirements and we applied them for the genetic characterization of louse flies. Four DNA extraction methods were studied: chloroform/isoamyl alcohol, HotShot procedure, Qiagen DNeasy(®) Tissue and Blood Kit and DNA Kit Maxwell(®) 16LEV. All the louse flies were morphologically identified as Ornithophila gestroi and a single COI-based haplotype was identified. The number of positive amplifications did not differ significantly among DNA extraction procedures. However, the quality of the sequences was significantly lower for the case of the chloroform/isoamyl alcohol procedure with respect to the rest of methods tested here. These results may be useful for the genetic characterization of louse flies, leaving most of the remaining insect as a voucher. © 2015 The Society for Vector Ecology.

  6. Extraction of low molecular weight RNA from Citrus trifolita tissues ...

    African Journals Online (AJOL)

    We employed a simple and quick method involving trizol for total RNA extraction from citrus tissues, then generation of LMW RNA using 4M LiCl, which have been successfully utilized in studies in our laboratory. Compared with traditional methods, this method is less expensive and produced high RNA yields while avoiding ...

  7. Rapid methods for the extraction and archiving of molecular grade fungal genomic DNA.

    Science.gov (United States)

    Borman, Andrew M; Palmer, Michael; Johnson, Elizabeth M

    2013-01-01

    The rapid and inexpensive extraction of fungal genomic DNA that is of sufficient quality for molecular approaches is central to the molecular identification, epidemiological analysis, taxonomy, and strain typing of pathogenic fungi. Although many commercially available and in-house extraction procedures do eliminate the majority of contaminants that commonly inhibit molecular approaches, the inherent difficulties in breaking fungal cell walls lead to protocols that are labor intensive and that routinely take several hours to complete. Here we describe several methods that we have developed in our laboratory that allow the extremely rapid and inexpensive preparation of fungal genomic DNA.

  8. Determination of molecular weight and other characteristics of co- and terpolymers using automatic continuous online monitoring of polymerization reactions (ACOMP)

    Science.gov (United States)

    Enohnyaket, Pascal E. A.

    The Automatic Continuous Online Monitoring of Polymerization reactions (ACOMP), is a technique developed by the Reed Research Group at Tulane University. By simultaneously monitoring and combining signals from a continuously dilute reactor stream, detectors such as a multi-angle light scattering detector, near infra-red spectrometer, viscometer, differential refractive index, and a full wavelength UV/Visible detector were used in a model-independent fashion to follow the weight-average molecular weight, intrinsic viscosity, the concentrations of each comonomer, and hence the evolution of the average instantaneous and cumulative compositions along the chains as comonomers are consumed. The goal of this dissertation is to make the ACOMP system more useful in very complex polymerization situations by improving it with additional detectors and formalisms (such as a new expression for computing the molecular weight a copolymer of nth degree) and to exploit its robustness in situations where traditional routes fail or are of limited value. By providing a continuum of data, ACOMP allows polymer scientists to better understand and control new reaction schemes. At the pilot plant, it can be used to optimize reaction conditions. Because the ACOMP system is relatively cheap, user friendly, can be environmentally friendly, less bulky and very efficient, it is my desire to use ACOMP to solve some of the problems in the petroleum, plastic and drug manufacturing industries in Cameroon (and Africa).

  9. Automatic labeling of molecular biomarkers of immunohistochemistry images using fully convolutional networks

    Science.gov (United States)

    Ward, Rabab K.; van Niekerk, Dirk; Guillaud, Martial

    2018-01-01

    This paper addresses the problem of quantifying biomarkers in multi-stained tissues based on the color and spatial information of microscopy images of the tissue. A deep learning-based method that can automatically localize and quantify the regions expressing biomarker(s) in any selected area on a whole slide image is proposed. The deep learning network, which we refer to as Whole Image (WI)-Net, is a fully convolutional network whose input is the true RGB color image of a tissue and output is a map showing the locations of each biomarker. The WI-Net relies on a different network, Nuclei (N)-Net, which is a convolutional neural network that classifies each nucleus separately according to the biomarker(s) it expresses. In this study, images of immunohistochemistry (IHC)-stained slides were collected and used. Images of nuclei (4679 RGB images) were manually labeled based on the expressing biomarkers in each nucleus (as p16 positive, Ki-67 positive, p16 and Ki-67 positive, p16 and Ki-67 negative). The labeled nuclei images were used to train the N-Net (obtaining an accuracy of 92% in a test set). The trained N-Net was then extended to WI-Net that generated a map of all biomarkers in any selected sub-image of the whole slide image acquired by the scanner (instead of classifying every nucleus image). The results of our method compare well with the manual labeling by humans (average F-score of 0.96). In addition, we carried a layer-based immunohistochemical analysis of cervical epithelium, and showed that our method can be used by pathologists to differentiate between different grades of cervical intraepithelial neoplasia by quantitatively assessing the percentage of proliferating cells in the different layers of HPV positive lesions. PMID:29351281

  10. Pressurized liquid extraction of selected molecular biomarkers in deep sea sediments used as proxies in paleoceanography.

    Science.gov (United States)

    Calvo, Eva; Pelejero, Carles; Logan, Graham A

    2003-03-14

    Pressurized liquid extraction has been performed on a suite of deep-sea sediments to assess its capability as an extraction technique in the analysis of molecular biomarkers used in paleoceanography. Specific compounds assessed comprise long-chain alkenones, n-alkanes, n-alcohols and, additionally, one diol and one keto-ol. These have been extracted by both pressurized liquid extraction and ultrasonication for comparison. One key result is that the U37(K') index (based on the degree of unsaturation of the alkenones and used as a paleothermometer in paleoceanography) remains intact after both extraction techniques. In terms of biomarker concentrations, which are often used to qualitatively assess changes in marine productivity and/or terrigenous inputs, pressurized liquid extraction is substantially more efficient than ultrasonication, providing higher amounts of extracted constituents, particularly for polar compounds.

  11. Automatic 3D segmentation of the kidney in MR images using wavelet feature extraction and probability shape model

    Science.gov (United States)

    Akbari, Hamed; Fei, Baowei

    2012-02-01

    Numerical estimation of the size of the kidney is useful in evaluating conditions of the kidney, especially, when serial MR imaging is performed to evaluate the kidney function. This paper presents a new method for automatic segmentation of the kidney in three-dimensional (3D) MR images, by extracting texture features and statistical matching of geometrical shape of the kidney. A set of Wavelet-based support vector machines (W-SVMs) is trained on the MR images. The W-SVMs capture texture priors of MRI for classification of the kidney and non-kidney tissues in different zones around the kidney boundary. In the segmentation procedure, these W-SVMs are trained to tentatively label each voxel around the kidney model as a kidney or non-kidney voxel by texture matching. A probability kidney model is created using 10 segmented MRI data. The model is initially localized based on the intensity profiles in three directions. The weight functions are defined for each labeled voxel for each Wavelet-based, intensity-based, and model-based label. Consequently, each voxel has three labels and three weights for the Wavelet feature, intensity, and probability model. Using a 3D edge detection method, the model is re-localized and the segmented kidney is modified based on a region growing method in the model region. The probability model is re-localized based on the results and this loop continues until the segmentation converges. Experimental results with mouse MRI data show the good performance of the proposed method in segmenting the kidney in MR images.

  12. DNA extraction from sea anemone (Cnidaria: Actiniaria tissues for molecular analyses

    Directory of Open Access Journals (Sweden)

    Pinto S.M.

    2000-01-01

    Full Text Available A specific DNA extraction method for sea anemones is described in which extraction of total DNA from eight species of sea anemones and one species of corallimorpharian was achieved by changing the standard extraction protocols. DNA extraction from sea anemone tissue is made more difficult both by the tissue consistency and the presence of symbiotic zooxanthellae. The technique described here is an efficient way to avoid problems of DNA contamination and obtain large amounts of purified and integral DNA which can be used in different kinds of molecular analyses.

  13. Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction.

    Science.gov (United States)

    Xu, Youjun; Pei, Jianfeng; Lai, Luhua

    2017-11-27

    Median lethal death, LD 50 , is a general indicator of compound acute oral toxicity (AOT). Various in silico methods were developed for AOT prediction to reduce costs and time. In this study, we developed an improved molecular graph encoding convolutional neural networks (MGE-CNN) architecture to construct three types of high-quality AOT models: regression model (deepAOT-R), multiclassification model (deepAOT-C), and multitask model (deepAOT-CR). These predictive models highly outperformed previously reported models. For the two external data sets containing 1673 (test set I) and 375 (test set II) compounds, the R 2 and mean absolute errors (MAEs) of deepAOT-R on the test set I were 0.864 and 0.195, and the prediction accuracies of deepAOT-C were 95.5% and 96.3% on test sets I and II, respectively. The two external prediction accuracies of deepAOT-CR are 95.0% and 94.1%, while the R 2 and MAE are 0.861 and 0.204 for test set I, respectively. We then performed forward and backward exploration of deepAOT models for deep fingerprints, which could support shallow machine learning methods more efficiently than traditional fingerprints or descriptors. We further performed automatic feature learning, a key essence of deep learning, to map the corresponding activation values into fragment space and derive AOT-related chemical substructures by reverse mining of the features. Our deep learning architecture for AOT is generally applicable in predicting and exploring other toxicity or property end points of chemical compounds. The two deepAOT models are freely available at http://repharma.pku.edu.cn/DLAOT/DLAOThome.php or http://www.pkumdl.cn/DLAOT/DLAOThome.php .

  14. Optimisation of the synthesis of vancomycin-selective molecularly imprinted polymer nanoparticles using automatic photoreactor

    Science.gov (United States)

    Muzyka, Kateryna; Karim, Khalku; Guerreiro, Antonio; Poma, Alessandro; Piletsky, Sergey

    2014-03-01

    A novel optimized protocol for solid-state synthesis of molecularly imprinted polymer nanoparticles (nanoMIPs) with specificity for antibiotic vancomycin is described. The experimental objective was optimization of the synthesis parameters (factors) affecting the yield of obtained nanoparticles which have been synthesized using the first prototype of an automated solid-phase synthesizer. Applications of experimental design (or design of experiments) in optimization of nanoMIP yield were carried out using MODDE 9.0 software. The factors chosen in the model were the amount of functional monomers in the polymerization mixture, irradiation time, temperature during polymerization, and elution temperature. In general, it could be concluded that the irradiation time is the most important and the temperature was the least important factor which influences the yield of nanoparticles. Overall, the response surface methodology proved to be an effective tool in reducing time required for optimization of complex experimental conditions.

  15. Molecular Techniques for Dicistrovirus Detection without RNA Extraction or Purification

    Directory of Open Access Journals (Sweden)

    Jailson F. B. Querido

    2013-01-01

    Full Text Available Dicistroviridae is a new family of small, nonenveloped, and +ssRNA viruses pathogenic to both beneficial arthropods and insect pests as well. Triatoma virus (TrV, a dicistrovirus, is a pathogen of Triatoma infestans (Hemiptera: Reduviidae, one of the main vectors of Chagas disease. In this work, we report a single-step method to identify TrV, a dicistrovirus, isolated from fecal samples of triatomines. The identification method proved to be quite sensitive, even without the extraction and purification of RNA virus.

  16. Extraction Kinetics and Molecular Size Fractionation of Humic Substances From Two Brazilian Soils

    Directory of Open Access Journals (Sweden)

    Dick Deborah Pinheiro

    1999-01-01

    Full Text Available In the present study, the extraction behaviour of humic substances (HS from an Oxisol and a Mollisol from South Brazil, by using 0.1 and 0.5 mol L-1 NaOH and 0.15 mol L-1 neutral pyrophosphate solutions, respectively, was systematically studied. The kinetics and efficiency of HS extraction were evaluated by means of UV/Vis spectroscopy. The isolated humic acids (HA and fulvic acids (FA were size-classified by multistage ultrafiltration (six fractions in the molecular weight range of 1 to 100 kDa. The obtained data show that the HS extraction yield depended not only on the extractant, but also on the soil type. Within 3 h approximately 90% of the soluble HS could be extracted following complex extraction kinetics by both methods and none or little structural modification was verified as observed from their stable extinction ratio E350/E550. In the Mollisol the pyrophosphate extraction was more effective, suggesting that a great part of HS occurred as macromolecules bonded to clay minerals and aggregated between themselves through cationic bridges. In the Oxisol a higher HS yield was verified with the alkaline method, presumably due to HS fixation onto the oxide surface by H-bonds and/or surface complexation reactions. In general, HS extracted by the pyrophosphate procedure showed higher molecular weights than those extracted by NaOH.

  17. Molecular characteristics of Illicium verum extractives to activate acquired immune response.

    Science.gov (United States)

    Peng, Wanxi; Lin, Zhi; Wang, Lansheng; Chang, Junbo; Gu, Fangliang; Zhu, Xiangwei

    2016-05-01

    Illicium verum, whose extractives can activate the demic acquired immune response, is an expensive medicinal plant. However, the rich extractives in I. verum biomass were seriously wasted for the inefficient extraction and separation processes. In order to further utilize the biomedical resources for the good acquired immune response, the four extractives were obtained by SJYB extraction, and then the immunology moleculars of SJYB extractives were identified and analyzed by GC-MS. The result showed that the first-stage extractives contained 108 components including anethole (40.27%), 4-methoxy-benzaldehyde (4.25%), etc.; the second-stage extractives had 5 components including anethole (84.82%), 2-hydroxy-2-(4-methoxy-phenyl)-n-methyl-acetamide (7.11%), etc.; the third-stage extractives contained one component namely anethole (100%); and the fourth-stage extractives contained 5 components including cyclohexyl-benzene (64.64%), 1-(1-methylethenyl)-3-(1-methylethyl)-benzene (17.17%), etc. The SJYB extractives of I. verum biomass had a main retention time between 10 and 20 min what's more, the SJYB extractives contained many biomedical moleculars, such as anethole, eucalyptol, [1S-(1α,4aα,10aβ)]-1,2,3,4,4a,9,10,10a-octahydro-1,4a-dimethyl-7-(1-methylethyl)-1-phenanthrenecarboxylic acid, stigmast-4-en-3-one, γ-sitosterol, and so on. So the functional analytical results suggested that the SJYB extractives of I. verum had a function in activating the acquired immune response and a huge potential in biomedicine.

  18. Pomegranate Extracts and Cancer Prevention: Molecular and Cellular Activities

    Science.gov (United States)

    Syed, Deeba N.; Chamcheu, Jean-Christopher; Adhami, Vaqar M.; Mukhtar, Hasan

    2014-01-01

    There is increased appreciation by the scientific community that dietary phytochemicals can be potential weapons in the fight against cancer. Emerging data has provided new insights into the molecular and cellular framework needed to establish novel mechanism-based strategies for cancer prevention by selective bioactive food components. The unique chemical composition of the pomegranate fruit, rich in antioxidant tannins and flavonoids has drawn the attention of many investigators. Polyphenol rich fractions derived from the pomegranate fruit have been studied for their potential chemopreventive and/or cancer therapeutic effects in several animal models. Although data from in vitro and in vivo studies look convincing, well designed clinical trials in humans are needed to ascertain whether pomegranate can become part of our armamentarium against cancer. This review summarizes the available literature on the effects of pomegranate against various cancers. PMID:23094914

  19. A Neutral-Network-Fusion Architecture for Automatic Extraction of Oceanographic Features from Satellite Remote Sensing Imagery

    National Research Council Canada - National Science Library

    Askari, Farid

    1999-01-01

    This report describes an approach for automatic feature detection from fusion of remote sensing imagery using a combination of neural network architecture and the Dempster-Shafer (DS) theory of evidence...

  20. A novel automatic molecular test for detection of multidrug resistance tuberculosis in sputum specimen: A case control study.

    Science.gov (United States)

    Li, Qiang; Ou, Xi C; Pang, Yu; Xia, Hui; Huang, Hai R; Zhao, Bing; Wang, Sheng F; Zhao, Yan L

    2017-07-01

    MiniLab tuberculosis (ML TB) assay is a new automatic diagnostic tool for diagnosis of multidrug resistance tuberculosis (MDR-TB). This study was conducted with aims to know the performance of this assay. Sputum sample from 224 TB suspects was collected from tuberculosis suspects seeking medical care at Beijing Chest hospital. The sputum samples were directly used for smear and ML TB test. The left sputum sample was used to conduct Xpert MTB/RIF, Bactec MGIT culture and drug susceptibility test (DST). All discrepancies between the results from DST, molecular and phenotypic methods were confirmed by DNA Sequencing. The sensitivity and specificity of ML TB test for detecting MTBC from TB suspects were 95.1% and 88.9%, respectively. The sensitivity for smear negative TB suspects was 64.3%. For detection of RIF resistance, the sensitivity and specificity of ML TB test were 89.2% and 95.7%, respectively. For detection of INH resistance, the sensitivity and specificity of ML TB test were 78.3% and 98.1%, respectively. ML TB test showed similar performance to Xpert MTB/RIF for detection of MTBC and RIF resistance. In addition, ML TB also had good performance for INH resistance detection. Copyright © 2017. Published by Elsevier Ltd.

  1. Nonequilibrium Phase Transitions in the Extraction of Membrane Tubes by Molecular Motors

    Science.gov (United States)

    Tailleur, J.; Evans, M. R.; Kafri, Y.

    2009-03-01

    The extraction of membrane tubes by molecular motors is known to play an important role for the transport properties of eukaryotic cells. By studying a generic class of models for the tube extraction, we discover a rich phase diagram. In particular we show that the density of motors along the tube can exhibit shocks, inverse shocks, and plateaux, depending on parameters which could in principle be probed experimentally. In addition the phase diagram exhibits interesting reentrant behavior.

  2. Automatic Object-Oriented, Spectral-Spatial Feature Extraction Driven by Tobler’s First Law of Geography for Very High Resolution Aerial Imagery Classification

    Directory of Open Access Journals (Sweden)

    Zhiyong Lv

    2017-03-01

    Full Text Available Aerial image classification has become popular and has attracted extensive research efforts in recent decades. The main challenge lies in its very high spatial resolution but relatively insufficient spectral information. To this end, spatial-spectral feature extraction is a popular strategy for classification. However, parameter determination for that feature extraction is usually time-consuming and depends excessively on experience. In this paper, an automatic spatial feature extraction approach based on image raster and segmental vector data cross-analysis is proposed for the classification of very high spatial resolution (VHSR aerial imagery. First, multi-resolution segmentation is used to generate strongly homogeneous image objects and extract corresponding vectors. Then, to automatically explore the region of a ground target, two rules, which are derived from Tobler’s First Law of Geography (TFL and a topological relationship of vector data, are integrated to constrain the extension of a region around a central object. Third, the shape and size of the extended region are described. A final classification map is achieved through a supervised classifier using shape, size, and spectral features. Experiments on three real aerial images of VHSR (0.1 to 0.32 m are done to evaluate effectiveness and robustness of the proposed approach. Comparisons to state-of-the-art methods demonstrate the superiority of the proposed method in VHSR image classification.

  3. Comparison of Landsat-8, ASTER and Sentinel 1 satellite remote sensing data in automatic lineaments extraction: A case study of Sidi Flah-Bouskour inlier, Moroccan Anti Atlas

    Science.gov (United States)

    Adiri, Zakaria; El Harti, Abderrazak; Jellouli, Amine; Lhissou, Rachid; Maacha, Lhou; Azmi, Mohamed; Zouhair, Mohamed; Bachaoui, El Mostafa

    2017-12-01

    Certainly, lineament mapping occupies an important place in several studies, including geology, hydrogeology and topography etc. With the help of remote sensing techniques, lineaments can be better identified due to strong advances in used data and methods. This allowed exceeding the usual classical procedures and achieving more precise results. The aim of this work is the comparison of ASTER, Landsat-8 and Sentinel 1 data sensors in automatic lineament extraction. In addition to image data, the followed approach includes the use of the pre-existing geological map, the Digital Elevation Model (DEM) as well as the ground truth. Through a fully automatic approach consisting of a combination of edge detection algorithm and line-linking algorithm, we have found the optimal parameters for automatic lineament extraction in the study area. Thereafter, the comparison and the validation of the obtained results showed that the Sentinel 1 data are more efficient in restitution of lineaments. This indicates the performance of the radar data compared to those optical in this kind of study.

  4. Enzymatic treatment of specimens before DNA extraction directly influences molecular detection of infectious agents.

    Directory of Open Access Journals (Sweden)

    Pablo Goldschmidt

    Full Text Available INTRODUCTION: Biological samples, pharmaceuticals or food contain proteins, lipids, polymers, ammoniums and macromolecules that alter the detection of infectious agents by DNA amplification techniques (PCR. Moreover the targeted DNA has to be released from the complex cell walls and the compact nucleoprotein matrixes and cleared from potential inhibitors. The goal of the present work was to assess the efficiency of enzymatic pretreatments on infectious agents to make DNA available for further extraction and amplification. METHODS: Staphylococcus epidermidis, Streptococcus mitis, Propionibacterium acnes, Escherichia coli, Pseudomonas aeruginosa, Candida albicans, Aspergillus niger and Fusarium solani were mixed with an internal control virus and treated with: 1 proteinase K; 2 lyticase and 3 lyticase followed by proteinase K. DNAs was manually extracted using the QIAmp DNA Mini kit or the MagNA Pure Compact automate. DNA extraction yields and the inhibitors were assessed with a phocid Herpesvirus. Bacterial detection was performed using TaqMan real-time PCR and yeasts and filamentous Fungi with HRM (real-time PCR followed by high-resolution melting analysis. RESULTS: Viral DNA was released, extracted and detected using manual and automatic methods without pre enzymatic treatments. Either the manual or the automatic DNA extraction systems did not meet the sensitivity expectations if enzymatic treatments were not performed before: lyticase for Fungi and Proteinase K for Bacteria. The addition of lyticase and proteinase K did not improve results. For Fungi the detection after lyticase was higher than for Proteinase K, for which melting analysis did not allow fungal specification. DISCUSSION: Columns and magnetic beads allowed collecting DNA and separate PCR inhibitors. Detection rates cannot be related to DNA-avidity of beads or to elution but to the lack of proteolysis.

  5. Molecularly imprinted polymer for solid-phase extraction of ephedrine and analogs from human plasma.

    Science.gov (United States)

    Lasáková, Martina; Thiébaut, Didier; Jandera, Pavel; Pichon, Valérie

    2009-04-01

    A molecularly imprinted polymer (MIP) was synthesized and evaluated to selectively extract ephedrine from human plasma. The MIP synthesis was performed in chloroform with methacrylic acid as a functional monomer and the target alkaloid as a template molecule. The resulting MIP was applied to the selective extraction of ephedrine from a pure aqueous medium. A recovery about 74% was obtained using the MIP with only 7% on the nonimprinted polymer (NIP). A very straightforward selective SPE procedure was then successfully applied to the direct extraction of ephedrine from spiked human plasma with a high extraction recovery (68%) on the MIP with no recovery on the NIP. Moreover, the MIP was used for the selective extraction of catecholamine neurotransmitters, i.e. adrenaline and noradrenaline.

  6. Automatic extraction of corpus callosum from midsagittal head MR image and examination of Alzheimer-type dementia objective diagnostic system in feature analysis

    International Nuclear Information System (INIS)

    Kaneko, Tomoyuki; Kodama, Naoki; Kaeriyama, Tomoharu; Fukumoto, Ichiro

    2004-01-01

    We studied the objective diagnosis of Alzheimer-type dementia based on changes in the corpus callosum. We examined midsagittal head MR images of 40 Alzheimer-type dementia patients (15 men and 25 women; mean age, 75.4±5.5 years) and 31 healthy elderly persons (10 men and 21 women; mean age, 73.4±7.5 years), 71 subjects altogether. First, the corpus callosum was automatically extracted from midsagittal head MR images. Next, Alzheimer-type dementia was compared with the healthy elderly individuals using the features of shape factor and six features of Co-occurrence Matrix from the corpus callosum. Automatic extraction of the corpus callosum succeeded in 64 of 71 individuals, for an extraction rate of 90.1%. A statistically significant difference was found in 7 of the 9 features between Alzheimer-type dementia patients and the healthy elderly adults. Discriminant analysis using the 7 features demonstrated a sensitivity rate of 82.4%, specificity of 89.3%, and overall accuracy of 85.5%. These results indicated the possibility of an objective diagnostic system for Alzheimer-type dementia using feature analysis based on change in the corpus callosum. (author)

  7. Subcritical Butane Extraction of Wheat Germ Oil and Its Deacidification by Molecular Distillation

    Directory of Open Access Journals (Sweden)

    Jinwei Li

    2016-12-01

    Full Text Available Extraction and deacidification are important stages for wheat germ oil (WGO production. Crude WGO was extracted using subcritical butane extraction (SBE and compared with traditional solvent extraction (SE and supercritical carbon dioxide extraction (SCE based on the yield, chemical index and fatty acid profile. Furthermore, the effects of the molecular distillation temperature on the quality of WGO were also investigated in this study. Results indicated that WGO extracted by SBE has a higher yield of 9.10% and better quality; at the same time, its fatty acid composition has no significant difference compared with that of SE and SCE. The molecular distillation experiment showed that the acid value, peroxide value and p-anisidine value of WGO were reduced with the increase of the evaporation temperatures, and the contents of the active constituents of tocopherol, polyphenols and phytosterols are simultaneously decreased. Generally, the distillation temperature of 150 °C is an appropriate condition for WGO deacidification with the higher deacidification efficiency of 77.78% and the higher retention rate of active constituents.

  8. Auto-OBSD: Automatic parameter selection for reliable Oscillatory Behavior-based Signal Decomposition with an application to bearing fault signature extraction

    Science.gov (United States)

    Huang, Huan; Baddour, Natalie; Liang, Ming

    2017-03-01

    Bearing signals are often contaminated by in-band interferences and random noise. Oscillatory Behavior-based Signal Decomposition (OBSD) is a new technique which decomposes a signal according to its oscillatory behavior, rather than frequency or scale. Due to the low oscillatory transients of bearing fault-induced signals, the OBSD can be used to effectively extract bearing fault signatures from a blurred signal. However, the quality of the result highly relies on the selection of method-related parameters. Such parameters are often subjectively selected and a systematic approach has not been reported in the literature. As such, this paper proposes a systematic approach to automatic selection of OBSD parameters for reliable extraction of bearing fault signatures. The OBSD utilizes the idea of Morphological Component Analysis (MCA) that optimally projects the original signal to low oscillatory wavelets and high oscillatory wavelets established via the Tunable Q-factor Wavelet Transform (TQWT). In this paper, the effects of the selection of each parameter on the performance of the OBSD for bearing fault signature extraction are investigated. It is found that some method-related parameters can be fixed at certain values due to the nature of bearing fault-induced impulses. To adaptively tune the remaining parameters, index-guided parameter selection algorithms are proposed. A Convergence Index (CI) is proposed and a CI-guided self-tuning algorithm is developed to tune the convergence-related parameters, namely, penalty factor and number of iterations. Furthermore, a Smoothness Index (SI) is employed to measure the effectiveness of the extracted low oscillatory component (i.e. bearing fault signature). It is shown that a minimum SI implies an optimal result with respect to the adjustment of relevant parameters. Thus, two SI-guided automatic parameter selection algorithms are also developed to specify two other parameters, i.e., Q-factor of high-oscillatory wavelets and

  9. A nanoscale study of charge extraction in organic solar cells: the impact of interfacial molecular configurations.

    Science.gov (United States)

    Tang, Fu-Ching; Wu, Fu-Chiao; Yen, Chia-Te; Chang, Jay; Chou, Wei-Yang; Gilbert Chang, Shih-Hui; Cheng, Horng-Long

    2015-01-07

    In the optimization of organic solar cells (OSCs), a key problem lies in the maximization of charge carriers from the active layer to the electrodes. Hence, this study focused on the interfacial molecular configurations in efficient OSC charge extraction by theoretical investigations and experiments, including small molecule-based bilayer-heterojunction (sm-BLHJ) and polymer-based bulk-heterojunction (p-BHJ) OSCs. We first examined a well-defined sm-BLHJ model system of OSC composed of p-type pentacene, an n-type perylene derivative, and a nanogroove-structured poly(3,4-ethylenedioxythiophene) (NS-PEDOT) hole extraction layer. The OSC with NS-PEDOT shows a 230% increment in the short circuit current density compared with that of the conventional planar PEDOT layer. Our theoretical calculations indicated that small variations in the microscopic intermolecular interaction among these interfacial configurations could induce significant differences in charge extraction efficiency. Experimentally, different interfacial configurations were generated between the photo-active layer and the nanostructured charge extraction layer with periodic nanogroove structures. In addition to pentacene, poly(3-hexylthiophene), the most commonly used electron-donor material system in p-BHJ OSCs was also explored in terms of its possible use as a photo-active layer. Local conductive atomic force microscopy was used to measure the nanoscale charge extraction efficiency at different locations within the nanogroove, thus highlighting the importance of interfacial molecular configurations in efficient charge extraction. This study enriches understanding regarding the optimization of the photovoltaic properties of several types of OSCs by conducting appropriate interfacial engineering based on organic/polymer molecular orientations. The ultimate power conversion efficiency beyond at least 15% is highly expected when the best state-of-the-art p-BHJ OSCs are combined with present arguments.

  10. Biochemical and molecular evidences for the antitumor potential of Ginkgo biloba leaves extract in rodents.

    Science.gov (United States)

    Ahmed, Hanaa H; Shousha, Wafaa Gh; El-Mezayen, Hatem A; El-Toumy, Sayed A; Sayed, Alaa H; Ramadan, Aesha R

    2017-01-01

    Hepatocellular carcinoma (HCC) is one of the deadliest primary cancers, with a 5-year survival rate of 10% or less. This study was undertaken to elucidate the underlying biochemical and molecular mechanisms in favor of N-nitrosodiethylamine-induced hepatocellular carcinoma. Furthermore, the aim of this work was extended to explore the efficacy of Ginkgo biloba leaves extract in deterioration of HCC in rats. In the current study, HCC group experienced significant downregulation of ING-3 gene expression and upregulation of Foxp-1 gene expression in liver. Treatment of HCC groups with Ginkgo biloba leaves extract resulted in upregulation of ING-3 and downregulation of Foxp-1 gene expression in liver. In addition, there was significant increase in serum alpha-fetoprotein (AFP), carcinoembryonic antigen (CEA) and glypican-3 (GPC-3) levels in HCC group versus the negative control group. In contrast, the groups with HCC subjected to either high or low dose of Ginkgo biloba leaves extract elicited significant reduction (PGinkgo biloba leaves extract elicited marked improvement in the histological feature of liver tissue in HCC groups. In conclusion, this research indicated that the carcinogenic potency of N-nitrosodiethylamine targeted multiple systems on the cellular and molecular levels. In addition, the results of the current study shed light on the promising anticancer activity of Ginkgo biloba leaves extract in treatment of hepatocellular carcinoma induced chemically in the experimental model through its apoptotic and antiproliferative properties.

  11. A Supporting Platform for Semi-Automatic Hyoid Bone Tracking and Parameter Extraction from Videofluoroscopic Images for the Diagnosis of Dysphagia Patients.

    Science.gov (United States)

    Lee, Jun Chang; Nam, Kyoung Won; Jang, Dong Pyo; Paik, Nam Jong; Ryu, Ju Seok; Kim, In Young

    2017-04-01

    Conventional kinematic analysis of videofluoroscopic (VF) swallowing image, most popular for dysphagia diagnosis, requires time-consuming and repetitive manual extraction of diagnostic information from multiple images representing one swallowing period, which results in a heavy work load for clinicians and excessive hospital visits for patients to receive counseling and prescriptions. In this study, a software platform was developed that can assist in the VF diagnosis of dysphagia by automatically extracting a two-dimensional moving trajectory of the hyoid bone as well as 11 temporal and kinematic parameters. Fifty VF swallowing videos containing both non-mandible-overlapped and mandible-overlapped cases from eight patients with dysphagia of various etiologies and 19 videos from ten healthy controls were utilized for performance verification. Percent errors of hyoid bone tracking were 1.7 ± 2.1% for non-overlapped images and 4.2 ± 4.8% for overlapped images. Correlation coefficients between manually extracted and automatically extracted moving trajectories of the hyoid bone were 0.986 ± 0.017 (X-axis) and 0.992 ± 0.006 (Y-axis) for non-overlapped images, and 0.988 ± 0.009 (X-axis) and 0.991 ± 0.006 (Y-axis) for overlapped images. Based on the experimental results, we believe that the proposed platform has the potential to improve the satisfaction of both clinicians and patients with dysphagia.

  12. Comparative Analysis of Music Recordings from Western and Non-Western traditions by Automatic Tonal Feature Extraction

    Directory of Open Access Journals (Sweden)

    Emilia Gómez

    2008-09-01

    Full Text Available The automatic analysis of large musical corpora by means of computational models overcomes some limitations of manual analysis, and the unavailability of scores for most existing music makes necessary to work with audio recordings. Until now, research on this area has focused on music from the Western tradition. Nevertheless, we might ask if the available methods are suitable when analyzing music from other cultures. We present an empirical approach to the comparative analysis of audio recordings, focusing on tonal features and data mining techniques. Tonal features are related to the pitch class distribution, pitch range and employed scale, gamut and tuning system. We provide our initial but promising results obtained when trying to automatically distinguish music from Western and non- Western traditions; we analyze which descriptors are most relevant and study their distribution over 1500 pieces from different traditions and styles. As a result, some feature distributions differ for Western and non-Western music, and the obtained classification accuracy is higher than 80% for different classification algorithms and an independent test set. These results show that automatic description of audio signals together with data mining techniques provide means to characterize huge music collections from different traditions and complement musicological manual analyses.

  13. Quantify Water Extraction by TBP/Dodecane via Molecular Dynamics Simulations

    International Nuclear Information System (INIS)

    Khomami, Bamin; Cui, Shengting; De Almeida, Valmor F.

    2013-01-01

    The purpose of this project is to quantify the interfacial transport of water into the most prevalent nuclear reprocessing solvent extractant mixture, namely tri-butyl- phosphate (TBP) and dodecane, via massively parallel molecular dynamics simulations on the most powerful machines available for open research. Specifically, we will accomplish this objective by evolving the water/TBP/dodecane system up to 1 ms elapsed time, and validate the simulation results by direct comparison with experimentally measured water solubility in the organic phase. The significance of this effort is to demonstrate for the first time that the combination of emerging simulation tools and state-of-the-art supercomputers can provide quantitative information on par to experimental measurements for solvent extraction systems of relevance to the nuclear fuel cycle. Results: Initially, the isolated single component, and single phase systems were studied followed by the two-phase, multicomponent counterpart. Specifically, the systems we studied were: pure TBP; pure n-dodecane; TBP/n-dodecane mixture; and the complete extraction system: water-TBP/n-dodecane two phase system to gain deep insight into the water extraction process. We have completely achieved our goal of simulating the molecular extraction of water molecules into the TBP/n-dodecane mixture up to the saturation point, and obtained favorable comparison with experimental data. Many insights into fundamental molecular level processes and physics were obtained from the process. Most importantly, we found that the dipole moment of the extracting agent is crucially important in affecting the interface roughness and the extraction rate of water molecules into the organic phase. In addition, we have identified shortcomings in the existing OPLS-AA force field potential for long-chain alkanes. The significance of this force field is that it is supposed to be optimized for molecular liquid simulations. We found that it failed for dodecane and

  14. Quantify Water Extraction by TBP/Dodecane via Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Khomami, Bamin [Univ. of Tennessee, Knoxville, TN (United States); Cui, Shengting [Univ. of Tennessee, Knoxville, TN (United States); de Almeida, Valmor F. [Oak Ridge National Lab., Oak Ridge, TN (United States); Felker, Kevin [Oak Ridge National Lab., Oak Ridge, TN (United States)

    2013-05-16

    The purpose of this project is to quantify the interfacial transport of water into the most prevalent nuclear reprocessing solvent extractant mixture, namely tri-butyl- phosphate (TBP) and dodecane, via massively parallel molecular dynamics simulations on the most powerful machines available for open research. Specifically, we will accomplish this objective by evolving the water/TBP/dodecane system up to 1 ms elapsed time, and validate the simulation results by direct comparison with experimentally measured water solubility in the organic phase. The significance of this effort is to demonstrate for the first time that the combination of emerging simulation tools and state-of-the-art supercomputers can provide quantitative information on par to experimental measurements for solvent extraction systems of relevance to the nuclear fuel cycle. Results: Initially, the isolated single component, and single phase systems were studied followed by the two-phase, multicomponent counterpart. Specifically, the systems we studied were: pure TBP; pure n-dodecane; TBP/n-dodecane mixture; and the complete extraction system: water-TBP/n-dodecane two phase system to gain deep insight into the water extraction process. We have completely achieved our goal of simulating the molecular extraction of water molecules into the TBP/n-dodecane mixture up to the saturation point, and obtained favorable comparison with experimental data. Many insights into fundamental molecular level processes and physics were obtained from the process. Most importantly, we found that the dipole moment of the extracting agent is crucially important in affecting the interface roughness and the extraction rate of water molecules into the organic phase. In addition, we have identified shortcomings in the existing OPLS-AA force field potential for long-chain alkanes. The significance of this force field is that it is supposed to be optimized for molecular liquid simulations. We found that it failed for dodecane and

  15. Development of automatic extraction of the corpus callosum from magnetic resonance imaging of the head and examination of the early dementia objective diagnostic technique in feature analysis

    International Nuclear Information System (INIS)

    Kodama, Naoki; Kaneko, Tomoyuki

    2005-01-01

    We examined the objective diagnosis of dementia based on changes in the corpus callosum. We examined midsagittal head MR images of 17 early dementia patients (2 men and 15 women; mean age, 77.2±3.3 years) and 18 healthy elderly controls (2 men and 16 women; mean age, 73.8±6.5 years), 35 subjects altogether. First, the corpus callosum was automatically extracted from the MR images. Next, early dementia was compared with the healthy elderly individuals using 5 features of the straight-line methods, 5 features of the Run-Length Matrix, and 6 features of the Co-occurrence Matrix from the corpus callosum. Automatic extraction of the corpus callosum showed an accuracy rate of 84.1±3.7%. A statistically significant difference was found in 6 of the 16 features between early dementia patients and healthy elderly controls. Discriminant analysis using the 6 features demonstrated a sensitivity of 88.2% and specificity of 77.8%, with an overall accuracy of 82.9%. These results indicate that feature analysis based on changes in the corpus callosum can be used as an objective diagnostic technique for early dementia. (author)

  16. Sequential injection system incorporating a micro extraction column for automatic fractionation of metal ions in solid samples

    DEFF Research Database (Denmark)

    Chomchoei, Roongrat; Miró, Manuel; Hansen, Elo Harald

    2005-01-01

    to conventional batch methods, this fully automated approach furthermore offers the potentials of a variety of operational extraction protocols. Employing the three-step sequential extraction BCR scheme to a certified homogeneous soil reference material (NIST, SRM 2710), this communication investigates four...

  17. Knickzone Extraction Tool (KET) - A new ArcGIS toolset for automatic extraction of knickzones from a DEM based on multi-scale stream gradients

    Science.gov (United States)

    Zahra, Tuba; Paudel, Uttam; Hayakawa, Yuichi S.; Oguchi, Takashi

    2017-04-01

    Extraction of knickpoints or knickzones from a Digital Elevation Model (DEM) has gained immense significance owing to the increasing implications of knickzones on landform development. However, existing methods for knickzone extraction tend to be subjective or require time-intensive data processing. This paper describes the proposed Knickzone Extraction Tool (KET), a new raster-based Python script deployed in the form of an ArcGIS toolset that automates the process of knickzone extraction and is both fast and more user-friendly. The KET is based on multi-scale analysis of slope gradients along a river course, where any locally steep segment (knickzone) can be extracted as an anomalously high local gradient. We also conducted a comparative analysis of the KET and other contemporary knickzone identification techniques. The relationship between knickzone distribution and its morphometric characteristics are also examined through a case study of a mountainous watershed in Japan.

  18. Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules.

    Science.gov (United States)

    Mayjonade, Baptiste; Gouzy, Jérôme; Donnadieu, Cécile; Pouilly, Nicolas; Marande, William; Callot, Caroline; Langlade, Nicolas; Muños, Stéphane

    2016-10-01

    De novo sequencing of complex genomes is one of the main challenges for researchers seeking high-quality reference sequences. Many de novo assemblies are based on short reads, producing fragmented genome sequences. Third-generation sequencing, with read lengths >10 kb, will improve the assembly of complex genomes, but these techniques require high-molecular-weight genomic DNA (gDNA), and gDNA extraction protocols used for obtaining smaller fragments for short-read sequencing are not suitable for this purpose. Methods of preparing gDNA for bacterial artificial chromosome (BAC) libraries could be adapted, but these approaches are time-consuming, and commercial kits for these methods are expensive. Here, we present a protocol for rapid, inexpensive extraction of high-molecular-weight gDNA from bacteria, plants, and animals. Our technique was validated using sunflower leaf samples, producing a mean read length of 12.6 kb and a maximum read length of 80 kb.

  19. Validation of the ICU-DaMa tool for automatically extracting variables for minimum dataset and quality indicators: The importance of data quality assessment.

    Science.gov (United States)

    Sirgo, Gonzalo; Esteban, Federico; Gómez, Josep; Moreno, Gerard; Rodríguez, Alejandro; Blanch, Lluis; Guardiola, Juan José; Gracia, Rafael; De Haro, Lluis; Bodí, María

    2018-04-01

    Big data analytics promise insights into healthcare processes and management, improving outcomes while reducing costs. However, data quality is a major challenge for reliable results. Business process discovery techniques and an associated data model were used to develop data management tool, ICU-DaMa, for extracting variables essential for overseeing the quality of care in the intensive care unit (ICU). To determine the feasibility of using ICU-DaMa to automatically extract variables for the minimum dataset and ICU quality indicators from the clinical information system (CIS). The Wilcoxon signed-rank test and Fisher's exact test were used to compare the values extracted from the CIS with ICU-DaMa for 25 variables from all patients attended in a polyvalent ICU during a two-month period against the gold standard of values manually extracted by two trained physicians. Discrepancies with the gold standard were classified into plausibility, conformance, and completeness errors. Data from 149 patients were included. Although there were no significant differences between the automatic method and the manual method, we detected differences in values for five variables, including one plausibility error and two conformance and completeness errors. Plausibility: 1) Sex, ICU-DaMa incorrectly classified one male patient as female (error generated by the Hospital's Admissions Department). Conformance: 2) Reason for isolation, ICU-DaMa failed to detect a human error in which a professional misclassified a patient's isolation. 3) Brain death, ICU-DaMa failed to detect another human error in which a professional likely entered two mutually exclusive values related to the death of the patient (brain death and controlled donation after circulatory death). Completeness: 4) Destination at ICU discharge, ICU-DaMa incorrectly classified two patients due to a professional failing to fill out the patient discharge form when thepatients died. 5) Length of continuous renal replacement

  20. A Simple Thermoplastic Substrate Containing Hierarchical Silica Lamellae for High-Molecular-Weight DNA Extraction.

    Science.gov (United States)

    Zhang, Ye; Zhang, Yi; Burke, Jeffrey M; Gleitsman, Kristin; Friedrich, Sarah M; Liu, Kelvin J; Wang, Tza-Huei

    2016-12-01

    An inexpensive, magnetic thermoplastic nanomaterial is developed utilizing a hierarchical layering of micro- and nanoscale silica lamellae to create a high-surface-area and low-shear substrate capable of capturing vast amounts of ultrahigh-molecular-weight DNA. Extraction is performed via a simple 45 min process and is capable of achieving binding capacities up to 1 000 000 times greater than silica microparticles. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. SU-F-R-05: Multidimensional Imaging Radiomics-Geodesics: A Novel Manifold Learning Based Automatic Feature Extraction Method for Diagnostic Prediction in Multiparametric Imaging

    International Nuclear Information System (INIS)

    Parekh, V; Jacobs, MA

    2016-01-01

    Purpose: Multiparametric radiological imaging is used for diagnosis in patients. Potentially extracting useful features specific to a patient’s pathology would be crucial step towards personalized medicine and assessing treatment options. In order to automatically extract features directly from multiparametric radiological imaging datasets, we developed an advanced unsupervised machine learning algorithm called the multidimensional imaging radiomics-geodesics(MIRaGe). Methods: Seventy-six breast tumor patients underwent 3T MRI breast imaging were used for this study. We tested the MIRaGe algorithm to extract features for classification of breast tumors into benign or malignant. The MRI parameters used were T1-weighted, T2-weighted, dynamic contrast enhanced MR imaging (DCE-MRI) and diffusion weighted imaging(DWI). The MIRaGe algorithm extracted the radiomics-geodesics features (RGFs) from multiparametric MRI datasets. This enable our method to learn the intrinsic manifold representations corresponding to the patients. To determine the informative RGF, a modified Isomap algorithm(t-Isomap) was created for a radiomics-geodesics feature space(tRGFS) to avoid overfitting. Final classification was performed using SVM. The predictive power of the RGFs was tested and validated using k-fold cross validation. Results: The RGFs extracted by the MIRaGe algorithm successfully classified malignant lesions from benign lesions with a sensitivity of 93% and a specificity of 91%. The top 50 RGFs identified as the most predictive by the t-Isomap procedure were consistent with the radiological parameters known to be associated with breast cancer diagnosis and were categorized as kinetic curve characterizing RGFs, wash-in rate characterizing RGFs, wash-out rate characterizing RGFs and morphology characterizing RGFs. Conclusion: In this paper, we developed a novel feature extraction algorithm for multiparametric radiological imaging. The results demonstrated the power of the MIRa

  2. SU-F-R-05: Multidimensional Imaging Radiomics-Geodesics: A Novel Manifold Learning Based Automatic Feature Extraction Method for Diagnostic Prediction in Multiparametric Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Parekh, V [The Johns Hopkins University, Computer Science. Baltimore, MD (United States); Jacobs, MA [The Johns Hopkins University School of Medicine, Dept of Radiology and Oncology. Baltimore, MD (United States)

    2016-06-15

    Purpose: Multiparametric radiological imaging is used for diagnosis in patients. Potentially extracting useful features specific to a patient’s pathology would be crucial step towards personalized medicine and assessing treatment options. In order to automatically extract features directly from multiparametric radiological imaging datasets, we developed an advanced unsupervised machine learning algorithm called the multidimensional imaging radiomics-geodesics(MIRaGe). Methods: Seventy-six breast tumor patients underwent 3T MRI breast imaging were used for this study. We tested the MIRaGe algorithm to extract features for classification of breast tumors into benign or malignant. The MRI parameters used were T1-weighted, T2-weighted, dynamic contrast enhanced MR imaging (DCE-MRI) and diffusion weighted imaging(DWI). The MIRaGe algorithm extracted the radiomics-geodesics features (RGFs) from multiparametric MRI datasets. This enable our method to learn the intrinsic manifold representations corresponding to the patients. To determine the informative RGF, a modified Isomap algorithm(t-Isomap) was created for a radiomics-geodesics feature space(tRGFS) to avoid overfitting. Final classification was performed using SVM. The predictive power of the RGFs was tested and validated using k-fold cross validation. Results: The RGFs extracted by the MIRaGe algorithm successfully classified malignant lesions from benign lesions with a sensitivity of 93% and a specificity of 91%. The top 50 RGFs identified as the most predictive by the t-Isomap procedure were consistent with the radiological parameters known to be associated with breast cancer diagnosis and were categorized as kinetic curve characterizing RGFs, wash-in rate characterizing RGFs, wash-out rate characterizing RGFs and morphology characterizing RGFs. Conclusion: In this paper, we developed a novel feature extraction algorithm for multiparametric radiological imaging. The results demonstrated the power of the MIRa

  3. Development of Molecularly Imprinted Polymers to Target Polyphenols Present in Plant Extracts

    Directory of Open Access Journals (Sweden)

    Catarina Gomes

    2017-11-01

    Full Text Available The development of molecularly imprinted polymers (MIPs to target polyphenols present in vegetable extracts was here addressed. Polydatin was selected as a template polyphenol due to its relatively high size and amphiphilic character. Different MIPs were synthesized to explore preferential interactions between the functional monomers and the template molecule. The effect of solvent polarity on the molecular imprinting efficiency, namely owing to hydrophobic interactions, was also assessed. Precipitation and suspension polymerization were examined as a possible way to change MIPs morphology and performance. Solid phase extraction and batch/continuous sorption processes were used to evaluate the polyphenols uptake/release in individual/competitive assays. Among the prepared MIPs, a suspension polymerization synthesized material, with 4-vinylpyridine as the functional monomer and water/methanol as solvent, showed a superior performance. The underlying cause of such a significant outcome is the likely surface imprinting process caused by the amphiphilic properties of polydatin. The uptake and subsequent selective release of polyphenols present in natural extracts was successfully demonstrated, considering a red wine solution as a case study. However, hydrophilic/hydrophobic interactions are inevitable (especially with complex natural extracts and the tuning of the polarity of the solvents is an important issue for the isolation of the different polyphenols.

  4. Molecular dynamics simulation of cyclodextrin aggregation and extraction of Anthracene from non-aqueous liquid phase

    International Nuclear Information System (INIS)

    Zhu, Xinzhe; Wu, Guozhong; Chen, Daoyi

    2016-01-01

    Cyclodextrin (CD) extraction is widely used for the remediation of polycyclic aromatic hydrocarbons (PAH) pollution, but it remains unclear about the influence of CD aggregation on the PAH transport from non-aqueous liquid phase to water. The atomistic adsorption and complexation of PAHs (32 anthracenes) by CD aggregates (48 β-cyclodextrins) were studied by molecular dynamics simulations at hundreds of nanoseconds time scale. Results indicated that high temperature promoted the βCD aggregation in bulk oil, which was not found in bulk water. Nevertheless, the fractions of anthracenes entrapped inside the βCDs cavity in both scenarios were significantly increased when temperature increased from 298 to 328 K. Free energy calculation for the sub-steps of CD extraction demonstrated that the anthracenes could be extracted when the βCDs arrived at the water-oil interface or after the βCDs entered the bulk oil. The former was kinetic-controlled while the latter was thermodynamic-limited process. Results also highlighted the formation of porous structures by CD aggregates in water, which was able to sequestrate PAH clusters with the size obviously larger than the cavity diameter of individual CD. This provided an opportunity for the extraction of recalcitrant PAHs with molecular size larger than anthracenes by cyclodextrins.

  5. Automatic extraction of the cingulum bundle in diffusion tensor tract-specific analysis. Feasibility study in Parkinson's disease with and without dementia

    International Nuclear Information System (INIS)

    Ito, Kenji; Masutani, Yoshitaka; Suzuki, Yuichi; Ino, Kenji; Kunimatsu, Akira; Ohtomo, Kuni; Kamagata, Koji; Yasmin, Hasina; Aoki, Shigeki

    2013-01-01

    Tract-specific analysis (TSA) measures diffusion parameters along a specific fiber that has been extracted by fiber tracking using manual regions of interest (ROIs), but TSA is limited by its requirement for manual operation, poor reproducibility, and high time consumption. We aimed to develop a fully automated extraction method for the cingulum bundle (CB) and to apply the method to TSA in neurobehavioral disorders such as Parkinson's disease (PD). We introduce the voxel classification (VC) and auto diffusion tensor fiber-tracking (AFT) methods of extraction. The VC method directly extracts the CB, skipping the fiber-tracking step, whereas the AFT method uses fiber tracking from automatically selected ROIs. We compared the results of VC and AFT to those obtained by manual diffusion tensor fiber tracking (MFT) performed by 3 operators. We quantified the Jaccard similarity index among the 3 methods in data from 20 subjects (10 normal controls [NC] and 10 patients with Parkinson's disease dementia [PDD]). We used all 3 extraction methods (VC, AFT, and MFT) to calculate the fractional anisotropy (FA) values of the anterior and posterior CB for 15 NC subjects, 15 with PD, and 15 with PDD. The Jaccard index between results of AFT and MFT, 0.72, was similar to the inter-operator Jaccard index of MFT. However, the Jaccard indices between VC and MFT and between VC and AFT were lower. Consequently, the VC method classified among 3 different groups (NC, PD, and PDD), whereas the others classified only 2 different groups (NC, PD or PDD). For TSA in Parkinson's disease, the VC method can be more useful than the AFT and MFT methods for extracting the CB. In addition, the results of patient data analysis suggest that a reduction of FA in the posterior CB may represent a useful biological index for monitoring PD and PDD. (author)

  6. Automatic on-line solid-phase extraction with ultra-high performance liquid chromatography and tandem mass spectrometry for the determination of ten antipsychotics in human plasma.

    Science.gov (United States)

    Zhong, Qisheng; Shen, Lingling; Liu, Jiaqi; Yu, Dianbao; Li, Simin; Li, Zhiru; Yao, Jinting; Huang, Taohong; Kawano, Shin-Ichi; Hashi, Yuki; Zhou, Ting

    2016-06-01

    An automatic on-line solid-phase extraction with ultra-high performance liquid chromatography and tandem mass spectrometry method was developed for the simultaneous determination of ten antipsychotics in human plasma. The plasma sample after filtration was injected directly into the system without any pretreatment. A Shim-pack MAYI-C8 (G) column was used as a solid-phase extraction column, and all the analytes were separated on a Shim-pack XR-ODS III column with a mobile phase consisting of 0.1% v/v formic acid in water with 5 mM ammonium acetate and acetonitrile. The method features were systematically investigated, including extraction conditions, desorption conditions, the equilibration solution, the valve switching time, and the dilution for column-head stacking. Under the optimized conditions, the whole analysis procedure took only 10 min. The limits of quantitation were in the range of 0.00321-2.75 μg/L and the recoveries ranged from 75.9 to 122%. Compared with the off-line ultra-high performance liquid chromatography and the reported methods, this validated on-line method showed significant advantages such as minimal pretreatment, shortest analysis time, and highest sensitivity. The results indicated that this automatic on-line method was rapid, sensitive, and reliable for the determination of antipsychotics in plasma and could be extended to other target analytes in biological samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Morphotectonic mapping from the analysis of automatically extracted lineaments using Landsat 8 images and SRTM data in the Hindukush-Pamir

    Science.gov (United States)

    Rahnama, Mehdi; Gloaguen, Richard

    2014-05-01

    Modern deformation, fault movements, and induced earthquakes in the Hindukush-Pamir region are driven by the collision between the northward-moving Indian subcontinent and Eurasia. We investigated neotectonic activity and generated tectonic maps of this area. We developed a Matlab based toolbox for the automatic extraction of image discontinuities. The approach consists of frequency domain filtering, edge detection in the spatial domain, Hough transformation, segment grouping, polynomial interpolation and geostatistical analysis of the lineaments patterns. Statistical quantification of counts, lengths, azimuth frequency, density distribution, and orientations are analyzed to understand the tectonic activities, to explain the prominent structural trends, and to demarcate the contribution of different faulting styles. Morphotectonic lineaments observed on the study area were automatically extracted from panchromatic band of Landsat 8 with 15-m resolution and SRTM digital elevation model (DEM) with 90-m resolution. Then, this data was analyzed to characterize the tectonic trends that dominated the geologic evolution of this area. We show that the SW-Pamir is mainly controlled by the Chaman-Herat-Central Badakhshan fault systems and, to a lesser extent by the Darvaz fault zone. Extracted lineaments and the intensity of the characterized tectonic trends correspond well with reference data. In Addition, results are consistent with the styles of faulting determined from focal mechanisms of the historical earthquake epicenters in the region. The presented results could be applicable in different geological aspects that are based on a good knowledge of the system patterns and the spatial relationship between them. These aspects included geodynamics, seismic and risk assessment, mineral exploration and hydrogeological research.

  8. Automatic extraction of plots from geo-registered UAS imagery of crop fields with complex planting schemes

    Science.gov (United States)

    Hearst, Anthony A.

    Complex planting schemes are common in experimental crop fields and can make it difficult to extract plots of interest from high-resolution imagery of the fields gathered by Unmanned Aircraft Systems (UAS). This prevents UAS imagery from being applied in High-Throughput Precision Phenotyping and other areas of agricultural research. If the imagery is accurately geo-registered, then it may be possible to extract plots from the imagery based on their map coordinates. To test this approach, a UAS was used to acquire visual imagery of 5 ha of soybean fields containing 6.0 m2 plots in a complex planting scheme. Sixteen artificial targets were setup in the fields before flights and different spatial configurations of 0 to 6 targets were used as Ground Control Points (GCPs) for geo-registration, resulting in a total of 175 geo-registered image mosaics with a broad range of geo-registration accuracies. Geo-registration accuracy was quantified based on the horizontal Root Mean Squared Error (RMSE) of targets used as checkpoints. Twenty test plots were extracted from the geo-registered imagery. Plot extraction accuracy was quantified based on the percentage of the desired plot area that was extracted. It was found that using 4 GCPs along the perimeter of the field minimized the horizontal RMSE and enabled a plot extraction accuracy of at least 70%, with a mean plot extraction accuracy of 92%. Future work will focus on further enhancing the plot extraction accuracy through additional image processing techniques so that it becomes sufficiently accurate for all practical purposes in agricultural research and potentially other areas of research.

  9. Molecularly imprinted solid-phase extraction for selective extraction of bisphenol analogues in beverages and canned food.

    Science.gov (United States)

    Yang, Yunjia; Yu, Jianlong; Yin, Jie; Shao, Bing; Zhang, Jing

    2014-11-19

    This study aimed to develop a selective analytical method for the simultaneous determination of seven bisphenol analogues in beverage and canned food samples by using a new molecularly imprinted polymer (MIP) as a sorbent for solid-phase extraction (SPE). Liquid chromatography coupled to triple-quadruple tandem mass spectrometry (LC-MS/MS) was used to identify and quantify the target analytes. The MIP-SPE method exhibited a higher level of selectivity and purification than the traditional SPE method. The developed procedures were further validated in terms of accuracy, precision, and sensitivity. The obtained recoveries varied from 50% to 103% at three fortification levels and yielded a relative standard deviation (RSD, %) of less than 15% for all of the analytes. The limits of quantification (LOQ) for the seven analytes varied from 0.002 to 0.15 ng/mL for beverage samples and from 0.03 to 1.5 ng/g for canned food samples. This method was used to analyze real samples that were collected from a supermarket in Beijing. Overall, the results revealed that bisphenol A and bisphenol F were the most frequently detected bisphenols in the beverage and canned food samples and that their concentrations were closely associated with the type of packaging material. This study provides an alternative method of traditional SPE extraction for screening bisphenol analogues in food matrices.

  10. Evaluation of growth conditions and DNA extraction techniques used in the molecular analysis of dermatophytes.

    Science.gov (United States)

    Gnat, S; Nowakiewicz, A; Ziółkowska, G; Trościańczyk, A; Majer-Dziedzic, B; Zięba, P

    2017-05-01

    Recent molecular methods for diagnosis of superficial mycoses have determined the need for a rapid and easy method of extracting DNA. The aim of study was to determine growth conditions and techniques of DNA extraction for Microsporum canis, Trichophyton mentagrophytes and T. verrucosum. Samples were prepared of each of the DNA extraction methods (phenol-chloroform, CTAB and four different kits) for all of the incubation periods (4, 7 and 10 days) of the cultures on the solid and in the liquid medium. The highest DNA concentrations were obtained using the phenol-chloroform method. The concentration of DNA extracted with the CTAB method accounted for 62·21%, for kits it corresponded from 35·53 to 15·41%. The analysis of the DNA weight yield revealed the highest isolation efficiency of the phenol-chloroform method, 1 mg of mycelium yielded 223·8 μg DNA. Lower DNA yield (by 39·32%) was obtained with the CTAB method; in the case of kits by 68·46-85·32%. In most of the techniques, the DNA yield on the solid medium was higher. In summary, the highest DNA yield was noted in the 7-day cultures and extraction with the phenol-chloroform method. Importantly, the type of culture was not relevant for the diagnostic result. Most mycoses are caused by fungi that reside in nature. The severity of the infection depends on the pathogenic attributes, socioeconomic factors and local environmental conditions. Recent diagnosis increasingly relies on not only the clinical features. Molecular identifications have determined the need for a rapid and easy method of extracting DNA. Usually two factors have to be considered: maximize the DNA yield and ensure that the extracted DNA is susceptible to enzymatic reactions. These data suggest that phenol-chloroform methods and a 7-day culture period may be useful for validation and constitute the first step of molecular diagnosis of dermatophytes. © 2017 The Society for Applied Microbiology.

  11. Quality assessment of biobanked nucleic acid extracts for downstream molecular analysis.

    Science.gov (United States)

    Wahlberg, Karin; Huggett, Jim; Sanders, Rebecca; Whale, Alexandra S; Bushell, Claire; Elaswarapu, Ramnath; Scott, Daniel J; Foy, Carole A

    2012-06-01

    Sample quality is of major importance when conducting molecular analysis of nucleic acids, and factors such as degradation, presence of impurities, and enzymatic inhibitors may have a significant impact on the quality of data. Issues of quality assessment become more important as the increased use of biobanking means that whole blood samples are being stored for longer periods. A range of commercially available kits/methods have been specifically developed for extraction of high quality nucleic acids from a variety of clinical samples, including blood, but there is limited information on how best to quality assess the extracts to determine their fitness for purpose in specific downstream applications. In this study, we have performed nucleic acid extractions from stored blood using a number of different methods. The resulting extracts were analyzed by a panel of quantity and quality metrics including UV spectrophotometry, PicoGreen fluorescence, electrophoresis, and a PCR approach. To evaluate the relevance of different metrics, DNA samples were subsequently assessed for their performance in real time PCR and microarray experiments. Our findings demonstrate that the most suitable extraction technique and quality assessment approach depends on the required downstream analytical method.

  12. Molecular identity and cytotoxicity of Lenzites quercina macrofungus extracts toward cancer cell lines

    Directory of Open Access Journals (Sweden)

    Olusola Clement Ogidi

    2017-05-01

    Full Text Available The medicinal uses of wild macrofungi have been attributed to their accumulated bioactive compounds. Several mushrooms have been reported to possess antitumor activity, but little, in this regard, is known about Lenzites quercina collected from Akure in Nigeria. Hence, the molecular identification and cytotoxic activity of extracts obtained from raw and fermented Lenzites quercina were assessed. The macrofungus Lenzites quercina was identified using Internal Transcribed Spacers (ITS sequence analysis. The basic local alignment search tool (BLAST analyzed on NCBI GenBank data revealed that the Lenzites species from Nigeria – accession number, JF689829.1 – was closely related to Lenzites quercina (a 100% relationship match. The cytotoxic activity of raw and fermented Lenzites quercina extracts was tested against human cervical cancer (HeLa, habdomyosarcoma (RD and African green monkey kidney (VERO cell lines. A tetrazolium yellow 3-(4,5-dimethyl thiazol-2-yl-2,5- diphenyl tetrazolium bromide (MTT colorimetric assay was used to evaluate the reduction in viability of cell cultures with or without the extracts of Lenzites quercina . Extracts of Lenzites quercina exhibited cytotoxic activity (6.0-84.5% against the tested cancer cell lines (HeLa, VERO and RD. The concentration of the bioactive compounds in the crude extract ranged from 0.01 to 1000 μg/ml. The results revealed that bioactive compounds in Lenzites quercina possess cytotoxic properties. These bioactive compounds may be isolated and used as alternative therapies to currently available anticancer drugs.

  13. Automatic flow-through dynamic extraction: A fast tool to evaluate char-based remediation of multi-element contaminated mine soils.

    Science.gov (United States)

    Rosende, María; Beesley, Luke; Moreno-Jimenez, Eduardo; Miró, Manuel

    2016-02-01

    An automatic in-vitro bioaccessibility test based upon dynamic microcolumn extraction in a programmable flow setup is herein proposed as a screening tool to evaluate bio-char based remediation of mine soils contaminated with trace elements as a compelling alternative to conventional phyto-availability tests. The feasibility of the proposed system was evaluated by extracting the readily bioaccessible pools of As, Pb and Zn in two contaminated mine soils before and after the addition of two biochars (9% (w:w)) of diverse source origin (pine and olive). Bioaccessible fractions under worst-case scenarios were measured using 0.001 mol L(-1) CaCl2 as extractant for mimicking plant uptake, and analysis of the extracts by inductively coupled optical emission spectrometry. The t-test of comparison of means revealed an efficient metal (mostly Pb and Zn) immobilization by the action of olive pruning-based biochar against the bare (control) soil at the 0.05 significance level. In-vitro flow-through bioaccessibility tests are compared for the first time with in-vivo phyto-toxicity assays in a microcosm soil study. By assessing seed germination and shoot elongation of Lolium perenne in contaminated soils with and without biochar amendments the dynamic flow-based bioaccessibility data proved to be in good agreement with the phyto-availability tests. Experimental results indicate that the dynamic extraction method is a viable and economical in-vitro tool in risk assessment explorations to evaluate the feasibility of a given biochar amendment for revegetation and remediation of metal contaminated soils in a mere 10 min against 4 days in case of phyto-toxicity assays. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Automatic Extraction of Appendix from Ultrasonography with Self-Organizing Map and Shape-Brightness Pattern Learning

    Directory of Open Access Journals (Sweden)

    Kwang Baek Kim

    2016-01-01

    Full Text Available Accurate diagnosis of acute appendicitis is a difficult problem in practice especially when the patient is too young or women in pregnancy. In this paper, we propose a fully automatic appendix extractor from ultrasonography by applying a series of image processing algorithms and an unsupervised neural learning algorithm, self-organizing map. From the suggestions of clinical practitioners, we define four shape patterns of appendix and self-organizing map learns those patterns in pixel clustering phase. In the experiment designed to test the performance for those four frequently found shape patterns, our method is successful in 3 types (1 failure out of 45 cases but leaves a question for one shape pattern (80% correct.

  15. Automatic Extraction of Appendix from Ultrasonography with Self-Organizing Map and Shape-Brightness Pattern Learning.

    Science.gov (United States)

    Kim, Kwang Baek; Song, Doo Heon; Park, Hyun Jun

    2016-01-01

    Accurate diagnosis of acute appendicitis is a difficult problem in practice especially when the patient is too young or women in pregnancy. In this paper, we propose a fully automatic appendix extractor from ultrasonography by applying a series of image processing algorithms and an unsupervised neural learning algorithm, self-organizing map. From the suggestions of clinical practitioners, we define four shape patterns of appendix and self-organizing map learns those patterns in pixel clustering phase. In the experiment designed to test the performance for those four frequently found shape patterns, our method is successful in 3 types (1 failure out of 45 cases) but leaves a question for one shape pattern (80% correct).

  16. An integrated automatic system to evaluate U and Th dynamic lixiviation from solid matrices, and to extract/pre-concentrate leached analytes previous ICP-MS detection.

    Science.gov (United States)

    Ceballos, Melisa Rodas; García-Tenorio, Rafael; Estela, José Manuel; Cerdà, Víctor; Ferrer, Laura

    2017-12-01

    Leached fractions of U and Th from different environmental solid matrices were evaluated by an automatic system enabling the on-line lixiviation and extraction/pre-concentration of these two elements previous ICP-MS detection. UTEVA resin was used as selective extraction material. Ten leached fraction, using artificial rainwater (pH 5.4) as leaching agent, and a residual fraction were analyzed for each sample, allowing the study of behavior of U and Th in dynamic lixiviation conditions. Multivariate techniques have been employed for the efficient optimization of the independent variables that affect the lixiviation process. The system reached LODs of 0.1 and 0.7ngkg -1 of U and Th, respectively. The method was satisfactorily validated for three solid matrices, by the analysis of a soil reference material (IAEA-375), a certified sediment reference material (BCR- 320R) and a phosphogypsum reference material (MatControl CSN-CIEMAT 2008). Besides, environmental samples were analyzed, showing a similar behavior, i.e. the content of radionuclides decreases with the successive extractions. In all cases, the accumulative leached fraction of U and Th for different solid matrices studied (soil, sediment and phosphogypsum) were extremely low, up to 0.05% and 0.005% of U and Th, respectively. However, a great variability was observed in terms of mass concentration released, e.g. between 44 and 13,967ngUkg -1 . Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Rapid, potentially automatable, method extract biomarkers for HPLC/ESI/MS/MS to detect and identify BW agents

    Energy Technology Data Exchange (ETDEWEB)

    White, D.C. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology]|[Oak Ridge National Lab., TN (United States). Environmental Science Div.; Burkhalter, R.S.; Smith, C. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; Whitaker, K.W. [Microbial Insights, Inc., Rockford, TN (United States)

    1997-12-31

    The program proposes to concentrate on the rapid recovery of signature biomarkers based on automated high-pressure, high-temperature solvent extraction (ASE) and/or supercritical fluid extraction (SFE) to produce lipids, nucleic acids and proteins sequentially concentrated and purified in minutes with yields especially from microeukaryotes, Gram-positive bacteria and spores. Lipids are extracted in higher proportions greater than classical one-phase, room temperature solvent extraction without major changes in lipid composition. High performance liquid chromatography (HPLC) with or without derivatization, electrospray ionization (ESI) and highly specific detection by mass spectrometry (MS) particularly with (MS){sup n} provides the detection, identification and because the signature lipid biomarkers are both phenotypic as well as genotypic biomarkers, insights into potential infectivity of BW agents. Feasibility has been demonstrated with detection, identification, and determination of infectious potential of Cryptosporidium parvum at the sensitivity of a single oocyst (which is unculturable in vitro) and accurate identification and prediction, pathogenicity, and drug-resistance of Mycobacteria spp.

  18. Automatic bone outer contour extraction from B-modes ultrasound images based on local phase symmetry and quadratic polynomial fitting

    Science.gov (United States)

    Karlita, Tita; Yuniarno, Eko Mulyanto; Purnama, I. Ketut Eddy; Purnomo, Mauridhi Hery

    2017-06-01

    Analyzing ultrasound (US) images to get the shapes and structures of particular anatomical regions is an interesting field of study since US imaging is a non-invasive method to capture internal structures of a human body. However, bone segmentation of US images is still challenging because it is strongly influenced by speckle noises and it has poor image quality. This paper proposes a combination of local phase symmetry and quadratic polynomial fitting methods to extract bone outer contour (BOC) from two dimensional (2D) B-modes US image as initial steps of three-dimensional (3D) bone surface reconstruction. By using local phase symmetry, the bone is initially extracted from US images. BOC is then extracted by scanning one pixel on the bone boundary in each column of the US images using first phase features searching method. Quadratic polynomial fitting is utilized to refine and estimate the pixel location that fails to be detected during the extraction process. Hole filling method is then applied by utilize the polynomial coefficients to fill the gaps with new pixel. The proposed method is able to estimate the new pixel position and ensures smoothness and continuity of the contour path. Evaluations are done using cow and goat bones by comparing the resulted BOCs with the contours produced by manual segmentation and contours produced by canny edge detection. The evaluation shows that our proposed methods produces an excellent result with average MSE before and after hole filling at the value of 0.65.

  19. Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case

    Directory of Open Access Journals (Sweden)

    Giuliano Malloci

    2016-01-01

    Full Text Available The accurate and exhaustive description of the conformational ensemble sampled by small molecules in solution, possibly at different physiological conditions, is of primary interest in many fields of medicinal chemistry and computational biology. Recently, we have built an on-line database of compounds with antimicrobial properties, where we provide all-atom force-field parameters and a set of molecular properties, including representative structures extracted from cluster analysis over μs-long molecular dynamics (MD trajectories. In the present work, we used a medium-sized antibiotic from our sample, namely ampicillin, to assess the quality of the conformational ensemble. To this aim, we compared the conformational landscape extracted from previous unbiased MD simulations to those obtained by means of Replica Exchange MD (REMD and those originating from three freely-available conformer generation tools widely adopted in computer-aided drug-design. In addition, for different charge/protonation states of ampicillin, we made available force-field parameters and static/dynamic properties derived from both Density Functional Theory and MD calculations. For the specific system investigated here, we found that: (i the conformational statistics extracted from plain MD simulations is consistent with that obtained from REMD simulations; (ii overall, our MD-based approach performs slightly better than any of the conformer generator tools if one takes into account both the diversity of the generated conformational set and the ability to reproduce experimentally-determined structures.

  20. Selective molecularly imprinted polymer obtained from a combinatorial library for the extraction of bisphenol A.

    Science.gov (United States)

    Martin-Esteban, Antonio; Tadeo, Jose Luis

    2006-12-01

    In the present work, an analytical methodology based on molecularly imprinted solid-phase extraction (MISPE) has been developed for the determination of bisphenol A (BPA) in environmental and food samples. In order to select the optimum material, a combinatorial library of molecularly imprinted polymers in small-scale (mini-MIPs) was prepared using BPA as template. Different monomers (methacrylic acid or 4-vinylpyridine), crosslinkers (ethylene glycol dimethacrylate or trimethylolpropane trimethacrylate) and porogens (methanol, acetonitrile or toluene) were used leading to 24 different polymerisation mixtures. After BPA removal, the ability of mini-MIPs to recognise BPA was evaluated by equilibrium rebinding-elution experiments. The copolymer of 4-vinylpyridine (4-VP) and trimethylolpropane trimethacrylate (TRIM) prepared in toluene showed the higher affinity for the template. Subsequently, a scaled-up version of the optimum polymer was prepared and used in the development of MISPE procedures for the extraction of BPA. The optimised MISPE protocols were successfully applied to the selective extraction of BPA from soils and aqueous canned peas samples.

  1. Development of andrographolide molecularly imprinted polymer for solid-phase extraction

    Science.gov (United States)

    Yin, Xiaoying; Liu, Qingshan; Jiang, Yifan; Luo, Yongming

    2011-06-01

    A method employing molecularly imprinted polymer (MIP) as selective sorbent for solid-phase extraction (SPE) to pretreat samples was developed. The polymers were prepared by precipitation polymerization with andrographolide as template molecule. The structure of MIP was characterized and its static adsorption capacity was measured by the Scatchard equation. In comparison with C 18-SPE and non-imprinted polymer (NIP) SPE column, MIP-SPE column displays high selectivity and good affinity for andrographolide and dehydroandrographolide for extract of herb Andrographis paniculata ( Burm.f.) Nees (APN). MIP-SPE column capacity was 11.9 ± 0.6 μmol/g and 12.1 ± 0.5 μmol/g for andrographolide and dehydroandrographolide, respectively and was 2-3 times higher than that of other two columns. The precision and accuracy of the method developed were satisfactory with recoveries between 96.4% and 103.8% (RSD 3.1-4.3%, n = 5) and 96.0% and 104.2% (RSD 2.9-3.7%, n = 5) for andrographolide and dehydroandrographolide, respectively. Various real samples were employed to confirm the feasibility of method. This developed method demonstrates the potential of molecularly imprinted solid phase extraction for rapid, selective, and effective sample pretreatment.

  2. Molecularly Imprinted Polymers as Extracting Media for the Chromatographic Determination of Antibiotics in Milk

    Directory of Open Access Journals (Sweden)

    Dimitrios Bitas

    2018-02-01

    Full Text Available Milk-producing animals are typically kept stationary in overcrowded large-scale farms and in most cases under unsanitary conditions, which promotes the development of infections. In order to maintain sufficient health status among the herd or promote growth and increase production, farmers administer preventative antibiotic doses to the animals through their feed. However, many antibiotics used in cattle farms are intended for the treatment of bacterial infections in humans. This results in the development of antibiotic-resistant bacteria which pose a great risk for public health. Additionally, antibiotic residues are found in milk and dairy products, with potential toxic effects for the consumers. Hence the need of antibiotic residues monitoring in milk arises. Analytical methods were developed for the determination of antibiotics in milk, with key priority given to the analyte extraction and preconcentration step. Extraction can benefit from the production of molecularly imprinted polymers (MIPs that can be applied as sorbents for the extraction of specific antibiotics. This review focuses on the principals of molecular imprinting technology and synthesis methods of MIPs, as well as the application of MIPs and MIPs composites for the chromatographic determination of various antibiotic categories in milk found in the recent literature.

  3. Extraction of tryptophan with ionic liquids studied with molecular dynamics simulations.

    Science.gov (United States)

    Seduraman, Abirami; Wu, Ping; Klähn, Marco

    2012-01-12

    Extraction of amino acids from aqueous solutions with ionic liquids (ILs) in biphasic systems is analyzed with molecular dynamics (MD) simulations. Extraction of tryptophan (TRP) with the imidazolium-based ILs [C(4)mim][PF(6)], [C(8)mim][PF(6)], and [C(8)mim][BF(4)] are considered as model cases. Solvation free energies of TRP are calculated with MD simulations and thermodynamic integration in combination with an empirical force field, whose parametrization is based on the liquid-phase charge distribution of the ILs. Calculated solvation free energies reproduce successfully all observed experimental trends according to the previously reported partition of TRP between water and IL phases. Water is present in ILs as a cosolvent, due to direct contact with the aqueous phase during extraction, and is found to play a major role in the extraction of TRP. Water improves solvation of cationic TRP by 7.8 and 5.1 kcal/mol in [C(4)mim][PF(6)] and [C(8)mim][PF(6)], respectively, which is in the case of [C(4)mim][PF(6)] sufficient to extract TRP. Extraction in [C(8)mim][PF(6)] is not feasible, since the hydrophobic octyl groups of the cations limit the water concentration in the IL. The solvation of cationic TRP is 2.4 kcal/mol less favorable in [C(8)mim][PF(6)] than in [C(4)mim][PF(6)]. Water improves the solvation of TRP in ILs mostly through dipole-dipole interactions with the polar backbone of TRP. Extraction is most efficient with [C(8)mim][BF(4)], where hydrophilic BF(4)(-) anions substantially increase the water concentration in the IL. Additionally, stronger direct electrostatic interactions of TRP with BF(4)(-) anions improve its solvation in the IL further. The solvation of cationic TRP in [C(8)mim][BF(4)] is 3.4 kcal/mol more favorable than in [C(8)mim][PF(6)]. Overall, the extractive power of the ILs correlates with the water saturation concentration of the IL phase, which in turn is determined by the hydrophilicity of the constituting ions. The results of this work

  4. Molecular mechanisms of bio-catalysis of heme extraction from hemoglobin.

    Science.gov (United States)

    Sakipov, Serzhan; Rafikova, Olga; Kurnikova, Maria G; Rafikov, Ruslan

    2017-04-01

    Red blood cell hemolysis in sickle cell disease (SCD) releases free hemoglobin. Extracellular hemoglobin and its degradation products, free heme and iron, are highly toxic due to oxidative stress induction and decrease in nitric oxide availability. We propose an approach that helps to eliminate extracellular hemoglobin toxicity in SCD by employing a bacterial protein system that evolved to extract heme from extracellular hemoglobin. NEAr heme Transporter (NEAT) domains from iron-regulated surface determinant proteins from Staphylococcus aureus specifically bind free heme as well as facilitate its extraction from hemoglobin. We demonstrate that a purified NEAT domain fused with human haptoglobin β-chain is able to remove heme from hemoglobin and reduce heme content and peroxidase activity of hemoglobin. We further use molecular dynamics (MD) simulations to resolve molecular pathway of heme transfer from hemoglobin to NEAT, and to elucidate molecular mechanism of such heme transferring process. Our study is the first of its kind, in which simulations are employed to characterize the process of heme leaving hemoglobin and subsequent rebinding with a NEAT domain. Our MD results highlight important amino acid residues that facilitate heme transfer and will guide further studies for the selection of best NEAT candidate to attenuate free hemoglobin toxicity. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  5. Proactive Response to Potential Material Shortages Arising from Environmental Restrictions Using Automatic Discovery and Extraction of Information from Technical Documents

    Science.gov (United States)

    2012-12-21

    documents is via web links on manufacturer and distributor product catalogs on the web . These links were discovered using XSB’s focused crawler technology...regulatory information with specific items Focused Crawler Data In addition to PDF documents, we made use of data collected from the web using XSB, Inc...listed in the catalog. As a rule, the focused crawler extracts attributes and values as they appear on the web page. To be useful for this project

  6. Comparative characterization of humic substances extracted from freshwater and peat of different apparent molecular sizes

    Directory of Open Access Journals (Sweden)

    Eliane Sloboda Rigobello

    2017-09-01

    Full Text Available This paper compares the structural characteristics of aquatic humic substances (AHS with humic substances from peat (HSP through different analytical techniques, including elemental analysis, solid state 13C cross polarization/magic-angle-spinning nuclear magnetic resonance spectroscopy (13C CP-MAS NMR, ultraviolet/visible (UV/Vis spectroscopy and Fourier transform infrared (FTIR spectroscopy and total organic carbon (TOC. The AHS were extracted from water collected in a tributary of the Itapanhaú River (Bertioga/SP using XAD 8 resin, and the HSP were extracted from peat collected in the Mogi Guaçu River bank (Luis Antonio/SP with a KOH solution. After dialysis, both AHS and HSP extracts were filtered in membrane of 0.45 µm pore size (Fraction F1: < 0.45 µm and fractioned by ultrafiltration in different apparent molecular sizes (AMS (F2: 100 kDa-0.45 μm; F3: 30 kDa-100 kDa and F4: < 30 kDa. The extracts with the lowest AMS (F3 and F4 showed a higher number of aliphatic carbons than aromatic carbons, a higher concentration of groups containing oxygen and a higher percentage of fulvic acids (FA than humic acids (HA for both AHS and HSP. However, the AHS presented higher FA than HA content in relation to the HSP and distinct structural properties.

  7. Comparison of DNA Extraction Protocols and Molecular Targets to Diagnose Tuberculous Meningitis

    Directory of Open Access Journals (Sweden)

    Flavia Silva Palomo

    2017-01-01

    Full Text Available Tuberculous meningitis (TBM is a severe form of extrapulmonary tuberculosis. The aims of this study were to evaluate in-house molecular diagnostic protocols of DNA extraction directly from CSF samples and the targets amplified by qPCR as an accurate and fast diagnosis of TBM. One hundred CSF samples from 68 patients suspected of TBM were studied. Four DNA extraction techniques (phenol-chloroform-thiocyanate guanidine, silica thiocyanate guanidine, resin, and resin with ethanol were compared and CSF samples were used to determine the best target (IS6110, MPB64, and hsp65 KDa by qPCR. The extraction protocol using the phenol-chloroform-thiocyanate guanidine showed the best results in terms of quantification and sensitivity of PCR amplification, presenting up to 10 times more DNA than the second best protocol, the silica guanidine thiocyanate. The target that showed the best result for TBM diagnosis was the IS6110. This target showed 91% sensitivity and 97% specificity when we analyzed the results by sample and showed 100% sensitivity and 98% specificity when we analyzed the results by patient. The DNA extraction with phenol-chloroform-thiocyanate guanidine followed by IS6110 target amplification has been shown to be suitable for diagnosis of TBM in our clinical setting.

  8. Extraction of High Quality RNA from Cannabis sativa Bast Fibres: A Vademecum for Molecular Biologists

    Directory of Open Access Journals (Sweden)

    Gea Guerriero

    2016-07-01

    Full Text Available In plants there is no universal protocol for RNA extraction, since optimizations are required depending on the species, tissues and developmental stages. Some plants/tissues are rich in secondary metabolites or synthesize thick cell walls, which hinder an efficient RNA extraction. One such example is bast fibres, long extraxylary cells characterized by a thick cellulosic cell wall. Given the economic importance of bast fibres, which are used in the textile sector, as well as in biocomposites as green substitutes of glass fibres, it is desirable to better understand their development from a molecular point of view. This knowledge favours the development of biotechnological strategies aimed at improving specific properties of bast fibres. To be able to perform high-throughput analyses, such as, for instance, transcriptomics of bast fibres, RNA extraction is a crucial and limiting step. We here detail a protocol enabling the rapid extraction of high quality RNA from the bast fibres of textile hemp, Cannabis sativa L., a multi-purpose fibre crop standing in the spotlight of research.

  9. Automatic segmentation of 4D cardiac MR images for extraction of ventricular chambers using a spatio-temporal approach

    Science.gov (United States)

    Atehortúa, Angélica; Zuluaga, Maria A.; Ourselin, Sébastien; Giraldo, Diana; Romero, Eduardo

    2016-03-01

    An accurate ventricular function quantification is important to support evaluation, diagnosis and prognosis of several cardiac pathologies. However, expert heart delineation, specifically for the right ventricle, is a time consuming task with high inter-and-intra observer variability. A fully automatic 3D+time heart segmentation framework is herein proposed for short-axis-cardiac MRI sequences. This approach estimates the heart using exclusively information from the sequence itself without tuning any parameters. The proposed framework uses a coarse-to-fine approach, which starts by localizing the heart via spatio-temporal analysis, followed by a segmentation of the basal heart that is then propagated to the apex by using a non-rigid-registration strategy. The obtained volume is then refined by estimating the ventricular muscle by locally searching a prior endocardium- pericardium intensity pattern. The proposed framework was applied to 48 patients datasets supplied by the organizers of the MICCAI 2012 Right Ventricle segmentation challenge. Results show the robustness, efficiency and competitiveness of the proposed method both in terms of accuracy and computational load.

  10. DynaPhoPy: A code for extracting phonon quasiparticles from molecular dynamics simulations

    Science.gov (United States)

    Carreras, Abel; Togo, Atsushi; Tanaka, Isao

    2017-12-01

    We have developed a computational code, DYNAPHOPY, that allows us to extract the microscopic anharmonic phonon properties from molecular dynamics (MD) simulations using the normal-mode-decomposition technique as presented by Sun et al. (2014). Using this code we calculated the quasiparticle phonon frequencies and linewidths of crystalline silicon at different temperatures using both of first-principles and the Tersoff empirical potential approaches. In this work we show the dependence of these properties on the temperature using both approaches and compare them with reported experimental data obtained by Raman spectroscopy (Balkanski et al., 1983; Tsu and Hernandez, 1982).

  11. Analysis of the relationship of automatically and manually extracted lineaments from DEM and geologically mapped tectonic faults around the Main Ethiopian Rift and the Ethiopian Highlands, Ethiopia

    Directory of Open Access Journals (Sweden)

    Michal Kusák

    2017-02-01

    Full Text Available The paper deals with the functions that automatically extract lineaments from the 90 m Shuttle Radar Topographic Mission (SRTM of Digital Elevation Model (DEM (Consortium for Spatial Information 2014 in the software ArcGIS 10.1 and PCI Geomatica. They were performed for the Main Ethiopian Rift and the Ethiopian Highlands (transregional scale 1,060,000 km2, which are one of the tectonically most active areas in the world. The values of input parameters – the RADI (filter radius value, GTHR (edge gradient threshold, LTHR (curve length, FTHR (line fitting error, ATHR (angular difference, and the DTHR (linked distance threshold – and their influence on the final shape and number of lineaments are discussed. A map of automated extracted lineaments was created and compared with 1 the tectonic faults on the geological map by Geological Survey of Ethiopia (Mangesha et al. 1996 and 2 the lineaments based on visual interpretation by the author from the same data set. The predominant azimuth of lineaments is similar to the azimuth of the faults on the geological map. The comparison of lineaments by automated visualization in GIS and visual interpretation of lineaments carried out by the authors around the Jemma River Basin (regional scale 16,000 km2 proved that both sets of lineaments are of the same NE–SW azimuth, which is the orientation of the rift. However, lineaments mapping by automated visualization in GIS identifies a larger number of shorter lineaments than lineaments created by visual interpretation.

  12. A new generic method for the semi-automatic extraction of river and road networks in low and mid-resolution satellite images

    Energy Technology Data Exchange (ETDEWEB)

    Grazzini, Jacopo [Los Alamos National Laboratory; Dillard, Scott [PNNL; Soille, Pierre [EC JRC

    2010-10-21

    This paper addresses the problem of semi-automatic extraction of road or hydrographic networks in satellite images. For that purpose, we propose an approach combining concepts arising from mathematical morphology and hydrology. The method exploits both geometrical and topological characteristics of rivers/roads and their tributaries in order to reconstruct the complete networks. It assumes that the images satisfy the following two general assumptions, which are the minimum conditions for a road/river network to be identifiable and are usually verified in low- to mid-resolution satellite images: (i) visual constraint: most pixels composing the network have similar spectral signature that is distinguishable from most of the surrounding areas; (ii) geometric constraint: a line is a region that is relatively long and narrow, compared with other objects in the image. While this approach fully exploits local (roads/rivers are modeled as elongated regions with a smooth spectral signature in the image and a maximum width) and global (they are structured like a tree) characteristics of the networks, further directional information about the image structures is incorporated. Namely, an appropriate anisotropic metric is designed by using both the characteristic features of the target network and the eigen-decomposition of the gradient structure tensor of the image. Following, the geodesic propagation from a given network seed with this metric is combined with hydrological operators for overland flow simulation to extract the paths which contain most line evidence and identify them with the target network.

  13. Automatic Mapping Extraction from Multiecho T2-Star Weighted Magnetic Resonance Images for Improving Morphological Evaluations in Human Brain

    Directory of Open Access Journals (Sweden)

    Shaode Yu

    2013-01-01

    Full Text Available Mapping extraction is useful in medical image analysis. Similarity coefficient mapping (SCM replaced signal response to time course in tissue similarity mapping with signal response to TE changes in multiecho T2-star weighted magnetic resonance imaging without contrast agent. Since different tissues are with different sensitivities to reference signals, a new algorithm is proposed by adding a sensitivity index to SCM. It generates two mappings. One measures relative signal strength (SSM and the other depicts fluctuation magnitude (FMM. Meanwhile, the new method is adaptive to generate a proper reference signal by maximizing the sum of contrast index (CI from SSM and FMM without manual delineation. Based on four groups of images from multiecho T2-star weighted magnetic resonance imaging, the capacity of SSM and FMM in enhancing image contrast and morphological evaluation is validated. Average contrast improvement index (CII of SSM is 1.57, 1.38, 1.34, and 1.41. Average CII of FMM is 2.42, 2.30, 2.24, and 2.35. Visual analysis of regions of interest demonstrates that SSM and FMM show better morphological structures than original images, T2-star mapping and SCM. These extracted mappings can be further applied in information fusion, signal investigation, and tissue segmentation.

  14. Automatic urban debris zone extraction from post-hurricane very high-resolution satellite and aerial imagery

    Directory of Open Access Journals (Sweden)

    Shasha Jiang

    2016-05-01

    Full Text Available Automated remote sensing methods have not gained widespread usage for damage assessment after hurricane events, especially for low-rise buildings, such as individual houses and small businesses. Hurricane wind, storm surge with waves, and inland flooding have unique damage signatures, further complicating the development of robust automated assessment methodologies. As a step toward realizing automated damage assessment for multi-hazard hurricane events, this paper presents a mono-temporal image classification methodology that quickly and accurately differentiates urban debris from non-debris areas using post-event images. Three classification approaches are presented: spectral, textural, and combined spectral–textural. The methodology is demonstrated for Gulfport, Mississippi, using IKONOS panchromatic satellite and NOAA aerial colour imagery collected after 2005 Hurricane Katrina. The results show that multivariate texture information significantly improves debris class detection performance by decreasing the confusion between debris and other land cover types, and the extracted debris zone accurately captures debris distribution. Additionally, the extracted debris boundary is approximately equivalent regardless of imagery type, demonstrating the flexibility and robustness of the debris mapping methodology. While the test case presents results for hurricane hazards, the proposed methodology is generally developed and expected to be effective in delineating debris zones for other natural hazards, including tsunamis, tornadoes, and earthquakes.

  15. Quercetin molecularly imprinted polymers: preparation, recognition characteristics and properties as sorbent for solid-phase extraction.

    Science.gov (United States)

    Song, Xingliang; Li, Jinhua; Wang, Jiangtao; Chen, Lingxin

    2009-12-15

    Molecular imprinted polymers (MIPs) were prepared through thermal polymerization by using quercetin as the template molecule, acrylamide (AA) as the functional monomer and ethylene glycol dimethacrylate (EDMA) as the cross-linker in the porogen of tetrahydrofuran (THF). The synthesized MIPs were identified by both Fourier transform infrared (FTIR) and scanning electron microscope (SEM). Systematic investigations of the influences of key synthetic conditions, including functional monomers, porogens and cross-linkers, on the recognition properties of the MIPs were conducted. Scatchard analysis revealed that the homogeneous binding sites were formed in the polymers. Besides quercetin, two structurally similar compounds of rutin and catechol were employed for molecular recognition specificity tests of MIPs. It was observed that the MIPs exhibited the highest selective rebinding to quercetin. Accordingly, the MIPs were used as a solid-phase extraction (SPE) sorbent for the extraction and enrichment of quercetin in cacumen platycladi samples, followed by HPLC-UV analysis. The application of MIPs with high affinity and excellent stereo-selectivity toward quercetin in SPE might offer a novel method for the enrichment and determination of flavonoid compounds in the natural products.

  16. Molecular Affinity of Mabolo Extracts to an Octopamine Receptor of a Fruit Fly

    Directory of Open Access Journals (Sweden)

    Francoise Neil D. Dacanay

    2017-10-01

    Full Text Available Essential oils extracted from plants are composed of volatile organic compounds that can affect insect behavior. Identifying the active components of the essential oils to their biochemical target is necessary to design novel biopesticides. In this study, essential oils extracted from Diospyros discolor (Willd. were analyzed using gas chromatography mass spectroscopy (GC-MS to create an untargeted metabolite profile. Subsequently, a conformational ensemble of the Drosophila melanogaster octopamine receptor in mushroom bodies (OAMB was created from a molecular dynamics simulation to resemble a flexible receptor for docking studies. GC-MS analysis revealed the presence of several metabolites, i.e. mostly aromatic esters. Interestingly, these aromatic esters were found to exhibit relatively higher binding affinities to OAMB than the receptor’s natural agonist, octopamine. The molecular origin of this observed enhanced affinity is the π -stacking interaction between the aromatic moieties of the residues and ligands. This strategy, computational inspection in tandem with untargeted metabolomics, may provide insights in screening the essential oils as potential OAMB inhibitors.

  17. Molecularly imprinted polymers as the extracted sorbents of clenbuterol ahead of liquid chromatographic determination*

    Science.gov (United States)

    Lay, Sovichea; Yu, Hai-ning; Hu, Bao-xiang; Shen, Sheng-rong

    2016-01-01

    A pre-treatment methodology for clenbuterol hydrochloride (CLEN) isolation and enrichment in a complex matrix environment was developed through exploiting molecularly imprinted polymers (MIPs). CLEN-imprinted polymers were synthesized by the combined use of ally-β-cyclodextrin (ally-β-CD) and methacrylic acid (MAA), allyl-β-CD and acrylonitrile (AN), and allyl-β-CD and methyl methacrylate (MMA) as the binary functional monomers. MAA-linked allyl-β-CD MIPs (M-MAA) were characterized by Fourier transform-infrared (FT-IR) spectroscopy and a scanning electron microscope (SEM). Based upon the results, M-MAA polymers generally proved to be an excellent selective extraction compared to its references: AN-linked allyl-β-CD MIPs (M-AN) and MMA-linked allyl-β-CD MIPs (M-MMA). M-MAA polymers were eventually chosen to run through a molecularly imprinted solid-phase extraction (MISPE) micro-column to enrich CLEN residues spiked in pig livers. A high recovery was achieved, ranging from 91.03% to 96.76% with relative standard deviation (RSD) ≤4.45%. PMID:27256680

  18. Molecularly imprinted polymers as the extracted sorbents of clenbuterol ahead of liquid chromatographic determination.

    Science.gov (United States)

    Lay, Sovichea; Yu, Hai-Ning; Hu, Bao-Xiang; Shen, Sheng-Rong

    2016-06-01

    A pre-treatment methodology for clenbuterol hydrochloride (CLEN) isolation and enrichment in a complex matrix environment was developed through exploiting molecularly imprinted polymers (MIPs). CLEN-imprinted polymers were synthesized by the combined use of ally-β-cyclodextrin (ally-β-CD) and methacrylic acid (MAA), allyl-β-CD and acrylonitrile (AN), and allyl-β-CD and methyl methacrylate (MMA) as the binary functional monomers. MAA-linked allyl-β-CD MIPs (M-MAA) were characterized by Fourier transform-infrared (FT-IR) spectroscopy and a scanning electron microscope (SEM). Based upon the results, M-MAA polymers generally proved to be an excellent selective extraction compared to its references: AN-linked allyl-β-CD MIPs (M-AN) and MMA-linked allyl-β-CD MIPs (M-MMA). M-MAA polymers were eventually chosen to run through a molecularly imprinted solid-phase extraction (MISPE) micro-column to enrich CLEN residues spiked in pig livers. A high recovery was achieved, ranging from 91.03% to 96.76% with relative standard deviation (RSD) ≤4.45%.

  19. A Novel Characteristic Frequency Bands Extraction Method for Automatic Bearing Fault Diagnosis Based on Hilbert Huang Transform.

    Science.gov (United States)

    Yu, Xiao; Ding, Enjie; Chen, Chunxu; Liu, Xiaoming; Li, Li

    2015-11-03

    Because roller element bearings (REBs) failures cause unexpected machinery breakdowns, their fault diagnosis has attracted considerable research attention. Established fault feature extraction methods focus on statistical characteristics of the vibration signal, which is an approach that loses sight of the continuous waveform features. Considering this weakness, this article proposes a novel feature extraction method for frequency bands, named Window Marginal Spectrum Clustering (WMSC) to select salient features from the marginal spectrum of vibration signals by Hilbert-Huang Transform (HHT). In WMSC, a sliding window is used to divide an entire HHT marginal spectrum (HMS) into window spectrums, following which Rand Index (RI) criterion of clustering method is used to evaluate each window. The windows returning higher RI values are selected to construct characteristic frequency bands (CFBs). Next, a hybrid REBs fault diagnosis is constructed, termed by its elements, HHT-WMSC-SVM (support vector machines). The effectiveness of HHT-WMSC-SVM is validated by running series of experiments on REBs defect datasets from the Bearing Data Center of Case Western Reserve University (CWRU). The said test results evidence three major advantages of the novel method. First, the fault classification accuracy of the HHT-WMSC-SVM model is higher than that of HHT-SVM and ST-SVM, which is a method that combines statistical characteristics with SVM. Second, with Gauss white noise added to the original REBs defect dataset, the HHT-WMSC-SVM model maintains high classification accuracy, while the classification accuracy of ST-SVM and HHT-SVM models are significantly reduced. Third, fault classification accuracy by HHT-WMSC-SVM can exceed 95% under a Pmin range of 500-800 and a m range of 50-300 for REBs defect dataset, adding Gauss white noise at Signal Noise Ratio (SNR) = 5. Experimental results indicate that the proposed WMSC method yields a high REBs fault classification accuracy and a

  20. Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature.

    Science.gov (United States)

    Doughty, Emily; Kertesz-Farkas, Attila; Bodenreider, Olivier; Thompson, Gary; Adadey, Asa; Peterson, Thomas; Kann, Maricel G

    2011-02-01

    A major goal of biomedical research in personalized medicine is to find relationships between mutations and their corresponding disease phenotypes. However, most of the disease-related mutational data are currently buried in the biomedical literature in textual form and lack the necessary structure to allow easy retrieval and visualization. We introduce a high-throughput computational method for the identification of relevant disease mutations in PubMed abstracts applied to prostate (PCa) and breast cancer (BCa) mutations. We developed the extractor of mutations (EMU) tool to identify mutations and their associated genes. We benchmarked EMU against MutationFinder--a tool to extract point mutations from text. Our results show that both methods achieve comparable performance on two manually curated datasets. We also benchmarked EMU's performance for extracting the complete mutational information and phenotype. Remarkably, we show that one of the steps in our approach, a filter based on sequence analysis, increases the precision for that task from 0.34 to 0.59 (PCa) and from 0.39 to 0.61 (BCa). We also show that this high-throughput approach can be extended to other diseases. Our method improves the current status of disease-mutation databases by significantly increasing the number of annotated mutations. We found 51 and 128 mutations manually verified to be related to PCa and Bca, respectively, that are not currently annotated for these cancer types in the OMIM or Swiss-Prot databases. EMU's retrieval performance represents a 2-fold improvement in the number of annotated mutations for PCa and BCa. We further show that our method can benefit from full-text analysis once there is an increase in Open Access availability of full-text articles. Freely available at: http://bioinf.umbc.edu/EMU/ftp.

  1. Switchable zipper-like thermoresponsive molecularly imprinted polymers for selective recognition and extraction of estradiol.

    Science.gov (United States)

    Xiong, Huihuang; Wu, Xiaqing; Lu, Wenhui; Fu, Junqing; Peng, Hailong; Li, Jinhua; Wang, Xiaoyan; Xiong, Hua; Chen, Lingxin

    2018-01-01

    Zipper-like thermoresponsive molecularly imprinted polymers (MIPs) were prepared based on interpolymer complexation via the synergy of dual functional monomers of acrylamide (AAm) and 2-acrylamide-2-methyl propanesulfonic acid (AMPS) for selective recognition and extraction of estradiol (E2) by temperature regulation. The resulting E2-MIPs attained controlled adsorption and release of E2 in response to temperature change, with higher adsorption capacity (8.78mg/g) and stronger selectivity (imprinting factor was 3.18) at 30°C compared with that at 20 and 40°C; the zipper-like interpolymer interaction between poly(AAm) and poly(AMPS) enabled switchable molecular recognition. The adsorption processes obeyed Langmuir isotherm and pseudo-second-order kinetic models. High recognition selectivity of the MIPs toward E2 was achieved over its structural analogues, and good reusability was displayed over 86% recovery after six adsorption-desorption cycles. Accordingly, the E2-MIPs were empolyed as new adsorbents for selective dispersive solid-phase extraction of E2, and offered low limits of detection and quantification of 4.81 and 16.03μg/L, respectively. Recoveries from goat milk samples ranged from 76.2% to 89.7% with the precisions (relative standard deviations, n = 3, %) of 2.8-3.7% at 30°C. The intelligent E2-MIPs combining good adsorption, special recognition and temperature sensitivity proved to be a promising alternative to the selective identification and controlled extraction/removal of E2 in complicated samples by simple temperature-responsive regulation. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Mass spectroscopic characteristics of low molecular weight proteins extracted from calcium oxalate stones: preliminary study.

    Science.gov (United States)

    Chen, Wen-Chi; Lai, Chien-Chen; Lai, Chein-Cheng; Tsai, Yuhsin; Tsai, Yu-Hsin; Lin, Wei-Yong; Tsai, Fuu-Jen

    2008-01-01

    It is believed that boundary compositions of matrix proteins might play a role in stone formation; however, few proteomic studies concerning matrix proteins in urinary stones have been conducted. In this study, we extracted low molecular weight proteins from calcium oxalate stones and measured their characteristic patterns by mass spectroscopy. A total of 10 stones were surgically removed from patients with urolithiasis. Proteins were extracted from the stones and identified by one-dimensional electrophoresis (sodium dodecyl sulfate buffer [SDS]-polyacrylamide gel electrophoresis [SDS-PAGE]). After in-gel digest, samples were analyzed by the surface-enhanced laser desorption ionization-time of flight (SELDI-TOF) technique. The peptide sequences were analyzed from the data of mass spectroscopy. Proteins were identified from Database Search (SwissProt Protein Database; Swiss Institute of Bioinformatics; http://www.expasy.org/sprot) on a MASCOT server (Matrix Science Ltd.; http://www.matrixscience.com). A total of three bands of proteins (27, 18, and 14 kDa) were identified from SDS-PAGE in each stone sample. A database search (SwissProt) on a MASCOT server revealed that the most frequently seen proteins from band 1 (27 kDa) were leukocyte elastase precursor, cathepsin G precursor, azurocidin precursor, and myeloblastin precursor (EC 3.4.21.76) (leukocyte proteinase 3); band 2 (18 kDa) comprised calgranulin B, eosinophil cationic protein precursor, and lysozyme C precursor; band 3 (14 kDa) showed neutrophil defensin 3 precursor, calgranulin A, calgranulin C, and histone H4. The modifications and deamidations found from the mass pattern of these proteins may provide information for the study of matrix proteins. Various lower molecular weight proteins can be extracted from calcium oxalate stones. The characteristic patterns and their functions of those proteins should be further tested to investigate their roles in stone formation. (c) 2008 Wiley-Liss, Inc.

  3. Determination of organophosphorus pesticides using molecularly imprinted polymer solid phase extraction

    International Nuclear Information System (INIS)

    Mohd Marsin Sanagi; Syairah Salleh; Wan Aini Wan Ibrahim

    2011-01-01

    Molecularly imprinted polymer solid phase extraction (MIP-SPE) method has been developed for the determination of organophosphorus pesticides (OPPs) in water samples. The MIP was prepared by thermo-polymerization method using methacrylic acid (MAA) as functional monomer, ethylene glycol dimethacrylate (EGDMA) as crosslinker, acetonitrile as porogenic solvent and quinalphos as the template molecule. The three OPPs (diazinon, quinalphos and chloropyrifos) were selected as target analytes as they are widely used in agriculture sector. Various parameters affecting the extraction efficiency of the imprinted polymers have been evaluated to optimize the selective preconcentration of OPPs from aqueous samples. The characteristics of the MIP-SPE method were validated by high performance liquid chromatography (HPLC). The accuracy and selectivity of the MIP-SPE process developed were verified using non-imprinted polymer solid phase extraction (NIP-SPE) and a commercial C 18 -SPE was used for comparison. The recoveries of the target analytes obtained using the MIPs as the solid phase sorbent ranged from 83% to 98% (RSDs 1.05 - 1.98 %; n=3) for water sample. The developed MIP-SPE method demonstrates that it could be applied for the determination of OPPs in water samples. (author)

  4. Development and application of novel clonazepam molecularly imprinted coatings for stir bar sorptive extraction.

    Science.gov (United States)

    Li, Xiaoxu; Mei, Xiaoliang; Xu, Lei; Shen, Xin; Zhu, Wanying; Hong, Junli; Zhou, Xuemin

    2016-04-15

    The molecularly imprinted magnetic stir bar coatings were created based on graft-functional Fe3O4 nanoparticles with magnetic field-induced self-assembly. The magnetic complex including clonazepam as template, the graft-functional Fe3O4 nanoparticles and methacrylic acid as monomers was pre-assembled through π-π interaction and hydrogen bonding, then was directionally adsorbed on the surface of magnetic stir bar under the magnetic induction. The molecularly imprinted coating with well-ordered structure was generated by one-step copolymerization based on the cross linking of ethylene glycol dimethacrylate. The molecularly imprinted coating with multiple recognition sites could be manufactured and applied in polar solvents, and showed superior selectivity and fast binding kinetics for benzodiazepines. The analytes in herbal health foods, treated by stir bar sorptive extraction, were determined by HPLC-UV. Good linearity was observed in the range of 0.01-2 μg mL(-1). The content of clonazepam in the herbal health foods was found to be 44 ng g(-1), and the average recoveries were 89.8-103.3% with a relative standard deviation (RSD) <6.5%, demonstrating the successful application in real sample analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Road Extraction from High-Resolution SAR Images via Automatic Local Detecting and Human-Guided Global Tracking

    Directory of Open Access Journals (Sweden)

    Jianghua Cheng

    2012-01-01

    Full Text Available Because of existence of various kinds of disturbances, layover effects, and shadowing, it is difficult to extract road from high-resolution SAR images. A new road center-point searching method is proposed by two alternant steps: local detection and global tracking. In local detection step, double window model is set, which consists of the outer fixed square window and the inner rotary rectangular one. The outer window is used to obtain the local road direction by using orientation histogram, based on the fact that the surrounding objects always range along with roads. The inner window rotates its orientation in accordance with the result of local road direction calculation and searches the center points of a road segment. In global tracking step, particle filter of variable-step is used to deal with the problem of tracking frequently broken by shelters along the roadside and obstacles on the road. Finally, the center-points are linked by quadratic curve fitting. In 1 m high-resolution airborne SAR image experiment, the results show that this method is effective.

  6. Two-dimensional Morlet wavelet transform and its application to wave recognition methodology of automatically extracting two-dimensional wave packets from lidar observations in Antarctica

    Science.gov (United States)

    Chen, Cao; Chu, Xinzhao

    2017-09-01

    Waves in the atmosphere and ocean are inherently intermittent, with amplitudes, frequencies, or wavelengths varying in time and space. Most waves exhibit wave packet-like properties, propagate at oblique angles, and are often observed in two-dimensional (2-D) datasets. These features make the wavelet transforms, especially the 2-D wavelet approach, more appealing than the traditional windowed Fourier analysis, because the former allows adaptive time-frequency window width (i.e., automatically narrowing window size at high frequencies and widening at low frequencies), while the latter uses a fixed envelope function. This study establishes the mathematical formalism of modified 1-D and 2-D Morlet wavelet transforms, ensuring that the power of the wavelet transform in the frequency/wavenumber domain is equivalent to the mean power of its counterpart in the time/space domain. Consequently, the modified wavelet transforms eliminate the bias against high-frequency/small-scale waves in the conventional wavelet methods and many existing codes. Based on the modified 2-D Morlet wavelet transform, we put forward a wave recognition methodology that automatically identifies and extracts 2-D quasi-monochromatic wave packets and then derives their wave properties including wave periods, wavelengths, phase speeds, and time/space spans. A step-by-step demonstration of this methodology is given on analyzing the lidar data taken during 28-30 June 2014 at McMurdo, Antarctica. The newly developed wave recognition methodology is then applied to two more lidar observations in May and July 2014, to analyze the recently discovered persistent gravity waves in Antarctica. The decomposed inertia-gravity wave characteristics are consistent with the conclusion in Chen et al. (2016a) that the 3-10 h waves are persistent and dominant, and exhibit lifetimes of multiple days. They have vertical wavelengths of 20-30 km, vertical phase speeds of 0.5-2 m/s, and horizontal wavelengths up to several

  7. Dietary administration of scallion extract effectively inhibits colorectal tumor growth: cellular and molecular mechanisms in mice.

    Directory of Open Access Journals (Sweden)

    Palanisamy Arulselvan

    Full Text Available Colorectal cancer is a common malignancy and a leading cause of cancer death worldwide. Diet is known to play an important role in the etiology of colon cancer and dietary chemoprevention is receiving increasing attention for prevention and/or alternative treatment of colon cancers. Allium fistulosum L., commonly known as scallion, is popularly used as a spice or vegetable worldwide, and as a traditional medicine in Asian cultures for treating a variety of diseases. In this study we evaluated the possible beneficial effects of dietary scallion on chemoprevention of colon cancer using a mouse model of colon carcinoma (CT-26 cells subcutaneously inoculated into BALB/c mice. Tumor lysates were subjected to western blotting for analysis of key inflammatory markers, ELISA for analysis of cytokines, and immunohistochemistry for analysis of inflammatory markers. Metabolite profiles of scallion extracts were analyzed by LC-MS/MS. Scallion extracts, particularly hot-water extract, orally fed to mice at 50 mg (dry weight/kg body weight resulted in significant suppression of tumor growth and enhanced the survival rate of test mice. At the molecular level, scallion extracts inhibited the key inflammatory markers COX-2 and iNOS, and suppressed the expression of various cellular markers known to be involved in tumor apoptosis (apoptosis index, proliferation (cyclin D1 and c-Myc, angiogenesis (VEGF and HIF-1α, and tumor invasion (MMP-9 and ICAM-1 when compared with vehicle control-treated mice. Our findings may warrant further investigation of the use of common scallion as a chemopreventive dietary agent to lower the risk of colon cancer.

  8. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  9. [The molecular mechanisms of curcuma wenyujin extract-mediated inhibitory effects on human esophageal carcinoma cells in vitro].

    Science.gov (United States)

    Jing, Zhao; Zou, Hai-Zhou; Xu, Fang

    2012-09-01

    To study the molecular mechanisms of Curcuma Wenyujin extract-mediated inhibitory effects on human esophageal carcinoma cells. The Curcuma Wenyujin extract was obtained by supercritical carbon dioxide extraction. TE-1 cells were divided into 4 groups after adherence. 100 microL RMPI-1640 culture medium containing 0.1% DMSO was added in Group 1 as the control group. 100 microL 25, 50, and 100 mg/L Curcuma Wenyujin extract complete culture medium was respectively added in the rest 3 groups as the low, middle, and high dose Curcuma Wenyujin extract groups. The effects of different doses of Curcuma Wenyujin extract (25, 50, and 100 mg/L) on the proliferation of human esophageal carcinoma cell line TE-1 in vitro were analyzed by MTT assay. The gene expression profile was identified by cDNA microarrays in esophageal carcinoma TE-1 cells exposed to Curcuma Wenyujin extract for 48 h. The differential expression genes were further analyzed by Gene Ontology function analysis. Compared with the control group, MTT results showed that Curcuma Wenyujin extract significantly inhibited the proliferation of TE-1 cells in a dose-dependent manner (PCurcuma Wenyujin extract could inhibit the growth of human esophageal carcinoma cell line TE-1 in vitro. The molecular mechanisms might be associated with regulating genes expressions at multi-levels.

  10. Molecular Docking Studies and Anti-Tyrosinase Activity of Thai Mango Seed Kernel Extract

    Directory of Open Access Journals (Sweden)

    Patchreenart Saparpakorn

    2009-01-01

    Full Text Available The alcoholic extract from seed kernels of Thai mango (Mangifera indica L. cv. ‘Fahlun’ (Anacardiaceae and its major phenolic principle (pentagalloylglucopyranose exhibited potent, dose-dependent inhibitory effects on tyrosinase with respect to L-DOPA. Molecular docking studies revealed that the binding orientations of the phenolic principles were in the tyrosinase binding pocket and their orientations were located in the hydrophobic binding pocket surrounding the binuclear copper active site. The results indicated a possible mechanism for their anti-tyrosinase activity which may involve an ability to chelate the copper atoms which are required for the catalytic activity of tyrosinase.

  11. Selective extraction of clonazepam from human plasma and urine samples by molecularly imprinted polymeric beads.

    Science.gov (United States)

    Panahi, Homayon Ahmad; Mehramizi, Ali; Ghassemi, Somayeh; Moniri, Elham

    2014-03-01

    A molecularly imprinted polymer (MIP) based on free-radical polymerization was prepared with 1-(N,N-biscarboxymethyl)amino-3-allylglycerol and N,N-dimethylacrylamide as functional monomers, N,N-methylene diacrylamide as the cross-linker, copper ion-clonazepam as the template and 2,2-azobis(2-methylbutyronitrile) as the initiator. The imprinted polymer was characterized by Fourier transform infrared spectroscopy, elemental analysis, thermo-gravimetric analysis, and SEM. The MIP of agglomerated microparticles with multipores was used for SPE. The imprinted polymer sorbent was selective for clonazepam. The optimum pH and sorption capacity were 5 and 0.18 mg/g at 20C, respectively. The profile of the drug uptake by the sorbent reflects good accessibility of the active sites in the imprinted polymer sorbent. The MIP-SPE was the most feasible technique for the extraction of clonazepam with a high recovery from human plasma and urine samples.

  12. Automatic Tie-point Extraction Based on Multiple-image Matching and Bundle Adjustment of Large Block of Oblique Aerial Images

    Directory of Open Access Journals (Sweden)

    ZHANG Li

    2017-05-01

    Full Text Available Due to advantages such as ease of interpretation, completeness through mitigation of occluding areas, as well as system accessibility, the aerial oblique images have found their place in numerous civil applications. However, for these applications high quality orientation data are essential. A fully automatic tie-point extraction procedure is developed to precisely orient the large block of oblique aerial images, in which a refined ASIFT algorithm and a window-based multiple-viewing image matching (WMVM method are combined. In this approach, the WMVM method is based on the concept of multi-image matching guided from object space and allows reconstruction of 3D objects by matching all available images simultaneously, and a square correlation window in the reference image can be correlated with windows of different size, shape and orientation in the search images.Then another key algorithms, i.e. the combined bundle adjustment method with gross-error detection & removal algorithm, which can be used for simultaneously orient the oblique and nearly-vertical images will be presented. Finally, through the experiments by using real oblique images over several test areas, the performance and accuracy of the proposed method is studied and presented.

  13. Liquid chromatography-mass spectrometry platform for both small neurotransmitters and neuropeptides in blood, with automatic and robust solid phase extraction

    Science.gov (United States)

    Johnsen, Elin; Leknes, Siri; Wilson, Steven Ray; Lundanes, Elsa

    2015-03-01

    Neurons communicate via chemical signals called neurotransmitters (NTs). The numerous identified NTs can have very different physiochemical properties (solubility, charge, size etc.), so quantification of the various NT classes traditionally requires several analytical platforms/methodologies. We here report that a diverse range of NTs, e.g. peptides oxytocin and vasopressin, monoamines adrenaline and serotonin, and amino acid GABA, can be simultaneously identified/measured in small samples, using an analytical platform based on liquid chromatography and high-resolution mass spectrometry (LC-MS). The automated platform is cost-efficient as manual sample preparation steps and one-time-use equipment are kept to a minimum. Zwitter-ionic HILIC stationary phases were used for both on-line solid phase extraction (SPE) and liquid chromatography (capillary format, cLC). This approach enabled compounds from all NT classes to elute in small volumes producing sharp and symmetric signals, and allowing precise quantifications of small samples, demonstrated with whole blood (100 microliters per sample). An additional robustness-enhancing feature is automatic filtration/filter back-flushing (AFFL), allowing hundreds of samples to be analyzed without any parts needing replacement. The platform can be installed by simple modification of a conventional LC-MS system.

  14. Microbes on building materials — Evaluation of DNA extraction protocols as common basis for molecular analysis

    International Nuclear Information System (INIS)

    Ettenauer, Jörg D.; Piñar, Guadalupe; Lopandic, Ksenija; Spangl, Bernhard; Ellersdorfer, Günther; Voitl, Christian; Sterflinger, Katja

    2012-01-01

    The study of microbial life in building materials is an emerging topic concerning biodeterioration of materials as well as health risks in houses and at working places. Biodegradation and potential health implications associated with microbial growth in our residues claim for more precise methods for quantification and identification. To date, cultivation experiments are commonly used to gain insight into the microbial diversity. Nowadays, molecular techniques for the identification of microorganisms provide efficient methods that can be applied in this field. The efficiency of DNA extraction is decisive in order to perform a reliable and reproducible quantification of the microorganisms by qPCR or to characterize the structure of the microbial community. In this study we tested thirteen DNA extraction methods and evaluated their efficiency for identifying (1) the quantity of DNA, (2) the quality and purity of DNA and (3) the ability of the DNA to be amplified in a PCR reaction using three universal primer sets for the ITS region of fungi as well as one primer pair targeting the 16S rRNA of bacteria with three typical building materials — common plaster, red brick and gypsum cardboard. DNA concentration measurements showed strong variations among the tested methods and materials. Measurement of the DNA yield showed up to three orders of magnitude variation from the same samples, whereas A260/A280 ratios often prognosticated biases in the PCR amplifications. Visualization of the crude DNA extracts and the comparison of DGGE fingerprints showed additional drawbacks of some methods. The FastDNA Spin kit for soil showed to be the best DNA extraction method and could provide positive results for all tests with the three building materials. Therefore, we suggest this method as a gold standard for quantification of indoor fungi and bacteria in building materials. -- Highlights: ► Up to thirteen extraction methods were evaluated with three building materials.

  15. Microbes on building materials - Evaluation of DNA extraction protocols as common basis for molecular analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ettenauer, Joerg D., E-mail: joerg.ettenauer@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria); Pinar, Guadalupe, E-mail: Guadalupe.Pinar@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria); Lopandic, Ksenija, E-mail: Ksenija.Lopandic@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria); Spangl, Bernhard, E-mail: Bernhard.Spangl@boku.ac.at [University of Natural Resources and Life Sciences, Department of Landscape, Spatial and Infrastructure Science, Institute of Applied Statistics and Computing (IASC), Gregor Mendel-Str. 33, A-1180 Vienna (Austria); Ellersdorfer, Guenther, E-mail: Guenther.Ellersdorfer@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria); Voitl, Christian, E-mail: Christian.Voitl@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria); Sterflinger, Katja, E-mail: Katja.Sterflinger@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria)

    2012-11-15

    The study of microbial life in building materials is an emerging topic concerning biodeterioration of materials as well as health risks in houses and at working places. Biodegradation and potential health implications associated with microbial growth in our residues claim for more precise methods for quantification and identification. To date, cultivation experiments are commonly used to gain insight into the microbial diversity. Nowadays, molecular techniques for the identification of microorganisms provide efficient methods that can be applied in this field. The efficiency of DNA extraction is decisive in order to perform a reliable and reproducible quantification of the microorganisms by qPCR or to characterize the structure of the microbial community. In this study we tested thirteen DNA extraction methods and evaluated their efficiency for identifying (1) the quantity of DNA, (2) the quality and purity of DNA and (3) the ability of the DNA to be amplified in a PCR reaction using three universal primer sets for the ITS region of fungi as well as one primer pair targeting the 16S rRNA of bacteria with three typical building materials - common plaster, red brick and gypsum cardboard. DNA concentration measurements showed strong variations among the tested methods and materials. Measurement of the DNA yield showed up to three orders of magnitude variation from the same samples, whereas A260/A280 ratios often prognosticated biases in the PCR amplifications. Visualization of the crude DNA extracts and the comparison of DGGE fingerprints showed additional drawbacks of some methods. The FastDNA Spin kit for soil showed to be the best DNA extraction method and could provide positive results for all tests with the three building materials. Therefore, we suggest this method as a gold standard for quantification of indoor fungi and bacteria in building materials. -- Highlights: Black-Right-Pointing-Pointer Up to thirteen extraction methods were evaluated with three

  16. Aluminum-induced molecular neurodegeneration: The protective role of genistein and chickpea extract.

    Science.gov (United States)

    Wahby, M M; Mohammed, D S; Newairy, A A; Abdou, H M; Zaky, A

    2017-09-01

    Neurotoxicity of Al is well established and linked to oxidative damage and neurodegeneration. This study investigated the protective role of genistein (Gen) and chickpea extract (CPE) against AlCl 3 -induced neurodegeneration. HPLC analysis revealed that biochanin A-7-O-β-D-glucoside and biochanin A are the major components of the CPE. Gene expression of TNF-α, APP, BACE1, PSEN-2 and ER-β were assessed in brain extract using RT-PCR. Also, NF-кB subunit P65 and COX-2 expression were evaluated by western blotting. The cholinergic function, histological examination and oxidative status were also estimated. The AlCl 3 significantly up regulated the expression of the NF-кB subunit P65, COX-2, TNF- α, BACE1and APP while it significantly down regulated PSEN-2 and ER-β expression. The activity of acetyl cholinesterase (AChE) and the oxidative stress parameters as well as the histological examination confirmed the deleterious effect of AlCl 3 . The administration of either CPE or Gen attenuated the expression of inflammatory cytokines, inhibited the amyloidogenesis and restored both the AChE activity and ER-β expression. Gen and CPE also inhibited the oxidative stress and ameliorated the histological alterations. Accordingly, the present study provides an insight on the molecular role of Gen and CPE as protective agents against neuronal injury. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Molecular characterization and enzymatic hydrolysis of naringin extracted from kinnow peel waste.

    Science.gov (United States)

    Puri, Munish; Kaur, Aneet; Schwarz, Wolfgang H; Singh, Satbir; Kennedy, J F

    2011-01-01

    Kinnow peel, a waste rich in glycosylated phenolic substances, is the principal by-product of the citrus fruit processing industry and its disposal is becoming a major problem. This peel is rich in naringin and may be used for rhamnose production by utilizing α-L-rhamnosidase (EC 3.2.1.40), an enzyme that catalyzes the cleavage of terminal rhamnosyl groups from naringin to yield prunin and rhamnose. In this work, infrared (IR) spectroscopy confirmed molecular characteristics of naringin extracted from kinnow peel waste. Further, recombinant α-L-rhamnosidase purified from Escherichia coli cells using immobilized metal-chelate affinity chromatography (IMAC) was used for naringin hydrolysis. The purified enzyme was inhibited by Hg2+ (1 mM), 4-hydroxymercuribenzoate (0.1 mM) and cyanamide (0.1 mM). The purified enzyme established hydrolysis of naringin extracted from kinnow peel and thus endorses its industrial applicability for producing rhamnose. Copyright © 2010 Elsevier B.V. All rights reserved.

  18. Extraction of High Molecular Weight DNA from Fungal Rust Spores for Long Read Sequencing.

    Science.gov (United States)

    Schwessinger, Benjamin; Rathjen, John P

    2017-01-01

    Wheat rust fungi are complex organisms with a complete life cycle that involves two different host plants and five different spore types. During the asexual infection cycle on wheat, rusts produce massive amounts of dikaryotic urediniospores. These spores are dikaryotic (two nuclei) with each nucleus containing one haploid genome. This dikaryotic state is likely to contribute to their evolutionary success, making them some of the major wheat pathogens globally. Despite this, most published wheat rust genomes are highly fragmented and contain very little haplotype-specific sequence information. Current long-read sequencing technologies hold great promise to provide more contiguous and haplotype-phased genome assemblies. Long reads are able to span repetitive regions and phase structural differences between the haplomes. This increased genome resolution enables the identification of complex loci and the study of genome evolution beyond simple nucleotide polymorphisms. Long-read technologies require pure high molecular weight DNA as an input for sequencing. Here, we describe a DNA extraction protocol for rust spores that yields pure double-stranded DNA molecules with molecular weight of >50 kilo-base pairs (kbp). The isolated DNA is of sufficient purity for PacBio long-read sequencing, but may require additional purification for other sequencing technologies such as Nanopore and 10× Genomics.

  19. Selective extraction of dimethoate from cucumber samples by use of molecularly imprinted microspheres

    Directory of Open Access Journals (Sweden)

    Jiao-Jiao Du

    2015-06-01

    Full Text Available Molecularly imprinted polymers for dimethoate recognition were synthesized by the precipitation polymerization technique using methyl methacrylate (MMA as the functional monomer and ethylene glycol dimethacrylate (EGDMA as the cross-linker. The morphology, adsorption and recognition properties were investigated by scanning electron microscopy (SEM, static adsorption test, and competitive adsorption test. To obtain the best selectivity and binding performance, the synthesis and adsorption conditions of MIPs were optimized through single factor experiments. Under the optimized conditions, the resultant polymers exhibited uniform size, satisfactory binding capacity and significant selectivity. Furthermore, the imprinted polymers were successfully applied as a specific solid-phase extractants combined with high performance liquid chromatography (HPLC for determination of dimethoate residues in the cucumber samples. The average recoveries of three spiked samples ranged from 78.5% to 87.9% with the relative standard deviations (RSDs less than 4.4% and the limit of detection (LOD obtained for dimethoate as low as 2.3 μg/mL. Keywords: Molecularly imprinted polymer, Precipitation polymerization, Dimethoate, Cucumber, HPLC

  20. Physiological and biochemical characterization of egg extract of black widow spiders to uncover molecular basis of egg toxicity

    Directory of Open Access Journals (Sweden)

    Yizhong Yan

    2014-01-01

    Full Text Available BACKGROUND: Black widow spider (L. tredecimguttatus has toxic components not only in the venomous glands, but also in other parts of the body and its eggs. It is biologically important to investigate the molecular basis of the egg toxicity. RESULTS: In the present work, an aqueous extract was prepared from the eggs of the spider and characterized using multiple physiological and biochemical strategies. Gel electrophoresis and mass spectrometry demonstrated that the eggs are rich in high-molecular-mass proteins and the peptides below 5 kDa. The lyophilized extract of the eggs had a protein content of 34.22% and was shown to have a strong toxicity towards mammals and insects. When applied at a concentration of 0.25 mg/mL, the extract could completely block the neuromuscular transmission in mouse isolated phrenic nerve-hemidiaphragm preparations within 12.0 ± 1.5 min. Using whole-cell patch-clamp technique, the egg extract was demonstrated to be able to inhibit the voltage-activated Na+, K+and Ca2+ currents in rat DRG neurons. In addition, the extract displayed activities of multiple hydrolases. Finally, the molecular basis of the egg toxicity was discussed. CONCLUSIONS: The eggs of black widow spiders are rich in proteinous compounds particularly the high-molecular-mass proteins with different types of biological activity The neurotoxic and other active compounds in the eggs are believed to play important roles in the eggs' toxic actions.

  1. Physiological and biochemical characterization of egg extract of black widow spiders to uncover molecular basis of egg toxicity.

    Science.gov (United States)

    Yan, Yizhong; Li, Jianjun; Zhang, Yiya; Peng, Xiaozhen; Guo, Tianyao; Wang, Jirong; Hu, Weijun; Duan, Zhigui; Wang, Xianchun

    2014-05-16

    Black widow spider (L. tredecimguttatus) has toxic components not only in the venomous glands, but also in other parts of the body and its eggs. It is biologically important to investigate the molecular basis of the egg toxicity. In the present work, an aqueous extract was prepared from the eggs of the spider and characterized using multiple physiological and biochemical strategies. Gel electrophoresis and mass spectrometry demonstrated that the eggs are rich in high-molecular-mass proteins and the peptides below 5 kDa. The lyophilized extract of the eggs had a protein content of 34.22% and was shown to have a strong toxicity towards mammals and insects. When applied at a concentration of 0.25 mg/mL, the extract could completely block the neuromuscular transmission in mouse isolated phrenic nerve-hemidiaphragm preparations within 12.0 ± 1.5 min. Using whole-cell patch-clamp technique, the egg extract was demonstrated to be able to inhibit the voltage-activated Na+, K+ and Ca2+ currents in rat DRG neurons. In addition, the extract displayed activities of multiple hydrolases. Finally, the molecular basis of the egg toxicity was discussed. The eggs of black widow spiders are rich in proteinous compounds particularly the high-molecular-mass proteins with different types of biological activity The neurotoxic and other active compounds in the eggs are believed to play important roles in the eggs' toxic actions.

  2. An automatic versatile system integrating solid-phase extraction with ultra-high performance liquid chromatography-tandem mass spectrometry using a dual-dilution strategy for direct analysis of auxins in plant extracts.

    Science.gov (United States)

    Zhong, Qisheng; Qiu, Xiongxiong; Lin, Caiyong; Shen, Lingling; Huo, Yin; Zhan, Song; Yao, Jinting; Huang, Taohong; Kawano, Shin-ichi; Hashi, Yuki; Xiao, Langtao; Zhou, Ting

    2014-09-12

    An automatic versatile system which integrated solid phase extraction (SPE) with ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) was developed. Diverse commercial SPE columns can be used under an ambient pressure in this online system realized by a dual-dilution strategy. The first dilution enabled the direct injection of complex samples with minimal pretreatment, and the second dilution realized direct introduction of large volume of strong eluent into the UHPLC column without causing peak broadening or distortion. In addition, a post-column compensation mode was also designed for the matrix-effects evaluation. The features of the online system were systematically investigated, including the dilution effect, the capture of desorption solution, the column-head stacking effect and the system recovery. Compared with the offline UHPLC system, this online system showed significant advantages such as larger injection volume, higher sensitivity, shorter analysis time and better repeatability. The feasibility of the system was demonstrated by the direct analysis of three auxins from different plant tissues, including leaves of Dracaena sanderiana, buds and petals of Bauhinia. Under the optimized conditions, the whole analysis procedure took only 7min. All the correlation coefficients were greater than 0.9987, the limits of detection and the limits of quantitation were in the range of 0.560-0.800ng/g and 1.80-2.60ng/g, respectively. The recoveries of the real samples ranged from 61.0 to 117%. Finally, the post-column compensation mode was applied and no matrix-effects were observed under the analysis conditions. The automatic versatile system was rapid, sensitive and reliable. We expect this system could be extended to other target analytes in complex samples utilizing diverse SPE columns. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Classifying visemes for automatic lipreading

    NARCIS (Netherlands)

    Visser, Michiel; Poel, Mannes; Nijholt, Antinus; Matousek, Vaclav; Mautner, Pavel; Ocelikovi, Jana; Sojka, Petr

    1999-01-01

    Automatic lipreading is automatic speech recognition that uses only visual information. The relevant data in a video signal is isolated and features are extracted from it. From a sequence of feature vectors, where every vector represents one video image, a sequence of higher level semantic elements

  4. Elucidation of the structure of organic solutions in solvent extraction by combining molecular dynamics and X-ray scattering

    International Nuclear Information System (INIS)

    Ferru, G.; Gomes Rodrigues, D.; Berthon, L.; Guilbaud, P.; Diat, O.; Bauduin, P.

    2014-01-01

    Knowledge of the supramolecular structure of the organic phase containing amphiphilic ligand molecules is mandatory for full comprehension of ionic separation during solvent extraction. Existing structural models are based on simple geometric aggregates, but no consensus exists on the interaction potentials. Herein, we show that molecular dynamics crossed with scattering techniques offers key insight into the complex fluid involving weak interactions without any long range ordering. Two systems containing mono- or diamide extractants in heptane and contacted with an aqueous phase were selected as examples to demonstrate the advantages of coupling the two approaches for furthering fundamental studies on solvent extraction. (authors)

  5. Development and optimisation of a novel three-way extraction technique based on a combination of Soxhlet extraction, membrane assisted solvent extraction and a molecularly imprinted polymer using sludge polycyclic aromatic hydrocarbons as model compounds.

    Science.gov (United States)

    Ncube, Somandla; Lekoto, Goitsemang; Cukrowska, Ewa; Chimuka, Luke

    2018-02-01

    A novel technique that integrates extraction and clean-up into a single step format is reported as part of the search for new sample preparation techniques in the analysis of persistent organic pollutants from complex samples. This was achieved by combining the extraction efficiency of the Soxhlet extractor, the selectivity of a size exclusion membrane and the specificity of a molecularly imprinted polymer for the extraction of polycyclic aromatic hydrocarbons from wastewater sludge followed by quantitation using gas chromatography with time-of-flight mass spectrometry. The approach is described as the Soxhlet extraction membrane-assisted solvent extraction molecularly imprinted polymer technique. This technique was optimised for various parameters such as extraction solvent, reflux time and membrane acceptor phase. The applicability of the developed technique was optimised using a wastewater sludge certified reference material and then tested on real wastewater sludge samples. The method detection limits ranged from 0.14 to 12.86 ng/g with relative standard deviation values for the extraction of the 16 US-EPA priority polycyclic aromatic hydrocarbons from wastewater sludge samples ranging from 0.78 to 18%. The extraction process was therefore reproducible and showed remarkable selectivity. The developed technique is a promising prospect that can be applied in the analysis of organic pollutants from complex solid samples. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Extraction and separation of mercury(II from succinate media with high molecular weight amine as an extractant

    Directory of Open Access Journals (Sweden)

    Chandrashekhar P. Mane

    2015-01-01

    Full Text Available The extraction of mercury(II from succinate solutions by 2-octylaminopyridine (2-OAP has been studied by metal distribution measurements. The optimum extraction conditions were determined from a critical study of effects of pH, sodium succinate concentration and 2-octylaminopyridine concentration. The probable composition of the species has been deduced from log–log plots. The extraction reaction proceeds with ion-pair formation and the stoichiometry of extracted species was found to be [(2OAPH+2 Hg(Succinate22−](org. The method has been used to separate mercury(II from commonly associated elements. The method has been further extended to separate and to estimate mercury in synthetic mixtures and real samples.

  7. Nanostructured conducting molecularly imprinted polymer for selective extraction of salicylate from urine and serum samples by electrochemically controlled solid-phase micro-extraction

    International Nuclear Information System (INIS)

    Ameli, Akram; Alizadeh, Naader

    2011-01-01

    Highlights: ► Overoxidized polypyrrole templated with salicylate has been utilized as conducting molecular imprinted polymer for EC-SPME. ► This first study reported on conducting molecular imprinted polymer was used to EC-SPME of salicylate. ► Proposed method, is particularly effective in sample clean-up and selective monitoring of salicylate in physiological samples. - Abstract: Overoxidized polypyrrole (OPPy) films templated with salicylate (SA) have been utilized as conducting molecular imprinted polymers (CMIPs) for potential-induced selective solid-phase micro-extraction processes. Various important fabrication factors for controlling the performance of the OPPy films have been investigated using fluorescence spectrometry. Several key parameters such as applied potential for uptake, release, pH of uptake and release solution were varied to achieve the optimum micro-extraction procedure. The film template with SA exhibited excellent selectivity over some interference. The calibration graphs were linear in the ranges of 5 × 10 −8 to 5 × 10 −4 and 1.2 × 10 −6 to 5 × 10 −4 mol mL −1 and the detection limit was 4 × 10 −8 mol L −1 . The OPPy film as the solid-phase micro-extraction absorbent has been applied for the selective clean-up and quantification of trace amounts of SA from physiological samples. The results of scanning electron microscopy (SEM) have confirmed the nano-structure morphologies of the films.

  8. Use of molecularly imprinted solid-phase extraction for the selective clean-up of clenbuterol from calf urine

    NARCIS (Netherlands)

    Berggren, C; Bayoudh, S; Sherrington, D; Ensing, K

    2000-01-01

    A feasibility study was performed in order to study the possibilities in using molecularly imprinted polymers (MIPs) as sorbent material in solid-phase extraction (MISPE) for clean-up of clenbuterol from urine. A binding study of clenbuterol in several solvents was performed on a clenbuterol

  9. [Determination of characteristic compound in manuka honey by automatic on-line solid phase extraction-liquid chromatography-high resolution mass spectrometry].

    Science.gov (United States)

    Shen, Chongyu; Guo, Siyan; Ding, Tao; Liu, Yun; Chen, Lei; Fei, Xiaoqing; Zhang, Rui; Wu, Bin; Shen, Weijian; Chen, Lei; Zhang, Feng; Feng, Feng; Deng, Xiaojun; Yi, Xionghai; Yang, Gongjun; Chen, Guoqiang

    2017-10-08

    A method for the determination of characteristic compound 3,5-dimethoxybenzoate-4-diglucoside (leptosperin) in manuka honey was developed by automatic on-line solid phase extraction-liquid chromatography-high resolution mass spectrometry (SPE-LC-HRMS). The samples were separated on a Dikma Diamonsil Plus C 18 column (150 mm×4.6 mm, 5 μm) using the mobile phases of 0.1% (v/v) formic acid aqueous solution and acetonitrile with gradient elution. The compound was detected with negative electrospray ionization (ESI - ) in Target-MS 2 mode. The results showed that the linear range was 0.5-100.0 mg/L, the correlation coefficient was 0.9993. The limit of detection (LOD, S/N ≥ 3) and limit of quantification (LOQ, S/N ≥ 10) of the method was 3 mg/kg and 10 mg/kg, respectively. The recoveries at the spiked levels of 50.0, 100.0, 200.0 mg/kg (10.0, 20.0, 50.0 mg/kg in black locust samples) were in the range of 82.0%-95.2% with the relative standard deviations ranging from 2.7% to 9.7% ( n =6). The proposed method was applied to 95 mature honey samples from hives in New Zealand including 12 different kinds and 50 commercial honey samples from four different countries. The method is fast, sensitive and accurate to provide technical support to solve the judgment of the manuka honey imported from New Zealand.

  10. PASBio: predicate-argument structures for event extraction in molecular biology

    Science.gov (United States)

    Wattarujeekrit, Tuangthong; Shah, Parantu K; Collier, Nigel

    2004-01-01

    Background The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sentence structure. A consensus in the IE community is emerging on the necessity for exploiting deeper knowledge structures such as through the relations between a verb and its arguments shown by predicate-argument structure (PAS). PAS is of interest as structures typically correspond to events of interest and their participating entities. For this to be realized within IE a key knowledge component is the definition of PAS frames. PAS frames for non-technical domains such as newswire are already being constructed in several projects such as PropBank, VerbNet, and FrameNet. Knowledge from PAS should enable more accurate applications in several areas where sentence understanding is required like machine translation and text summarization. In this article, we explore the need to adapt PAS for the MB domain and specify PAS frames to support IE, as well as outlining the major issues that require consideration in their construction. Results We introduce PASBio by extending a model based on PropBank to the MB domain. The hypothesis we explore is that PAS holds the key for understanding relationships describing the roles of genes and gene products in mediating their biological functions. We chose predicates describing gene expression, molecular interactions and signal transduction events with the aim of covering a number of research areas in MB. Analysis was performed on sentences containing a set of verbal predicates from MEDLINE and full text journals. Results confirm the necessity to analyze

  11. Online molecular characterisation of organic aerosols in an atmospheric chamber using extractive electrospray ionisation mass spectrometry

    Science.gov (United States)

    Gallimore, Peter J.; Giorio, Chiara; Mahon, Brendan M.; Kalberer, Markus

    2017-12-01

    The oxidation of biogenic volatile organic compounds (VOCs) represents a substantial source of secondary organic aerosol (SOA) in the atmosphere. In this study, we present online measurements of the molecular constituents formed in the gas and aerosol phases during α-pinene oxidation in the Cambridge Atmospheric Simulation Chamber (CASC). We focus on characterising the performance of extractive electrospray ionisation (EESI) mass spectrometry (MS) for particle analysis. A number of new aspects of EESI-MS performance are considered here. We show that relative quantification of organic analytes can be achieved in mixed organic-inorganic particles. A comprehensive assignment of mass spectra for α-pinene derived SOA in both positive and negative ion modes is obtained using an ultra-high-resolution mass spectrometer. We compare these online spectra to conventional offline ESI-MS spectra and find good agreement in terms of the compounds identified, without the need for complex sample work-up procedures. Under our experimental conditions, EESI-MS signals arise only from particle-phase analytes. High-time-resolution (7 min) EESI-MS spectra are compared with simulations from the near-explicit Master Chemical Mechanism (MCM) for a range of reaction conditions. We show that MS peak abundances scale with modelled concentrations for condensable products (pinonic acid, pinic acid, OH-pinonic acid). Relative quantification is achieved throughout SOA formation as the composition, size and mass (5-2400 µg m-3) of particles is evolving. This work provides a robust demonstration of the advantages of EESI-MS for chamber studies over offline ESI-MS (time resolution, relative quantification) and over hard online techniques (molecular information).

  12. Modification of Hewlett-Packard Chemstation (G1034C version C.02.00 and G1701AA version C.02.00 and C.03.00) data analysis program for addition of automatic extracted ion chromatographic groups.

    Science.gov (United States)

    Amick, G D

    1998-01-01

    A modification to data analysis macros to create "ion groups" and add a menu item to the data analysis menu bar is described. These "ion groups" consist of up to 10 ions for extracted ion chromatographs. The present manuscript describes modifications to yield a drop down menu in data analysis that contains user-defined names of groups (e.g., opiates, barbiturates, benzodiazepines) of ions that, when selected, will automatically perform extracted ion chromatographs with up to 10 ions in that group for the loaded datafile.

  13. Molecularly imprinted polymers based stir bar sorptive extraction for determination of cefaclor and cefalexin in environmental water.

    Science.gov (United States)

    Peng, Jun; Liu, Donghao; Shi, Tian; Tian, Huairu; Hui, Xuanhong; He, Hua

    2017-07-01

    Although stir bar sportive extraction was thought to be a highly efficiency and simple pretreatment approach, its wide application was limited by low selectivity, short service life, and relatively high cost. In order to improve the performance of the stir bar, molecular imprinted polymers and magnetic carbon nanotubes were combined in the present study. In addition, two monomers were utilized to intensify the selectivity of molecularly imprinted polymers. Fourier transform infrared spectroscopy, scanning electron microscopy, and selectivity experiments showed that the molecularly imprinted polymeric stir bar was successfully prepared. Then micro-extraction based on the obtained stir bar was coupled with HPLC for determination of trace cefaclor and cefalexin in environmental water. This approach had the advantages of stir bar sportive extraction, high selectivity of molecular imprinted polymers, and high sorption efficiency of carbon nanotubes. To utilize this pretreatment approach, pH, extraction time, stirring speed, elution solvent, and elution time were optimized. The LOD and LOQ of cefaclor were found to be 3.5 ng · mL -1 and 12.0 ng · mL -1 , respectively; the LOD and LOQ of cefalexin were found to be 3.0 ng · mL -1 and 10.0 ng · mL -1 , respectively. The recoveries of cefaclor and cefalexin were 86.5 ~ 98.6%. The within-run precision and between-run precision were acceptable (relative standard deviation bar did not decrease dramatically. This demonstrated that the molecularly imprinted polymeric stir bar based micro-extraction was a convenient, efficient, low-cost, and a specific method for enrichment of cefaclor and cefalexin in environmental samples.

  14. Novel DNA extraction assay for molecular identification of Aedes spp eggs.

    Science.gov (United States)

    Freitas, M T S; Gomes-Júnior, P P; Batista, M V A; Leal-Balbino, T C; Araujo, A L; Balbino, V Q

    2014-10-27

    Aedes aegypti and A. albopictus represent the two most important species of mosquitoes in relation to dengue virus transmission both in the Americas and Asia. However, the study of theses species generally requires the establishment of a colony for the larvae to hatch, or waiting for the adult development to perform its taxonomic classification, which is time consuming. Thus, the establishment of new methods aimed at obtaining DNA directly from the mosquito eggs is relevant. Accordingly, we compared a new approach based on Chelex(®) 100 resin with the standard STE method to extract DNA from the eggs of Aedes spp to molecularly identify these vectors. The Chelex(®) 100 resin approach was very efficient, as satisfactory amounts of DNA were obtained, making it possible to amplify and sequence a mitochondrial DNA barcode region widely used to identify species. The STE protocol yielded substantial amounts of DNA, but the 260/280 optical density ratio indicated a low quality, precluding amplification. This new method proved quite effective in obtaining DNA from even a single mosquito egg, and it can thus be applied in population genetic studies of various vector insects to enhance monitoring programs.

  15. Selective extraction of dimethoate from cucumber samples by use of molecularly imprinted microspheres.

    Science.gov (United States)

    Du, Jiao-Jiao; Gao, Rui-Xia; Yu, Hu; Li, Xiao-Jing; Mu, Hui

    2015-06-01

    Molecularly imprinted polymers for dimethoate recognition were synthesized by the precipitation polymerization technique using methyl methacrylate (MMA) as the functional monomer and ethylene glycol dimethacrylate (EGDMA) as the cross-linker. The morphology, adsorption and recognition properties were investigated by scanning electron microscopy (SEM), static adsorption test, and competitive adsorption test. To obtain the best selectivity and binding performance, the synthesis and adsorption conditions of MIPs were optimized through single factor experiments. Under the optimized conditions, the resultant polymers exhibited uniform size, satisfactory binding capacity and significant selectivity. Furthermore, the imprinted polymers were successfully applied as a specific solid-phase extractants combined with high performance liquid chromatography (HPLC) for determination of dimethoate residues in the cucumber samples. The average recoveries of three spiked samples ranged from 78.5% to 87.9% with the relative standard deviations (RSDs) less than 4.4% and the limit of detection (LOD) obtained for dimethoate as low as 2.3 μg/mL.

  16. Flow system for optical activity detection of vegetable extracts employing molecular exclusion continuous chromatographic detection

    Science.gov (United States)

    Fajer, V.; Rodríguez, C.; Naranjo, S.; Mesa, G.; Mora, W.; Arista, E.; Cepero, T.; Fernández, H.

    2006-02-01

    The combination of molecular exclusion chromatography and laser polarimetric detection has turned into a carbohydrate separation and quantification system for plant fluids of industrial value, making it possible the evaluation of the quality of sugarcane juices, agave juices and many other plant extracts. Some previous papers described a system where liquid chromatography separation and polarimetric detection using a LASERPOL 101M polarimeter with He-Ne light source allowed the collection and quantification of discrete samples for analytical purposes. In this paper, the authors are introducing a new improved system which accomplishes polarimetric measurements in a continuous flux. Chromatograms of several carbohydrates standard solutions were obtained as useful references to study juice quality of several sugarcane varieties under different physiological conditions. Results by either discrete or continuous flux systems were compared in order to test the validation of the new system. An application of the system to the diagnostics of scalded foliar is described. A computer program allowing the output of the chromatograms to a display on line and the possibility of digital storing, maxima detections, zone integration, and some other possibilities make this system very competitive and self-convincing.

  17. Simple Extraction and Molecular Weight Characterization of Fucoidan From Indonesian Sargassum SP.

    OpenAIRE

    Junaidi, Lukman

    2013-01-01

    Fucoidan is a complex polysaccharide compounds found in brown algae. Fucoidan exhibits various biological properties for disease prevention. There are various methods used to extract fucoidan from brown algae, such as using ethanol, acetone, HCl and microwave. This research aims to extract and characterize fucoidan from Sargassum sp. using simple methods with the variables on extracting solutions, temperature and time of extraction. Extraction solution used were water and HCl. Ttemperature us...

  18. Combining Pickering Emulsion Polymerization with Molecular Imprinting to Prepare Polymer Microspheres for Selective Solid-Phase Extraction of Malachite Green

    Directory of Open Access Journals (Sweden)

    Weixin Liang

    2017-08-01

    Full Text Available Malachite green (MG is currently posing a carcinogenic threat to the safety of human lives; therefore, it is highly desirable to develop an effective method for fast trace detection of MG. Herein, for the first time, this paper presents a systematic study on polymer microspheres, being prepared by combined Pickering emulsion polymerization and molecular imprinting, to detect and purify MG. The microspheres, molecularly imprinted with MG, show enhanced adsorption selectivity to MG, despite a somewhat lowered adsorption capacity, as compared to the counterpart without molecular imprinting. Structural features and adsorption performance of these microspheres are elucidated by different characterizations and kinetic and thermodynamic analyses. The surface of the molecularly imprinted polymer microspheres (M-PMs exhibits regular pores of uniform pore size distribution, endowing M-PMs with impressive adsorption selectivity to MG. In contrast, the microspheres without molecular imprinting show a larger average particle diameter and an uneven porous surface (with roughness and a large pore size, causing a lower adsorption selectivity to MG despite a higher adsorption capacity. Various adsorption conditions are investigated, such as pH and initial concentration of the solution with MG, for optimizing the adsorption performance of M-PMs in selectively tackling MG. The adsorption kinetics and thermodynamics are deeply discussed and analyzed, so as to provide a full picture of the adsorption behaviors of the polymer microspheres with and without the molecular imprinting. Significantly, M-PMs show promising solid-phase extraction column applications for recovering MG in a continuous extraction manner.

  19. EXTRACT

    DEFF Research Database (Denmark)

    Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra

    2016-01-01

    The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have...

  20. Molecularly Imprinted Polymers (MIP for Selective Solid Phase Extraction of Celecoxib in Urine Samples Followed by High Performance Liquid Chromatography

    Directory of Open Access Journals (Sweden)

    Saeedeh Ansari

    2017-09-01

    Full Text Available In this study, for the analysis of human urine samples, a novel method explained for the determination of celecoxib, a nonsteroidal anti-inflammatory drug (NSAID, using molecularly imprinted solid-phase extraction (MISPE coupled with high-performance liquid chromatography (HPLC. The synthesis of the MIP was performed by precipitation polymerization in methacrylic acid (MAA, ethylene glycol dimethacrylate (EGDMA, chloroform, 2,2′-azobisisobutyronitrile (AIBN and celecoxib as the functional monomer, cross-linker monomer, solvent, initiator and target drug, respectively. The celecoxib imprinted polymer was utilized as a specific sorbent for the solid phase extraction (SPE of celecoxib from samples. The molecularly imprinted polymer (MIP performance was compared with the synthesized non-molecularly imprinted polymer (NIP. Scanning electron microscopy (SEM, FT-IR spectroscopy, UV-VIS spectrophotometry and thermogravimetric analysis (TGA/DTG were used for characterizing the synthesized polymers. Moreover, the MISPE procedure parameters such as pH, eluent solvent flow rate, eluent volume and sorbent mass that probably influence the extraction process have been optimized to achieve the highest celecoxib extraction efficiency. The relative standard deviation (RSD %, recovery percent, limit of detection (LOD and limit of quantification (LOQ of this proposed method were 1.12%, 96%, 8 µg L-1 and 26.7 µg L-1, respectively. The proposed MISPE-HPLC-UV method can be used for the separation and enrichment of trace amounts of celecoxib in human urine and biological samples.

  1. Molecular characterization of inhibiting biochar water-extractable substances using electrospray ionization fourier transform ion cyclotron resonance mass spectrometry.

    Science.gov (United States)

    Smith, Cameron R; Sleighter, Rachel L; Hatcher, Patrick G; Lee, James W

    2013-01-01

    Biochar has gained significant interest worldwide for its potential use as both a carbon sequestration technique and soil amendment. Recently, research has shown that pinewood-derived biochar water extracts inhibited the growth of aquatic photosynthetic microorganisms, both prokaryotic and eukaryotic algae, while chicken litter- and peanut shell-derived biochar water extracts showed no growth inhibition. With the use of electrodialysis, the pinewood-derived biochar water extract is separated into 3 fractions (anode-isolated, center chamber retained, and cathode-isolated substances) all with varying toxic effects. Because of its ultrahigh resolution and mass precision, electrospray ionization (ESI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is utilized in this study to analyze biochar water extracts at a molecular level to enhance our understanding of the toxic nature of pinewood-derived biochar water extracts as compared to benign peanut shell-derived biochar water extracts. The molecular composition of pinewood-derived biochar water extracts shows unique carbohydrate ligneous components and sulfur containing condensed ligneous components that are both absent from the peanut shell water extracts and more prevalent in the anode-isolated substances. Using Kendrick mass defect analysis, we also determine that the most likely inhibitor species contain carboxyl and hydroxyl homologous series, both of which are characteristic functional groups hypothesized in our previous research for the inhibitor species. We have suggested that inhibition of aquatic photosynthetic microorganism growth is most likely due to degraded lignin-like species rich in oxygen containing functionalities. From the study conducted here, we show the potential of ultrahigh resolution FTICR-MS as a valuable analytical technique for determining whether certain biochars are safe and benign for use as carbon sequestration and soil amendment.

  2. Subcritical water extraction combined with molecular imprinting technology for sample preparation in the detection of triazine herbicides.

    Science.gov (United States)

    Zhao, Fengnian; Wang, Shanshan; She, Yongxin; Zhang, Chao; Zheng, Lufei; Jin, Maojun; Shao, Hua; Jin, Fen; Du, Xinwei; Wang, Jing

    2017-09-15

    A selective, environmentally friendly, and cost-effective sample extraction method based on a combination of subcritical water extraction (SWE) and molecularly imprinted solid-phase extraction (MISPE) was developed for the determination of eight triazine herbicides in soil samples by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In SWE, the highest extraction yields of triazine herbicides were obtained under 150°C for 15min using 20% ethanol as the organic modifier. Addition of MIP during SWE increased the extraction efficiency, and using MIP as a selective SPE sorbent improved the enrichment capability. Soil samples were treated with the optimized extraction MIP/SWE-MISPE method and analyzed by LC-MS/MS. The novel technique was then applied to soil samples for the determination of triazine herbicides, and better recoveries (78.9%-101%) were obtained compared with using SWE-MISPE (30%-67%). Moreover, this newly developed method displayed good linearity (R 2 >0.99) and precision (2.7-9.8%), and low enough detection limits (0.4-3.3μgkg -1 ). This combination of SWE and MIP technology is a simple, effective and promising method to selectively extract class-specific compounds in complex samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. The effects of Bombyx mori silk strain and extraction time on the molecular and biological characteristics of sericin.

    Science.gov (United States)

    Siritientong, Tippawan; Bonani, Walter; Motta, Antonella; Migliaresi, Claudio; Aramwit, Pornanong

    2016-01-01

    Sericin was extracted from three strains of Thai Bombyx mori silk cocoons (white shell Chul1/1, greenish shell Chul3/2, and yellow shell Chul4/2) by a high-pressure and high-temperature technique. The characteristics of sericin extracted from different fractions (15, 45, and 60 min extraction process) were compared. No differences in amino acid composition were observed among the three fractions. For all silk strains, sericin extracted from a 15-min process presented the highest molecular weight. The biological potential of the different sericin samples as a bioadditive for 3T3 fibroblast cells was assessed. When comparing sericin extracted from three silk strains, sericin fractions extracted from Chul4/2 improved cell proliferation, while sericin from Chul 1/1 activated Type I collagen production to the highest extent. This study allows the natural variability of sericin obtained from different sources and extraction conditions to be addressed and provides clues for the selection of sericin sources.

  4. Logic minimization and rule extraction for identification of functional sites in molecular sequences

    Directory of Open Access Journals (Sweden)

    Cruz-Cano Raul

    2012-08-01

    Full Text Available Abstract Background Logic minimization is the application of algebraic axioms to a binary dataset with the purpose of reducing the number of digital variables and/or rules needed to express it. Although logic minimization techniques have been applied to bioinformatics datasets before, they have not been used in classification and rule discovery problems. In this paper, we propose a method based on logic minimization to extract predictive rules for two bioinformatics problems involving the identification of functional sites in molecular sequences: transcription factor binding sites (TFBS in DNA and O-glycosylation sites in proteins. TFBS are important in various developmental processes and glycosylation is a posttranslational modification critical to protein functions. Methods In the present study, we first transformed the original biological dataset into a suitable binary form. Logic minimization was then applied to generate sets of simple rules to describe the transformed dataset. These rules were used to predict TFBS and O-glycosylation sites. The TFBS dataset is obtained from the TRANSFAC database, while the glycosylation dataset was compiled using information from OGLYCBASE and the Swiss-Prot Database. We performed the same predictions using two standard classification techniques, Artificial Neural Networks (ANN and Support Vector Machines (SVM, and used their sensitivities and positive predictive values as benchmarks for the performance of our proposed algorithm. SVM were also used to reduce the number of variables included in the logic minimization approach. Results For both TFBS and O-glycosylation sites, the prediction performance of the proposed logic minimization method was generally comparable and, in some cases, superior to the standard ANN and SVM classification methods with the advantage of providing intelligible rules to describe the datasets. In TFBS prediction, logic minimization produced a very small set of simple rules. In

  5. Flavonoids-Rich Orthosiphon stamineus Extract as New Candidate for Angiotensin I-Converting Enzyme Inhibition: A Molecular Docking Study.

    Science.gov (United States)

    Shafaei, Armaghan; Sultan Khan, Md Shamsuddin; F A Aisha, Abdalrahim; Abdul Majid, Amin Malik Shah; Hamdan, Mohammad Razak; Mordi, Mohd Nizam; Ismail, Zhari

    2016-11-09

    This study aims to evaluate the in vitro angiotensin-converting enzyme (ACE) inhibition activity of different extracts of Orthosiphon stamineus (OS) leaves and their main flavonoids, namely rosmarinic acid (RA), sinensetin (SIN), eupatorin (EUP) and 3'-hydroxy-5,6,7,4'-tetramethoxyflavone (TMF). Furthermore, to identify possible mechanisms of action based on structure-activity relationships and molecular docking. The in vitro ACE inhibition activity relied on determining hippuric acid (HA) formation from ACE-specific substrate (hippuryl-histidyl-leucine (HHL)) by the action of ACE enzyme. A High Performance Liquid Chromatography method combined with UV detection was developed and validated for measurement the concentration of produced HA. The chelation ability of OS extract and its reference compounds was evaluated by tetramethylmurexide reagent. Furthermore, molecular docking study was performed by LeadIT-FlexX : BioSolveIT's LeadIT program. OS ethanolic extract (OS-E) exhibited highest inhibition and lowest IC 50 value (45.77 ± 1.17 µg/mL) against ACE compared to the other extracts. Among the tested reference compounds, EUP with IC 50 15.35 ± 4.49 µg/mL had highest inhibition against ACE and binding ability with Zn (II) (56.03% ± 1.26%) compared to RA, TMF and SIN. Molecular docking studies also confirmed that flavonoids inhibit ACE via interaction with the zinc ion and this interaction is stabilized by other interactions with amino acids in the active site. In this study, we have demonstrated that changes in flavonoids active core affect their capacity to inhibit ACE. Moreover, we showed that ACE inhibition activity of flavonoids compounds is directly related to their ability to bind with zinc ion in the active site of ACE enzyme. It was also revealed that OS extract contained high amount of flavonoids other than RA, TMF, SIN and EUP. As such, application of OS extract is useful as inhibitors of ACE.

  6. High-capacity thermo-responsive magnetic molecularly imprinted polymers for selective extraction of curcuminoids.

    Science.gov (United States)

    You, Qingping; Zhang, Yuping; Zhang, Qingwen; Guo, Junfang; Huang, Weihua; Shi, Shuyun; Chen, Xiaoqin

    2014-08-08

    Thermo-responsive magnetic molecularly imprinted polymers (TMMIPs) for selective recognition of curcuminoids with high capacity and selectivity have firstly been developed. The resulting TMMIPs were characterized by TEM, FT-IR, TGA, VSM and UV, which indicated that TMMIPs showed thermo-responsiveness [lower critical solution temperature (LCST) at 33.71°C] and rapid magnetic separation (5s). The polymerization, adsorption and release conditions were optimized in detail to obtain the highest binding capacity, selectivity and release ratio. We found that the adopted thermo-responsive monomer [N-isopropylacrylamide (NIPAm)] could be considered not only as inert polymer backbone for thermo-responsiveness but also as functional co-monomers combination with basic monomer (4-VP) for more specific binding sites when ethanol was added in binding solution. The maximum adsorption capacity with highest selectivity of curcumin was 440.3μg/g (1.93 times that on MMIPs with no thermosensitivity) at 45°C (above LCST) in 20% (v/v) ethanol solution on shrunk TMMIPs, and the maximum release proportion was about 98% at 20°C (below LCST) in methanol-acetic acid (9/1, v/v) solution on swelled TMMIPs. The adsorption process between curcumin and TMMIPs followed Langumuir adsorption isotherm and pseudo-first-order reaction kinetics. The prepared TMMIPs also showed high reproducibility (RSD<6% for batch-to-batch evaluation) and stability (only 7% decrease after five cycles). Subsequently, the TMMIPs were successfully applied for selective extraction of curcuminoids from complex natural product, Curcuma longa. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Nanostructured conducting molecularly imprinted polymer for selective extraction of salicylate from urine and serum samples by electrochemically controlled solid-phase micro-extraction

    Energy Technology Data Exchange (ETDEWEB)

    Ameli, Akram [Department of Chemistry, Faculty of Science, Tarbiat Modares University, P.O. Box 14115-175, Tehran (Iran, Islamic Republic of); Alizadeh, Naader, E-mail: alizaden@modares.ac.ir [Department of Chemistry, Faculty of Science, Tarbiat Modares University, P.O. Box 14115-175, Tehran (Iran, Islamic Republic of)

    2011-11-30

    Highlights: Black-Right-Pointing-Pointer Overoxidized polypyrrole templated with salicylate has been utilized as conducting molecular imprinted polymer for EC-SPME. Black-Right-Pointing-Pointer This first study reported on conducting molecular imprinted polymer was used to EC-SPME of salicylate. Black-Right-Pointing-Pointer Proposed method, is particularly effective in sample clean-up and selective monitoring of salicylate in physiological samples. - Abstract: Overoxidized polypyrrole (OPPy) films templated with salicylate (SA) have been utilized as conducting molecular imprinted polymers (CMIPs) for potential-induced selective solid-phase micro-extraction processes. Various important fabrication factors for controlling the performance of the OPPy films have been investigated using fluorescence spectrometry. Several key parameters such as applied potential for uptake, release, pH of uptake and release solution were varied to achieve the optimum micro-extraction procedure. The film template with SA exhibited excellent selectivity over some interference. The calibration graphs were linear in the ranges of 5 Multiplication-Sign 10{sup -8} to 5 Multiplication-Sign 10{sup -4} and 1.2 Multiplication-Sign 10{sup -6} to 5 Multiplication-Sign 10{sup -4} mol mL{sup -1} and the detection limit was 4 Multiplication-Sign 10{sup -8} mol L{sup -1}. The OPPy film as the solid-phase micro-extraction absorbent has been applied for the selective clean-up and quantification of trace amounts of SA from physiological samples. The results of scanning electron microscopy (SEM) have confirmed the nano-structure morphologies of the films.

  8. Development of a selective molecularly imprinted polymer-based solid-phase extraction for indomethacin from water samples.

    Science.gov (United States)

    Yang, Tao; Li, Ya-Hui; Wei, Shuang; Li, Yuan; Deng, Anping

    2008-08-01

    A selective molecularly imprinted solid-phase extraction (MISPE) for indomethacin (IDM) from water samples was developed. Using IDM as template molecule, acrylamide (AM) or methacrylic acid (MAA) as functional monomer, ethylene dimethacrylate (EDMA) as crosslinker, and bulk or suspension polymerization as the synthetic method, three molecularly imprinted polymers (MIPs) were synthesized and characterized with a rebinding experiment. It was found that the MIP of AM-EDMA produced by bulk polymerization showed the highest binding capacity for IDM, and so it was chosen for subsequent experiments, such as those testing the selectivity and recognition binding sites. Scatchard analysis revealed that at least two kinds of binding sites formed in the MIP, with the dissociation constants of 7.8 micromol L(-1) and 127.2 micromol L(-1), respectively. Besides IDM, three structurally related compounds--acemetacin, oxaprozin and ibuprofen--were employed for selectivity tests. It was observed that the MIP exhibited the highest selective rebinding to IDM. Accordingly, the MIP was used as a solid-phase extraction sorbent for the extraction and enrichment of IDM in water samples. The extraction conditions of the MISPE column for IDM were optimized to be: chloroform or water as loading solvent, chloroform with 20% acetonitrile as washing solution, and methanol as eluting solvent. Water samples with or without spiking were extracted by the MISPE column and analyzed by HPLC. No detectable IDM was observed in tap water and the content of IDM in a river water sample was found to be 1.8 ng mL(-1). The extraction efficiencies of the MISPE column for IDM in spiked tap and river water were acceptable (87.2% and 83.5%, respectively), demonstrating the feasibility of the prepared MIP for IDM extraction.

  9. Molecular alterations of tropoelastin and proteoglycans induced by tobacco smoke extracts and ultraviolet A in cultured skin fibroblasts

    International Nuclear Information System (INIS)

    Yin, Lei; Morita, Akimichi; Tsuji, Takuo

    2002-01-01

    Functional integrity of normal skin is dependent on the balance between the biosynthesis and degradation of extracellular matrix, primarily composed of collagen, elastin and proteoglycans. In our previous studies, we found that tobacco smoke extracts decreased expressions of type I and III procollagen and induced matrix metalloproteinase-1 (MMP-1) and MMP-3 in the cultured skin fibroblasts. We here further investigated the effects of tobacco smoke extracts or ultraviolet A (UVA) treatments on the expression of tropoelastin (soluble elastin protein), and versican and decorin (proteoglycans) in cultured skin fibroblasts. The mRNA of tropoelastin increased by tobacco smoke extracts or UVA irradiation. Versican was markedly shown to decrease after these treatments by using western blotting and the mRNA of versican V0 also significantly decreased. UVA treatment did not show remarkable change in decorin protein, but resulted in marked decrease of decorin D1 mRNA. In contrast to UVA irradiation, the treatments of tobacco smoke extracts resulted in significant increase in decorin, while mRNA of decorin D1 decreased as compared to the control. MMP-7 increased after the treatment of tobacco smoke extracts or UVA. These results indicated that common molecular features might underlie the skin premature aging induced by tobacco smoke extracts and UVA, including abnormal regulation of extracellular matrix deposition through elevated MMPs, reduced collagen production, abnormal tropoelastin accumulation, and altered proteoglycans. (author)

  10. Rapid preparation of molecularly imprinted polymers by microwave-assisted emulsion polymerization for the extraction of florfenicol in milk.

    Science.gov (United States)

    Chen, Haiyan; Son, Sunil; Zhang, Fengshuang; Yan, Jin; Li, Yi; Ding, Hong; Ding, Lan

    2015-03-01

    In this study, we proposed a rapid and simple method for the preparation of molecularly imprinted polymers (MIPs) by emulsion polymerization. The polymerization process was accelerated by microwave heating, and the reaction time was greatly shortened. The obtained MIPs were spherical in shape and exhibited a uniform morphology. The MIPs with selectivity and high affinity to florfenicol were successfully applied as solid-phase extraction materials to extract and clean up the florfenicol in milk, followed by liquid chromatography-tandem mass spectrometry (LC-MS) analysis. The parameters affecting the performance of extraction and LC-MS analysis were evaluated. The detection limit of the method was 4.1ngmL(-1). The relative standard deviations of intra- and inter-day were in the range of 3.5-4.7% and 3.9-7.5%, respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Molecularly imprinted macroporous monoliths for solid-phase extraction: Effect of pore size and column length on recognition properties.

    Science.gov (United States)

    Vlakh, E G; Stepanova, M A; Korneeva, Yu M; Tennikova, T B

    2016-09-01

    The series of macroporous monolithic molecularly imprinted monoliths differed by pore size, column length (volume) and amount of template used for imprinting was synthesized using methacrylic acid and glycerol dimethacrylate as co-monomers and antibiotic ciprofloxacin as a template. The prepared monoliths were characterized regarding to their permeability, pore size, porosity, and resistance to the flow of a mobile phase. The surface morphology was also analyzed. The slight dependence of imprinting factor on flow rate, as well as its independence on pore size of macroporous molecularly imprinted monolithic media was observed. The column obtained at different conditions exhibited different affinity of ciprofloxacin to the imprinted sites that was characterized with Kdiss values in the range of 10(-5)-10(-4)M. The solid-phase extraction of ciprofloxacin from such biological liquids as human blood serum, human urine and cow milk serum was performed using the developed monolithic columns. In all cases, the extraction was found to be 95.0-98.6%. Additionally, the comparison of extraction of three fluoroqinolone analogues, e.g. ciprofloxacin, levofloxacin and moxifloxacin, from human blood plasma was carried out. Contrary to ciprofloxacin extracted with more than 95%, this parameter did not exceed 40% for its analogues. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Novel dummy molecularly imprinted polymers for matrix solid-phase dispersion extraction of eight fluoroquinolones from fish samples.

    Science.gov (United States)

    Sun, Xiaoli; Wang, Jincheng; Li, Yun; Yang, Jiajia; Jin, Jing; Shah, Syed Mazhar; Chen, Jiping

    2014-09-12

    A series of novel dummy molecularly imprinted polymers (DMIPs) were prepared as highly class-selective sorbents for fluoroquinolones. A non-poisonous dummy template, daidzein, was used for the first time to create specific molecular recognition sites for fluoroquinolones in the synthesized polymers. The influence of porogen polarity on dummy molecular imprinting effect was studied. The DMIP prepared using dimethylsulfoxide-acetonitrile (1:1.8, v/v) as porogen achieved the highest imprinting factors (IF) for fluoroquinolones over a range of IF 13.4-84.0. This DMIP was then used for selective extraction of eight fluoroquinolones (fleroxacin, ofloxacin, norfloxacin, pefloxacin, ciprofloxacin, lomefloxacin, enrofloxacin and gatifloxacin) from fish samples based on dummy molecularly imprinted matrix solid-phase dispersion (DMI-MSPD). The extracted fluoroquinolones were subsequently analyzed by high-performance liquid chromatography (HPLC) equipped with a fluorescence detector (FLD). The developed method had acceptable recoveries (64.4-102.7%) and precision (RSDs: 1.7-8.5%, n=5) for determination of fluoroquinolones in fish samples fortified at levels of 10 and 100ngg(-1). The limits of detection (LODs) for identification of eight fluoroquinolones ranged between 0.06 and 0.22ngg(-1). The results demonstrated great potential of the optimized method for sample preparation in routine analysis of trace fluoroquinolones in fish samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Molecular dynamics simulations of the interactions of medicinal plant extracts and drugs with lipid bilayer membranes

    DEFF Research Database (Denmark)

    Kopec, Wojciech; Telenius, Jelena; Khandelia, Himanshu

    2013-01-01

    Several small drugs and medicinal plant extracts, such as the Indian spice extract curcumin, have a wide range of useful pharmacological properties that cannot be ascribed to binding to a single protein target alone. The lipid bilayer membrane is thought to mediate the effects of many such molecu......Several small drugs and medicinal plant extracts, such as the Indian spice extract curcumin, have a wide range of useful pharmacological properties that cannot be ascribed to binding to a single protein target alone. The lipid bilayer membrane is thought to mediate the effects of many...

  14. An automatic image recognition approach

    Directory of Open Access Journals (Sweden)

    Tudor Barbu

    2007-07-01

    Full Text Available Our paper focuses on the graphical analysis domain. We propose an automatic image recognition technique. This approach consists of two main pattern recognition steps. First, it performs an image feature extraction operation on an input image set, using statistical dispersion features. Then, an unsupervised classification process is performed on the previously obtained graphical feature vectors. An automatic region-growing based clustering procedure is proposed and utilized in the classification stage.

  15. RNA Polymerase II Second Largest Subunit Molecular Identification of Boletus griseipurpureus Corner From Thailand and Antibacterial Activity of Basidiocarp Extracts.

    Science.gov (United States)

    Aung-Aud-Chariya, Amornrat; Bangrak, Phuwadol; Lumyong, Saisamorn; Phupong, Worrapong; Aggangan, Nelly Siababa; Kamlangdee, Niyom

    2015-03-01

    Boletus griseipurpureus Corner, an edible mushroom, is a putative ectomycorrhizal fungus. Currently, the taxonomic boundary of this mushroom is unclear and its bitter taste makes it interesting for evaluating its antibacterial properties. The purpose of this study was to identify the genetic variation of this mushroom and also to evaluate any antibacterial activities. Basidiocarps were collected from 2 north-eastern provinces, Roi Et and Ubon Ratchathani, and from 2 southern provinces, Songkhla and Surat Thani, in Thailand. Genomic DNA was extracted and molecular structure was examined using the RNA polymerase II (RPB2) analysis. Antibacterial activities of basidiocarp extracts were conducted with Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 29523 and methicillin-resistant Staphylococcus aureus (MRSA) 189 using the agar-well diffusion method. All the samples collected for this study constituted a monophyletic clade, which was closely related with the Boletus group of polypore fungi. For the antibacterial study, it was found that the crude methanol extract of basidiomes inhibited the growth of all bacteria in vitro more than the crude ethyl acetate extract. Basidomes collected from four locations in Thailand had low genetic variation and their extracts inhibited the growth of all tested bacteria. The health benefits of this edible species should be evaluated further.

  16. Molecular identification of polymers and anthropogenic particles extracted from oceanic water and fish stomach - A Raman micro-spectroscopy study.

    Science.gov (United States)

    Ghosal, Sutapa; Chen, Michael; Wagner, Jeff; Wang, Zhong-Min; Wall, Stephen

    2018-02-01

    Pacific Ocean trawl samples, stomach contents of laboratory-raised fish as well as fish from the subtropical gyres were analyzed by Raman micro-spectroscopy (RMS) to identify polymer residues and any detectable persistent organic pollutants (POP). The goal was to access specific molecular information at the individual particle level in order to identify polymer debris in the natural environment. The identification process was aided by a laboratory generated automated fluorescence removal algorithm. Pacific Ocean trawl samples of plastic debris associated with fish collection sites were analyzed to determine the types of polymers commonly present. Subsequently, stomach contents of fish from these locations were analyzed for ingested polymer debris. Extraction of polymer debris from fish stomach using KOH versus ultrapure water were evaluated to determine the optimal method of extraction. Pulsed ultrasonic extraction in ultrapure water was determined to be the method of choice for extraction with minimal chemical intrusion. The Pacific Ocean trawl samples yielded primarily polyethylene (PE) and polypropylene (PP) particles >1 mm, PE being the most prevalent type. Additional microplastic residues (1 mm - 10 μm) extracted by filtration, included a polystyrene (PS) particle in addition to PE and PP. Flame retardant, deca-BDE was tentatively identified on some of the PP trawl particles. Polymer residues were also extracted from the stomachs of Atlantic and Pacific Ocean fish. Two types of polymer related debris were identified in the Atlantic Ocean fish: (1) polymer fragments and (2) fragments with combined polymer and fatty acid signatures. In terms of polymer fragments, only PE and PP were detected in the fish stomachs from both locations. A variety of particles were extracted from oceanic fish as potential plastic pieces based on optical examination. However, subsequent RMS examination identified them as various non-plastic fragments, highlighting the importance

  17. Selective solid-phase extraction of cholesterol using molecularly imprinted polymers and its application in different biological samples.

    Science.gov (United States)

    Shi, Yun; Zhang, Jiang-Hua; Shi, Dan; Jiang, Ming; Zhu, Ye-Xiang; Mei, Su-Rong; Zhou, Yi-Kai; Dai, Kang; Lu, Bin

    2006-11-16

    Non-covalent molecularly imprinted polymers (MIPs) of cholesterol were prepared by UV initiated polymerization. A polymer that had the highest binding selectivity and capability was used as solid-phase extraction (SPE) sorbents for direct extraction of cholesterol from different biological samples (human serum, cow milk, yolk, shrimp, pork and beef). The extraction conditions of molecularly imprinted SPE (MISPE) were optimized and the optimum protocol was: conditioning MISPE cartridges with n-hexane, loading with n-hexane, washing with n-hexane and n-hexane:toluene=9:1, respectively, then eluting with chloroform:ethanol:acetic acid=3:1:1. Cholesterol MISPE selectively recognized, effectively trapped and pre-concentrated cholesterol over a concentration range of 10-80 microg/mL. Recoveries ranged from 80.6% to 92.7%, with R.S.D. lower than 9.8%. Under the optimal condition, MISPE recoveries of spiked human serum, yolk, cow milk, shrimp, pork and beef were 91.1%, 80.4%, 86.6%, 78.2%, 81.4% and 80.1%, respectively. Compared with C18 SPE, almost all of the matrix interferences were removed after MISPE, and better baselines and higher selectivity were achieved.

  18. Flavonoids-Rich Orthosiphon stamineus Extract as New Candidate for Angiotensin I-Converting Enzyme Inhibition: A Molecular Docking Study

    Directory of Open Access Journals (Sweden)

    Armaghan Shafaei

    2016-11-01

    Full Text Available This study aims to evaluate the in vitro angiotensin-converting enzyme (ACE inhibition activity of different extracts of Orthosiphon stamineus (OS leaves and their main flavonoids, namely rosmarinic acid (RA, sinensetin (SIN, eupatorin (EUP and 3′-hydroxy-5,6,7,4′-tetramethoxyflavone (TMF. Furthermore, to identify possible mechanisms of action based on structure–activity relationships and molecular docking. The in vitro ACE inhibition activity relied on determining hippuric acid (HA formation from ACE-specific substrate (hippuryl-histidyl-leucine (HHL by the action of ACE enzyme. A High Performance Liquid Chromatography method combined with UV detection was developed and validated for measurement the concentration of produced HA. The chelation ability of OS extract and its reference compounds was evaluated by tetramethylmurexide reagent. Furthermore, molecular docking study was performed by LeadIT-FlexX: BioSolveIT’s LeadIT program. OS ethanolic extract (OS-E exhibited highest inhibition and lowest IC50 value (45.77 ± 1.17 µg/mL against ACE compared to the other extracts. Among the tested reference compounds, EUP with IC50 15.35 ± 4.49 µg/mL had highest inhibition against ACE and binding ability with Zn (II (56.03% ± 1.26% compared to RA, TMF and SIN. Molecular docking studies also confirmed that flavonoids inhibit ACE via interaction with the zinc ion and this interaction is stabilized by other interactions with amino acids in the active site. In this study, we have demonstrated that changes in flavonoids active core affect their capacity to inhibit ACE. Moreover, we showed that ACE inhibition activity of flavonoids compounds is directly related to their ability to bind with zinc ion in the active site of ACE enzyme. It was also revealed that OS extract contained high amount of flavonoids other than RA, TMF, SIN and EUP. As such, application of OS extract is useful as inhibitors of ACE.

  19. Testing a low molecular mass fraction of a mushroom (Lentinus edodes) extract formulated as an oral rinse in a cohort of volunteers

    NARCIS (Netherlands)

    Signoretto, C.; Burlacchini, G.; Marchi, A.; Grillenzoni, M.; Cavalleri, G.; Ciric, L.; Lingström, P.; Pezzati, E.; Daglia, M.; Zaura, E.; Pratten, J.; Spratt, D.A.; Wilson, M.; Canepari, P.

    2011-01-01

    Although foods are considered enhancing factors for dental caries and periodontitis, laboratory researches indicate that several foods and beverages contain components endowed with antimicrobial and antiplaque activities. A low molecular mass (LMM) fraction of an aqueous mushroom extract has been

  20. Extraction chromatographic method of uranium(VI) with high molecular mass amine (ALIQUAT - 336)

    International Nuclear Information System (INIS)

    Roy, Uday Sankar; Dutta, Keshab Kumar

    1999-01-01

    A selective method has been developed for reversed phase extraction chromatographic studies of uranium(VI) with Aliquat - 336 (liquid anion exchanger) coated on silica gel as stationary phase. Quantitative extraction of uranium has been achieved in HCl - medium from 1.25(M)-4(M). The effect of different acids with various concentrations stripping agents, flow rate on extraction and elution have been investigated. The exchange capacity of the prepared exchanger has been determined. Uranium(VI) has been separated quantitatively from Th, Ce, Zr, Pb, Ga, Hg, Fe, La, Pr, Nd, Sm and Cr from a binary mixture by controlling the extraction and elution conditions. The separation of U(VI) from ternary and quarternary mixtures of various metal ions has also been achieved. (author)

  1. Online coupling of fully automatic in-syringe dispersive liquid-liquid microextraction with oxidative back-extraction to inductively coupled plasma spectrometry for sample clean-up in elemental analysis: A proof of concept.

    Science.gov (United States)

    Horstkotte, Burkhard; Fikarová, Kateřina; Cocovi-Solberg, David J; Sklenářová, Hana; Solich, Petr; Miró, Manuel

    2017-10-01

    A proof of concept of a novel automatic sample cleanup approach for metal assays in troublesome matrixes as a front-end sample pre-treatment to inductively coupled plasma optical emission spectroscopy - ICP-OES - is herein presented. Target metals, namely, copper, lead, and cadmium were complexed in-system quantitatively using ammonium pyrrolidine dithiocarbamate (APDC) and transferred into a minute volume of toluene as extractant employing lab-in-syringe magnetic stirring-assisted dispersive liquid-liquid microextraction (LIS-MSA-DLLME). After discharge of the sample, the analytes were back-extracted into nitric acid and injected on-line into ICP-OES. To promote and expedite this process in-syringe, advantage was taken from oxidative decomposition of the chelate by potassium iodate, reported in this article for the first time. Experimental conditions for LIS-MSA-DLLME were optimized by Box-Benkhen multivariate analysis using the geometric mean of analyte recoveries as the desirability function. Times of extraction and back-extraction of 300s and 100s, respectively, pH 5.5 at 30mmol/L acetate, 300µL of extraction solvent, and 600µmol/L of APDC were finally applied. Online interfacing to ICP-OES for back-extract analysis yielded average repeatabilities for Cd, Cu, and Pb of 2.9%, 3.5%, and 3.5% with limits of detections (3s) of 1.9, 1.4, and 5.6ng/mL, respectively. Oxidative back-extraction was proven reliable for the determination of metal species in coastal seawater, surrogate digestive fluids and soil leachates with recovery values for Cd, Cu, and Pb ranging from 90% to 118%, 68% to 104%, and 86% to 112%, respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Wild Roman chamomile extracts and phenolic compounds: enzymatic assays and molecular modelling studies with VEGFR-2 tyrosine kinase.

    Science.gov (United States)

    Guimarães, Rafaela; Calhelha, Ricardo C; Froufe, Hugo J C; Abreu, Rui M V; Carvalho, Ana Maria; Queiroz, Maria João R P; Ferreira, Isabel C F R

    2016-01-01

    Angiogenesis is a process by which new blood vessels are formed from the pre-existing vasculature, and it is a key process that leads to tumour development. Some studies have recognized phenolic compounds as chemopreventive agents; flavonoids, in particular, seem to suppress the growth of tumor cells modifying the cell cycle. Herein, the antiangiogenic activity of Roman chamomile (Chamaemelum nobile L.) extracts (methanolic extract and infusion) and the main phenolic compounds present (apigenin, apigenin-7-O-glucoside, caffeic acid, chlorogenic acid, luteolin, and luteolin-7-O-glucoside) was evaluated through enzymatic assays using the tyrosine kinase intracellular domain of the Vascular Endothelium Growth Factor Receptor-2 (VEGFR-2), which is a transmembrane receptor expressed fundamentally in endothelial cells involved in angiogenesis, and molecular modelling studies. The methanolic extract showed a lower IC50 value (concentration that provided 50% of VEGFR-2 inhibition) than the infusion, 269 and 301 μg mL(-1), respectively. Regarding phenolic compounds, luteolin and apigenin showed the highest capacity to inhibit the phosphorylation of VEGFR-2, leading us to believe that these compounds are involved in the activity revealed by the methanolic extract.

  3. Magnetic molecularly imprinted polymer for the selective extraction of hesperetin from the dried pericarp of Citrus reticulata Blanco.

    Science.gov (United States)

    Wang, Dan-Dan; Gao, Die; Xu, Wan-Jun; Li, Fan; Yin, Man-Ni; Fu, Qi-Feng; Xia, Zhi-Ning

    2018-07-01

    In present study, novel magnetic molecularly imprinted polymers for hesperetin were successfully prepared by surface molecular imprinting method using functionalized Fe 3 O 4 particles as the magnetic cores. Hesperetin as the template, N-Isopropylacrylamide as the functional monomer, ethylene glycol dimethyl acrylate as the crosslinker, 2,2-azobisisobutyonnitrile as initiator and acetonitrile-methanol (3:1, v/v) as the porogen were applied in the preparation process. Fourier transform infrared spectroscopy, scanning electron microscopy, transmission electron microscope, x-ray diffraction and vibrating sample magnetometry were applied to characterize the magnetic molecularly imprinted polymers. The adsorption experiments indicated that the magnetic molecularly imprinted polymers performed high selective recognition property to hesperetin. The selectivity experiment indicated that the adsorption capacity and selectivity of polymers to hesperetin was higher than that of luteolin, baicalein and ombuin. Furthermore, the magnetic molecularly imprinted polymers were employed as adsorbents for extraction and enrichment of hesperetin from the dried pericarp of Citrus reticulata Blanco. The recoveries of hesperetin in the dried pericarp of Citrus reticulata Blanco ranged from 90.5% to 96.9%. The linear range of 0.15-110.72 µg/mL was obtained with correlation coefficient of greater than 0.9991. The limit of detection and quantification of the proposed method was 0.06 µg/mL and 0.15 µg/mL, respectively. Based on three replicate measurements, intra-day RSD was 0.71% and inter-day RSD was 2.31%. These results demonstrated that the prepared magnetic molecularly imprinted polymers were proven to be an effective material for the selective adsorption and enrichment of hesperetin from natural medicines, fruits and et al. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Extraction and isotopic analysis of medium molecular weight hydrocarbons from Murchison using supercritical carbon dioxide

    Science.gov (United States)

    Gilmour, Iain; Pillinger, Colin

    1993-03-01

    The large variety of organic compounds present in carbonaceous chondrites poses particular problems in their analysis not the least of which is terrestrial contamination. Conventional analytical approaches employ simple chromatographic techniques to fractionate the extractable compounds into broad classes of similar chemical structure. However, the use of organic solvents and their subsequent removal by evaporation results in the depletion or loss of semi-volatile compounds as well as requiring considerable preparative work to assure solvent purity. Supercritical fluids have been shown to provide a powerful alternative to conventional liquid organic solvents used for analytical extractions. A sample of Murchison from the Field Museum was analyzed. Two interior fragments were used; the first (2.85 g) was crushed in an agate pestel and mortar to a grain size of ca. 50-100 micron, the second (1.80 g) was broken into chips 3-8 mm in size. Each sample was loaded into a stainless steel bomb and placed in the extraction chamber of an Isco supercritical fluid extractor maintained at 35 C. High purity (99.9995 percent) carbon dioxide was used and was pressurized using an Isco syringe pump. The samples were extracted dynamically by flowing CO2 under pressure through the bomb and venting via a 50 micron fused filica capillary into 5 mls of hexane used as a collection solvent. The hexane was maintained at a temperature of 0.5 C. A series of extractions were done on each sample using CO2 of increasing density. The principal components extracted in each fraction are summarized.

  5. Mass spectrometric identification of molecular species of phosphatidylcholine and lysophosphatidycholine extracted from shark liver

    NARCIS (Netherlands)

    Chen, S.; Li, K.W.

    2007-01-01

    The profile and structural characterization of molecular species of phosphatidylcholine (PC) and lysophosphatidylcholine (LysoPC) from shark liver using liquid chromatographic/electrospray ionization mass spectrometry (LC-ESI/MS) and tandem mass spectrometry (MS/MS) are described for the first time

  6. Structuring and extracting knowledge for the support of hypothesis generation in molecular biology

    NARCIS (Netherlands)

    Roos, M.; Marshall, M.S.; Gibson, A.P.; Schuemie, M.; Meij, E.; Katrenko, S.; van Hage, W.R.; Krommydas, K.; Adriaans, P.W.

    2009-01-01

    Background: Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. The requirement of automated support is exemplified by the difficulty of considering all relevant facts that are

  7. One-step column chromatographic extraction with gradient elution followed by automatic separation of volatiles, flavonoids and polysaccharides from Citrus grandis.

    Science.gov (United States)

    Han, Han-Bing; Li, Hui; Hao, Rui-Lin; Chen, Ya-Fei; Ni, He; Li, Hai-Hang

    2014-02-15

    Citrus grandis Tomentosa is widely used in traditional Chinese medicine and health foods. Its functional components include volatiles, flavonoids and polysaccharides which cannot be effectively extracted through traditional methods. A column chromatographic extraction with gradient elution was developed for one-step extraction of all bioactive substances from C. grandis. Dried material was loaded into a column with petroleum ether: ethanol (8:2, PE) and sequentially eluted with 2-fold PE, 3-fold ethanol: water (6:4) and 8-fold water. The elutes was separated into an ether fraction containing volatiles and an ethanol-water fraction containing flavonoids and polysaccharides. The later was separated into flavonoids and polysaccharides by 80% ethanol precipitation of polysaccharides. Through this procedure, volatiles, flavonoids and polysaccharides in C. grandis were simultaneously extracted at 98% extraction rates and simply separated at higher than 95% recovery rates. The method provides a simple and high-efficient extraction and separation of wide range bioactive substances. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Chemical composition and molecular structure of polysaccharide-protein biopolymer from Durio zibethinus seed: extraction and purification process

    Directory of Open Access Journals (Sweden)

    Amid Bahareh

    2012-10-01

    Full Text Available Abstract Background The biological functions of natural biopolymers from plant sources depend on their chemical composition and molecular structure. In addition, the extraction and further processing conditions significantly influence the chemical and molecular structure of the plant biopolymer. The main objective of the present study was to characterize the chemical and molecular structure of a natural biopolymer from Durio zibethinus seed. A size-exclusion chromatography coupled to multi angle laser light-scattering (SEC-MALS was applied to analyze the molecular weight (Mw, number average molecular weight (Mn, and polydispersity index (Mw/Mn. Results The most abundant monosaccharide in the carbohydrate composition of durian seed gum were galactose (48.6-59.9%, glucose (37.1-45.1%, arabinose (0.58-3.41%, and xylose (0.3-3.21%. The predominant fatty acid of the lipid fraction from the durian seed gum were palmitic acid (C16:0, palmitoleic acid (C16:1, stearic acid (C18:0, oleic acid (C18:1, linoleic acid (C18:2, and linolenic acid (C18:2. The most abundant amino acids of durian seed gum were: leucine (30.9-37.3%, lysine (6.04-8.36%, aspartic acid (6.10-7.19%, glycine (6.07-7.42%, alanine (5.24-6.14%, glutamic acid (5.57-7.09%, valine (4.5-5.50%, proline (3.87-4.81%, serine (4.39-5.18%, threonine (3.44-6.50%, isoleucine (3.30-4.07%, and phenylalanine (3.11-9.04%. Conclusion The presence of essential amino acids in the chemical structure of durian seed gum reinforces its nutritional value.

  9. Automatic Evaluation Of Interferograms

    Science.gov (United States)

    Becker, Friedhelm; Meier, Gerd E. A.; Wegner, Horst

    1983-03-01

    A system for the automatic evaluation of interference patterns has been developed. After digitizing the interferograms from classical and holografic interferometers with a television digitizer and performing different picture enhancement operations the fringe loci are extracted by use of a floating-threshold method. The fringes are numbered using a special scheme after the removal of any fringe disconnections which might appear if there was insufficient contrast in the interferograms. The reconstruction of the object function from the numbered fringe field is achieved by a local polynomial least-squares approximation. Applications are given, demonstrating the evaluation of interferograms of supersonic flow fields and the analysis of holografic interferograms of car-tyres.

  10. Solid phase extraction using molecular imprinting polymers (MISPE for the determination of estrogens in surface water by HPLC

    Directory of Open Access Journals (Sweden)

    Viviane do Nascimento Bianchi

    2017-05-01

    Full Text Available Estrogens are emerging pollutants and traditional sewage treatments unable to remove them. They are harmful to human health and to the environment. It is therefore important to evaluate the presence and concentration of estrogens in water bodies and environmental matrices. This work presents the development and application of a methodology for the determination of E1, E3, EE2 and E2 in surface waters using solid phase extraction with molecular imprinting polymers (MISPE followed by identification and quantification by HPLC-DAD. Acetonitrile and water deionized acidified with phosphoric acid pH 3 (1:1, v/v, a flow rate of 1.0 ml min-1, at 40°C and an injection volume of 5 µL. The method was validated according to the protocol ICH Q2R. Reproducibility and repeatability tests resulted in a smaller variation coefficient of 10%; the calibration curves in the concentration ranged from 1 to 20 mg L-1, with return linearity values greater than 0.99. The limits of detection and quantification were less than 1 mg L-1 and the method was satisfactory for specificity and selectivity tests using caffeine, which is often found in water bodies receiving effluent, and DES, an estrogen used in the treatment of prostate cancer. Selected samples underwent clean-up and pre-concentration treatments using solid phase extraction with commercial phase (C18 and molecularly imprinted polymers (MISPE. The analysis of MISPE extracts indicate that it is possible to obtain results with greater sensitivity and precision for analyses of complex environmental matrices, demonstrating that the developed method can be applied in complex environmental matrices.

  11. Fast and selective extraction of chloramphenicol from soil by matrix solid-phase dispersion using molecularly imprinted polymer as dispersant.

    Science.gov (United States)

    Wang, Ting; Tong, Jia; Sun, Mingli; Chen, Ligang

    2011-08-01

    The molecularly imprinted polymer (MIP) was synthesized and used as dispersant of matrix solid-phase dispersion (MSPD) for the extraction of chloramphenicol (CAP) in soil samples. The satisfactory recovery of CAP was obtained by the optimized extraction conditions: 1:2 as the ratio of sample to MIPs; 5 min as the dispersion time; 30% aqueous methanol as washing solvent and methanol as elution solvent. The CAP extracted from soil was determined by LC-MS/MS. The slight ion suppression phenomenon was observed for the CAP when the sample was cleaned up by MSPD with MIP as dispersant, when compared with C18 as MSPD dispersant, which caused significant ion suppression. LOD of CAP is 4.1 ng/g. RSDs of intra- and inter-day tests ranging from 3.1 to 6.2% and from 3.9 to 8.3% are obtained. At all three fortified levels (20, 100 and 500 ng/g), recoveries of CAP are in the range of 86.9-92.6%. The effect of ageing time of spiked soil sample on the CAP recovery was examined. The CAP recovery decreased from 91.0 to 36.9% when the ageing time changed from 1 day to 4 wk. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Fast HPLC-MS/MS Method for Determining Penicillin Antibiotics in Infant Formulas Using Molecularly Imprinted Solid-Phase Extraction

    Directory of Open Access Journals (Sweden)

    Mónica Díaz-Bao

    2015-01-01

    Full Text Available The dairy cattle may suffer from different infections relatively often, but the inflammation of the mammary gland is very important to the farmer. These infections are frequently treated with penicillin antimicrobial drugs. However, their use may result in the presence of residues in animal products, such as milk powder and/or infant formulas, and it represents a potential risk for consumers. To monitor this, the EU has defined safe maximum residue limits (MRLs through Commission Regulation (EU number 37/2010. Although LC-MS is a trustful option for confirmation and quantification of antibiotics, the analysis of real samples with complex matrices frequently implies previous clean-up steps. In this work, precipitation polymerization has been used and different molecularly imprinted polymer (MIP sorbents were tested and optimized for the fast and simultaneous solid-phase extraction (MISPE of eight common penicillins (ampicillin, amoxicillin, oxacillin, penicillin G, penicillin V, cloxacillin, dicloxacillin, and nafcillin. The extracts were analyzed using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS and the applicability of these polymers as sorbents for the extraction of penicillins at MRL levels in milk powder (infant formulas was proved. The limits of detection and quantification were below the legal tolerances, except for LOQ for oxacillin and cloxacillin.

  13. Determination of 14 aminoglycosides by LC-MS/MS using molecularly imprinted polymer solid phase extraction for clean-up.

    Science.gov (United States)

    Savoy, Marie-Claude; Woo, Pei Mun; Ulrich, Pauline; Tarres, Adrienne; Mottier, Pascal; Desmarchelier, Aurélien

    2018-04-01

    An LC-MS/MS method for screening 14 aminoglycosides in foodstuffs of animal origin is presented. Its scope includes raw materials and processed ingredients but also finished products composed of milk, meat, fish, egg or fat. Aminoglycosides are extracted in an acidic aqueous solution, which is first recovered after centrifugation, then diluted with a basic buffer and finally purified by molecularly imprinted polymer-solid phase extraction (MIP-SPE). Analytes are detected within 8 min by ion-pair reversed phase LC-MS/MS. Due to the large range of foodstuffs involved, the variability of matrix effects led to significant MS signal variations. This was circumvented by systematically extracting each sample twice, i.e. 'unspiked' and 'spiked' at the screening target concentration of 50 µg kg -1 . The method was validated according to the European Community Reference Laboratories Residues Guidelines giving false-negative and false-positive rates ≤3% for all compounds. Ruggedness of the method was further demonstrated in quality control operations by a second laboratory. The 14 aminoglycosides in water-based standard solutions were stable for up to 6 months when stored at either -80°C, -20°C or at 4°C storage temperatures.

  14. Effective synthesis of magnetic porous molecularly imprinted polymers for efficient and selective extraction of cinnamic acid from apple juices.

    Science.gov (United States)

    Shi, Shuyun; Fan, Dengxin; Xiang, Haiyan; Li, Huan

    2017-12-15

    An effective strategy was proposed to prepare novel magnetic porous molecularly imprinted polymers (MPMIPs) for highly selective extraction of cinnamic acid (CMA) from complex matrices. Characterization and various parameters affecting adsorption and desorption behaviors were investigated. Results revealed adsorption behavior between CMA and MPMIPs followed Freundlich equation adsorption isotherm with a maximum adsorption capacity at 4.35mg/g and pseudo-second-order reaction kinetics with equilibrium time at 60min. Subsequently, MPMIPs were successfully used to selectively extract CMA from apple juice with a relatively satisfactory recovery (92.7-101.4%). Coupling with high-performance liquid chromatography and ultraviolet detection (HPLC-UV), the limit of detection (LOD) for CMA was 0.006µg/mL, and the linear range (0.02-10μg/mL) was wide with correlation coefficient at 0.9995. Finally, the contents of CMA in two kinds of apple juices were determined as 0.132 and 0.120μg/mL. Results indicated the superiority of MPMIPs in the selective extraction field. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. The role of association of ions in ionic liquid/molecular solvent mixtures on metal extraction.

    Science.gov (United States)

    Andanson, J-M; Papaiconomou, N; Cable, P-A; Traïkia, M; Billard, I; Husson, P

    2017-11-01

    Several mixtures of butyl acetate (BA) and an ionic liquid (1-methyl-3-octylpyrrolidinium bis(trifluoromethylsulfonyl)imide, [C 1 C 8 Pyrro][NTf 2 ], 1-octyl-pyridinium bis(trifluoromethylsulfonyl)imide, [C 8 Pyr][NTf 2 ], 1-butyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide, [C 1 C 4 Im][NTf 2 ] or 1-octyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide, [C 1 C 8 Im][NTf 2 ]) have been characterized by measuring density, viscosity and conductivity, from pure BA to pure ILs at 298.15 K. The ionicity of these mixtures has been determined on the basis of electrical conductivity and NMR spectroscopy. IR spectra of these mixtures were used to examine the interactions between ions. In parallel, Pt(iv) was extracted from the acidic aqueous phase towards mixtures of BA and [C 1 C 8 Im][NTf 2 ] over the entire composition range. A drastic modification in the distribution coefficient of Pt(iv) was observed at ca x AB = 0.8. A drop was also observed in the ionicity of the extracting phase (IL + BA) at a similar composition. The variation of the distribution coefficient is ascribed to changes in the interactions in the mixtures, which in turn could induce changes in the extraction mechanism.

  16. Synthetic approaches to parabens molecularly imprinted polymers and their applications to the solid-phase extraction of river water samples.

    Science.gov (United States)

    Beltran, A; Marcé, R M; Cormack, P A G; Borrull, F

    2010-09-10

    In this paper we describe the synthesis, characterisation and use of two distinct molecularly imprinted polymers (MIPs) prepared using esters of p-hydroxybenzoic acid (parabens) as templates: one MIP was synthesised by precipitation polymerisation using a semi-covalent molecularly imprinting strategy with methyl paraben as the template/target (MIP 1); the second MIP was prepared in monolithic form through a conventional non-covalent molecular imprinting strategy, with butyl paraben as the template (MIP 2). MIP 1 recognized methyl paraben, showed cross-selectivity for other parabens analytes used in the study and higher affinity towards these compounds than did a non-imprinted control polymer. Similarly, MIP 2 demonstrated higher affinity towards paraben analytes than a non-imprinted control polymer. For the analysis of environmental water samples, a solid-phase extraction (SPE) protocol was developed using MIP 2 as sorbent, and results were compared to a SPE using a commercial sorbent (Oasis HLB). With MIP 2 as sorbent and butyl paraben as target, when percolating 500 mL of river water spiked at 1 μg L(-1) through the SPE cartridge, and using 1 mL of isopropanol as cleaning solvent, a higher recovery of butyl 4-hydroxybenzoate (butyl paraben) and a cleaner chromatogram where achievable when using the MIP compared to the commercial sorbent. Copyright © 2010 Elsevier B.V. All rights reserved.

  17. ADSORPTION PROCESS OF MOLECULARLY IMPRINTED SILICA FOR EXTRACTION OF LACTOSE FROM MILK

    Directory of Open Access Journals (Sweden)

    A. L. Balieiro

    Full Text Available Abstract In Brazil, about 25-30% of the population has some degree of intolerance to lactose, a disorder associated with the inability of the body to digest lactose due to a disability or absence of the enzyme lactase. The goal of this study was to evaluate the performance of adsorption of lactose from fresh milk using a fixed bed column of molecularly imprinted polymer (MIP. The polymeric material was characterized using Scanning electron microscopy (SEM analysis, thermal analysis (e.g., differential scanning calorimetric (DSC and thermogravimetric analysis (TGA, Fourier Transform Infrared Spectroscopy (FTIR, and the method of Braunauer, Emmet and Teller (BET. The adsorption column dynamics and performance were studied by the breakthrough curves using a 24-1 fractional factorial design. The chemical and structural characterization of the pure matrix and imprinted polymers confirmed the molecularly imprinted polymer (MIP imprinted with lactose. The highest capacity was 62.21 mgg-1, obtained at 307.1 K and a flow rate of 12.5 mL.min-1, with central point conditions, 320.1 K and 9 mL.min-1, with an average value of 50.9 mg.g-1. The results indicate that the molecularly imprinted polymer is efficient.

  18. Molecularly imprinted coated graphene oxide solid-phase extraction monolithic capillary column for selective extraction and sensitive determination of phloxine B in coffee bean

    Energy Technology Data Exchange (ETDEWEB)

    Zhai, Haiyun, E-mail: zhaihaiyun@126.com [College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006 (China); Su, Zihao [College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006 (China); Chen, Zuanguang, E-mail: chenzg@mail.sysu.edu.cn [School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou 510006 (China); Liu, Zhenping; Yuan, Kaisong; Huang, Lu [College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006 (China)

    2015-03-20

    Highlights: • A new GO-MISPE monolithic capillary column was prepared. • The column showed ability of impurities removal and excellent selectivity. • Phloxine B existed in real sample was enriched more than 90 times. • The GO-MISPE column presented good recovery and high stability. • The method was prospered to analyze phloxine B and LOD achieved 0.3 ng g{sup −1}. - Abstract: A method was developed to sensitively determine phloxine B in coffee bean by molecularly imprinted polymers (MIPs) coated graphene oxide (GO) solid-phase extraction (GO-MISPE) coupled with high-performance liquid chromatography and laser-induced fluorescence detection (HPLC–LIF). The GO-MISPE capillary monolithic column was prepared by water-bath in situ polymerization, using GO as supporting material, phloxine B, methacrylic acid (MAA), and ethylene dimethacrylate (EDMA) as template, functional monomer, and cross-linker, respectively. The properties of the homemade GO-MISPE capillary monolithic column, including capacity and specificity, were investigated under optimized conditions. The GO-MIPs were characterized by scanning electron microscopy (SEM) and Fourier transform-infrared spectroscopy (FT-IR). The mean recoveries of phloxine B in coffee bean ranged from 89.5% to 91.4% and the intra-day and inter-day relative standard deviation (RSD) values all ranged from 3.6% to 4.7%. Good linearity was obtained over 0.001–2.0 μg mL{sup −1} (r = 0.9995) with the detection limit (S/N = 3) of 0.075 ng mL{sup −1}. Under the selected conditions, enrichment factors of over 90-fold were obtained and extraction on the monolithic column effectively cleaned up the coffee bean matrix. The results demonstrated that the proposed GO-MISPE HPLC–LIF method can be applied to sensitively determine phloxine B in coffee bean.

  19. Molecularly imprinted coated graphene oxide solid-phase extraction monolithic capillary column for selective extraction and sensitive determination of phloxine B in coffee bean

    International Nuclear Information System (INIS)

    Zhai, Haiyun; Su, Zihao; Chen, Zuanguang; Liu, Zhenping; Yuan, Kaisong; Huang, Lu

    2015-01-01

    Highlights: • A new GO-MISPE monolithic capillary column was prepared. • The column showed ability of impurities removal and excellent selectivity. • Phloxine B existed in real sample was enriched more than 90 times. • The GO-MISPE column presented good recovery and high stability. • The method was prospered to analyze phloxine B and LOD achieved 0.3 ng g −1 . - Abstract: A method was developed to sensitively determine phloxine B in coffee bean by molecularly imprinted polymers (MIPs) coated graphene oxide (GO) solid-phase extraction (GO-MISPE) coupled with high-performance liquid chromatography and laser-induced fluorescence detection (HPLC–LIF). The GO-MISPE capillary monolithic column was prepared by water-bath in situ polymerization, using GO as supporting material, phloxine B, methacrylic acid (MAA), and ethylene dimethacrylate (EDMA) as template, functional monomer, and cross-linker, respectively. The properties of the homemade GO-MISPE capillary monolithic column, including capacity and specificity, were investigated under optimized conditions. The GO-MIPs were characterized by scanning electron microscopy (SEM) and Fourier transform-infrared spectroscopy (FT-IR). The mean recoveries of phloxine B in coffee bean ranged from 89.5% to 91.4% and the intra-day and inter-day relative standard deviation (RSD) values all ranged from 3.6% to 4.7%. Good linearity was obtained over 0.001–2.0 μg mL −1 (r = 0.9995) with the detection limit (S/N = 3) of 0.075 ng mL −1 . Under the selected conditions, enrichment factors of over 90-fold were obtained and extraction on the monolithic column effectively cleaned up the coffee bean matrix. The results demonstrated that the proposed GO-MISPE HPLC–LIF method can be applied to sensitively determine phloxine B in coffee bean

  20. Synthesis and application of molecularly imprinted polymers for the selective extraction of organophosphorus pesticides from vegetable oils.

    Science.gov (United States)

    Boulanouar, Sara; Combès, Audrey; Mezzache, Sakina; Pichon, Valérie

    2017-09-01

    The increasing use of pesticides in agriculture causes environmental issues and possible serious health risks to humans and animals. Their determination at trace concentrations in vegetable oils constitutes a significant analytical challenge. Therefore, their analysis often requires both an extraction and a purification step prior to separation with liquid chromatography (LC) and mass spectrometry (MS) detection. This work aimed at developing sorbents that are able to selectively extract from vegetable oil samples several organophosphorus (OPs) pesticides presenting a wide range of physico-chemical properties. Therefore, different conditions were screened to prepare molecularly imprinted polymers (MIPs) by a non-covalent approach. The selectivity of the resulting polymers was evaluated by studying the OPs retention in pure media on both MIPs and non-imprinted polymers (NIP) used as control. The most promising MIP sorbent was obtained using monocrotophos (MCP) as the template, methacrylic acid (MAA) as the monomer and ethylene glycol dimethacrylate (EGDMA) as the cross-linker with a molar ratio of 1/4/20 respectively. The repeatability of the extraction procedure and of the synthesis procedure was demonstrated in pure media. The capacity of this MIP was 1mg/g for malathion. This MIP was also able to selectively extract three OPs from almond oil by applying the optimized SPE procedure. Recoveries were between 73 and 99% with SD values between 4 and 6% in this oil sample. The calculated LOQs (between 0.3 and 2μg/kg) in almond seeds with a SD between 0.1 and 0.4μg/kg were lower than the Maximum Residue Levels (MRLs) established for the corresponding compounds in almond seed. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Matrix molecularly imprinted mesoporous sol-gel sorbent for efficient solid-phase extraction of chloramphenicol from milk.

    Science.gov (United States)

    Samanidou, Victoria; Kehagia, Maria; Kabir, Abuzar; Furton, Kenneth G

    2016-03-31

    Highly selective and efficient chloramphenicol imprinted sol-gel silica based inorganic polymeric sorbent (sol-gel MIP) was synthesized via matrix imprinting approach for the extraction of chloramphenicol in milk. Chloramphenicol was used as the template molecule, 3-aminopropyltriethoxysilane (3-APTES) and triethoxyphenylsilane (TEPS) as the functional precursors, tetramethyl orthosilicate (TMOS) as the cross-linker, isopropanol as the solvent/porogen, and HCl as the sol-gel catalyst. Non-imprinted sol-gel polymer (sol-gel NIP) was synthesized under identical conditions in absence of template molecules for comparison purpose. Both synthesized materials were characterized by Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FT-IR) and nitrogen adsorption porosimetry, which unambiguously confirmed their significant structural and morphological differences. The synthesized MIP and NIP materials were evaluated as sorbents for molecularly imprinted solid phase extraction (MISPE) of chloramphenicol in milk. The effect of critical extraction parameters (flow rate, elution solvent, sample and eluent volume, selectivity coefficient, retention capacity) was studied in terms of retention and desorption of chloramphenicol. Competition and cross reactivity tests have proved that sol-gel MIP sorbent possesses significantly higher specific retention and enrichment capacity for chloramphenicol compared to its non-imprinted analogue. The maximum imprinting factor (IF) was found as 9.7, whereas the highest adsorption capacity of chloramphenicol by sol-gel MIP was 23 mg/g. The sol-gel MIP was found to be adequately selective towards chloramphenicol to provide the necessary minimum required performance limit (MRPL) of 0.3 μg/kg set forth by European Commission after analysis by LC-MS even without requiring time consuming solvent evaporation and sample reconstitution step, often considered as an integral part in solid phase extraction work-flow. Intra and

  2. Presentation video retrieval using automatically recovered slide and spoken text

    Science.gov (United States)

    Cooper, Matthew

    2013-03-01

    Video is becoming a prevalent medium for e-learning. Lecture videos contain text information in both the presentation slides and lecturer's speech. This paper examines the relative utility of automatically recovered text from these sources for lecture video retrieval. To extract the visual information, we automatically detect slides within the videos and apply optical character recognition to obtain their text. Automatic speech recognition is used similarly to extract spoken text from the recorded audio. We perform controlled experiments with manually created ground truth for both the slide and spoken text from more than 60 hours of lecture video. We compare the automatically extracted slide and spoken text in terms of accuracy relative to ground truth, overlap with one another, and utility for video retrieval. Results reveal that automatically recovered slide text and spoken text contain different content with varying error profiles. Experiments demonstrate that automatically extracted slide text enables higher precision video retrieval than automatically recovered spoken text.

  3. A simple and cost-effective method of DNA extraction from small formalin-fixed paraffin-embedded tissue for molecular oncologic testing.

    Science.gov (United States)

    Snow, Anthony N; Stence, Aaron A; Pruessner, Jonathan A; Bossler, Aaron D; Ma, Deqin

    2014-01-01

    Extraction of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is a critical step in molecular oncologic testing. As molecular oncology testing becomes more important for prognostic and therapeutic decision making and tissue specimens become smaller due to earlier detection of suspicious lesions and the use of fine needle aspiration methods for tissue collection, it becomes more challenging for the typical molecular pathology laboratory to obtain reliable test results. We developed a DNA extraction method to obtain sufficient quantity and high quality genomic DNA from limited FFPE tissue for molecular oncology testing using a combination of H&E stained slides, a matrix capture method and the Qiagen DNA column. THREE DNA EXTRACTION METHODS WERE COMPARED: our standard procedure of manually scraping tissue from unstained slides followed by DNA extraction using the QIAamp FFPE column (Qiagen, Valencia, CA), a glue capture method (Pinpoint Solution, Zymo Research Corp, Inc) on H&E stained slides followed by DNA extraction using either the QIAamp column or the column included with the Pinpoint kit (Zymo Research). The DNA extraction protocol was optimized. Statistical analysis was performed using the paired two-sample student's t-test. The combination of the matrix capture method with the QIAamp column gave an equivalent amount of DNA as our standard extraction method using the unstained slides and a 4.6-fold higher DNA yield than using the Zymo column included in the Pinpoint Slide Solution kit. Several molecular tests were performed and DNA purified using the new method gave the same results as for the previous methods. Using H&E stained slides allows visual confirmation of tumor cells during microdissection. The Pinpoint solution made removal of specific tissue from the slides easier and reduced the risk of contamination and tissue loss. This DNA extraction method is simple, cost-effective, and blends with our current workflow requiring no additional equipment.

  4. Matrix molecularly imprinted mesoporous sol–gel sorbent for efficient solid-phase extraction of chloramphenicol from milk

    Energy Technology Data Exchange (ETDEWEB)

    Samanidou, Victoria, E-mail: samanidu@chem.auth.gr [Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki (Greece); Kehagia, Maria [Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki (Greece); Kabir, Abuzar, E-mail: akabir@fiu.edu [International Forensic Research Institute, Department of Chemistry and Biochemistry, Florida International University, Miami, FL (United States); Furton, Kenneth G. [International Forensic Research Institute, Department of Chemistry and Biochemistry, Florida International University, Miami, FL (United States)

    2016-03-31

    Highly selective and efficient chloramphenicol imprinted sol–gel silica based inorganic polymeric sorbent (sol–gel MIP) was synthesized via matrix imprinting approach for the extraction of chloramphenicol in milk. Chloramphenicol was used as the template molecule, 3-aminopropyltriethoxysilane (3-APTES) and triethoxyphenylsilane (TEPS) as the functional precursors, tetramethyl orthosilicate (TMOS) as the cross-linker, isopropanol as the solvent/porogen, and HCl as the sol–gel catalyst. Non-imprinted sol–gel polymer (sol–gel NIP) was synthesized under identical conditions in absence of template molecules for comparison purpose. Both synthesized materials were characterized by Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FT-IR) and nitrogen adsorption porosimetry, which unambiguously confirmed their significant structural and morphological differences. The synthesized MIP and NIP materials were evaluated as sorbents for molecularly imprinted solid phase extraction (MISPE) of chloramphenicol in milk. The effect of critical extraction parameters (flow rate, elution solvent, sample and eluent volume, selectivity coefficient, retention capacity) was studied in terms of retention and desorption of chloramphenicol. Competition and cross reactivity tests have proved that sol–gel MIP sorbent possesses significantly higher specific retention and enrichment capacity for chloramphenicol compared to its non-imprinted analogue. The maximum imprinting factor (IF) was found as 9.7, whereas the highest adsorption capacity of chloramphenicol by sol–gel MIP was 23 mg/g. The sol–gel MIP was found to be adequately selective towards chloramphenicol to provide the necessary minimum required performance limit (MRPL) of 0.3 μg/kg set forth by European Commission after analysis by LC-MS even without requiring time consuming solvent evaporation and sample reconstitution step, often considered as an integral part in solid phase extraction work

  5. Preparation of molecularly imprinted polymers for strychnine by precipitation polymerization and multistep swelling and polymerization and their application for the selective extraction of strychnine from nux-vomica extract powder.

    Science.gov (United States)

    Nakamura, Yukari; Matsunaga, Hisami; Haginaka, Jun

    2016-04-01

    Monodisperse molecularly imprinted polymers for strychnine were prepared by precipitation polymerization and multistep swelling and polymerization, respectively. In precipitation polymerization, methacrylic acid and divinylbenzene were used as a functional monomer and crosslinker, respectively, while in multistep swelling and polymerization, methacrylic acid and ethylene glycol dimethacrylate were used as a functional monomer and crosslinker, respectively. The retention and molecular recognition properties of the molecularly imprinted polymers prepared by both methods for strychnine were evaluated using a mixture of sodium phosphate buffer and acetonitrile as a mobile phase by liquid chromatography. In addition to shape recognition, ionic and hydrophobic interactions could affect the retention of strychnine in low acetonitrile content. Furthermore, molecularly imprinted polymers prepared by both methods could selectively recognize strychnine among solutes tested. The retention factors and imprinting factors of strychnine on the molecularly imprinted polymer prepared by precipitation polymerization were 220 and 58, respectively, using 20 mM sodium phosphate buffer (pH 6.0)/acetonitrile (50:50, v/v) as a mobile phase, and those on the molecularly imprinted polymer prepared by multistep swelling and polymerization were 73 and 4.5. These results indicate that precipitation polymerization is suitable for the preparation of a molecularly imprinted polymer for strychnine. Furthermore, the molecularly imprinted polymer could be successfully applied for selective extraction of strychnine in nux-vomica extract powder. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Wavelet analysis of molecular dynamics: Efficient extraction of time-frequency information in ultrafast optical processes

    International Nuclear Information System (INIS)

    Prior, Javier; Castro, Enrique; Chin, Alex W.; Almeida, Javier; Huelga, Susana F.; Plenio, Martin B.

    2013-01-01

    New experimental techniques based on nonlinear ultrafast spectroscopies have been developed over the last few years, and have been demonstrated to provide powerful probes of quantum dynamics in different types of molecular aggregates, including both natural and artificial light harvesting complexes. Fourier transform-based spectroscopies have been particularly successful, yet “complete” spectral information normally necessitates the loss of all information on the temporal sequence of events in a signal. This information though is particularly important in transient or multi-stage processes, in which the spectral decomposition of the data evolves in time. By going through several examples of ultrafast quantum dynamics, we demonstrate that the use of wavelets provide an efficient and accurate way to simultaneously acquire both temporal and frequency information about a signal, and argue that this greatly aids the elucidation and interpretation of physical process responsible for non-stationary spectroscopic features, such as those encountered in coherent excitonic energy transport

  7. A molecular dynamics study for the extraction of Cs+ and Na+ ions using dicyclohexano-18-crown-6 with octanol

    International Nuclear Information System (INIS)

    Biswas, Rima; Ghosh, Pallab; Banerjee, Tamal; Ali, Sk. Musharaf

    2016-01-01

    In this work we report a molecular dynamics study of the interfacial behavior involved in the cesium and sodium ion extraction by dicyclohexano-18-crown-6 (DCH18C6). Thereafter to understand the mechanism of complexation and the behavior of crown ether ligand, crown ether (CE) molecules, Cs + NO 3 - and Na + NO 3 - ions were inserted randomly in the Octanol-water biphasic system. In case of Na + NO 3 and Cs + NO 3 mixed system, it was observed that Cs + ion was extracted from water phase to octanol phase. The Na + ion was found to prefer to remain at the interface without complexation with DCH18C6. For the individual systems consisting of only Na + NO 3 , the complexed moiety (Na + -CE) formed during the simulation was found to diffuse slowly as compared to other free species. The binding energies during complexation of Na + cations with crown ether (DCH18C6) were further computed. The RDF peak height of 80 suggesting a high stability and a strong interaction for the complexed species is shown. The large magnitude of the RDF peak between sodium and oxygen is similar to that obtained by Pooja et al. and Maerzke et.al. The non bonded interaction energies during complexation of Na + cation with DCH18C6 were also analyzed. (author)

  8. Extraction/oxidation kinetics of low molecular weight compounds in wine brandy resulting from different ageing technologies.

    Science.gov (United States)

    Canas, Sara; Caldeira, Ilda; Belchior, A Pedro

    2013-06-15

    This study provides innovative information on the influence of new technologies of ageing (stainless steel tanks with wood staves or wood tablets of chestnut or Limousin oak), in comparison with traditional technology (oak wooden barrels), on the extraction/oxidation kinetics of low molecular weight compounds of wine brandy. The brandy was sampled and analysed by HPLC during the first year of ageing. The results show that most of the compounds tend to increase over the time, but their extraction/oxidation kinetics depend on the ageing technology. The wooden barrels promote greater enrichment in the majority of the compounds. However, gallic acid, ellagic acid and syringaldehyde, and vanillin and 5-methylfurfural, which are strong antioxidants and key-odourant compounds, respectively, present higher contents in the brandy aged with the alternative technologies. Chestnut proves to be a suitable alternative to Limousin oak for the ageing of brandy in all the studied technologies, inducing faster evolution and high quality. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Molecular characterization of two microalgal strains in Egypt and investigation of the antimicrobial activity of their extracts

    Directory of Open Access Journals (Sweden)

    El Semary, NA.

    2013-01-01

    Full Text Available The emergence of new pathogens and the increasing drug-resistance of recognized ones pose a difficult challenge. One way that this challenge is being addressed is through the discovery of new cost-effective drug resources in the form of bioactive compounds. Algae represent a promising source of bioactive compounds in this regard. In the present research, we used molecular and phylogenetic analysis to isolate and identify two microalgal strains. We found that one strain belonged to the phylum chrysophyta and the other to the cyanobacteria. We also investigated the antimicrobial activity of some of the lipophilic extracts of the two microalgal strains. Several fractions showed high individual antimicrobial bioactivity against multidrug-resistant Salmonella sp., Citrobacter sp., Aspergillus niger and Aspergillus flavus. Fraction III from Poterioochromonas malhamensis showed the highest level of activity against two multidrug-resistant bacterial pathogens. The inhibition zone diameter was 1.4 cm for Salmonella and 1.4 cm for Citrobacter. Meanwhile, another lipophilic fraction from the cyanobacterium Synechocystis salina showed broad-spectrum bioactivity (inhibition zone diameter of 0.9 cm for Aspergillus niger, 1 cm for Citrobacter and 0.9 cm for Salmonella. One lipophilic fraction from Aphanizomenon showed antifungal bioactivity against Aspergillus niger and Aspergillus flavus, where the inhibition zone diameter was 1.1 cm and 1.0 cm, respectively. The study highlights the antimicrobial bioactivity of extracts from local microalgae and emphasizes the importance of carrying out screening programs for those microorganisms.

  10. Determination of diethylstilbestrol in seawater by molecularly imprinted solid-phase extraction coupled with high-performance liquid chromatography.

    Science.gov (United States)

    He, Xiuping; Mei, Xiaoqi; Wang, Jiangtao; Lian, Ziru; Tan, Liju; Wu, Wei

    2016-01-15

    An effective and highly selective molecularly imprinted material was prepared by suspension polymerization for the isolation and pre-concentration of synthetic estrogen diethylstilbestrol (DES) in seawater. The obtained MIPMs were proved to have more uniform size and porous structure, with maximum adsorption capacity of 8.43 mg g(-1) almost two times more than NIPMs (4.43 mg g(-1)). The MIPMs showed no significant deterioration of the adsorption capacity after five rounds of regeneration. An off-line molecularly imprinted solid phase extraction (MISPE) method followed by HPLC-DAD was proposed for the detection of DES in seawater, and recoveries were satisfactorily higher than 77%. Four seawater samples in aquaculture area were analyzed and 0.61 ng mL(-1) DES was detected in one sample. The result demonstrated that this method can be used for the rapid separation and clean up of trace residual of DES in seawater. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Molecular marker study of extractable organic matter in aerosols from urban areas of China

    Science.gov (United States)

    Simoneit, Bernd R. T.; Sheng, Guoying; Chen, Xiaojing; Fu, Jiamo; Zhang, Jian; Xu, Yuping

    The solvent-extractable compounds (lipids) of aerosol samples, which were collected from a western suburb of Beijing, in the city of Guiyang and on the outskirts of Guangzhou, P.R. China, using a standard high volume air sampler, were investigated to determine the distributions of homologous compounds and biomarkers. These preliminary results show that all samples contain aliphatic hydrocarbons including n-alkanes, steranes and triterpanes, derived from both biogenic sources (vascular plant wax input) and fossil fuel contamination (coal, crude oil, etc.). Polynuclear aromatic hydrocarbons, which are considered to be combustion products from fossil fuels such as petroleum and, especially in this case, coal burning, are also widely distributed in all samples. Oxygenated compounds (e.g. alkanoic acids, alkanones and alkanols) are present as major fractions and are derived from mainly natural sources. Furthermore, some compositional differences are observed for the organic compounds in samples from different heights above ground. This is interpreted to be due to dilution at higher levels of locally generated aerosol with upper air aerosol transported over longer distances.

  12. Molecular properties and antioxidant activities of polysaccharides isolated from alkaline extract of wild Armillaria ostoyae mushrooms.

    Science.gov (United States)

    Siu, Ka-Chai; Xu, Lijian; Chen, Xia; Wu, Jian-Yong

    2016-02-10

    This study aims to discover novel and bioactive polysaccharides (PS) from wild Armillaria ostoyae, a honey mushroom species. Two PS designated AkPS1V-1 (66.6 kDa) and AkPS1V-2 (15.3 kDa) were isolated and fractionated by anion ion exchange (IEC) and size exclusion chromatography (SEC) from the alkaline extract of A. ostoyae mushrooms. AkPS1V-1 was a glucan composed of solely glucose residues and AkPS1V-2 a heteropolysaccharide composed of glucose and galactose at 6:1 molar ratio. AkPS1V-2 exhibited higher antioxidant activities than AkPS1V-1 based on reducing power, radical scavenging and metal chelating assays. The structure of AkPS1V-2 was further analyzed and elucidated as a branched galactoglucan with a backbone composed of (1→6)-β-D-glucopyranosyl, (1→3)-β-D-glucopyranosyl, (1→3)-α-D-galactopyranosyl and (1→3,6)-β-D-glucopyranosyl residues at 3:1:1:1 ratio, and side chain of (1→3)-β-D-glucopyranosyl residue. This is the first report on a pure PS structure and its antioxidant activities from this mushroom species. Copyright © 2015. Published by Elsevier Ltd.

  13. Extracting physics of life at the molecular level: A review of single-molecule data analyses.

    Science.gov (United States)

    Colomb, Warren; Sarkar, Susanta K

    2015-06-01

    Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Critical comparison of the on-line and off-line molecularly imprinted solid-phase extraction of patulin coupled with liquid chromatography.

    Science.gov (United States)

    Lhotská, Ivona; Holznerová, Anežka; Solich, Petr; Šatínský, Dalibor

    2017-12-01

    Reaching trace amounts of mycotoxin contamination requires sensitive and selective analytical tools for their determination. Improving the selectivity of sample pretreatment steps covering new and modern extraction techniques is one way to achieve it. Molecularly imprinted polymers as selective sorbent for extraction undoubtedly meet these criteria. The presented work is focused on the hyphenation of on-line molecularly imprinted solid-phase extraction with a chromatography system using a column-switching approach. Making a critical comparison with a simultaneously developed off-line extraction procedure, evaluation of pros and cons of each method, and determining the reliability of both methods on a real sample analysis were carried out. Both high-performance liquid chromatography methods, using off-line extraction on molecularly imprinted polymer and an on-line column-switching approach, were validated, and the validation results were compared against each other. Although automation leads to significant time savings, fewer human errors, and required no handling of toxic solvents, it reached worse detection limits (15 versus 6 μg/L), worse recovery values (68.3-123.5 versus 81.2-109.9%), and worse efficiency throughout the entire clean-up process in comparison with the off-line extraction method. The difficulties encountered, the compromises made during the optimization of on-line coupling and their critical evaluation are presented in detail. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. On-line dynamic extraction system hyphenated to inductively coupled plasma optical emission spectrometry for automatic determination of oral bioaccessible trace metal fractions in airborne particulate matter.

    Science.gov (United States)

    Mohr, Victoria; Miró, Manuel; Limbeck, Andreas

    2017-04-01

    For a realistic evaluation of the potential hazard emanating from airborne particulate matter (APM), the determination of the total inhaled metal amounts associated with APM is insufficient in risk assessment. Additional information about metal fractions that can be mobilized by the human body is necessary, because only those soluble (also called bioaccessible) fractions can be absorbed by the human body, and thus potentially cause adverse health effects. In the present study, a dynamic flow-through approach as a front end to inductively coupled plasma optical emission spectrometry (ICP-OES) exploiting advanced flow analysis is employed for on-line handling of multiple APM samples and determination of bioaccessible trace metals under worst case extraction scenarios. The method is based on on-line continuous extraction of filter samples with synthetic gastric fluid followed by on-line ICP-OES measurement of the dissolved fraction of trace metals. The assembly permits an automated successive measurement of three sample replicates in less than 19 min. The on-line extraction procedure offers increased sample throughput and reduced risk of sample contamination and overcomes metal re-adsorption processes compared to the traditional batch-wise counterparts. Furthermore, it provides deeper information on the kinetics of the leaching process. The developed procedure was applied to the determination of bioaccessible metal fractions (Al, Ba, Cu, Fe and Mn as model analytes) in PM10 samples from Palma de Mallorca (Spain) and Vienna (Austria). Graphical Abstract On-line gastric bioaccessibility of elements in airborne particulate matter.

  16. Extraction of a dual-chamber pacemaker and inserting of a new automatic implantable cardioverter defibrillator: The easy procedure almost became catastrophic: a case report.

    Science.gov (United States)

    Kiuchi, Márcio Galindo; Lobato, Guilherme Miglioli; Chen, Shaojie

    2017-09-01

    The cardiovascular illnesses are in the middle of the foremost reasons of death around the world. Deaths in Europe, from sudden cardiac death (SCD), reach nearby 700,000 individuals every year. In the United States, statistics point to the existence of nearly 1 million yearly deaths from cardiovascular sickness, of which 330,000 are the consequence of abrupt. The significance of automatic implantable cardioverter-defibrillator (ICD) has been proven in subjects with preceding myocardial infarction and stark systolic left ventricular dysfunction (secondary prevention). In this case, we describe a female patient, 94 years old, with a dual-chamber pacemaker since 2014, normal functioning, and controlled hypertension. The patient was in use of bisoprolol 10 mg daily, hydrochlorothiazide 25 mg daily, and candesartan cilexetil 16 mg daily. She presented 2 episodes of syncope associated with the high ventricular rate (HVR), which characterizes sustained ventricular tachycardia (SVT) due to its instability, besides 1 episode of cardiorespiratory arrest. During an attempt to position the active monocoil shock lead in the right ventricle, there was perforation of the upper posterolateral wall of the right atrium, transfixing the pericardium and constituting a pericardial-pleural fistula with hemothorax formation in the right hemithorax. We chose to remove the electrodes and suture the left pocket. There was no cardiac tamponade or pericardial effusion, verified by a pericardial puncture. Thoracic drainage was introduced into the right hemithorax, and 3 L of blood were drained acutely with volume replacement and hemotransfusion. We maintained thoracic drainage in water seal. The ICD was implanted on the right side. So, in this case, we reported a rare complication during pacemakers or ICD implantation that is the pericardial-pleural fistula with hemothorax formation in the contralateral hemithorax. Despite the patient's advanced age, we had the dexterity and luck to

  17. Sensitive, automatic method for the determination of diazepam and its five metabolites in human oral fluid by online solid-phase extraction and liquid chromatography with tandem mass spectrometry.

    Science.gov (United States)

    Jiang, Fengli; Rao, Yulan; Wang, Rong; Johansen, Sys Stybe; Ni, Chunfang; Liang, Chen; Zheng, Shuiqing; Ye, Haiying; Zhang, Yurong

    2016-05-01

    A novel and simple online solid-phase extraction liquid chromatography-tandem mass spectrometry method was developed and validated for the simultaneous determination of diazepam and its five metabolites including nordazepam, oxazepam, temazepam, oxazepam glucuronide, and temazepam glucuronide in human oral fluid. Human oral fluid was obtained using the Salivette(®) collection device, and 100 μL of oral fluid samples were loaded onto HySphere Resin GP cartridge for extraction. Analytes were separated on a Waters Xterra C18 column and quantified by liquid chromatography with tandem mass spectrometry using the multiple reaction monitoring mode. The whole procedure was automatic, and the total run time was 21 min. The limit of detection was in the range of 0.05-0.1 ng/mL for all analytes. The linearity ranged from 0.25 to 250 ng/mL for oxazepam, and 0.1 to 100 ng/mL for the other five analytes. Intraday and interday precision for all analytes was 0.6-12.8 and 1.0-9.2%, respectively. Accuracy ranged from 95.6 to 114.7%. Method recoveries were in the range of 65.1-80.8%. This method was fully automated, simple, and sensitive. Authentic oral fluid samples collected from two volunteers after consuming a single oral dose of 10 mg diazepam were analyzed to demonstrate the applicability of this method. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Computational approach to radiogenomics of breast cancer: Luminal A and luminal B molecular subtypes are associated with imaging features on routine breast MRI extracted using computer vision algorithms.

    Science.gov (United States)

    Grimm, Lars J; Zhang, Jing; Mazurowski, Maciej A

    2015-10-01

    To identify associations between semiautomatically extracted MRI features and breast cancer molecular subtypes. We analyzed routine clinical pre-operative breast MRIs from 275 breast cancer patients at a single institution in this retrospective, Institutional Review Board-approved study. Six fellowship-trained breast imagers reviewed the MRIs and annotated the cancers. Computer vision algorithms were then used to extract 56 imaging features from the cancers including morphologic, texture, and dynamic features. Surrogate markers (estrogen receptor [ER], progesterone receptor [PR], human epidermal growth factor receptor-2 [HER2]) were used to categorize tumors by molecular subtype: ER/PR+, HER2- (luminal A); ER/PR+, HER2+ (luminal B); ER/PR-, HER2+ (HER2); ER/PR/HER2- (basal). A multivariate analysis was used to determine associations between the imaging features and molecular subtype. The imaging features were associated with both luminal A (P = 0.0007) and luminal B (P = 0.0063) molecular subtypes. No association was found for either HER2 (P = 0.2465) or basal (P = 0.1014) molecular subtype and the imaging features. A P-value of 0.0125 (0.05/4) was considered significant. Luminal A and luminal B molecular subtype breast cancer are associated with semiautomatically extracted features from routine contrast enhanced breast MRI. © 2015 Wiley Periodicals, Inc.

  19. Molecular and Biochemical Effects of a Kola Nut Extract on Androgen Receptor-Mediated Pathways

    Directory of Open Access Journals (Sweden)

    Rajasree Solipuram

    2009-01-01

    Full Text Available The low incidence of prostate cancer in Asians has been attributed to chemopreventative properties of certain chemicals found in their diet. This study characterized the androgenic and chemopreventative properties of the Jamaican bush tea “Bizzy,” using androgen receptor positive and negative cell lines. Exposure of prostate cells to Biz-2 resulted in a growth inhibition (GI50 of 15 ppm in LNCaP cells and 3.6 ppm in DU145 cells. Biz-2 elicited a 2-fold increase in the mRNA of the anti-apoptotic gene Bcl2, with a 10-fold increase in that of the proapoptotic gene Bax. We observed a 2.4- to 7.5-fold change in apoptotic cells in both cell lines. Biz-2 at 10 ppm elicited a time- and dose-dependent stimulation of both the protein and mRNA levels of several androgen-regulated genes. Biz-2 caused a 36% decrease in PSA secretion and a significant increase in PSA mRNA. The relative binding affinity (IC50 of Biz-2 for AR was 2- to 5-fold lower than that of the synthetic androgen R1881. Biz-2 was found to be a specific ligand for the AR in that the natural ligand, DHT, and the anti-androgen, flutamide, displaced Biz-2 bound to AR and inhibited Biz-2-induced transcription and PSA secretion. This study provided evidence that Biz-2 extract possesses the ability to modulate prostate cancer cell biology in an AR-dependent manner.

  20. Liquid chromatography with tandem mass spectrometry for the determination of flufenoxuron in blood using automatic solid phase extraction and its application to a fatal case of flufenoxuron poisoning.

    Science.gov (United States)

    Rhee, Jongsook; Cho, Byungsuk; Lee, Juseon; Moon, Sungmin; Yum, Hyesun

    2015-12-01

    A liquid chromatography/tandem mass spectrometry method with solid phase extraction for the detection and the quantitation of flufenoxuron in an aliquot of blood was developed and validated. Flufenoxuron belongs to a benzoylurea insecticide and is the active ingredient of Cascade™. The analyte in postmortem specimens was extracted by solid-phase extraction with Bond Elut Certify cartridge. After the elution layer was evaporated, the residue was reconstituted with 70% methanol for LC/MS/MS analysis. Separations were carried out on a Synergi(®) 2.5u Fusion-RP 100 A column with column temperature kept at 40 °C at a flow rate of 0.4 mL/min. The mobile phase was composed of 5mM ammonium formate in 10% methanol and 5 mM ammonium formate in 90% methanol using gradient elution. A triple quadruple mass spectrometer equipped with an electrospray ionization source operated in a positive ion mode with selective reaction monitoring mode. Atrazine-d5 was used as internal standard. The assay was linear over 0.02-1.0 mg/L (r(2)=0.999). Limit of detection (LOD) and limit of quantitation (LOQ) in blood were 0.009 mg/L (S/N=3) and 0.02 mg/L (S/N=10), respectively. The accuracy and the precision were toxicology laboratory guidelines. Relative recoveries with 0.02, 0.1 and 1.0mg/L (in blood) were 112.3%, 101.2% and 111.0% (n=5), respectively. The developed method was applied in forensic toxicology to determine flufenoxuron in postmortem specimens in a fatal case of flufenoxuron intoxication in a 48-year-old-man who was found dead on bed in a small room after vomiting on the floor. The postmortem heart blood, peripheral blood and gastric contents were analyzed for flufenoxuron with the result of 6.3 mg/L in heart blood, 3.2 mg/L in peripheral blood and 30.6 mg/kg in gastric contents, respectively. The concentration ratio of the heart/peripheral blood of flufenoxuron was 2.0, and the ratio of gastric contents/peripheral blood was 9.4, suggesting possible postmortem redistribution and

  1. SwathProfiler and NProfiler: Two new ArcGIS Add-ins for the automatic extraction of swath and normalized river profiles

    Science.gov (United States)

    Pérez-Peña, J. V.; Al-Awabdeh, M.; Azañón, J. M.; Galve, J. P.; Booth-Rea, G.; Notti, D.

    2017-07-01

    The present-day great availability of high-resolution Digital Elevation Models has improved tectonic geomorphology analyses in their methodological aspects and geological meaning. Analyses based on topographic profiles are valuable to explore the short and long-term landscape response to tectonic activity and climate changes. Swath and river longitudinal profiles are two of the most used analysis to explore the long and short-term landscape responses. Most of these morphometric analyses are conducted in GIS software, which have become standard tools for analyzing drainage network metrics. In this work we present two ArcGIS Add-Ins to automatically delineate swath and normalized river profiles. Both tools are programmed in Visual Basic . NET and use ArcObjects library-architecture to access directly to vector and raster data. The SwathProfiler Add-In allows analyzing the topography within a swath or band by representing maximum-minimum-mean elevations, first and third quartile, local relief and hypsometry. We have defined a new transverse hypsometric integral index (THi) that analyzes hypsometry along the swath and offer valuable information in these kind of graphics. The NProfiler Add-In allows representing longitudinal normalized river profiles and their related morphometric indexes as normalized concavity (CT), maximum concavity (Cmax) and length of maximum concavity (Lmax). Both tools facilitate the spatial analysis of topography and drainage networks directly in a GIS environment as ArcMap and provide graphical outputs. To illustrate how these tools work, we analyzed two study areas, the Sierra Alhamilla mountain range (Betic Cordillera, SE Spain) and the Eastern margin of the Dead Sea (Jordan). The first study area has been recently studied from a morphotectonic perspective and these new tools can show an added value to the previous studies. The second study area has not been analyzed by quantitative tectonic geomorphology and the results suggest a landscape

  2. Gas chromatographic determination of N-nitrosamines, aromatic amines, and melamine in milk and dairy products using an automatic solid-phase extraction system.

    Science.gov (United States)

    Jurado-Sanchez, Beatriz; Ballesteros, Evaristo; Gallego, Mercedes

    2011-07-13

    A reliable analytical method was presented for the simultaneous determination of six N-nitrosamines, nine aromatic amines, and melamine in milk and dairy products using gas chromatography coupled with mass spectrometry. The sample treatment includes the precipitation of proteins with acetonitrile, centrifugation, solvent changeover by evaporation, and continuous solid-phase extraction for cleanup and preconcentration purposes. Samples (5 g) containing 0.15-500 ng of each amine were analyzed, and low detection limits (15-130 ng/kg) were achieved. Recoveries for milk and dairy products samples spiked with 1, 10, and 50 μg/kg ranged from 92% to 101%, with intraday and interday relative standard deviation values below 7.5%. The method was successfully applied to determine amine residues in several milk types (human breast, cow, and goat) and dairy products.

  3. Analysis of fusaric acid in maize using molecularly imprinted solid phase extraction (MISPE) clean-up and ion-pair LC with diode array UV detection

    Science.gov (United States)

    Fusaric acid is a phytotoxin and mycotoxin occasionally found in maize contaminated with Fusarium fungi. A selective sample clean-up procedure was developed to detect fusaric acid in maize using molecularly imprinted solid phase extraction (MISPE) clean-up coupled with ion-pair liquid chromatography...

  4. Selective extraction and determination of chlorogenic acids as combined quality markers in herbal medicines using molecularly imprinted polymers based on a mimic template.

    Science.gov (United States)

    Ji, Wenhua; Zhang, Mingming; Yan, Huijiao; Zhao, Hengqiang; Mu, Yan; Guo, Lanping; Wang, Xiao

    2017-12-01

    We describe a solid-phase extraction adsorbent based on molecularly imprinted polymers (MIPs), prepared with use of a mimic template. The MIPs were used for the selective extraction and determination of three chlorogenic acids as combined quality markers for Lonicera japonica and Lianhua qingwen granules. The morphologies and surface groups of the MIPs were assessed by scanning electron microscopy, Brunauer-Emmett-Teller surface area analysis, and Fourier transform infrared spectroscopy. The adsorption isotherms, kinetics, and selectivity of the MIPs were systematically compared with those of non-molecularly imprinted polymers. The MIPs showed high selectivity toward three structurally similar chlorogenic acids (chlorogenic acid, cryptochlorogenic acid, and neochlorogenic acid). A procedure using molecularly imprinted solid-phase extraction coupled with high-performance liquid chromatography was established for the determination of three chlorogenic acids from Lonicera japonica and Lianhua qingwen granules. The recoveries of the chlorogenic acids ranged from 93.1% to 101.4%. The limits of detection and limits of quantification for the three chlorogenic acids were 0.003 mg g -1 and 0.01 mg g -1 , respectively. The newly developed method is thus a promising technique for the enrichment and determination of chlorogenic acids from herbal medicines. Graphical Abstract Mimic molecularly imprinted polymers for the selective extraction of chlorogenic acids.

  5. Enhancement of human adaptive immune responses by administration of a high-molecular-weight polysaccharide extract from the cyanobacterium Arthrospira platensis

    DEFF Research Database (Denmark)

    Pedersen, Morten Løbner; Walsted, Anette; Larsen, Rune

    2008-01-01

    The effect of consumption of Immulina, a high-molecular-weight polysaccharide extract from the cyanobacterium Arthrospira platensis, on adaptive immune responses was investigated by evaluation of changes in leukocyte responsiveness to two foreign recall antigens, Candida albicans (CA) and tetanus...

  6. TBP assisted uranyl extraction from water to water/organic interface to organic phase: molecular dynamics of uranyl complex with water, acid and TBP

    International Nuclear Information System (INIS)

    Sahu, P.; Ali, Sk. M.; Shenoy, K.T.

    2016-01-01

    Reprocessing of the used fuel, not only diminishes the volume and toxicity of high level waste but is also required to produce the new fuel for nuclear reactors. It has been observed that the extraction of uranyl ions from dissolver solution to the organic phase is influenced by co extraction of other species, such as water and nitric acid and it is assumed that the presence of water or acid droplets in the organic phase intensifies the coordination mechanism of TBP. Present study is dedicated to revisit the molecular process of uranyl extraction from aqueous phase to organic phase, using molecular dynamic (MD) simulations. Here, we consider the biphasic systems to gain insights into the characteristics of the interface and humidity of organic phase under different acidic and neutral conditions. The consequences regarding the interfacial landscape, in the extraction process are considered by comparing the MD results of interfacial systems with various TBP and acid concentration. Further, the importance of charge transferability during uranyl-TBP complexation have been investigated with NO 3 - counter ions. Overall, this study aims at improving the description of molecular composition of various species and the structure of interface, in order to better understand the molecular-level complexation reaction occurring at the interface in different neutral and acidic environment

  7. Effect of the Ethanolic Extract of Salvia officinalis on Ovarian Angiogenesis in Mice at Preimplantation: A Morphological and Molecular Analysis

    Directory of Open Access Journals (Sweden)

    Nasim Beigi Boroujeni

    2017-02-01

    Full Text Available Background Salvia officinalis is a phytoestrogen, which is used to reduce clinical signs of pregnancy and improve the female infertility in herbal medicine treatment. The effect of S. officinalis on ovarian angiogenesis at the preimplantation time is unknown. Objectives This research was a histomorphometric and quantitative real-time study on angiogenic activity in the ovarian tissue in mice after exposure to S. officinalis at preimplantaion. Methods The extract of S. officinalis leaves, which was analyzed by phytochemical methods, administered at a dose of 100 mg/kg daily for 14 days to female mice. Then, pseudopregnancy was induced and ovarian tissue samples were removed for histological and molecular assessment. Results Data analysis on the space-solid phase micro extraction/gas chromatography-mass spectrometry demonstrated α-thujone (33.90%, camphor (19.34%, cineole (11.01% and ß-thujone (9.48% were the dominating compounds in the leaves of S. officinalis. Data analysis on histomorphometric parameters showed a significant difference in the vascular parameters between the test and control groups. Furthermore, gene expression analysis implied an increased level of the vascular endothelial growth factor (VEGF (3.175 and was also associated with an increase in the level of Kinase insert domain protein receptor (KDR/Flk gene expression (3.556 and FMS-like tyrosine kinase (Flt gene expression (3.437 in the test group compared to the control group. Conclusions Increased ovarian angiogenesis after exposure to S. officinalis may induce vascular permeability and finally contribute to a variety of disorders including clinical signs similar to the ovarian hyperstimulation syndrome.

  8. Enantioselective separation and electrochemical sensing of D- and L-tryptophan at ultratrace level using molecularly imprinted micro-solid phase extraction fiber coupled with complementary molecularly imprinted polymer-fiber sensor.

    Science.gov (United States)

    Prasad, Bhim Bali; Tiwari, Mahavir Prasad; Madhuri, Rashmi; Sharma, Piyush Sindhu

    2011-02-15

    Highly efficient enantioselective separation and quantitative recoveries of D- and L-tryptophan in aqueous and real samples can be achieved, with a monolithic molecularly imprinted polymeric fiber that serves both for micro-solid phase extraction and ultratrace sensing, without any false-positive (non-specific) contribution and cross-reactivity, in the range of 0.15-30.00 ng mL(-1) with detection limit as low as 0.0261 ng mL(-1) (relative standard deviation=0.64%, signal/noise=3). The proposed method combining molecularly imprinted micro-solid phase extraction fiber and a complementary molecularly imprinted polymer-carbon composite fiber sensor is proven to be useful for clinical diagnosis of stress-related diseases caused by acute tryptophan depletion. Copyright © 2010 Elsevier B.V. All rights reserved.

  9. Improving molecular detection of Candida DNA in whole blood: comparison of seven fungal DNA extraction protocols using real-time PCR.

    Science.gov (United States)

    Metwally, L; Fairley, D J; Coyle, P V; Hay, R J; Hedderwick, S; McCloskey, B; O'Neill, H J; Webb, C H; Elbaz, W; McMullan, R

    2008-03-01

    The limitations of classical diagnostic methods for invasive Candida infections have led to the development of molecular techniques such as real-time PCR to improve diagnosis. However, the detection of low titres of Candida DNA in blood from patients with candidaemia requires the use of extraction methods that efficiently lyse yeast cells and recover small amounts of DNA suitable for amplification. In this study, a Candida-specific real-time PCR assay was used to detect Candida albicans DNA in inoculated whole blood specimens extracted using seven different extraction protocols. The yield and quality of total nucleic acids were estimated using UV absorbance, and specific recovery of C. albicans genomic DNA was estimated quantitatively in comparison with a reference (Qiagen kit/lyticase) method currently in use in our laboratory. The extraction protocols were also compared with respect to sensitivity, cost and time required for completion. The TaqMan PCR assay used to amplify the DNA extracts achieved high levels of specificity, sensitivity and reproducibility. Of the seven extraction protocols evaluated, only the MasterPure yeast DNA extraction reagent kit gave significantly higher total nucleic acid yields than the reference method, although nucleic acid purity was highest using either the reference or YeaStar genomic DNA kit methods. More importantly, the YeaStar method enabled C. albicans DNA to be detected with highest sensitivity over the entire range of copy numbers evaluated, and appears to be an optimal method for extracting Candida DNA from whole blood.

  10. Probing the molecular forces involved in binding of selected volatile flavour compounds to salt-extracted pea proteins.

    Science.gov (United States)

    Wang, Kun; Arntfield, Susan D

    2016-11-15

    Molecular interactions between heterologous classes of flavour compounds with salt-extracted pea protein isolates (PPIs) were determined using various bond disrupting agents followed by GC/MS analysis. Flavour bound by proteins decreased in the order: dibutyl disulfide>octanal>hexyl acetate>2-octanone=benzaldehyde. Benzaldehyde, 2-octanone and hexyl acetate interacted non-covalently with PPIs, whereas octanal bound PPIs via covalent and non-covalent forces. Dibutyl disulfide reacted with PPIs covalently, as its retention was not diminished by urea and guanidine hydrochloride. Using propylene glycol, H-bonding and ionic interactions were implicated for hexyl acetate, benzaldehyde, and 2-octanone. A protein-destabilising salt (Cl3CCOONa) reduced bindings for 2-octanone, hexyl acetate, and benzaldehyde; however, retention for octanal and dibutyl disulfide increased. Conversely, a protein-stabilising salt (Na2SO4) enhanced retention for benzaldehyde, 2-octanone, hexyl acetate and octanal. Formation of a volatile flavour by-product, 1-butanethiol, from dibutyl disulfide when PPIs were treated with dithiothreitol indicated occurrence of sulfhydryl-disulfide interchange reactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Cellular and molecular mechanisms in vascular smooth muscle cells by which total saponin extracted from Tribulus terrestris protects against artherosclerosis.

    Science.gov (United States)

    Li, Mengquan; Guan, Yue; Liu, Jiaqi; Zhai, Fengguo; Zhang, Xiuping; Guan, Lixin

    2013-01-01

    Total saponin extracted from Tribulus terrestris (TSETT) has been reported to protect against atherosclerosis. We here investigate the cellular and molecular mechanisms of TSETT underlying protection against atherosclerosis. Cell proliferation was measured with Methyl thiazolyl tetrazolium (MTT); Intracellular H2O2 was measured with DCFH-DA, a fluorescent dye; Intracellular free Ca(2+) was measured with a confocal laser scanning microscopy; Genes expression was measured with gene array and real-time quantitative polymerase chain reaction (RT-PCR); Phosphorylation of extracellular signal-regulated kinase 1/2 (phospho-ERK1/2) was measured with cell-based enzyme-linked immunosorbent assay (ELISA) and western blotting. TSETT significantly suppressed the increase in cells proliferation induced by angiotensin II, significantly suppressed the increase in the intracellular production of H2O2 induced by angiotensin II, significantly inhibited the increase in intracellular free Ca(2+) induced by H2O2, significantly inhibited the increase in phospho-ERK1/2 induced by angiotensin II; significantly inhibited the increase in mRNA expression of c-fos, c-jun and pkc-α induced by angiotensin II. These findings provide a new insight into the antiatherosclerotic properties of TSETT and provide a pharmacological basis for the clinical application of TSETT in anti-atherosclerosis. © 2013 S. Karger AG, Basel.

  12. Cellular and Molecular Mechanisms in Vascular Smooth Muscle Cells by which Total Saponin Extracted from Tribulus Terrestris Protects Against Artherosclerosis

    Directory of Open Access Journals (Sweden)

    Mengquan Li

    2013-11-01

    Full Text Available Background/Aims: Total saponin extracted from Tribulus terrestris (TSETT has been reported to protect against atherosclerosis. We here investigate the cellular and molecular mechanisms of TSETT underlying protection against atherosclerosis. Methods: Cell proliferation was measured with Methyl thiazolyl tetrazolium (MTT; Intracellular H2O2 was measured with DCFH-DA, a fluorescent dye; Intracellular free Ca2+ was measured with a confocal laser scanning microscopy; Genes expression was measured with gene array and real-time quantitative polymerase chain reaction (RT-PCR; Phosphorylation of extracellular signal-regulated kinase 1/2 (phospho-ERK1/2 was measured with cell-based enzyme-linked immunosorbent assay (ELISA and western blotting. Results: TSETT significantly suppressed the increase in cells proliferation induced by angiotensin II, significantly suppressed the increase in the intracellular production of H2O2 induced by angiotensin II, significantly inhibited the increase in intracellular free Ca2+ induced by H2O2, significantly inhibited the increase in phospho-ERK1/2 induced by angiotensin II; significantly inhibited the increase in mRNA expression of c-fos, c-jun and pkc-α induced by angiotensin II. Conclusion: These findings provide a new insight into the antiatherosclerotic properties of TSETT and provide a pharmacological basis for the clinical application of TSETT in anti-atherosclerosis.

  13. A needle extraction utilizing a molecularly imprinted-sol-gel xerogel for on-line microextraction of the lung cancer biomarker bilirubin from plasma and urine samples.

    Science.gov (United States)

    Moein, Mohammad Mahdi; Jabbar, Dunia; Colmsjö, Anders; Abdel-Rehim, Mohamed

    2014-10-31

    In the present work, a needle trap utilizing a molecularly imprinted sol-gel xerogel was prepared for the on-line microextraction of bilirubin from plasma and urine samples. Each prepared needle could be used for approximately one hundred extractions before it was discarded. Imprinted and non-imprinted sol-gel xerogel were applied for the extraction of bilirubin from plasma and urine samples. The produced molecularly imprinted sol-gel xerogel polymer showed high binding capacity and fast adsorption/desorption kinetics for bilirubin in plasma and urine samples. The adsorption capacity of molecularly imprinted sol-gel xerogel polymer was approximately 60% higher than that of non-imprinted polymer. The effect of the conditioning, washing and elution solvents, pH, extraction time, adsorption capacity and imprinting factor were investigated. The limit of detection and the lower limit of quantification were set to 1.6 and 5nmolL(-1), respectively using plasma or urine samples. The standard calibration curves were obtained within the concentration range of 5-1000nmolL(-1) in both plasma and urine samples. The coefficients of determination values (R(2)) were ≥0.998 for all runs. The extraction recovery was approximately 80% for BR in the human plasma and urine samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection

    Directory of Open Access Journals (Sweden)

    Zhang Yanxin

    2012-11-01

    Full Text Available Abstract Background Sesame (Sesamum indicum L. is one of the four major oil crops in China. A sesame core collection (CC was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC. Results Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525. The Shannon-Weaver diversity index (I and Nei genetic diversity index (h were higher (I = 0.9537, h = 0.5490 when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218. A mini-core collection (MC containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%, low variance difference percentage (VD, 22.58%, large variable rate of coefficient of variance (VR, 114.86%, and large coincidence rate of range (CR, 95.76%. For molecular data, the diversity indices and the polymorphism information content (PIC for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. Conclusions This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and

  15. Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection

    Science.gov (United States)

    2012-01-01

    Background Sesame (Sesamum indicum L.) is one of the four major oil crops in China. A sesame core collection (CC) was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC). Results Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525). The Shannon-Weaver diversity index (I) and Nei genetic diversity index (h) were higher (I = 0.9537, h = 0.5490) when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218). A mini-core collection (MC) containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%), low variance difference percentage (VD, 22.58%), large variable rate of coefficient of variance (VR, 114.86%), and large coincidence rate of range (CR, 95.76%). For molecular data, the diversity indices and the polymorphism information content (PIC) for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. Conclusions This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and large VR% and CR

  16. Molecularly imprinted polymer for selective extraction of malachite green from seawater and seafood coupled with high-performance liquid chromatographic determination

    International Nuclear Information System (INIS)

    Lian Ziru; Wang Jiangtao

    2012-01-01

    Highlights: ► The malachite green molecularly imprinted polymer (MG-MIP) was prepared. ► The characteristics and regeneration property of MIP were studied. ► An off-line method for MG was developed using MIP as solid-phase extraction. ► The MG concentrations from seawater and seafood samples were determined. - Abstract: In this paper, a highly selective sample cleanup procedure combining molecular imprinting technique (MIT) and solid-phase extraction (SPE) was developed for the isolation of malachite green in seawater and seafood samples. The molecularly imprinted polymer (MIP) was prepared using malachite green as the template molecule, methacrylic acid as the functional monomer and ethylene glycol dimethacrylate as the cross-linking monomer. The imprinted polymer and non-imprinted polymer were characterized by scanning electron microscope and static adsorption experiments. The MIP showed a high adsorption capacity and was used as selective sorbent for the SPE of malachite green. An off-line molecularly imprinted solid-phase extraction (MISPE) method followed by high-performance liquid chromatography with diodearray detection for the analysis of malachite green in seawater and seafood samples was also established. Finally, five samples were determined. The results showed that malachite green concentration in one seawater sample was at 1.30 μg L −1 and the RSD (n = 3) was 4.15%.

  17. Intramembranous bone healing process subsequent to tooth extraction in mice: micro-computed tomography, histomorphometric and molecular characterization.

    Science.gov (United States)

    Vieira, Andreia Espindola; Repeke, Carlos Eduardo; Ferreira Junior, Samuel de Barros; Colavite, Priscila Maria; Biguetti, Claudia Cristina; Oliveira, Rodrigo Cardoso; Assis, Gerson Francisco; Taga, Rumio; Trombone, Ana Paula Favaro; Garlet, Gustavo Pompermaier

    2015-01-01

    Bone tissue has a significant potential for healing, which involves a significant the interplay between bone and immune cells. While fracture healing represents a useful model to investigate endochondral bone healing, intramembranous bone healing models are yet to be developed and characterized. In this study, a micro-computed tomography, histomorphometric and molecular (RealTimePCRarray) characterization of post tooth-extraction alveolar bone healing was performed on C57Bl/6 WT mice. After the initial clot dominance (0 h), the development of a provisional immature granulation tissue is evident (7 d), characterized by marked cell proliferation, angiogenesis and inflammatory cells infiltration; associated with peaks of growth factors (BMP-2-4-7,TGFβ1,VEGFa), cytokines (TNFα, IL-10), chemokines & receptors (CXCL12, CCL25, CCR5, CXCR4), matrix (Col1a1-2, ITGA4, VTN, MMP1a) and MSCs (CD105, CD106, OCT4, NANOG, CD34, CD146) markers expression. Granulation tissue is sequentially replaced by more mature connective tissue (14 d), characterized by inflammatory infiltrate reduction along the increased bone formation, marked expression of matrix remodeling enzymes (MMP-2-9), bone formation/maturation (RUNX2, ALP, DMP1, PHEX, SOST) markers, and chemokines & receptors associated with healing (CCL2, CCL17, CCR2). No evidences of cartilage cells or tissue were observed, strengthening the intramembranous nature of bone healing. Bone microarchitecture analysis supports the evolving healing, with total tissue and bone volumes as trabecular number and thickness showing a progressive increase over time. The extraction socket healing process is considered complete (21 d) when the dental socket is filled by trabeculae bone with well-defined medullary canals; it being the expression of mature bone markers prevalent at this period. Our data confirms the intramembranous bone healing nature of the model used, revealing parallels between the gene expression profile and the

  18. Intramembranous bone healing process subsequent to tooth extraction in mice: micro-computed tomography, histomorphometric and molecular characterization.

    Directory of Open Access Journals (Sweden)

    Andreia Espindola Vieira

    Full Text Available Bone tissue has a significant potential for healing, which involves a significant the interplay between bone and immune cells. While fracture healing represents a useful model to investigate endochondral bone healing, intramembranous bone healing models are yet to be developed and characterized. In this study, a micro-computed tomography, histomorphometric and molecular (RealTimePCRarray characterization of post tooth-extraction alveolar bone healing was performed on C57Bl/6 WT mice. After the initial clot dominance (0 h, the development of a provisional immature granulation tissue is evident (7 d, characterized by marked cell proliferation, angiogenesis and inflammatory cells infiltration; associated with peaks of growth factors (BMP-2-4-7,TGFβ1,VEGFa, cytokines (TNFα, IL-10, chemokines & receptors (CXCL12, CCL25, CCR5, CXCR4, matrix (Col1a1-2, ITGA4, VTN, MMP1a and MSCs (CD105, CD106, OCT4, NANOG, CD34, CD146 markers expression. Granulation tissue is sequentially replaced by more mature connective tissue (14 d, characterized by inflammatory infiltrate reduction along the increased bone formation, marked expression of matrix remodeling enzymes (MMP-2-9, bone formation/maturation (RUNX2, ALP, DMP1, PHEX, SOST markers, and chemokines & receptors associated with healing (CCL2, CCL17, CCR2. No evidences of cartilage cells or tissue were observed, strengthening the intramembranous nature of bone healing. Bone microarchitecture analysis supports the evolving healing, with total tissue and bone volumes as trabecular number and thickness showing a progressive increase over time. The extraction socket healing process is considered complete (21 d when the dental socket is filled by trabeculae bone with well-defined medullary canals; it being the expression of mature bone markers prevalent at this period. Our data confirms the intramembranous bone healing nature of the model used, revealing parallels between the gene expression profile and the

  19. Simultaneous molecular formula determinations of natural compounds in a plant extract using 15 T Fourier transform ion cyclotron resonance mass spectrometry.

    Science.gov (United States)

    Park, Kyu Hwan; Kim, Min Sun; Baek, Sun Jong; Bae, Ik Hyun; Seo, Sang-Wan; Kim, Jongjin; Shin, Yong Kook; Lee, Yong-Moon; Kim, Hyun Sik

    2013-01-01

    Plant extracts are a reservoir of pharmacologically active substances; however, conventional analytical methods can analyze only a small portion of an extract. Here, we report a high-throughput analytical method capable of determining most phytochemicals in a plant extract and of providing their molecular formulae from a single experiment using ultra-high-resolution electrospray ionization mass spectrometry (UHR ESI MS). UHR mass profiling was used to analyze natural compounds in a 70% ethanol ginseng extract, which was directly infused into a 15 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer for less than 10 min without a separation process. The UHR FT-ICR MS yielded a mass accuracy of 0.5 ppm and a mass resolving power (m/Δm) of 1,000,000-270,000 for the range m/z 290-1,100. The mass resolution was sufficient to resolve the isotopic fine structure (IFS) of many compounds in the extract. After noise removal from 1,552 peaks, 405 compounds were detected. The molecular formulae of 123 compounds, including 33 ginsenosides, were determined using the observed IFS, exact monoisotopic mass, and exact mass difference. Liquid chromatography (LC)/FT-ICR MS of the extract was performed to compare the high-throughput performance of UHR ESI FT-ICR MS. The LC/FT-ICR MS detected only 129 compounds, including 19 ginsenosides. The result showed that UHR ESI FT-ICR MS identified three times more compounds than LC/FT-ICR MS and in a relatively shorter time. The molecular formula determination by UHR FT-ICR MS was validated by LC and tandem MS analyses of three known ginsenosides. UHR mass profiling of a plant extract by 15 T FT-ICR MS showed that multiple compounds were simultaneously detected and their molecular formulae were decisively determined by a single experiment with ultra-high mass resolution and mass accuracy. Simultaneous molecular determination of multiple natural products by UHR ESI FT-ICR MS would be a powerful method to profile a wide

  20. Characterization of Extractable Organic Fine Particulate Matter in the Atmosphere of Houston and Source Apportionment Calculations Using Organic Molecular Markers

    Science.gov (United States)

    Fraser, M. P.; Yue, Z. W.; Buzco, B.

    2002-12-01

    Samples of atmospheric PM2.5 were collected in Houston, TX every second day during the summer of 2000 as part of the EPA sponsored Houston Fine Particle Matter Supersite program. Sampling occurred at three sites, including one industrial location (HRM-3), one suburban location (Aldine) and one coastal location (La Porte). Twenty samples collected over a 24 hour period have been analyzed to quantify the concentration of 95 individual organic compounds, including: n-alkanes (C20 to C36), aromatic hydrocarbons (PAHs), n-alkanoic acids (C5 to C34), n-alkenoic acids (C18:1 and C18:2), carboxylic diacids (C3 to C10), petroleum biomarkers and others. As a whole, the extractable compounds were dominated by acids, especially by octadecanoic acid and hexadecanoic acid. The measured concentration of n-alkanes exhibited a peak at C29, with carbon preference index (CPI) values in the range of 0.97 to 2.0. Using organic molecular markers, including seven alkanes, four petroleum biomarkers, seven PAH, one alkanoic acid, one alkenoic acid, levoglucosan, and three chemical components (Al, Si and Elemental Carbon), Chemical Mass Balancing (CMB) calculations have been performed on the ambient speciation data. These calculations are used to determine the contribution of seven different primary emission sources including: diesel powered vehicles, gasoline vehicles, wood combustion, fuel oil combustion, road dusts, meat cooking and vegetation waxes. The contribution of diesel powered vehicles and gasoline powered vehicles are the most important primary sources at all three sampling locations, with road dusts important at the industrial location. Meat cooking emissions were significant at all three locations. Wood combustion is an important contribution during a four-day period when uncontrolled wildfires in eastern Texas and Louisiana brought biomass combustion aerosols into the sampling region.

  1. Contribution of molecular modeling and of structure-activity relations to the liquid-liquid extraction. Application to the case of U(VI) extraction by monoamides; Apport de la modelisation moleculaire et des relations structure -activite a l`extraction liquide-liquide. Application au cas de l`extraction d`U(VI) par les monoamides

    Energy Technology Data Exchange (ETDEWEB)

    Rabbe, C.

    1996-06-07

    In France, spent fuels are in most cases reprocessed. The aim of the reprocessing is to separate the recyclable fissile materials (for instance, uranium and plutonium) of radioactive wastes. The industrial process used until now is the Purex (Plutonium Uranium Refining by EXtraction) process. Recently (1991), the CEA has undertaken researches on the fields of separation and transmutation of long-lived radionuclides as minor actinides. Some molecules with an amide function have been at first considered especially for the uranium extraction. In order to rationalize the research of new extracting molecules, some molecular modeling methods (quantum chemistry calculations, molecular mechanics) have been used. In fact, there are three determining parameters for a molecule to be a good extractant: it has to own: (1) one or several sites which present a sufficient electron density in order that the metallic cation be complexed (2) the smallest possible substituents to avoid interferences with the complexation (3) a sufficient lipophilic effect. (O.M.). 139 refs., 43 figs., 36 tabs.

  2. Automatic fluid dispenser

    Science.gov (United States)

    Sakellaris, P. C. (Inventor)

    1977-01-01

    Fluid automatically flows to individual dispensing units at predetermined times from a fluid supply and is available only for a predetermined interval of time after which an automatic control causes the fluid to drain from the individual dispensing units. Fluid deprivation continues until the beginning of a new cycle when the fluid is once again automatically made available at the individual dispensing units.

  3. Enhancement of human adaptive immune responses by administration of a high-molecular-weight polysaccharide extract from the cyanobacterium Arthrospira platensis

    DEFF Research Database (Denmark)

    Løbner, Morten; Walsted, Anette; Larsen, Rune

    2008-01-01

    The effect of consumption of Immulina, a high-molecular-weight polysaccharide extract from the cyanobacterium Arthrospira platensis, on adaptive immune responses was investigated by evaluation of changes in leukocyte responsiveness to two foreign recall antigens, Candida albicans (CA) and tetanus......beta, and IL-6 responses, indicating that it acts by inducing a pro-inflammatory state. Taken together, the data suggest that Immulina causes an age-dependent, temporary enhancement of adaptive immune responses....

  4. FERMENTATION BY Lactobacillus paracasei OF GALACTOOLIGOSACCHARIDES AND LOW-MOLECULAR-WEIGHT CARBOHYDRATES EXTRACTED FROM SQUASH (Curcubita maxima AND LUPIN (Lupinus albus SEEDS

    Directory of Open Access Journals (Sweden)

    María I. Palacio

    2014-02-01

    Full Text Available The in vitro prebiotic activity of galactooligosaccharides (GOS and low-molecular-weight carbohydrates (LMWC extracted from lupin and squash seeds on the growth of Lactobacillus paracasei BGP1 was studied. To this end, the change in cell density after 24 h of L. paracasei growth on 1% (w/v glucose, 1% (w/v raffinose, 1% (w/v commercial inulin GR, 1% (w/v lupin extract, and 1% (w/v squash extract relative to the change in cell density of a mixture of enteric strains under the same culture conditions were evaluated. Additionally, the principal components of GOS and LMWC in the extracts were identified using Thin Layer Chromatography. The highest prebiotic activity score was for L. paracasei grown on squash extract (0.55±0.03, followed by lupin extract (0.49±0.02, inulin (0.38±0.05 and raffinose (0.37±0.05. These results will contribute to selecting plant species as potential sources of prebiotic ingredients for the development of functional foods.

  5. Antiviral activity of the Indian medicinal plant extract, Swertia chirata against herpes simplex viruses: A study by in-vitro and molecular approach

    Directory of Open Access Journals (Sweden)

    Verma H

    2008-01-01

    Full Text Available Purpose: The antiviral activity of Indian Medicinal plant extract Swertia chirata was tested against Herpes simplex virus (HSV type-1, using multiple approaches both at cellular and molecular level. Methods: Cytotoxicity, plaque reduction, virus infectivity, antigen expression and polymerase chain reaction (PCR assays were conducted to test the antiviral activity of the plant extract. Results: Swertia plant crude extract (1gm/mL at 1:64 dilution inhibited HSV-1, plaque formation at more than 70% level. HSV antigen expression and time kinetics experiments conducted by indirect immunofluorescence (IFA test, revealed a characteristic pattern of small foci of single fluorescent cells in Swertia extract treated HSV-1 infected cells at 4 hours post infection dose, suggested drug inhibited viral dissemination. Infected cell cultures treated with Swertia extract at various time intervals, tested by PCR, failed to show amplification at 12, 24-72 hours. HSV-1 infected cells treated with Acyclovir (antiviral drug did not show any amplification by PCR. Conclusions: In this preliminary study, the Indian medicinal plant extract, Swertia chirata showed antiviral properties against Herpes simplex virus type-1.

  6. Extraction: a system for automatic eddy current diagnosis of steam generator tubes in nuclear power plants; Extracsion: un systeme de controle automatique par courants de Foucault des tubes de generateurs de vapeur de centrales nucleaires

    Energy Technology Data Exchange (ETDEWEB)

    Georgel, B.; Zorgati, R.

    1994-12-31

    Improving speed and quality of Eddy Current non-destructive testing of steam generator tubes leads to automatize all processes that contribute to diagnosis. This paper describes how we use signal processing, pattern recognition and artificial intelligence to build a software package that is able to automatically provide an efficient diagnosis. (authors). 2 figs., 5 refs.

  7. Selective Dispersive Solid Phase Extraction of Ser-traline Using Surface Molecularly Imprinted Polymer Grafted on SiO2/Graphene Oxide

    Directory of Open Access Journals (Sweden)

    Faezeh Khalilian

    2017-01-01

    Full Text Available A surface molecularly imprinted dispersive solid phase extraction coupled with liquid chromatography–ultraviolet detection is proposed as a selective and fast clean-up technique for the determination of sertraline in biological sample. Surface sertraline-molecular imprinted polymer was grafted and synthesized on the SiO2/graphene oxide surface. Firstly SiO2 was coated on synthesized graphene oxide sheet using sol-gel technique. Prior to polymerization, the vinyl group was incorporated on to the surface of SiO2/graphene oxide to direct selective polymerization on the surface. Methacrylic acid, ethylene glycol dimethacrylate and ethanol were used as monomer, cross-linker and progen, respectively. Non-imprinted polymer was also prepared for comparing purposes. The properties of the molecular imprinted polymer were characterized using field emission-scanning electron microscopy and Fourier transform infrared spectroscopy methods. The surface molecular imprinted polymer was utilized as an adsorbent of dispersive solid phase extraction for separation and preconcentration of sertraline. The effects of the different parameters influencing the extraction efficiency, such as sample pH were investigated and optimized. The specificity of the molecular imprinted polymer over the non-imprinted polymer was examined in absence and presence of competitive drugs. Sertraline calibration curve showed linearity in the ranges 1–500 µg L-1. The limits of detection and quantification under optimized conditions were obtained 0.2 and 0.5 µg L-1. The within-day and between-day relative standard deviations (n=3 were 4.3 and 7.1%, respectively. Furthermore, the relative recoveries for spiked biological samples were above 92%.

  8. Extraction and identification of matrine-type alkaloids from Sophora moorcroftiana using double-templated molecularly imprinted polymers with HPLC-MS/MS.

    Science.gov (United States)

    Ma, Xingbin; Lin, Hongling; Zhang, Jiyu; She, Yongxin; Zhou, Xuzheng; Li, Xiaozhong; Cui, Yan; Wang, Jing; Rabah, Tsdan; Shao, Yong

    2018-01-05

    Double-templated molecularly imprinted polymers with specific recognition of three matrine-type alkaloids were prepared using matrine and oxymatrine as the template molecules. An approach based on double-templated molecularly imprinted solid-phase extraction coupled with high-performance liquid chromatography and tandem mass spectrometry was then developed to extract and purify matrine, oxymatrine, and sophocarpine from Sophora moorcroftiana in the Tibetan plateau herbs. The polymers were characterized by Fourier-transform infrared spectroscopy and scanning electron microscopy. Their adsorption characteristics were evaluated using adsorption kinetics, isotherms, selectivity, and recycling experiments. This polymer exhibited excellent molecular recognition ability and good selectivity. The obtained polymers as adsorbent was further used for the determination of three matrine-type alkaloids coupled to high-performance liquid chromatography with tandem mass spectrometry, the recoveries of three matrines spiked at three concentration levels in samples were 73.25-98.42% (n = 5) with a relative standard deviation less than 6.82%. The limits of detection for the method were 9.23-15.42 μg/kg (S/N = 3). This proposed method was assessed to be an effective method for simultaneous extraction, isolation, and identification of matrine, oxymatrine, and sophocarpine from Sophora moorcroftiana. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Automatic emotional expression analysis from eye area

    Science.gov (United States)

    Akkoç, Betül; Arslan, Ahmet

    2015-02-01

    Eyes play an important role in expressing emotions in nonverbal communication. In the present study, emotional expression classification was performed based on the features that were automatically extracted from the eye area. Fırst, the face area and the eye area were automatically extracted from the captured image. Afterwards, the parameters to be used for the analysis through discrete wavelet transformation were obtained from the eye area. Using these parameters, emotional expression analysis was performed through artificial intelligence techniques. As the result of the experimental studies, 6 universal emotions consisting of expressions of happiness, sadness, surprise, disgust, anger and fear were classified at a success rate of 84% using artificial neural networks.

  10. Analysis of iminosugars and other low molecular weight carbohydrates in Aglaonema sp. extracts by hydrophilic interaction liquid chromatography coupled to mass spectrometry.

    Science.gov (United States)

    Rodríguez-Sánchez, S; García-Sarrió, M J; Quintanilla-López, J E; Soria, A C; Sanz, M L

    2015-12-04

    A method by hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry (HILIC-MS(2)) has been successfully developed for the simultaneous analysis of bioactive iminosugars and other low molecular weight carbohydrates in Aglaonema leaf extracts. Among other experimental chromatographic conditions, mobile phase eluents, additives and column temperature were evaluated in terms of retention time, resolution, peak width and symmetry provided for target carbohydrates. In general, narrow peaks (wh: 0.2-0.6min) with good symmetry (As: 0.9-1.3) and excellent resolution (Rs>1.8) were obtained for iminosugars using an acetonitrile:water gradient with 5mM ammonium acetate in both eluents at 55°C. Tandem mass spectra were used to confirm the presence of previously detected iminosugars in Aglaonema extracts and to tentatively identify for the first time others such as miglitol isomer, glycosyl-miglitol isomers and glycosyl-DMDP isomers. Concentration of total iminosugars varied from 1.35 to 2.84mgg(-1) in the extracts of the different Aglaonema samples analyzed. To the best of our knowledge, this is the first time that a HILIC-MS(2) method has been proposed for the simultaneous analysis of iminosugars and other low molecular weight carbohydrates of Aglaonema sp. extracts. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Image matching as a data source for forest inventory - Comparison of Semi-Global Matching and Next-Generation Automatic Terrain Extraction algorithms in a typical managed boreal forest environment

    Science.gov (United States)

    Kukkonen, M.; Maltamo, M.; Packalen, P.

    2017-08-01

    Image matching is emerging as a compelling alternative to airborne laser scanning (ALS) as a data source for forest inventory and management. There is currently an open discussion in the forest inventory community about whether, and to what extent, the new method can be applied to practical inventory campaigns. This paper aims to contribute to this discussion by comparing two different image matching algorithms (Semi-Global Matching [SGM] and Next-Generation Automatic Terrain Extraction [NGATE]) and ALS in a typical managed boreal forest environment in southern Finland. Spectral features from unrectified aerial images were included in the modeling and the potential of image matching in areas without a high resolution digital terrain model (DTM) was also explored. Plot level predictions for total volume, stem number, basal area, height of basal area median tree and diameter of basal area median tree were modeled using an area-based approach. Plot level dominant tree species were predicted using a random forest algorithm, also using an area-based approach. The statistical difference between the error rates from different datasets was evaluated using a bootstrap method. Results showed that ALS outperformed image matching with every forest attribute, even when a high resolution DTM was used for height normalization and spectral information from images was included. Dominant tree species classification with image matching achieved accuracy levels similar to ALS regardless of the resolution of the DTM when spectral metrics were used. Neither of the image matching algorithms consistently outperformed the other, but there were noticeably different error rates depending on the parameter configuration, spectral band, resolution of DTM, or response variable. This study showed that image matching provides reasonable point cloud data for forest inventory purposes, especially when a high resolution DTM is available and information from the understory is redundant.

  12. Physics of Automatic Target Recognition

    CERN Document Server

    Sadjadi, Firooz

    2007-01-01

    Physics of Automatic Target Recognition addresses the fundamental physical bases of sensing, and information extraction in the state-of-the art automatic target recognition field. It explores both passive and active multispectral sensing, polarimetric diversity, complex signature exploitation, sensor and processing adaptation, transformation of electromagnetic and acoustic waves in their interactions with targets, background clutter, transmission media, and sensing elements. The general inverse scattering, and advanced signal processing techniques and scientific evaluation methodologies being used in this multi disciplinary field will be part of this exposition. The issues of modeling of target signatures in various spectral modalities, LADAR, IR, SAR, high resolution radar, acoustic, seismic, visible, hyperspectral, in diverse geometric aspects will be addressed. The methods for signal processing and classification will cover concepts such as sensor adaptive and artificial neural networks, time reversal filt...

  13. Selective and simultaneous determination of trace bisphenol A and tebuconazole in vegetable and juice samples by membrane-based molecularly imprinted solid-phase extraction and HPLC.

    Science.gov (United States)

    Wu, Ya-Ting; Zhang, Yan-Hong; Zhang, Meng; Liu, Fei; Wan, Ying-Chun; Huang, Zheng; Ye, Lei; Zhou, Qi; Shi, Yun; Lu, Bin

    2014-12-01

    Nanofibrous molecularly imprinted membranes (nano-MIMs) with multi-analyte selectivity were prepared by encapsulating two types of molecularly imprinted polymer nanoparticles (MIP-NPs) into electrospun polyvinyl alcohol nanofibers. The obtained nano-MIMs maintained high molecular selectivity offered by each of the MIP-NPs. Nano-MIM embedding BPA-imprinted nanoparticles and TBZ-imprinted nanoparticles together showed the highest binding selectivity for acid bisphenol A (BPA) and basic tebuconazole (TBZ). This nano-MIM was used as affinity material of membrane-based molecularly imprinted solid-phase extraction (m-MISPE) to extract trace BPA and TBZ in vegetables and juices simultaneously. The recoveries of BPA and TBZ from different samples were higher than 70.33% with RSDs lower than 9.57%. m-MISPE gave better HPLC separation efficiencies and higher recoveries than conventional SPE based on C18/SCX. Multi-analyte selective m-MISPE combined with HPLC realized selective and simultaneous determination of several trace analytes with opposite charges/polarities in different food samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Molecular and supramolecular speciations of solvent extraction systems based on malonamide and/or dialkyl-phosphoric acids for An(III)/Ln(III)

    International Nuclear Information System (INIS)

    Gannaz, B.

    2006-06-01

    The solvent extraction system used in the DIAMEX-SANEX process, developed for the actinide(III)/lanthanide(III) separation, is based on the use of mixtures of the malonamide DMDOHEMA and a dialkyl-phosphoric acid (HDEHP or HDHP), in hydrogenated tetra-propylene. The complexity of these systems urges on a novel approach to improve the conventional methods (thermodynamics, solvent extraction) which hardly explain the macroscopic behaviors observed (3. phase, over-stoichiometry). This approach combines studies on both supramolecular (VPO, SANS, SAXS) and molecular (liquid-liquid extraction, ESI-MS, IR, EXAFS) speciations of single extractant systems (DMDOHEMA or HDHP in in n-dodecane) and their mixture. In spite of safety constraints due to the handling of radio-material, they were used in the studies as much as possible, like for SAXS measurements on americium-containing samples, a worldwide first-time. In each of the investigated systems, actinides(III) and lanthanides(III) are extracted to the organic phase in polar cores of reversed micelles, the inner and outer-sphere compositions of which are proposed. Thus, the 4f and 5f cations are extracted by reversed micelles such as [(DMDOHEMA) 2 M(NO 3 ) 3 ] inn (DMDOHEMA) x (HNO 3 ) z (H 2 O) w ] out and M(DHP) 3 (HDHP) y-3 (H 2 O) w with y = 3 to 6, for the single extractant systems. In the case of the two extractants system, the less concentrated one acts like a co-surfactant regarding the mixed aggregate formation [(DMDOHEMA) 2 M(NO 3 ) 3-v (DHP) v ] inn [(DMDOFIEMA) x (HDHP) y (HNO 3 )z(H 2 O) w ] out . (author)

  15. Molecularly imprinted polymer for the selective extraction of cocaine and its metabolites, benzoylecgonine and ecgonine methyl ester, from biological fluids before LC-MS analysis.

    Science.gov (United States)

    Thibert, Valérie; Legeay, Patrice; Chapuis-Hugon, Florence; Pichon, Valérie

    2014-02-15

    Considering the important complexity of biological samples, a molecularly imprinted polymer (MIP) was applied to the selective extraction of cocaine and its two main metabolites, benzoylecgonine and ecgonine methyl ester from biological samples. The MIP was imprinted with cocaine and it was synthesized in acetonitrile with methacrylic acid as a functional monomer and ethylene glycol dimethacrylate as a crosslinker. The selectivity of the MIP was first assessed for the three target analytes in acetonitrile with recoveries higher than 80% on the MIP and lower than 30% on the non-imprinted polymer (NIP). The MIP was then evaluated for the selective extraction of these targets from real aqueous media, i.e. serum and urine samples. The pH adjustment of the sample as well as the optimization of the washing step led to a very selective extraction of cocaine from these media. A LOQ of 0.5ng/mL was obtained for cocaine in urine. Concerning cocaine metabolites, benzoylecgonine and ecgonine methyl ester, they were first extracted from urine by liquid-liquid extraction and the resulting extract was purified on the MIP. The results obtained with the MIP as compared to the LLE alone showed the great potential of the MIP extraction for the clean-up of the biological matrix. This procedure was tested for the extraction of the analytes from urine samples, leading to a very selective protocol with LOQs of 0.09ng/mL, 0.4ng/mL and 1.1ng/mL for cocaine, benzolecgonine and ecgonine methyl ester respectively in urine samples. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Preparation and evaluation of a novel molecularly imprinted polymer coating for selective extraction of indomethacin from biological samples by electrochemically controlled in-tube solid phase microextraction

    Energy Technology Data Exchange (ETDEWEB)

    Asiabi, Hamid [Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran (Iran, Islamic Republic of); Yamini, Yadollah, E-mail: yyamini@modares.ac.ir [Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran (Iran, Islamic Republic of); Seidi, Shahram; Ghahramanifard, Fazel [Department of Analytical Chemistry, Faculty of Chemistry, K.N. Toosi University of Technology, Tehran (Iran, Islamic Republic of)

    2016-03-24

    In the present work, an automated on-line electrochemically controlled in-tube solid-phase microextraction (EC-in-tube SPME) coupled with HPLC-UV was developed for the selective extraction and preconcentration of indomethacin as a model analyte in biological samples. Applying an electrical potential can improve the extraction efficiency and provide more convenient manipulation of different properties of the extraction system including selectivity, clean-up, rate, and efficiency. For more enhancement of the selectivity and applicability of this method, a novel molecularly imprinted polymer coated tube was prepared and applied for extraction of indomethacin. For this purpose, nanostructured copolymer coating consisting of polypyrrole doped with ethylene glycol dimethacrylate was prepared on the inner surface of a stainless-steel tube by electrochemical synthesis. The characteristics and application of the tubes were investigated. Electron microscopy provided a cross linked porous surface and the average thickness of the MIP coating was 45 μm. Compared with the non-imprinted polymer coated tubes, the special selectivity for indomethacin was discovered with the molecularly imprinted coated tube. Moreover, stable and reproducible responses were obtained without being considerably influenced by interferences commonly existing in biological samples. Under the optimal conditions, the limits of detection were in the range of 0.07–2.0 μg L{sup −1} in different matrices. This method showed good linearity for indomethacin in the range of 0.1–200 μg L{sup −1}, with coefficients of determination better than 0.996. The inter- and intra-assay precisions (RSD%, n = 3) were respectively in the range of 3.5–8.4% and 2.3–7.6% at three concentration levels of 7, 70 and 150 μg L{sup −1}. The results showed that the proposed method can be successfully applied for selective analysis of indomethacin in biological samples. - Graphical abstract: An automated on

  17. Evaluation and optimization of nucleic acid extraction methods for the molecular analysis of bacterial communities associated with corrored steel

    NARCIS (Netherlands)

    Marty, F.; Ghiglione, J.-F.; Païsse, S.; Gueuné, H.; Quillet, L.; van Loosdrecht, M.C.M.; Muyzer, G.

    2012-01-01

    Different DNA and RNA extraction approaches were evaluated and protocols optimized on in situ corrosion products from carbon steel in marine environments. Protocols adapted from the PowerSoil DNA/RNA Isolation methods resulted in the best nucleic acid (NA) extraction performances (ie combining high

  18. Liquid–liquid anion exchange extraction studies of samarium(III from salicylate media using high molecular weight amine

    Directory of Open Access Journals (Sweden)

    Aniruddha M. Mandhare

    2015-07-01

    Full Text Available Liquid–liquid extraction and separation of samarium(III were carried out by using 0.025 mol dm−3 2-octylaminopyridine(2-OAP in xylene at 298 K. The extraction behavior of samarium was studied as a function of pH, weak acid concentration, extractant concentration, diluent, and equilibration time. Samarium was quantitatively extracted at pH 7.5 to 10.0 from 0.01 mol dm−3 sodium salicylate solution with 0.025 mol dm−3 2-OAP. The possible composition of the extracted species in organic phase has been determined by using model of slope analysis method and extraction mechanism was found to proceed via an anion exchange mechanism. The stripping efficiency was found to be quantitative in HNO3, HCl and CH3COOH. The robustness of the procedure was demonstrated by the average recoveries obtained (>99.6% for samarium(III extraction in the presence of several cations and anions which are commonly associated with it. The proposed method facilitates the separation and determination of samarium(III from binary and synthetic mixtures. The various thermodynamic functions like free energy (ΔG, enthalpy (ΔH and entropy (ΔS of extraction mechanism were discussed.

  19. Molecularly imprinted polymers with synthetic dummy template for simultaneously selective removal and enrichment of ginkgolic acids from Ginkgo biloba L. leaves extracts.

    Science.gov (United States)

    Ji, Wenhua; Ma, Xiuli; Xie, Hongkai; Chen, Lingxiao; Wang, Xiao; Zhao, Hengqiang; Huang, Luqi

    2014-11-14

    Dummy molecularly imprinted polymers (DMIPs) for simultaneously selective removal and enrichment of ginkgolic acids (GAs) during the processing of Ginkgo biloba leaves have been prepared. Two dummy template molecule with similar structural skeleton to GAs, 6-methoxysalicylic acid (MOSA, DT-1) and 6-hexadecyloxysalicylic acid (HOSA, DT-2), have been designed and synthesized. The performance of the DMIPs and NIPs were evaluated including selective recognition capacity, adsorption isotherm, and adsorption kinetics. The selective recognition capacity of the three GAs with four analogues on the sorbents illustrated that the DMIPs sorbents have high specificity for GAs. An efficient method based on DMIP-HOSA coupled with solid-phase extraction (SPE) was developed for simultaneously selective removal and enrichment of ginkgolic acids (GAs) during the processing of Ginkgo biloba leaves. The method showed excellent recoveries (82.5-88.7%) and precision (RSD 0.5-2.6%, n=5) for licorice extracts, Gastrodia elata extracts and pepper extracts spiked at three concentration levels each (50, 100, 200 μg mL(-1)). The results indicated that GAs and standardized Ginkgo biloba leaves extracts could be obtained simultaneously through the DMIP-SPE. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Molecularly imprinted polymer-sol-gel tablet toward micro-solid phase extraction: II. Determination of amphetamine in human urine samples by liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    El-Beqqali, Aziza; Andersson, Lars I; Jeppsson, Amin Dadoun; Abdel-Rehim, Mohamed

    2017-09-15

    Amphetamine selective molecularly imprinted sol-gel polymer tablets, MIP-tablets, for solid-phase microextraction of biofluid samples were prepared. An acetonitrile solution of deuterated amphetamine template and silane precursor, 3-(propylmethacrylate) trimethoxysilane, was soaked into the pores of polyethylene tablet substrates and polymerized by an acid-catalysed sol-gel process. Application of the resultant MIP-tablets to extract amphetamine from human urine samples followed by LC-MS/MS analysis was investigated. The extraction protocol was optimised with respect to pH of sample, addition of sodium chloride, extraction time, desorption solvent and desorption time. The final analysis method determined amphetamine in human urine with a limit of detection (LOD) of 1.0ng/mL and a lower limit of quantification (LLOQ) of 5ng/mL. Validation demonstrated accuracy of the method was 91.0-104.0% and inter-assay precision was 4.8-8.5% (RSD). Extraction recovery was 80%. The MIP-tablets could be re-used and the same tablet could be employed for more than twenty extractions. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Application of cytoplasmic Ca2+ fluorescence imaging techniques to study the molecular mechanisms of exercise-induced fatigue eliminated by Chinese medicine ginseng extract

    Science.gov (United States)

    Liu, Yi; Zhao, Yanping; Zhang, Heming; Liu, Songhao

    2009-11-01

    The exercise-induced fatigue eliminated by Chinese medicine offers advantages including good efficiency and smaller side-effects, however, the exact mechanisms have not been classified. A lot of literatures indicated the cytosolic free Ca2+ concentrations of skeletal muscle cells increased significantly during exercise-induced fatigue. This study is aimed to establish a rat skeletal muscle cell model of exercise-induced fatigue. We applied cytoplasmic Ca2+ fluorescence imaging techniques to study the molecular mechanisms of exercise-induced fatigue eliminated by Chinese medicine ginseng extract. In our research, the muscle tissues from the newborn 3 days rats were taken out and digested into cells. The cells were randomly divided into the ginseng extract group and the control group. The cells from the two groups were cultured in the medium respectively added 2mg/ml ginseng extract and 2mg/ml D-hanks solution. After differentiating into myotubes, the two groups of cells treated with a fluorescent probe Fluo-3 AM were put on the confocal microscope and the fluorescence intensity of cells pre- and post- stimulation with dexamethasone were detected. It was found that cytoplasmic Ca2+ concentrations of the two groups of cells both increased post-stimulation, however, the increasing amplitude of fluorescence intensity of the ginseng extract group was significantly lower than that of the control group. In conclusion, stimulating the cells with dexamethasone is a kind of workable cell models of exercise-induced fatigue, and the molecular mechanisms of exercise-induced fatigue eliminated by ginseng extract may be connected to regulatating cytosolic free Ca2+ concentrations.

  2. Preparation of High Purity, High Molecular-Weight Chitin from Ionic Liquids for Use as an Adsorbate for the Extraction of Uranium from Seawater

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, Robin [Univ. of Alabama, Tuscaloosa, AL (United States)

    2013-12-21

    Ensuring a domestic supply of uranium is a key issue facing the wider implementation of nuclear power. Uranium is mostly mined in Kazakhstan, Australia, and Canada, and there are few high-grade uranium reserves left worldwide. Therefore, one of the most appealing potential sources of uranium is the vast quantity dissolved in the oceans (estimated to be 4.4 billion tons worldwide). There have been research efforts centered on finding a means to extract uranium from seawater for decades, but so far none have resulted in an economically viable product, due in part to the fact that the materials that have been successfully demonstrated to date are too costly (in terms of money and energy) to produce on the necessary scale. Ionic Liquids (salts which melt below 100{degrees}C) can completely dissolve raw crustacean shells, leading to recovery of a high purity, high molecular weight chitin powder and to fibers and films which can be spun directly from the extract solution suggesting that continuous processing might be feasible. The work proposed here will utilize the unprecedented control this makes possible over the chitin fiber a) to prepare electrospun nanofibers of very high surface area and in specific architectures, b) to modify the fiber surfaces chemically with selective extractant capacity, and c) to demonstrate their utility in the direct extraction and recovery of uranium from seawater. This approach will 1) provide direct extraction of chitin from shellfish waste thus saving energy over the current industrial process for obtaining chitin; 2) allow continuous processing of nanofibers for very high surface area fibers in an economical operation; 3) provide a unique high molecular weight chitin not available from the current industrial process, leading to stronger, more durable fibers; and 4) allow easy chemical modification of the large surface areas of the fibers for appending uranyl selective functionality providing selectivity and ease of stripping. The

  3. Preparation of High Purity, High Molecular-Weight Chitin from Ionic Liquids for Use as an Adsorbate for the Extraction of Uranium from Seawater

    International Nuclear Information System (INIS)

    Rogers, Robin

    2013-01-01

    Ensuring a domestic supply of uranium is a key issue facing the wider implementation of nuclear power. Uranium is mostly mined in Kazakhstan, Australia, and Canada, and there are few high-grade uranium reserves left worldwide. Therefore, one of the most appealing potential sources of uranium is the vast quantity dissolved in the oceans (estimated to be 4.4 billion tons worldwide). There have been research efforts centered on finding a means to extract uranium from seawater for decades, but so far none have resulted in an economically viable product, due in part to the fact that the materials that have been successfully demonstrated to date are too costly (in terms of money and energy) to produce on the necessary scale. Ionic Liquids (salts which melt below 100 deg C) can completely dissolve raw crustacean shells, leading to recovery of a high purity, high molecular weight chitin powder and to fibers and films which can be spun directly from the extract solution suggesting that continuous processing might be feasible. The work proposed here will utilize the unprecedented control this makes possible over the chitin fiber a) to prepare electrospun nanofibers of very high surface area and in specific architectures, b) to modify the fiber surfaces chemically with selective extractant capacity, and c) to demonstrate their utility in the direct extraction and recovery of uranium from seawater. This approach will 1) provide direct extraction of chitin from shellfish waste thus saving energy over the current industrial process for obtaining chitin; 2) allow continuous processing of nanofibers for very high surface area fibers in an economical operation; 3) provide a unique high molecular weight chitin not available from the current industrial process, leading to stronger, more durable fibers; and 4) allow easy chemical modification of the large surface areas of the fibers for appending uranyl selective functionality providing selectivity and ease of stripping. The resulting

  4. Automatic Fiscal Stabilizers

    Directory of Open Access Journals (Sweden)

    Narcis Eduard Mitu

    2013-11-01

    Full Text Available Policies or institutions (built into an economic system that automatically tend to dampen economic cycle fluctuations in income, employment, etc., without direct government intervention. For example, in boom times, progressive income tax automatically reduces money supply as incomes and spendings rise. Similarly, in recessionary times, payment of unemployment benefits injects more money in the system and stimulates demand. Also called automatic stabilizers or built-in stabilizers.

  5. Molecularly imprinted microspheres synthesized by a simple, fast, and universal suspension polymerization for selective extraction of the topical anesthetic benzocaine in human serum and fish tissues.

    Science.gov (United States)

    Sun, Hui; Lai, Jia-Ping; Chen, Fang; Zhu, De-Rong

    2015-02-01

    A simple, fast, and universal suspension polymerization method was used to synthesize the molecularly imprinted microspheres (MIMs) for the topical anesthetic benzocaine (BZC). The desired diameter (10-20 μm) and uniform morphology of the MIMs were obtained easily by changing one or more of the synthesis conditions, including type and amount of surfactant, stirring rate, and ratio of organic to water phase. The MIMs obtained were used as a molecular-imprinting solid-phase-extraction (MISPE) material for extraction of BZC in human serum and fish tissues. The MISPE results revealed that the BZC in these biosamples could be enriched effectively after the MISPE operation. The recoveries of BZC on MIMs cartridges were higher than 90% (n = 3). Finally, an MISPE-HPLC method with UV detection was developed for highly selective extraction and fast detection of trace BZC in human serum and fish tissues. The developed method could also be used for the enrichment and detection of BZC in other complex biosamples.

  6. Phytochemical Characterization, Biological Activity Evaluation of Ethanolic Extract of Cinnamomum zeylanicum and Molecular Docking Analysis of Active Component Cinnamaldehyde against Selected Protein Targets.

    Science.gov (United States)

    Husain, Ishrat; Ahmad, Rumana; Chandra, Anu; Raza, Syed Tasleem; Shukla, Yogeshwer; Mahdi, Farzana

    2018-02-02

    India being a multicultural nation, every region of the country offers a distinct culinary flavor and taste. These flavours are attributed to spices and condiments which form the mainstay of Indian cuisine. Most of these spices and condiments are derived from various biodiversity hotspots in India and form the crux of India's multidiverse and multicultural cuisine. Apart from their varying aromas, flavors and tastes, these spices and condiments are known to possess several medicinal properties also. Most of these spices find considerable mention in Ayurveda, the indigenous system of medicine, as panaceas for several aliments. Cinnamomum zeylanicum (CZ), belonging to family Lauraceae and commonly known as cinnamon is one such spice known to have diverse medicinal properties since time immemorial. In the present study, apoptotic and anti-microbial activity of ethanolic extract of CZ was evaluated against human breast cancer cell line MDA-MB-231 and compared for its effect on normal kidney epithelial cell line Vero. Ethanolic extract of tree bark of CZ was used to determine the cytotoxic effect on MDA-MB-231 using Trypan blue dye exclusion method and cytometry. The tested dose of the extract was 10-100µg/mL. Antibacterial activity was determined using disc diffusion method against Staphylococcus aureus and Escherichia coli in the range 2-10mg/mL. Apoptotic activity was determined using DNA fragmentation assay. Molecular docking analysis of cinnamaldehyde, the major active component found in CZ bark, was carried out using AutoDock 4.0.1 to study its inhibitory action against selected protein targets. Ethanolic extract of CZ was found to have an IC 50 value of 25µg/mL against MDA cell line. On the other hand, CZ extract did not have any significant effect on Vero cells even at 100µg/mL (IC 50 >100µg/mL). The ethanolic extract of CZ bark showed significant antibacterial activity against S. aureus at 10mg/mL while no appreciable activity was detected against E. coli

  7. Automatic differentiation bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Corliss, G.F. (comp.)

    1992-07-01

    This is a bibliography of work related to automatic differentiation. Automatic differentiation is a technique for the fast, accurate propagation of derivative values using the chain rule. It is neither symbolic nor numeric. Automatic differentiation is a fundamental tool for scientific computation, with applications in optimization, nonlinear equations, nonlinear least squares approximation, stiff ordinary differential equation, partial differential equations, continuation methods, and sensitivity analysis. This report is an updated version of the bibliography which originally appeared in Automatic Differentiation of Algorithms: Theory, Implementation, and Application.

  8. Automatic characterization of dynamics in Absence Epilepsy

    DEFF Research Database (Denmark)

    Petersen, Katrine N. H.; Nielsen, Trine N.; Kjær, Troels W.

    2013-01-01

    Dynamics of the spike-wave paroxysms in Childhood Absence Epilepsy (CAE) are automatically characterized using novel approaches. Features are extracted from scalograms formed by Continuous Wavelet Transform (CWT). Detection algorithms are designed to identify an estimate of the temporal development...

  9. Extraction chromatography of indium (III) on silica gel impregnated with high molecular weight carboxylic acid and its analytical applications

    International Nuclear Information System (INIS)

    Majumdar, P.S.; Ray, U.S.

    1991-01-01

    Indium(III) was separated by extraction chromatography with Versatic 10 as a stationary phase on a column of silica gel from acetic acid and sodium acetate solution (pH 4.5-6.0). The optimum condition for extraction was studied based on the critical study of the relevant factors as effects of pH, flow rate on extraction and elution. Role of stripping agents on the elution was studied. The separation of indium from a number of elements was carried out. Indium(III) was separated from Alsup(III), Gasup(III), Tlsup(III), Zrsup(IV) and trivalent lanthanides which interfere under the recommended extraction condition by exploiting the differences in their stripping behaviour. (author). 7 refs., 1 tab., 1 fig

  10. Wild Roman chamomile extracts and phenolic compounds: enzymatic assays and molecular modelling studies with VEGFR-2 tyrosine kinase

    OpenAIRE

    Guimarães, Rafaela; Calhelha, Ricardo C.; Froufe, Hugo J.C.; Abreu, Rui M.V.; Carvalho, Ana Maria; Queiroz, Maria João R.P.; Ferreira, Isabel C.F.R.

    2016-01-01

    Angiogenesis is a process by which new blood vessels are formed from the pre-existing vasculature, and it is a key process that leads to tumour development. Some studies have recognized phenolic compounds as chemopreventive agents; flavonoids, in particular, seem to suppress the growth of tumor cells modifying the cell cycle. Herein, the antiangiogenic activity of Roman chamomile (Chamaemelum nobile L.) extracts (methanolic extract and infusion) and the main phenolic compounds present (apigen...

  11. Comparative analysis of different methods of Hedera helix DNA extraction and molecular evidence of the functionality in PCR

    Directory of Open Access Journals (Sweden)

    Danka Bošeľová

    2016-12-01

    Full Text Available The most suitable method of total DNA extraction still remains the crucial step for many plant species, although there are many different protocols and commercial kits for DNA isolation. In this study, five different extraction protocols were analysed to find out the most appropriate method for DNA extraction from Hedera helix L. This species has numerous medical and pharmaceutical uses and is also characterized by antioxidant effects on human body. In spite of its wide medical utilization, it belongs to those plant species, where the genomic information is very limited. Comparing of different protocols resulted in the yield of extracted DNA that has ranged from 6.3 to 487 ng μl-1. The purity of extracted DNA has ranged from 1.4 up to 2.0 A260/A280. All the extraction methods used in this study were evaluated not only in term of quantity and purity of DNA but also its functionality in the restriction endonuclease digestion and polymerase chain reaction based downstream analysis was performed.

  12. Automatic segmentation of clinical texts.

    Science.gov (United States)

    Apostolova, Emilia; Channin, David S; Demner-Fushman, Dina; Furst, Jacob; Lytinen, Steven; Raicu, Daniela

    2009-01-01

    Clinical narratives, such as radiology and pathology reports, are commonly available in electronic form. However, they are also commonly entered and stored as free text. Knowledge of the structure of clinical narratives is necessary for enhancing the productivity of healthcare departments and facilitating research. This study attempts to automatically segment medical reports into semantic sections. Our goal is to develop a robust and scalable medical report segmentation system requiring minimum user input for efficient retrieval and extraction of information from free-text clinical narratives. Hand-crafted rules were used to automatically identify a high-confidence training set. This automatically created training dataset was later used to develop metrics and an algorithm that determines the semantic structure of the medical reports. A word-vector cosine similarity metric combined with several heuristics was used to classify each report sentence into one of several pre-defined semantic sections. This baseline algorithm achieved 79% accuracy. A Support Vector Machine (SVM) classifier trained on additional formatting and contextual features was able to achieve 90% accuracy. Plans for future work include developing a configurable system that could accommodate various medical report formatting and content standards.

  13. Solid-phase extraction of chlorophenols in seawater using a magnetic ionic liquid molecularly imprinted polymer with incorporated silicon dioxide as a sorbent.

    Science.gov (United States)

    Ma, Wanwan; Row, Kyung Ho

    2018-01-06

    A type of magnetic ionic liquid based molecularly imprinted polymer coated on SiO 2 (Fe 3 O 4 @SiO 2 @IL-MIPs) was prepared with 1-vinyl-3-ethylimidazole ionic liquid as functional monomer, and 1,4-butane-3,3'-bis-1-ethylimidazole ionic liquid as cross linker, 4-Chlorophenol as template was successfully applied as a selective adsorbent for selective extraction of 5 chlorophenols in seawater samples by using the magnetic solid-phase extraction (MSPE) method. 11 types of Fe 3 O 4 @SiO 2 @IL-MIPs were synthesized and investigated for their different compositions of functional monomer (such as [C 2 min][Br], [C 2 min][BF 4 ], [C 2 min][PF 6 ], acrylamide, methacrylic acid and 4-vinyl pyridine) and cross-linker (such as [C 4 min 2 ][Br], [C 4 min 2 ][BF 4 ], [C 4 min 2 ][PF 6 ], divinylbenzene, and ethylene glycol dimethacrylate), respectively. The [C 2 min][BF 4 ] and [C 4 min 2 ][PF 6 ] based Fe 3 O 4 @SiO 2 @IL-MIP with the highest extraction efficiencies was applied to the optimization experiment of MSPE process (including extraction time, adsorbent mass and desorption solvents). Good linearity was obtained with correlation coefficients (R 2 ) over 0.9990 and the relative standard deviations for the intra-day and inter-day determination were less than 3.10% with the extraction recoveries ranged from 85.0% to 98.4%. The results indicated that the proposed Fe 3 O 4 @SiO 2 @IL-MIPs possesses great identification and adsorption properties, and could be used as a good sorbent for selective extraction of CPs in environment waters. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Phytochemical Characterization of Low Molecular Weight Constituents from Marshmallow Roots (Althaea officinalis) and Inhibiting Effects of the Aqueous Extract on Human Hyaluronidase-1.

    Science.gov (United States)

    Sendker, Jandirk; Böker, Ines; Lengers, Isabelle; Brandt, Simone; Jose, Joachim; Stark, Timo; Hofmann, Thomas; Fink, Careen; Abdel-Aziz, Heba; Hensel, Andreas

    2017-02-24

    Extract RE was obtained from the roots of Althaea officinalis in a yield of 8.1%, related to the dried plant material, by extraction with MeOH-H 2 O (1:1), followed by precipitation with EtOH to remove high molecular weight constituents. Phytochemical investigation of RE revealed the presence of N-phenylpropenoyl-l-amino acid amides 1-5, 8% glycine betaine 6, about 9% total amino acids with proline as the main compound, and about 61% mono- and oligomeric carbohydrates with sucrose as the main compound. Further fractionation revealed the presence of a hypolaetin diglycoside (12) and four hypolaetin glycosides (7-9 and 11) with O-sulfocarbohydrate moieties; additionally, 4'-O-methylisoscutellarein-8-O-β-d-(3″-O-sulfo)glucuronopyranoside (10) and the diglycosylated coumarin haploperoside D (13) were identified. The hypolaetin-O-sulfoglycosides 7-10 are new natural products. RE inhibited the enzymatic activity of surface-displayed human hyaluronidase-1 on Escherichia coli F470 cells with an IC 50 of 7.7 mg/mL. RE downregulated mRNA expression of hyal-1 in HaCaT keratinocytes at 125 and 250 μg/mL, respectively. These data contribute to a deeper phytochemical understanding of marshmallow root extracts and to the positive influence of extracts used for therapy of irritated and inflamed buccal tissue and cough.

  15. Evaluation of different hydrophilic stationary phases for the simultaneous determination of iminosugars and other low molecular weight carbohydrates in vegetable extracts by liquid chromatography tandem mass spectrometry.

    Science.gov (United States)

    Rodríguez-Sánchez, S; Quintanilla-López, J E; Soria, A C; Sanz, M L

    2014-11-01

    Iminosugars are considered potential drug candidates for the treatment of several diseases, mainly as a result of their α-glycosidase inhibition properties. A method by hydrophilic interaction liquid chromatography tandem mass spectrometry has been optimized for the first time for the simultaneous determination of complex mixtures of bioactive iminosugars and other low molecular weight carbohydrates (LMWC) in vegetable extracts. Three hydrophilic stationary phases (sulfoalkylbetaine zwitterionic, polyhydroxyethyl aspartamide and ethylene bridge hybrid (BEH) with trifunctionally bonded amide) were compared under both basic and acidic conditions. The best sensitivity (limits of detection between 0.025 and 0.28ngmL -1 ) and overall chromatographic performance in terms of resolution, peak width and analysis time were obtained with the BEH amide column using 0.1% ammonium hydroxide as a mobile phase additive. The optimized method was applied to the analysis of extracts of hyacinth bulbs, buckwheat seeds and mulberry leaves. Iminosugar and other LMWC structures were tentatively assigned by their high resolution daughter ions mass spectra. Several iminosugars such as glycosyl-fagomine in mulberry extract were also described for the first time. Among the extracts analysed, mulberry showed the widest diversity of iminosugars, whereas the highest content of them was found in hyacinth bulb (2.5mgg -1 ) followed by mulberry (1.95 mgg -1 ). Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Multiresidue analysis of cephalosporin antibiotics in bovine milk based on molecularly imprinted polymer extraction followed by liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Baeza, A N; Urraca, J L; Chamorro, R; Orellana, G; Castellari, M; Moreno-Bondi, M C

    2016-11-25

    This work reports the preparation of molecularly imprinted polymers (MIPs) selective to cephalosporin (CF) antibiotics, and their application as molecularly imprinted solid-phase extraction (MISPE) sorbents for the determination of these antimicrobials in milk samples. Several functional monomers and cross-linkers have been screened to select the best combination that provides high selectivity for the simultaneous multiresidue extraction of cefthiofur (THIO), cefazolin (AZO), cefquinome (QUI), cephapirin (API), cephalexin (ALE) and cephalonium (ALO) from the samples. The novel MIPs were prepared by a non-covalent imprinting approach in the form of spherical microparticles using the synthetic surrogate molecule sodium 7-(2-biphenylylcarboxamido)-3-methyl-3-cepheme-4-carboxylate, N-3,5-bis(trifluoromethyl)phenyl-N'-4-vinylphenyl urea (VPU) as functional monomer, and divinylbenzene (DVB) as crosslinking agent in a 1:2:20 molar ratio. The optimized MISPE method allowed the extraction of the target antimicrobials from raw cow milk samples using a selective washing with 5mL methanol/2-[4-(2-hydroxyethyl)-1-piperazinyl]ethanesulfonic acid (HEPES) buffer (0.1M, pH 7.5) (2:98, v/v) to remove the non-specifically retained compounds, followed by elution with 1mL of trifluoroacetic acid (TFA) in methanol (0.1:99.9, v/v). The extracts have been analysed by UHPLC-MS/MS and the analytical method has been validated according to EU guideline 2002/657/EC. The limits of quantification (S/N=10) were in the 1.7-12.5μgkg -1 range, well below the maximum residue limits (MRLs) currently established for the quantified cephalosporins in milk samples. The developed MIP allows mutiresidual determination of the six cephalosporin antibiotics mentioned above, significantly broadening the application to food analysis of MISPE methods. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Non-targeted molecular characterisation of a rose flower ethyl acetate extract using Ultra-HPLC with atmospheric pressure photoionisation and quadrupole time-of-flight MS/MS.

    Science.gov (United States)

    Riffault, Ludivine; Colas, Cyril; Destandau, Emilie; Pasquier, Laure; André, Patrice; Elfakir, Claire

    2015-01-01

    A non-targeted approach to characterise the phytochemical composition of the flower organ of an original rose cultivar 'Jardin de Granville'® was developed. Particular attention was paid to the less documented molecular families of intermediate polarity, compared with the polyphenol family (anthocyanins, flavonoids, tannins) and volatile compounds. To develop a molecular fingerprinting method for the rapid qualitative phytochemical characterisation of the rose flower ethyl acetate extract. An ultra-HPLC with atmospheric pressure photoionisation (APPI) and quadrupole time-of-flight (QTOF) MS/MS combined with microwave-assisted extraction was carried out for ethyl acetate extracts as an intermediate polarity extraction solvent in order to obtain the most exhaustive extract containing a large range of molecular families. An optimised methodology based on the coupling of the UHPLC and APPI source with a QTOF analyser was developed to characterise the extracted molecules. Sixty-one compounds were identified in the extract, covering eight molecular families of intermediate polarity ranging from polyphenols to triglycerides. The presence of flavonoids with anti-oxidant properties and of triterpenoids with potential anti-inflammatory activity was evidenced and cell-wall constituents such as fatty acids, glycolipids, sphingolipids and acylated sterol glycosides were characterised. Some chlorophyll derivatives were also detected. The method developed is appropriate for fast phytochemical evaluation of rose ethyl acetate extract. It produced accurate mass and MS/MS spectra, which permitted identification of a wide range of compounds of intermediate polarity. Copyright © 2015 John Wiley & Sons, Ltd.

  18. Inter Genre Similarity Modelling For Automatic Music Genre Classification

    OpenAIRE

    Bagci, Ulas; Erzin, Engin

    2009-01-01

    Music genre classification is an essential tool for music information retrieval systems and it has been finding critical applications in various media platforms. Two important problems of the automatic music genre classification are feature extraction and classifier design. This paper investigates inter-genre similarity modelling (IGS) to improve the performance of automatic music genre classification. Inter-genre similarity information is extracted over the mis-classified feature population....

  19. Preparation of a magnetic molecularly imprinted polymer by atom-transfer radical polymerization for the extraction of parabens from fruit juices.

    Science.gov (United States)

    You, Xiaoxiao; Piao, Chungying; Chen, Ligang

    2016-07-01

    A silica-based surface magnetic molecularly imprinted polymer for the selective recognition of parabens was prepared using a facile and general method that combined atom-transfer radical polymerization with surface imprinting technique. The prepared magnetic molecularly imprinted polymer was characterized by transmission electron microscopy, Fourier transform infrared spectrometry and physical property measurement. The isothermal adsorption experiment and kinetics adsorption experiment investigated the adsorption property of magnetic molecularly imprinted polymer to template molecule. The four parabens including methylparaben, ethylparaben, propylparaben, and butylparaben were used to assess the rebinding selectivity. An extraction method, which used magnetic molecularly imprinted polymer as adsorbents coupled with high-performance liquid chromatography for the determination of the four parabens in fruit juice samples was developed. Under the optimal conditions, the limits of detections of the four parabens were 0.028, 0.026, 0.021, and 0.026 mg/L, respectively. The precision expressed as relative standard deviation ranging from 2.6 to 8.9% was obtained. In all three fortified levels, recoveries of parabens were in the range of 72.5-89.4%. The proposed method has been applied to different fruit juice samples including orange juice, grape juice, apple juice and peach juice, and satisfactory results were obtained. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Automatic control systems engineering

    International Nuclear Information System (INIS)

    Shin, Yun Gi

    2004-01-01

    This book gives descriptions of automatic control for electrical electronics, which indicates history of automatic control, Laplace transform, block diagram and signal flow diagram, electrometer, linearization of system, space of situation, state space analysis of electric system, sensor, hydro controlling system, stability, time response of linear dynamic system, conception of root locus, procedure to draw root locus, frequency response, and design of control system.

  1. Neural Bases of Automaticity

    Science.gov (United States)

    Servant, Mathieu; Cassey, Peter; Woodman, Geoffrey F.; Logan, Gordon D.

    2018-01-01

    Automaticity allows us to perform tasks in a fast, efficient, and effortless manner after sufficient practice. Theories of automaticity propose that across practice processing transitions from being controlled by working memory to being controlled by long-term memory retrieval. Recent event-related potential (ERP) studies have sought to test this…

  2. Focusing Automatic Code Inspections

    NARCIS (Netherlands)

    Boogerd, C.J.

    2010-01-01

    Automatic Code Inspection tools help developers in early detection of defects in software. A well-known drawback of many automatic inspection approaches is that they yield too many warnings and require a clearer focus. In this thesis, we provide such focus by proposing two methods to prioritize

  3. Automatic differentiation of functions

    International Nuclear Information System (INIS)

    Douglas, S.R.

    1990-06-01

    Automatic differentiation is a method of computing derivatives of functions to any order in any number of variables. The functions must be expressible as combinations of elementary functions. When evaluated at specific numerical points, the derivatives have no truncation error and are automatically found. The method is illustrated by simple examples. Source code in FORTRAN is provided

  4. AUTOMATIC INTRAVENOUS DRIP CONTROLLER*

    African Journals Online (AJOL)

    Both the nursing staff shortage and the need for precise control in the administration of dangerous drugs intra- venously have led to the development of various devices to achieve an automatic system. The continuous automatic control of the drip rate eliminates errors due to any physical effect such as movement of the ...

  5. Automatic Camera Control

    DEFF Research Database (Denmark)

    Burelli, Paolo; Preuss, Mike

    2014-01-01

    Automatically generating computer animations is a challenging and complex problem with applications in games and film production. In this paper, we investigate howto translate a shot list for a virtual scene into a series of virtual camera configurations — i.e automatically controlling the virtual...

  6. Molecularly imprinted polymers applied to the clean-up of zearalenone and alpha-zearalenol from cereal and swine feed sample extracts.

    Science.gov (United States)

    Urraca, Javier L; Marazuela, María Dolores; Moreno-Bondi, María C

    2006-08-01

    A molecularly imprinted polymer prepared using 1-allylpiperazine (1-ALPP) as the functional monomer, trimethyltrimethacrylate (TRIM) as the crosslinker and the zearalenone (ZON)-mimicking template cyclododecanyl-2,4-dihydroxybenzoate (CDHB) has been applied to the clean-up and preconcentration of this mycotoxin (zearalenone) and a related metabolite, alpha-zearalenol (alpha-ZOL), from cereal and swine feed sample extracts. The extraction of ZON and alpha-ZOL from the food samples was accomplished using pressurized liquid extraction (PLE) with MeOH/ACN (50:50, v/v) as the extraction solvent, at 50 degrees C and 1500 psi. The extracted samples were cleaned up and preconcentrated through the MIP cartridge and analyzed using HPLC with fluorescence detection (lambda (exc)=271/ lambda (em)=452 nm). The stationary phase was a polar endcapped C18 column, and ACN/MeOH/water 10/55/35 (v/v/v, 15 mM ammonium acetate) at a flow rate of 1.0 mL min(-1) was used as the mobile phase. The method was applied to the analysis of ZON and alpha-ZOL in wheat, corn, barley, rye, rice and swine feed samples fortified with 50, 100 and 400 ng g(-1) of both mycotoxins, and it gave recoveries of between 85 and 97% (RSD 2.1-6.7%, n=3) and 87-97% (RSD 2.3-5.6%, n=3) for alpha-ZOL and ZON, respectively. The method was validated using a corn reference material for ZON.

  7. Preparation of molecularly imprinted solid-phase microextraction fiber for the selective removal and extraction of the antiviral drug abacavir in environmental and biological matrices

    International Nuclear Information System (INIS)

    Terzopoulou, Zoi; Papageorgiou, Myrsini; Kyzas, George Z.; Bikiaris, Dimitrios N.; Lambropoulou, Dimitra A.

    2016-01-01

    In the present study, a molecularly imprinted solid-phase microextraction fiber (MIP-SPME f ) was synthesized and applied for the selective removal and extraction of the antiviral drug, abacavir (ABA). Morphology and structure characterization of fibers were performed by scanning electron microscopy and Fourier transform infrared spectra, respectively. The effects on the adsorption behavior of the process parameters were studied and the equilibrium data were fitted by the Langmuir, Freundlich and Langmuir-Freundlich models. The maximum adsorption capability (Q max ) was determined by Langmuir- Freundlich model and was 149 mg/g for MIP-SPME f . In the next step, SPME methodology followed by liquid desorption and liquid chromatography with mass spectrometry (LC/MS) has been developed and evaluated for the determination of the target compound in environmental and biological matrices (surface waters, wastewaters and urine). Parameters that could influence SPME efficiency were investigated. Then, optimization of stirring speed, extraction time and salt content was carried out by using a central composite design (CCD) and response surface methodology (RSM). A quadratic model between dependent and independent variables was built. Under the optimum conditions (extraction time 40 min, stirring rate 650 rpm and salt content 0.3% NaCl w/v) the validated method presented a high sensitivity and selectivity with LODs and LOQs in the range of 10.1–13.6 and 33.3–43.9 ng/L, respectively. The developed method was successfully applied to the analysis of ABA in real samples. The percentage extraction efficiency ranged from 88 to 99% revealing good accuracy and absence of matrix effects. - Highlights: • Preparation of a novel SPME MIP fiber with remarkable recognition properties. • Selective removal and extraction of abacavir from environmental & biological media. • Detailed adsorbent characterization and adsorption studies. • Successful application of synthesized MIPs

  8. Automatic identification of species with neural networks

    Directory of Open Access Journals (Sweden)

    Andrés Hernández-Serna

    2014-11-01

    Full Text Available A new automatic identification system using photographic images has been designed to recognize fish, plant, and butterfly species from Europe and South America. The automatic classification system integrates multiple image processing tools to extract the geometry, morphology, and texture of the images. Artificial neural networks (ANNs were used as the pattern recognition method. We tested a data set that included 740 species and 11,198 individuals. Our results show that the system performed with high accuracy, reaching 91.65% of true positive fish identifications, 92.87% of plants and 93.25% of butterflies. Our results highlight how the neural networks are complementary to species identification.

  9. Preparation and Evaluation of Core–Shell Magnetic Molecularly Imprinted Polymers for Solid-Phase Extraction and Determination of Sterigmatocystin in Food

    Directory of Open Access Journals (Sweden)

    Jing-Min Liu

    2017-10-01

    Full Text Available Magnetic molecularly imprinted polymers (MMIPs, combination of outstanding magnetism with specific selective binding capability for target molecules, have proven to be attractive in separation science and bio-applications. Herein, we proposed the core–shell magnetic molecularly imprinted polymers for food analysis, employing the Fe3O4 particles prepared by co-precipitation protocol as the magnetic core and MMIP film onto the silica layer as the recognition and adsorption of target analytes. The obtained MMIPs materials have been fully characterized by scanning electron microscope (SEM, Fourier transform infrared spectrometer (FT-IR, vibrating sample magnetometer (VSM, and re-binding experiments. Under the optimal conditions, the fabricated Fe3O4@MIPs demonstrated fast adsorption equilibrium, a highly improved imprinting capacity, and excellent specificity to target sterigmatocystin (ST, which have been successfully applied as highly efficient solid-phase extraction materials followed by high-performance liquid chromatography (HPLC analysis. The MMIP-based solid phase extraction (SPE method gave linear response in the range of 0.05–5.0 mg·L−1 with a detection limit of 9.1 µg·L−1. Finally, the proposed method was used for the selective isolation and enrichment of ST in food samples with recoveries in the range 80.6–88.7% and the relative standard deviation (RSD <5.6%.

  10. A molecularly imprinted polymer as the sorptive phase immobilized in a rotating disk extraction device for the determination of diclofenac and mefenamic acid in wastewater

    International Nuclear Information System (INIS)

    Manzo, Valentina; Ulisse, Karla; Rodríguez, Inés; Pereira, Eduardo; Richter, Pablo

    2015-01-01

    The microextraction of diclofenac and mefenamic acid from water samples was performed by using rotating disk sorptive extraction (RDSE) with molecularly imprinted polymer (MIP) as the sorptive phase. The MIP was synthesized from the monomer 1-vinylimidazol (VI) together with the cross-linker divinylbenzene (DVB) using diphenylamine as the template molecule. Scanning electron microscopy (SEM) analyses of the MIP revealed clusters of spherical particles having a narrow size distribution, with diameters of approximately 1 μm. The optimized extraction conditions involved a disk rotation velocity of 3000 rpm, an extraction time of 120 min, a sample volume of 50 mL, and a sample pH of 2 as well as 25 mg of MIP immobilized in the disk. Desorption of the extracted analytes was performed with 5 mL of methanol for 10 min. Analysis by gas chromatography-mass spectrometry (GC–MS) was carried out after derivatization of the analytes with N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA). Nonmolecularly imprinted polymer (NIP) was also synthesized for comparison. It was observed that under the same conditions, MIP extracted significantly more NSAIDs containing diphenylamine (or part of this molecule) in their structure than NIP. Higher significant differences between MIP and NIP were observed for diclofenac, mefenamic acid and paracetamol, clearly indicating the effect of the template on the extraction. Recoveries of the method were between 100 and 112%, with relative standard deviations of 5–6%. The limits of detection were between 60 and 223 ng L −1 . Water samples from a wastewater treatment plant (WWTP) of Santiago de Chile, were found to contain concentrations of these acidic drugs between 1.6 and 4.3 μg L −1 and between 1.4 and 3.3 μg L −1 in the influent and effluent, respectively. - Highlights: • A MIP immobilized in a rotating disk sucessfully extracts NSAIDs from wastewater. • MIP had remarkably superior binding properties

  11. A molecularly imprinted polymer as the sorptive phase immobilized in a rotating disk extraction device for the determination of diclofenac and mefenamic acid in wastewater

    Energy Technology Data Exchange (ETDEWEB)

    Manzo, Valentina; Ulisse, Karla [Department of Inorganic and Analytical Chemistry, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, P.O. Box 653, Santiago (Chile); Rodríguez, Inés [Department of Analytical and Inorganic Chemistry, Faculty of Chemical Sciences, University of Concepción (Chile); Pereira, Eduardo, E-mail: epereira@udec.cl [Department of Analytical and Inorganic Chemistry, Faculty of Chemical Sciences, University of Concepción (Chile); Richter, Pablo, E-mail: prichter@ciq.uchile.cl [Department of Inorganic and Analytical Chemistry, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, P.O. Box 653, Santiago (Chile)

    2015-08-19

    The microextraction of diclofenac and mefenamic acid from water samples was performed by using rotating disk sorptive extraction (RDSE) with molecularly imprinted polymer (MIP) as the sorptive phase. The MIP was synthesized from the monomer 1-vinylimidazol (VI) together with the cross-linker divinylbenzene (DVB) using diphenylamine as the template molecule. Scanning electron microscopy (SEM) analyses of the MIP revealed clusters of spherical particles having a narrow size distribution, with diameters of approximately 1 μm. The optimized extraction conditions involved a disk rotation velocity of 3000 rpm, an extraction time of 120 min, a sample volume of 50 mL, and a sample pH of 2 as well as 25 mg of MIP immobilized in the disk. Desorption of the extracted analytes was performed with 5 mL of methanol for 10 min. Analysis by gas chromatography-mass spectrometry (GC–MS) was carried out after derivatization of the analytes with N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA). Nonmolecularly imprinted polymer (NIP) was also synthesized for comparison. It was observed that under the same conditions, MIP extracted significantly more NSAIDs containing diphenylamine (or part of this molecule) in their structure than NIP. Higher significant differences between MIP and NIP were observed for diclofenac, mefenamic acid and paracetamol, clearly indicating the effect of the template on the extraction. Recoveries of the method were between 100 and 112%, with relative standard deviations of 5–6%. The limits of detection were between 60 and 223 ng L{sup −1}. Water samples from a wastewater treatment plant (WWTP) of Santiago de Chile, were found to contain concentrations of these acidic drugs between 1.6 and 4.3 μg L{sup −1} and between 1.4 and 3.3 μg L{sup −1} in the influent and effluent, respectively. - Highlights: • A MIP immobilized in a rotating disk sucessfully extracts NSAIDs from wastewater. • MIP had remarkably superior binding

  12. Structural Characterization and Antioxidative Activity of Low-Molecular-Weights Beta-1,3-Glucan from the Residue of Extracted Ganoderma lucidum Fruiting Bodies

    Directory of Open Access Journals (Sweden)

    Pai-Feng Kao

    2012-01-01

    Full Text Available The major cell wall constituent of Ganoderma lucidum (G. lucidum is β-1,3-glucan. This study examined the polysaccharide from the residues of alkaline-extracted fruiting bodies using high-performance anion-exchange chromatography (HPAEC, and it employed nuclear magnetic resonance (NMR and mass spectrometry (MS to confirm the structures. We have successfully isolated low-molecular-weight β-1,3-glucan (LMG, in high yields, from the waste residue of extracted fruiting bodies of G. lucidum. The 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyl tetrazolium bromide (MTT assay evaluated the capability of LMG to suppress H2O2-induced cell death in RAW264.7 cells, identifying that LMG protected cells from H2O2-induced damage. LMG treatment decreased H2O2-induced intracellular reactive oxygen species (ROS production. LMG also influenced sphingomyelinase (SMase activity, stimulated by cell death to induce ceramide formation, and then increase cell ROS production. Estimation of the activities of neutral and acid SMases in vitro showed that LMG suppressed the activities of both neutral and acid SMases in a concentration-dependent manner. These results suggest that LMG, a water-soluble β-1,3-glucan recycled from extracted residue of G. lucidum, possesses antioxidant capability against H2O2-induced cell death by attenuating intracellular ROS and inhibiting SMase activity.

  13. Salting-out assisted liquid-liquid extraction and partial least squares regression to assay low molecular weight polycyclic aromatic hydrocarbons leached from soils and sediments

    Science.gov (United States)

    Bressan, Lucas P.; do Nascimento, Paulo Cícero; Schmidt, Marcella E. P.; Faccin, Henrique; de Machado, Leandro Carvalho; Bohrer, Denise

    2017-02-01

    A novel method was developed to determine low molecular weight polycyclic aromatic hydrocarbons in aqueous leachates from soils and sediments using a salting-out assisted liquid-liquid extraction, synchronous fluorescence spectrometry and a multivariate calibration technique. Several experimental parameters were controlled and the optimum conditions were: sodium carbonate as the salting-out agent at concentration of 2 mol L- 1, 3 mL of acetonitrile as extraction solvent, 6 mL of aqueous leachate, vortexing for 5 min and centrifuging at 4000 rpm for 5 min. The partial least squares calibration was optimized to the lowest values of root mean squared error and five latent variables were chosen for each of the targeted compounds. The regression coefficients for the true versus predicted concentrations were higher than 0.99. Figures of merit for the multivariate method were calculated, namely sensitivity, multivariate detection limit and multivariate quantification limit. The selectivity was also evaluated and other polycyclic aromatic hydrocarbons did not interfere in the analysis. Likewise, high performance liquid chromatography was used as a comparative methodology, and the regression analysis between the methods showed no statistical difference (t-test). The proposed methodology was applied to soils and sediments of a Brazilian river and the recoveries ranged from 74.3% to 105.8%. Overall, the proposed methodology was suitable for the targeted compounds, showing that the extraction method can be applied to spectrofluorometric analysis and that the multivariate calibration is also suitable for these compounds in leachates from real samples.

  14. Automatic Test Systems Aquisition

    National Research Council Canada - National Science Library

    1994-01-01

    We are providing this final memorandum report for your information and use. This report discusses the efforts to achieve commonality in standards among the Military Departments as part of the DoD policy for automatic test systems (ATS...

  15. Reexamining the molecular/macromolecular model of coal from comparative in situ variable-temperature {sup 1}H NMR studies of Argonne Premium coal 601 and its pyridine extraction residue

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, J.; Maciel, G.E. [Colorado State University, Fort Collins, CO (United States). Dept. of Chemistry

    2002-06-01

    We have carried out the first systematic in situ variable-temperature {sup 1}H NMR study, using the CRAMPS (combined rotation and multiple pulse spectroscopy) technique of the residue from pyridine extraction of Argonne premium coal 601. The change of molecular mobility in the residue under various thermal treatments and pyridine swelling conditions were monitored quantitatively through a proton dipolar-dephasing experiment based on CRAMPS detection. Correlations among molecular structure, molecular mobility and solvent-extraction components were established through comparative variable-temperature {sup 1}H CRAMPS studies on the C{sub 5}D{sub 5}N-saturated original coal and its extraction residue. A critical review of the molecular/macromolecular (M/M) structural model of coal has been made on the basis of the new results, showing that the relationships between the M/M model and molecular dynamics is much more complicated than previously thought. Both the molecular phase and the macromolecular phase can show molecular dynamics behavior ranging from a lack of substantial motion to extremely mobile behaviour with correlation times as short as 30 ns. Without systematic variable temperature studies, correlation between molecular mobility and the M/M model cannot be established correctly by NMR. 28 refs., 7 figs., 6 tabs.

  16. Automatic requirements traceability

    OpenAIRE

    Andžiulytė, Justė

    2017-01-01

    This paper focuses on automatic requirements traceability and algorithms that automatically find recommendation links for requirements. The main objective of this paper is the evaluation of these algorithms and preparation of the method defining algorithms to be used in different cases. This paper presents and examines probabilistic, vector space and latent semantic indexing models of information retrieval and association rule mining using authors own implementations of these algorithms and o...

  17. Position automatic determination technology

    International Nuclear Information System (INIS)

    1985-10-01

    This book tells of method of position determination and characteristic, control method of position determination and point of design, point of sensor choice for position detector, position determination of digital control system, application of clutch break in high frequency position determination, automation technique of position determination, position determination by electromagnetic clutch and break, air cylinder, cam and solenoid, stop position control of automatic guide vehicle, stacker crane and automatic transfer control.

  18. Oocytes Polar Body Detection for Automatic Enucleation

    Directory of Open Access Journals (Sweden)

    Di Chen

    2016-02-01

    Full Text Available Enucleation is a crucial step in cloning. In order to achieve automatic blind enucleation, we should detect the polar body of the oocyte automatically. The conventional polar body detection approaches have low success rate or low efficiency. We propose a polar body detection method based on machine learning in this paper. On one hand, the improved Histogram of Oriented Gradient (HOG algorithm is employed to extract features of polar body images, which will increase success rate. On the other hand, a position prediction method is put forward to narrow the search range of polar body, which will improve efficiency. Experiment results show that the success rate is 96% for various types of polar bodies. Furthermore, the method is applied to an enucleation experiment and improves the degree of automatic enucleation.

  19. Unification of automatic target tracking and automatic target recognition

    Science.gov (United States)

    Schachter, Bruce J.

    2014-06-01

    The subject being addressed is how an automatic target tracker (ATT) and an automatic target recognizer (ATR) can be fused together so tightly and so well that their distinctiveness becomes lost in the merger. This has historically not been the case outside of biology and a few academic papers. The biological model of ATT∪ATR arises from dynamic patterns of activity distributed across many neural circuits and structures (including retina). The information that the brain receives from the eyes is "old news" at the time that it receives it. The eyes and brain forecast a tracked object's future position, rather than relying on received retinal position. Anticipation of the next moment - building up a consistent perception - is accomplished under difficult conditions: motion (eyes, head, body, scene background, target) and processing limitations (neural noise, delays, eye jitter, distractions). Not only does the human vision system surmount these problems, but it has innate mechanisms to exploit motion in support of target detection and classification. Biological vision doesn't normally operate on snapshots. Feature extraction, detection and recognition are spatiotemporal. When vision is viewed as a spatiotemporal process, target detection, recognition, tracking, event detection and activity recognition, do not seem as distinct as they are in current ATT and ATR designs. They appear as similar mechanism taking place at varying time scales. A framework is provided for unifying ATT and ATR.

  20. Electrophoretic extraction of low molecular weight cationic analytes from sodium dodecyl sulfate containing sample matrices for their direct electrospray ionization mass spectrometry.

    Science.gov (United States)

    Kinde, Tristan F; Lopez, Thomas D; Dutta, Debashis

    2015-03-03

    While the use of sodium dodecyl sulfate (SDS) in separation buffers allows efficient analysis of complex mixtures, its presence in the sample matrix is known to severely interfere with the mass-spectrometric characterization of analyte molecules. In this article, we report a microfluidic device that addresses this analytical challenge by enabling inline electrospray ionization mass spectrometry (ESI-MS) of low molecular weight cationic samples prepared in SDS containing matrices. The functionality of this device relies on the continuous extraction of analyte molecules into an SDS-free solvent stream based on the free-flow zone electrophoresis (FFZE) technique prior to their ESI-MS analysis. The reported extraction was accomplished in our current work in a glass channel with microelectrodes fabricated along its sidewalls to realize the desired electric field. Our experiments show that a key challenge to successfully operating such a device is to suppress the electroosmotically driven fluid circulations generated in its extraction channel that otherwise tend to vigorously mix the liquid streams flowing through this duct. A new coating medium, N-(2-triethoxysilylpropyl) formamide, recently demonstrated by our laboratory to nearly eliminate electroosmotic flow in glass microchannels was employed to address this issue. Applying this surface modifier, we were able to efficiently extract two different peptides, human angiotensin I and MRFA, individually from an SDS containing matrix using the FFZE method and detect them at concentrations down to 3.7 and 6.3 μg/mL, respectively, in samples containing as much as 10 mM SDS. Notice that in addition to greatly reducing the amount of SDS entering the MS instrument, the reported approach allows rapid solvent exchange for facilitating efficient analyte ionization desired in ESI-MS analysis.

  1. Biomimetic polymers in analytical chemistry. Part 1: preparation and applications of MIP (Molecularly Imprinted Polymers) in extraction and separation techniques

    International Nuclear Information System (INIS)

    Tarley, Cesar Ricardo Teixeira; Sotomayor, Maria del Pilar Taboada; Kubota, Lauro Tatsuo

    2005-01-01

    MIPs are synthetic polymers that are used as biomimetic materials simulating the mechanism verified in natural entities such as antibodies and enzymes. Although MIPs have been successfully used as an outstanding tool for enhancing the selectivity or different analytical approaches, such as separation science and electrochemical and optical sensors, several parameters must be optimized during their synthesis. Therefore, the state-of-the-art of MIP production as well as the different polymerization methods are discussed. The potential selectivity of MIPs in the extraction and separation techniques focusing mainly on environmental, clinical and pharmaceutical samples as applications for analytical purposes is presented. (author)

  2. Hybrid molecularly imprinted poly(methacrylic acid-TRIM)-silica chemically modified with (3-glycidyloxypropyl)trimethoxysilane for the extraction of folic acid in aqueous medium

    Energy Technology Data Exchange (ETDEWEB)

    Midori de Oliveira, Fernanda; Gava Segatelli, Mariana [Departamento de Química, Universidade Estadual de Londrina, Rod. Celso Garcia Cid, PR 445 Km 380, Campus Universitário, Londrina, PR CEP 86051-990 (Brazil); Tarley, César Ricardo Teixeira, E-mail: ctarleyquim@yahoo.com.br [Departamento de Química, Universidade Estadual de Londrina, Rod. Celso Garcia Cid, PR 445 Km 380, Campus Universitário, Londrina, PR CEP 86051-990 (Brazil); Instituto Nacional de Ciência e Tecnologia (INCT) de Bioanalítica, Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Departamento de Química Analítica, Cidade Universitária Zeferino Vaz s/n, CEP 13083-970 Campinas, SP (Brazil)

    2016-02-01

    In the present study a hybrid molecularly imprinted poly(methacrylic acid-trimethylolpropane trimethacrylate)-silica (MIP) was synthesized and modified with (3-glycidyloxypropyl)trimethoxysilane (GPTMS) with posterior opening of epoxy ring to provide hydrophilic properties of material in the extraction of folic acid from aqueous medium. The chemical and structural aggregates of hybrid material were characterized by means of Fourier Transform Infrared (FT-IR), Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Thermogravimetric analysis (TGA) and textural data. Selectivity data of MIP were compared to non-imprinted polymer (NIP) through competitive sorption studies in the presence of caffeine, paracetamol or 4-aminobenzamide yielding relative selectivity coefficients (k′) higher than one unit, thus confirming the selective character of MIP even in the presence of structurally smaller compounds than the folic acid. The lower hydrophobic sorption by bovine serum albumin (BSA) in the MIP as compared to unmodified MIP proves the hydrophilicity of polymer surface by using GPTMS with opening ring. Under acid medium (pH 1.5) the sorption of folic acid onto MIP from batch experiments was higher than the one achieved for NIP. Equilibrium sorption of folic acid was reached at 120 min for MIP, NIP and MIP without GPTMS and kinetic sorption data were well described by pseudo-second-order, Elovich and intraparticle diffusion models. Thus, these results indicate the existence of different binding energy sites in the polymers and a complex mechanism consisting of both surface sorption and intraparticle transport of folic acid within the pores of polymers. - Highlights: • The molecularly imprinted hybrid polymer showed high adsorption capacity for folic acid. • The molecularly imprinted hybrid polymer showed high selectivity for folic acid. • The molecularly imprinted hybrid polymer modified with GPTMS excludes higher amount of BSA.

  3. Knowledge environments representing molecular entities for the virtual physiological human.

    Science.gov (United States)

    Hofmann-Apitius, Martin; Fluck, Juliane; Furlong, Laura; Fornes, Oriol; Kolárik, Corinna; Hanser, Susanne; Boeker, Martin; Schulz, Stefan; Sanz, Ferran; Klinger, Roman; Mevissen, Theo; Gattermayer, Tobias; Oliva, Baldo; Friedrich, Christoph M

    2008-09-13

    In essence, the virtual physiological human (VPH) is a multiscale representation of human physiology spanning from the molecular level via cellular processes and multicellular organization of tissues to complex organ function. The different scales of the VPH deal with different entities, relationships and processes, and in consequence the models used to describe and simulate biological functions vary significantly. Here, we describe methods and strategies to generate knowledge environments representing molecular entities that can be used for modelling the molecular scale of the VPH. Our strategy to generate knowledge environments representing molecular entities is based on the combination of information extraction from scientific text and the integration of information from biomolecular databases. We introduce @neuLink, a first prototype of an automatically generated, disease-specific knowledge environment combining biomolecular, chemical, genetic and medical information. Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH.

  4. Automatic target identification using neural networks

    Science.gov (United States)

    Abdallah, Mahmoud A.; Samu, Tayib I.; Grissom, William A.

    1995-10-01

    Neural network theories are applied to attain human-like performance in areas such as speech recognition, statistical mapping, and target recognition or identification. In target identification, one of the difficult tasks has been the extraction of features to be used to train the neural network which is subsequently used for the target's identification. The purpose of this paper is to describe the development of an automatic target identification system using features extracted from a specific class of targets. The extracted features were the graphical representations of the silhouettes of the targets. Image processing techniques and some Fast Fourier Transform (FFT) properties were implemented to extract the features. The FFT eliminates variations in the extracted features due to rotation or scaling. A Neural Network was trained with the extracted features using the Learning Vector Quantization paradigm. An identification system was set up to test the algorithm. The image processing software was interfaced with MATLAB Neural Network Toolbox via a computer program written in C language to automate the target identification process. The system performed well as at classified the objects used to train it irrespective of rotation, scaling, and translation. This automatic target identification system had a classification success rate of about 95%.

  5. Automatic Power Line Inspection Using UAV Images

    Directory of Open Access Journals (Sweden)

    Yong Zhang

    2017-08-01

    Full Text Available Power line inspection ensures the safe operation of a power transmission grid. Using unmanned aerial vehicle (UAV images of power line corridors is an effective way to carry out these vital inspections. In this paper, we propose an automatic inspection method for power lines using UAV images. This method, known as the power line automatic measurement method based on epipolar constraints (PLAMEC, acquires the spatial position of the power lines. Then, the semi patch matching based on epipolar constraints (SPMEC dense matching method is applied to automatically extract dense point clouds within the power line corridor. Obstacles can then be automatically detected by calculating the spatial distance between a power line and the point cloud representing the ground. Experimental results show that the PLAMEC automatically measures power lines effectively with a measurement accuracy consistent with that of manual stereo measurements. The height root mean square (RMS error of the point cloud was 0.233 m, and the RMS error of the power line was 0.205 m. In addition, we verified the detected obstacles in the field and measured the distance between the canopy and power line using a laser range finder. The results show that the difference of these two distances was within ±0.5 m.

  6. Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer.

    Science.gov (United States)

    Al-Attas, Asmaa; Assidi, Mourad; Al-Maghrabi, Jaudah; Dallol, Ashraf; Schulten, Hans-Juergen; Abu-Elmagd, Muhammad; Chaudhary, Adeel; Abuzenadah, Adel; Budowle, Bruce; Buhmeida, Abdelbaset; Al-Qahtani, Mohammed

    To date, the conventional formalin-fixed, paraffin-embedded (FFPE) technique is the gold-standard for preserving histomorphology. Once FFPE tissues are stained, slides are routinely archived along with their blocks at biobanks/hospitals. However, the reuse of fixed and stained biospecimens as DNA source is not a common routine practice worldwide and, thus, indicates the need of studies to investigate the feasibility of extracting DNA from already immunohistochemistry (IHC) FFPE-stained slides and its possible reuse in subsequent downstream molecular analyses. FFPE IHC slides from colorectal cancer (CRC) patients were prepared and stored in the CEGMR Biobank. The workflow consists of digitalization of IHC stained slide's image, removing the slide cover-slip, crude dissection and DNA extraction. Following DNA quality assessment, mutation analysis of CTNNB1 and methylation profile of CDH1 were performed. High-quality DNA was obtained allowing 60% concordance between CDH1 methylation and membranous E-cadherin expression pattern. Clean CTNNB1 DNA chromatograms with evenly-spaced peaks were observed. This study is a proof of concept to recycle and reuse DNA from IHC stained slides with suitable concentration and integrity for further downstream molecular applications. These findings will enhance the pathologists' knowledge, attitudes and practices (KAP) towards the use of these biospecimens and support the implementation of this approach in clinical pathology practice. Therefore, the scientific community will benefit from the largest comprehensive database of human fully annotated FFPE biospecimens already available at their disposal in order to demystify the complexity and the heterogeneity of many challenging diseases and foster the transition towards precision medicine. Copyright© 2016, International Institute of Anticancer Research (Dr. John G. Delinasios), All rights reserved.

  7. On-line flow injection molecularly imprinted solid phase extraction for the preconcentration and determination of 1-hydroxypyrene in urine samples.

    Science.gov (United States)

    Serrano, Montserrat; Bartolomé, Mónica; Bravo, Juan Carlos; Paniagua, Gema; Gañan, Judith; Gallego-Picó, Alejandrina; Garcinuño, Rosa María

    2017-05-01

    New analytical strategies tend to automation of sample pre-treatment and flow analysis techniques provided a number of enhanced analytical methods allowing high throughput. Flow techniques are usually faster, more robust and more flexible than their batch equivalents. In addition, flow methods use less sample and reagent amounts and reduce analytical costs and waste. A flow injection solid-phase extraction pre-concentration system using a molecularly imprinted polymer (MIP) packed micro-column was developed for the determination of 1-hydroxypyrene in human urine with fluorescence detection. The pre-concentration of 1-hydroxypyrene on the MIP was carried out based on the specific retention of analyte by on-line introducing the sample into the micro-column system. Methanol and dichloromethane mixture was used to elute the retained analyte for fluorometric analysis. Important influencing factors were studied in detail, in batch and in flow (MISPE procedure optimisation, sample and eluent volumes, flow rate, dimensions of MIP micro-column and amounts of packing material, etc). To the best of our knowledge, this is the first on-line flow injection molecularly imprinted solid phase extraction for the pre-concentration and determination of hydroxylate PAH metabolite in urine samples. The optimised method was successfully applied to the determination of 1-Hydroxypyrene in spiked urine samples, with recoveries in the range of 74-85% and RSD0.996. We obtained limit of detection and quantification of 3.1μgL -1 and 10.5μgL -1 , respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Analysis of in vitro bioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds

    Directory of Open Access Journals (Sweden)

    Southan Christopher

    2011-05-01

    Full Text Available Abstract Background Since the classic Hopkins and Groom druggable genome review in 2002, there have been a number of publications updating both the hypothetical and successful human drug target statistics. However, listings of research targets that define the area between these two extremes are sparse because of the challenges of collating published information at the necessary scale. We have addressed this by interrogating databases, populated by expert curation, of bioactivity data extracted from patents and journal papers over the last 30 years. Results From a subset of just over 27,000 documents we have extracted a set of compound-to-target relationships for biochemical in vitro binding-type assay data for 1,736 human proteins and 1,654 gene identifiers. These are linked to 1,671,951 compound records derived from 823,179 unique chemical structures. The distribution showed a compounds-per-target average of 964 with a maximum of 42,869 (Factor Xa. The list includes non-targets, failed targets and cross-screening targets. The top-278 most actively pursued targets cover 90% of the compounds. We further investigated target ranking by determining the number of molecular frameworks and scaffolds. These were compared to the compound counts as alternative measures of chemical diversity on a per-target basis. Conclusions The compounds-per-protein listing generated in this work (provided as a supplementary file represents the major proportion of the human drug target landscape defined by published data. We supplemented the simple ranking by the number of compounds assayed with additional rankings by molecular topology. These showed significant differences and provide complementary assessments of chemical tractability.

  9. Analysis of in vitro bioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds.

    Science.gov (United States)

    Southan, Christopher; Boppana, Kiran; Jagarlapudi, Sarma Arp; Muresan, Sorel

    2011-05-13

    Since the classic Hopkins and Groom druggable genome review in 2002, there have been a number of publications updating both the hypothetical and successful human drug target statistics. However, listings of research targets that define the area between these two extremes are sparse because of the challenges of collating published information at the necessary scale. We have addressed this by interrogating databases, populated by expert curation, of bioactivity data extracted from patents and journal papers over the last 30 years. From a subset of just over 27,000 documents we have extracted a set of compound-to-target relationships for biochemical in vitro binding-type assay data for 1,736 human proteins and 1,654 gene identifiers. These are linked to 1,671,951 compound records derived from 823,179 unique chemical structures. The distribution showed a compounds-per-target average of 964 with a maximum of 42,869 (Factor Xa). The list includes non-targets, failed targets and cross-screening targets. The top-278 most actively pursued targets cover 90% of the compounds. We further investigated target ranking by determining the number of molecular frameworks and scaffolds. These were compared to the compound counts as alternative measures of chemical diversity on a per-target basis. The compounds-per-protein listing generated in this work (provided as a supplementary file) represents the major proportion of the human drug target landscape defined by published data. We supplemented the simple ranking by the number of compounds assayed with additional rankings by molecular topology. These showed significant differences and provide complementary assessments of chemical tractability.

  10. Preparation of molecularly imprinted solid-phase microextraction fiber for the selective removal and extraction of the antiviral drug abacavir in environmental and biological matrices

    Energy Technology Data Exchange (ETDEWEB)

    Terzopoulou, Zoi [Laboratory of Polymer Chemistry and Technology, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24, Thessaloniki (Greece); Papageorgiou, Myrsini [Laboratory of Environmental Pollution Control, Department of Chemistry, Aristotle University of Thessaloniki, GR–541 24, Thessaloniki (Greece); Kyzas, George Z.; Bikiaris, Dimitrios N. [Laboratory of Polymer Chemistry and Technology, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24, Thessaloniki (Greece); Lambropoulou, Dimitra A., E-mail: dlambro@chem.auth.gr [Laboratory of Environmental Pollution Control, Department of Chemistry, Aristotle University of Thessaloniki, GR–541 24, Thessaloniki (Greece)

    2016-03-24

    In the present study, a molecularly imprinted solid-phase microextraction fiber (MIP-SPME{sub f}) was synthesized and applied for the selective removal and extraction of the antiviral drug, abacavir (ABA). Morphology and structure characterization of fibers were performed by scanning electron microscopy and Fourier transform infrared spectra, respectively. The effects on the adsorption behavior of the process parameters were studied and the equilibrium data were fitted by the Langmuir, Freundlich and Langmuir-Freundlich models. The maximum adsorption capability (Q{sub max}) was determined by Langmuir- Freundlich model and was 149 mg/g for MIP-SPME{sub f}. In the next step, SPME methodology followed by liquid desorption and liquid chromatography with mass spectrometry (LC/MS) has been developed and evaluated for the determination of the target compound in environmental and biological matrices (surface waters, wastewaters and urine). Parameters that could influence SPME efficiency were investigated. Then, optimization of stirring speed, extraction time and salt content was carried out by using a central composite design (CCD) and response surface methodology (RSM). A quadratic model between dependent and independent variables was built. Under the optimum conditions (extraction time 40 min, stirring rate 650 rpm and salt content 0.3% NaCl w/v) the validated method presented a high sensitivity and selectivity with LODs and LOQs in the range of 10.1–13.6 and 33.3–43.9 ng/L, respectively. The developed method was successfully applied to the analysis of ABA in real samples. The percentage extraction efficiency ranged from 88 to 99% revealing good accuracy and absence of matrix effects. - Highlights: • Preparation of a novel SPME MIP fiber with remarkable recognition properties. • Selective removal and extraction of abacavir from environmental & biological media. • Detailed adsorbent characterization and adsorption studies. • Successful application of

  11. On automatic machine translation evaluation

    Directory of Open Access Journals (Sweden)

    Darinka Verdonik

    2013-05-01

    Full Text Available An important task of developing machine translation (MT is evaluating system performance. Automatic measures are most commonly used for this task, as manual evaluation is time-consuming and costly. However, to perform an objective evaluation is not a trivial task. Automatic measures, such as BLEU, TER, NIST, METEOR etc., have their own weaknesses, while manual evaluations are also problematic since they are always to some extent subjective. In this paper we test the influence of a test set on the results of automatic MT evaluation for the subtitling domain. Translating subtitles is a rather specific task for MT, since subtitles are a sort of summarization of spoken text rather than a direct translation of (written text. Additional problem when translating language pair that does not include English, in our example Slovene-Serbian, is that commonly the translations are done from English to Serbian and from English to Slovenian, and not directly, since most of the TV production is originally filmed in English. All this poses additional challenges to MT and consequently to MT evaluation. Automatic evaluation is based on a reference translation, which is usually taken from an existing parallel corpus and marked as a test set. In our experiments, we compare the evaluation results for the same MT system output using three types of test set. In the first round, the test set are 4000 subtitles from the parallel corpus of subtitles SUMAT. These subtitles are not direct translations from Serbian to Slovene or vice versa, but are based on an English original. In the second round, the test set are 1000 subtitles randomly extracted from the first test set and translated anew, from Serbian to Slovenian, based solely on the Serbian written subtitles. In the third round, the test set are the same 1000 subtitles, however this time the Slovene translations were obtained by manually correcting the Slovene MT outputs so that they are correct translations of the

  12. Automatic genre classification of music content

    OpenAIRE

    Scaringella, N.; Zoia, G.; Mlynek, D.

    2006-01-01

    This paper reviews the state-of-the-art in automatic genre classification of music collections through three main paradigms: expert systems, unsupervised classification, and supervised classification. The paper discusses the importance of music genres with their definitions and hierarchies. It also presents techniques to extract meaningful information from audio data to characterize musical excerpts. The paper also presents the results of new emerging research fields and techniques that inves...

  13. Synthesis and application of mesoporous molecular sieve for miniaturized matrix solid-phase dispersion extraction of bioactive flavonoids from toothpaste, plant, and saliva.

    Science.gov (United States)

    Cao, Wan; Cao, Jun; Ye, Li-Hong; Xu, Jing-Jing; Hu, Shuai-Shuai; Peng, Li-Qing

    2015-12-01

    This article describes the use of the mesoporous molecular sieve KIT-6 as a sorbent in miniaturized matrix solid-phase dispersion (MSPD) in combination with ultra-performance LC for the determination of bioactive flavonoids in toothpaste, Scutellariae Radix, and saliva. In this study, for the first time, KIT-6 was used as a sorbent material for this mode of extraction. Compared with common silica-based sorbents (C18 and activated silica gel), the proposed KIT-6 dispersant with a three-dimensional cubic Ia3d structure and highly ordered arrays of mesoporous channels exhibits excellent adsorption capability of the tested compounds. In addition, several experimental variables, such as the mass ratio of sample to dispersant, grinding time, and elution solvent, were optimized to maximize the extraction efficiency. The proposed analytical method is simple, fast, and entails low consumption of samples, dispersants and elution solvents, thereby meeting "green chemistry" requirements. Under the optimized conditions, the recoveries of three bioactive flavonoids obtained by analyzing the spiked samples were from 89.22 to 101.17%. Also, the LODs and LOQs for determining the analytes were in the range of 0.02-0.04 μg/mL and 0.07-0.13 μg/mL, respectively. Finally, the miniaturized matrix solid-phase dispersion method was successfully applied to the analysis of target solutes in real samples, and satisfactory results were obtained. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Determination of 16 polycyclic aromatic hydrocarbons in seawater using molecularly imprinted solid-phase extraction coupled with gas chromatography-mass spectrometry.

    Science.gov (United States)

    Song, Xingliang; Li, Jinhua; Xu, Shoufang; Ying, Rongjian; Ma, Jiping; Liao, Chunyang; Liu, Dongyan; Yu, Junbao; Chen, Lingxin

    2012-09-15

    A method of solid-phase extraction (SPE) using molecularly imprinted polymers (MIPs) as adsorbent coupled with gas chromatography-mass spectrometry (GC-MS) was developed for the determination of 16 types of polycyclic aromatic hydrocarbons (PAHs) in seawater samples. The MIPs were prepared through non-covalent polymerization by using the 16 PAHs mixture as a template based on sol-gel surface imprinting. Compared with the non-imprinted polymers (NIPs), the MIPs exhibited excellent affinity towards 16 PAHs with binding capacity of 111.0-195.0 μg g(-1), and imprinting factor of 1.50-3.12. The significant binding specificity towards PAHs even in the presence of environmental parameters such as dissolved organic matter and various metal ions, suggested that this new imprinting material was capable of removing 93.2% PAHs in natural seawater. High sensitivity was attained, with the low limits of detection for 16 PAHs in natural seawater ranging from 5.2-12.6 ng L(-1). The application of MIPs with high affinity and excellent stereo-selectivity toward PAHs in SPE might offer a more attractive alternative to conventional sorbents for extraction and abatement of PAH-contaminated seawater. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Molecularly imprinted layer-coated silica nanoparticles for selective solid-phase extraction of bisphenol A from chemical cleansing and cosmetics samples

    International Nuclear Information System (INIS)

    Zhu Rong; Zhao Wenhui; Zhai Meijuan; Wei Fangdi; Cai Zheng; Sheng Na; Hu Qin

    2010-01-01

    Highly selective molecularly imprinted layer-coated silica nanoparticles for bisphenol A (BPA) were synthesized by molecular imprinting technique with a sol-gel process on the supporter of silica nanoparticles. The BPA-imprinted silica nanoparticles were characterized by fourier transform infrared spectrometer, transmission electron microscope, dynamic adsorption and static adsorption tests. The equilibrium association constant, K a , and the apparent maximum number of binding sites, Q max , were estimated to be 1.25 x 10 5 mL μmol -1 and 16.4 μmol g -1 , respectively. The BPA-imprinted silica nanoparticles solid-phase extraction (SPE) column had higher selectivity for BPA than the commercial C18-SPE column. The results of the study indicated that the prepared BPA-imprinted silica nanoparticles exhibited high adsorption capacity and selectivity, and offered a fast kinetics for the rebinding of BPA. The BPA-imprinted silica nanoparticles were successfully used in SPE to selectively enrich and determine BPA from shampoo, bath lotion and cosmetic cream samples.

  16. Natural Korean Medicine Dang-Gui: Biosynthesis, Effective Extraction and Formulations of Major Active Pyranocoumarins, Their Molecular Action Mechanism in Cancer, and Other Biological Activities

    Directory of Open Access Journals (Sweden)

    Chinreddy Subramanyam Reddy

    2017-12-01

    Full Text Available Angelica gigas Nakai (AGN is a crucial oriental medicinal herb that grows especially in Korea and the Far-East countries. It contains chemically active compounds like pyranocoumarins, polyacetylenes and essential oils, which might be useful for treatment of several chronic diseases. It has been used for centuries as a traditional medicine in Southeast Asia, but in Western countries is used as a functional food and a major ingredient of several herbal products. The genus Angelica is also known as ‘female ginseng’ due to its critical therapeutic role in female afflictions, such as gynecological problems. However, it is well-documented that the AGN pyranocoumarins may play vital beneficial roles against cancer, neurodisorders, inflammation, osteoporosis, amnesia, allergies, depression, fungi, diabetes, ischemia, dermatitis, reactive oxygen species (ROS and androgen. Though numerous studies revealed the role of AGN pyranocoumarins as therapeutic agents, none of the reviews have published their molecular mechanism of action. To the best of our knowledge, this would be the first review that aims to appraise the biosynthesis of AGN’s major active pyranocoumarins, discuss effective extraction and formulation methods, and detail the molecular action mechanism of decursin (D, decursinol angelate (DA and decursinol (DOH in chronic diseases, which would further help extension of research in this area.

  17. Characterization of particle morphology of biochanin A molecularly imprinted polymers and their properties as a potential sorbent for solid-phase extraction

    Energy Technology Data Exchange (ETDEWEB)

    Chrzanowska, Anna M.; Poliwoda, Anna, E-mail: Anna.Poliwoda@uni.opole.pl; Wieczorek, Piotr P.

    2015-04-01

    Molecularly imprinted polymers (MIPs) with biochanin A as a template were obtained using a bulk polymerization with non-covalent imprinting approach. The polymers were prepared in acetonitrile as porogen, using ethylene glycol dimethacrylate (EDMA) as cross-linking agent. The synthesis, with an application of 1′,1′-azobis(cyclohexanecarbonitrile) (ACHN) as an initiator, has been performed thermally. During the synthesis process the effect of different functional monomers such as methacrylic acid (MAA), acrylamide (AA) and 4-vinylpyridine (4-VP) was investigated. The application of nitrogen sorption porosimetry, scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR) permitted the characterization and evaluation of synthesized polymers. The adsorption capacity of obtained MIPs was checked by using the binding testing. All synthesized polymers were evaluated as solid-phase extraction (SPE) sorbents for isolation and preconcentration of biochanin A and its analogues, daidzein and genistein. The MIPs exhibited higher affinity for biochanin A over competitive compounds. - Highlights: • The molecularly imprinted polymers with biochanin A as a template were synthesized. • The surface of synthesized monoliths was formed mainly from mesopores (73–77%). • Biochanin A was effectively concentrated in each of the synthesized polymers (recovery > 89.8%). • The results show potential ability of synthesized MIPs in analysis of phytoestrogens in real samples.

  18. Automatic Planning of External Search Engine Optimization

    Directory of Open Access Journals (Sweden)

    Vita Jasevičiūtė

    2015-07-01

    Full Text Available This paper describes an investigation of the external search engine optimization (SEO action planning tool, dedicated to automatically extract a small set of most important keywords for each month during whole year period. The keywords in the set are extracted accordingly to external measured parameters, such as average number of searches during the year and for every month individually. Additionally the position of the optimized web site for each keyword is taken into account. The generated optimization plan is similar to the optimization plans prepared manually by the SEO professionals and can be successfully used as a support tool for web site search engine optimization.

  19. Cellular and molecular mechanisms of the Ganoderma applanatum extracts induces apoptosis on SGC-7901 gastric cancer cells.

    Science.gov (United States)

    Ma, Jieqiong; Liu, Chanmin; Chen, Yongqiang; Jiang, Jihong; Qin, Zhihong

    2011-04-01

    To investigate the inhibition effect of Ganoderma applanatum extract (GAEAE) on human gastric cancer cell lines and apoptosis mechanism, Alamar Blue assay was used to assess the inhibition and apoptosis-inducing effect of the GAEAE on proliferation of SGC-7901 cells, the DNA ladders of the apoptosis cells was done, the mRNA expression of p53, Bax, Bcl-2 and JNK were analysed by reverse transcription-polymerase chain reaction. The levels of the Cyt C and the p53, Bax/Bcl-2, JNK proteins and the caspase-3 activity in the SGC-7901 cells were measured with ELISA kits. Our data showed that the GAEAE markedly inhibited the proliferation of SGC-7901 cells in a dose-dependent manner. The expression of Bcl-2 protein was down-regulated and Bax, c-jun, p53 protein expressions were up-regulated by the GAEAE treatment in SGC-7901 cells. The activity of caspase-3 was markedly increased and the Cty C was markedly released into cytoplasm from the mitochondria after GAEAE action. In conclusion, our results indicated that the GAEAE could enhance the sensitivity of SGC-7901 cells to the c-jun, p53, Bax and Bcl-2 induced apoptosis and provided a promising approach to anti-human gastric cancer therapy with Ganoderma applanatum. Copyright © 2011 John Wiley & Sons, Ltd.

  20. Molecular mechanisms of anti-hyperglycemic effects of Costus speciosus extract in streptozotocin-induced diabetic rats

    Science.gov (United States)

    Ali, Haytham A.; Almaghrabi, Omar A.; Afifi, Mohamed E.

    2014-01-01

    Objectives: To investigate the mechanisms of the anti-hyperglycemic effect of Costus speciosus (C. speciosus) root ethanolic extracts (CSREt) by assessing its action on insulin synthesis and glucose catabolic enzyme gene expression and activities in streptozotocin (STZ) diabetic rats. Methods: This study was carried out at the Biochemical Laboratory, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt between July and August 2013. Sixty male albino rats (120 ± 20 g weight, and 6 months old) were used and divided into 6 groups (n=10). Two groups served as diabetic and nondiabetic controls. Four groups of STZ diabetic animals were given oral C. speciosus (CSREt) in doses of 200, 400, and 600 mg/kg body weight, and 600 µg/kg body weight of the standard drug glibenclamide for 4 weeks. Results: The CSREt 400 and 600 mg/kg body weight induced a decrease in blood glucose and an increase in serum insulin level, glucokinase (GK), aldolase, pyruvate kinase (PK), succinate dehydrogenase (SDH), and glycogen synthase activities in addition to a higher expression level of insulin, insulin receptor A (IRA), GK, PK, SDH, and glucose transporting protein. Conclusion: The C. speciosus has anti-hyperglycemic activity. It induces insulin secretion and release from cells, as well as stimulates the tissue’s insulin sensitivity leading to an increase of the tissues’ glucose uptake, storage, and oxidation. PMID:25491216

  1. Automatic text summarization

    CERN Document Server

    Torres Moreno, Juan Manuel

    2014-01-01

    This new textbook examines the motivations and the different algorithms for automatic document summarization (ADS). We performed a recent state of the art. The book shows the main problems of ADS, difficulties and the solutions provided by the community. It presents recent advances in ADS, as well as current applications and trends. The approaches are statistical, linguistic and symbolic. Several exemples are included in order to clarify the theoretical concepts.  The books currently available in the area of Automatic Document Summarization are not recent. Powerful algorithms have been develop

  2. Automatic Ultrasound Scanning

    DEFF Research Database (Denmark)

    Moshavegh, Ramin

    on the scanners, and to improve the computer-aided diagnosis (CAD) in ultrasound by introducing new quantitative measures. Thus, four major issues concerning automation of the medical ultrasound are addressed in this PhD project. They touch upon gain adjustments in ultrasound, automatic synthetic aperture image...... on the user adjustments on the scanner interface to optimize the scan settings. This explains the huge interest in the subject of this PhD project entitled “AUTOMATIC ULTRASOUND SCANNING”. The key goals of the project have been to develop automated techniques to minimize the unnecessary settings...

  3. The Dual Edema-Preventing Molecular Mechanism of the Crataegus Extract WS 1442 Can Be Assigned to Distinct Phytochemical Fractions.

    Science.gov (United States)

    Fuchs, Simone; Bischoff, Iris; Willer, Elisabeth A; Bräutigam, Jacqueline; Bubik, Martin F; Erdelmeier, Clemens A J; Koch, Egon; Faleschini, Maria T; De Mieri, Maria; Bauhart, Milena; Zahler, Stefan; Hensel, Andreas; Hamburger, Matthias; Potterat, Olivier; Fürst, Robert

    2017-05-01

    The hawthorn ( Crataegus spp.) extract WS 1442 is used against mild forms of chronic heart failure. This disease is associated with endothelial barrier dysfunction and edema formation. We have recently shown that WS 1442 protects against this dysfunction by a dual mechanism: it both promotes endothelial barrier integrity by activation of a barrier-enhancing pathway (cortactin activation) and inhibits endothelial hyperpermeability by blocking a barrier disruptive pathway (calcium signaling). In this study, we aimed to identify the bioactive compounds responsible for these actions by using a bioactivity-guided fractionation approach. From the four fractions generated from WS 1442 by successive elution with water, 95 % ethanol, methanol, and 70 % acetone, only the water fraction was inactive, whereas the other three triggered a reduction of endothelial hyperpermeability. Analyses of intracellular calcium levels and cortactin phosphorylation were used as readouts to estimate the bioactivity of subfractions and isolated compounds. Interestingly, only the ethanolic fraction interfered with the calcium signaling, whereas only the methanolic fraction led to an activation of cortactin. Thus, the dual mode of action of WS 1442 could be clearly assigned to two distinct fractions. Although the identification of the calcium-active substance(s) was not successful, we could exclude an involvement of phenolic compounds. Cortactin activation, however, could be clearly attributed to oligomeric procyanidins with a distinct degree of polymerization. Taken together, our study provides the first approach to identify the active constituents of WS 1442 that address different cellular pathways leading to the inhibition of endothelial barrier dysfunction. Georg Thieme Verlag KG Stuttgart · New York.

  4. Reactor component automatic grapple

    International Nuclear Information System (INIS)

    Greenaway, P.R.

    1982-01-01

    A grapple for handling nuclear reactor components in a medium such as liquid sodium which, upon proper seating and alignment of the grapple with the component as sensed by a mechanical logic integral to the grapple, automatically seizes the component. The mechanical logic system also precludes seizure in the absence of proper seating and alignment. (author)

  5. Automatic Commercial Permit Sets

    Energy Technology Data Exchange (ETDEWEB)

    Grana, Paul [Folsom Labs, Inc., San Francisco, CA (United States)

    2017-12-21

    Final report for Folsom Labs’ Solar Permit Generator project, which has successfully completed, resulting in the development and commercialization of a software toolkit within the cloud-based HelioScope software environment that enables solar engineers to automatically generate and manage draft documents for permit submission.

  6. Automatic Complexity Analysis

    DEFF Research Database (Denmark)

    Rosendahl, Mads

    1989-01-01

    One way to analyse programs is to to derive expressions for their computational behaviour. A time bound function (or worst-case complexity) gives an upper bound for the computation time as a function of the size of input. We describe a system to derive such time bounds automatically using abstrac...

  7. Automatic Prosodic Segmentation by F0 Clustering Using Superpositional Modeling.

    OpenAIRE

    Nakai, Mitsuru; Harald, Singer; Sagisaka, Yoshinori; Shimodaira, Hiroshi

    1995-01-01

    In this paper, we propose an automatic method for detecting accent phrase boundaries in Japanese continuous speech by using F0 information. In the training phase, hand labeled accent patterns are parameterized according to a superpositional model proposed by Fujisaki, and assigned to some clusters by a clustering method, in which accent templates are calculated as centroid of each cluster. In the segmentation phase, automatic N-best extraction of boundaries is performe...

  8. A molecular exploration of human DNA/RNA co-extracted from the palmar surface of the hands and fingers.

    Science.gov (United States)

    Lacerenza, D; Aneli, S; Omedei, M; Gino, S; Pasino, S; Berchialla, P; Robino, C

    2016-05-01

    "Touch DNA" refers to the DNA that is left behind when a person touches or comes into contact with an item. However, the source of touch DNA is still debated and the large variability in DNA yield from casework samples suggests that, besides skin, various body fluids can be transferred through contact. Another important issue concerning touch DNA is the possible occurrence of secondary transfer, but the data published in the literature in relation to the background levels of foreign DNA present on the hand surfaces of the general population are very limited. As the present study aimed at better understanding the nature and characteristics of touch DNA, samples were collected from the palmar surface of the hands and fingers ("PHF" samples) of 30 male and 30 female donors by tape-lifting/swabbing and subjected to DNA/RNA co-extraction. Multiplex mRNA profiling showed that cellular material different from skin could be observed in 15% of the PHF samples. The total amount of DNA recovered from these samples (median 5.1 ng) was significantly higher than that obtained from samples containing skin cells only (median 1.6 ng). The integrity of the DNA isolated from the donors' hands and fingers as well as the prevalence of DNA mixtures were evaluated by STR typing and compared with reference STR profiles from buccal swabs. DNA integrity appeared significantly higher in the male rather than in the female subsample, as the average percentage of the donors' alleles effectively detected in PHF profiles was 75.1% and 60.1%, respectively. The prevalence of mixtures with a foreign DNA contribution ≥20% was 19.2% (30.0% in the female PHF samples and 8.3% in the male PHF samples). The obtained results support the hypothesis that transfer of cellular material different from skin may underlie the occasional recovery of quality STR profiles from handled items. These results also suggest that gender may represent an important factor influencing the propensity of individuals to carry

  9. Preparation and characterization of molecularly-imprinted polymers for extraction of sanshool acid amide compounds followed by their separation from pepper oil resin derived from Chinese prickly ash (Zanthoxylum bungeanum).

    Science.gov (United States)

    Chen, Xiaolong; Jin, Xinkai; Li, Yao; Chen, Guangjing; Chen, Kewei; Kan, Jianquan

    2018-01-01

    Molecularly imprinted polymers were prepared using the molecular structure analogs of sanshool as template molecule, 2-vinylpyridine and β-cyclodextrin as double functional monomers, ethylene dimethacrylate as cross linker, and azobisisobutyronitrile as initiator. The structural characteristics of the polymers were determined by Fourier-transform infrared spectroscopy and scanning electron microscopy. Dynamic adsorption and isothermal adsorption were also investigated. The molecularly imprinted polymers were used to prepare a molecularly imprinted solid-phase extraction column in order to separate acid amide components from pepper oil resin derived from Chinese prickly ash (Zanthoxylum bungeanum). After eluting, the percentage of acid amide components was enhanced to 92.40 ± 1.41% compared with 23.34 ± 1.21% in the initial pepper oil resin, indicating good properties of purification of molecularly imprinted polymers and potential industrial application. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Biochemical and molecular aspects of aluminium chloride-induced neurotoxicity in mice and the protective role of Crocus sativus L. extraction and honey syrup.

    Science.gov (United States)

    Shati, A A; Elsaid, F G; Hafez, E E

    2011-02-23

    -spondin gene was up-regulated in all examined animals except the control ones but the other two genes were only induced in the animals treated with AlCl(3) and honey syrup. We conclude that the biochemical and molecular studies showed the neurotoxicity of AlCl(3) in the brains of mice. In addition, there was an ameliorative change with saffron extract and honey syrup against AlCl(3) neurotoxicity. The obtained molecular results suggest that AlCl(3) made induction for BCL-W gene, which is an anticancer gene or belongs to the DNA repair system in the brain cells, as well as for R-spondin and inositol polyphosphate 4-phosphatase genes, which help in cell proliferation. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

  11. A Hybrid Human-Computer Approach to the Extraction of Scientific Facts from the Literature.

    Science.gov (United States)

    Tchoua, Roselyne B; Chard, Kyle; Audus, Debra; Qin, Jian; de Pablo, Juan; Foster, Ian

    2016-01-01

    A wealth of valuable data is locked within the millions of research articles published each year. Reading and extracting pertinent information from those articles has become an unmanageable task for scientists. This problem hinders scientific progress by making it hard to build on results buried in literature. Moreover, these data are loosely structured, encoded in manuscripts of various formats, embedded in different content types, and are, in general, not machine accessible. We present a hybrid human-computer solution for semi-automatically extracting scientific facts from literature. This solution combines an automated discovery, download, and extraction phase with a semi-expert crowd assembled from students to extract specific scientific facts. To evaluate our approach we apply it to a challenging molecular engineering scenario, extraction of a polymer property: the Flory-Huggins interaction parameter. We demonstrate useful contributions to a comprehensive database of polymer properties.

  12. Determination of fluoroquinolone antibiotics in environmental water samples based on magnetic molecularly imprinted polymer extraction followed by liquid chromatography-tandem mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Chen Ligang; Zhang Xiaopan; Xu Yang [College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, Jilin (China); Du Xiaobo; Sun Xin [College of Physics, Jilin University, 2699 Qianjin Street, Changchun 130012 (China); Sun Lei; Wang Hui; Zhao Qi; Yu Aimin; Zhang Hanqi [College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, Jilin (China); Ding Lan, E-mail: dinglan@jlu.edu.cn [College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, Jilin (China)

    2010-03-03

    A simple method based on magnetic separation for selective extraction of fluoroquinolones (FQs) from environmental water samples has been developed using magnetic molecularly imprinted polymer (MMIP) as sorbent. The MMIP has been prepared using ciprofloxacin as template molecule, methacrylic acid as functional monomer, ethylene glycol dimethacrylate as cross-linking agent and Fe{sub 3}O{sub 4} magnetite as magnetic component. The polymer has been characterized by scanning electron microscopy, Fourier-transform infrared spectrometry and vibrating sample magnetometry. Various parameters affecting the extraction efficiency were evaluated in order to achieve optimal concentration and reduce non-specific interactions. The analytes desorbed from the polymers were determined by liquid chromatography-tandem mass spectrometry. The matrix effect was evaluated by using different washing solvents for removing interfering compounds from the MMIPs after sample loading. Under the optimal conditions, the linearity of the method obtained is in the range of 20-2000 ng L{sup -1}. The detection limits of FQs are in the range of 3.2-6.2 ng L{sup -1}. The relative standard deviations of intra- and inter-day tests ranging from 2.5 to 7.2% and from 3.6 to 9.1% are obtained. In all three spiked levels (20, 100 and 200 ng L{sup -1}), the recoveries of FQs are in the range of 76.3-94.2%. The proposed method was successfully applied to determine FQs including ciprofloxacin, enrofloxacin, lomefloxacin, levofloxacin, fleroxacin and sparfloxacin in different water samples, such as lake water, river water, primary and final sewage effluent. Ciprofloxacin and fleroxacin were found in primary and final sewage effluent samples with the contents in the range of 26-87 ng L{sup -1}.

  13. A novel restricted access material combined to molecularly imprinted polymers for selective solid-phase extraction and high performance liquid chromatography determination of 2-methoxyestradiol in plasma samples.

    Science.gov (United States)

    Du, Bin; Qu, Tiantian; Chen, Zheng; Cao, Xiaohui; Han, Shuping; Shen, Guopeng; Wang, Lei

    2014-11-01

    A feasibility study was performed in order to ensure the possibilities in using a restricted access material combined to molecularly imprinted polymers (RAM-MIP) as sorbent material in solid phase extraction (SPE) for clean-up of 2-methoxyestradiol (2-ME) from plasma samples. The MIP with hydrophilic external layer was designed by precipitation polymerization. The polymer was characterized by thermogravimetric analysis (TGA) and scanning electron microscope (SEM). The use of analogs of 2-ME as templates, in combination with a chromatographic separation of the analytes in the sample, overcame the problem of the template bleeding. To demonstrate the property of the RAM-MIP obtained, a comparison of commercially available C18 SPE was performed. The results showed that the RAM-MISPE recoveries were significantly higher than that of C18 SPE for 2-ME in trace concentration. During the extraction process, 2-ME was sufficiently cleaned for further chromatographic analysis with no interferences from template leakage and matrix. Good linearity was obtained from 0.06 to 20 μg mL(-1) with the correlation coefficient r>0.9991. The coefficient of variation of the inter-assay precision was less than 11.9%. The recoveries of 2-ME in rat plasma at three spiked levels were in the range of 99.10-101.00%. Based on the analytical validation results, the proposed method (RAM-MIP off-line SPE/HPLC) can be a useful tool to determine 2-ME in rat plasma samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Ultrasound assisted combined molecularly imprinted polymer for selective extraction of nicotinamide in human urine and milk samples: Spectrophotometric determination and optimization study.

    Science.gov (United States)

    Asfaram, Arash; Ghaedi, Mehrorang; Dashtian, Kheibar

    2017-01-01

    Ultrasound-assisted dispersive solid phase microextraction followed by UV-vis spectrophotometer (UA-DSPME-UV-vis) was designed for extraction and preconcentration of nicotinamide (vitamin B 3 ) by HKUST-1 metal organic framework (MOF) based molecularly imprinted polymer (MIP). This new material was characterized by FTIR and FE-SEM techniques. The preliminary Plackett-Burman design was used for screening and subsequently the central composite design justifies significant terms and possible construction of mathematical equation which give the individual and cooperative contribution of variables like HKUST-1-MOF-NA-MIP mass, sonication time, temperature, eluent volume, pH and vortex time. Accordingly the optimum condition was set as: 2.0mg HKUST-1-MOF-NA-MIP, 200μL eluent and 5.0min sonication time in center points other variables were determined as the best conditions to reach the maximum recovery of the analyte. The UA-DSPME-UV-vis method performances like excellent linearity (LR), limits of detection (LOD), limits of quantification of 10-5000μgL -1 with R 2 of 0.99, LOD (1.96ngmL -1 ), LOQ (6.53μgL -1 ), respectively show successful and accurate applicability of the present method for monitoring analytes with within- and between-day precision of 0.96-3.38%. The average absolute recoveries of the nicotinamide extracted from the urine, milk and water samples were 95.85-101.27%. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Highly selective dummy molecularly imprinted polymer as a solid-phase extraction sorbent for five bisphenols in tap and river water.

    Science.gov (United States)

    Sun, Xiaoli; Wang, Jincheng; Li, Yun; Jin, Jing; Zhang, Baoqin; Shah, Syed Mazhar; Wang, Xueli; Chen, Jiping

    2014-05-23

    A simple and fast method for both dummy template selection and polymer composition optimization is proposed here. A series of dummy templates for bisphenols imprinting were screened by running them on a non-imprinted polymer (NIP) column with porogen solvent as mobile phase. The tested dummy templates mainly involved bisphenol S (BPS), bromobisphenol A (TBBPA), bisphenol F (BPF), bisphenol E (BPE), bisphenol B (BPB), bisphenol AF (BPAF), 2,2',6,6'-tetramethyl-4,4'-sulfonyldiphenol (BS-TM) and 4,4'-diaminodiphenylmethane (DADPM). Different monomers and porogens were also investigated for BPS and DADPM using the same method. BPS dummy template was finally selected with acetonitrile and 4-VP as porogen and monomer. The resulting dummy molecularly imprinted polymer (DMIP) achieved superior affinities for BPF, BPE, BPA, BPB and BPAF with imprinting factors 14.5, 13.8, 8.7, 5.7 and 4.2, respectively. An efficient method based on BPS-DMIP-SPE coupled with HPLC-UV was developed for selective extraction of BPF, BPE, BPA, BPB and BPAF in water samples. The method showed excellent recoveries (89.4-102.0%) and precision (RSD 0.3-4.8%, n=5) for tap and river water samples spiked at three concentration levels each (40, 200 and 1000ngL(-1)). The detection limits ranged between 2.2 and 3.8ngL(-1) with a sample volume of 500mL. The result demonstrated the superiority of the optimized method for selective extraction of BPs in water samples at the ngL(-1) level. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Automatic trend estimation

    CERN Document Server

    Vamos¸, C˘alin

    2013-01-01

    Our book introduces a method to evaluate the accuracy of trend estimation algorithms under conditions similar to those encountered in real time series processing. This method is based on Monte Carlo experiments with artificial time series numerically generated by an original algorithm. The second part of the book contains several automatic algorithms for trend estimation and time series partitioning. The source codes of the computer programs implementing these original automatic algorithms are given in the appendix and will be freely available on the web. The book contains clear statement of the conditions and the approximations under which the algorithms work, as well as the proper interpretation of their results. We illustrate the functioning of the analyzed algorithms by processing time series from astrophysics, finance, biophysics, and paleoclimatology. The numerical experiment method extensively used in our book is already in common use in computational and statistical physics.

  17. Automatic Program Development

    DEFF Research Database (Denmark)

    Automatic Program Development is a tribute to Robert Paige (1947-1999), our accomplished and respected colleague, and moreover our good friend, whose untimely passing was a loss to our academic and research community. We have collected the revised, updated versions of the papers published in his ...... a renewed stimulus for continuing and deepening Bob's research visions. A familiar touch is given to the book by some pictures kindly provided to us by his wife Nieba, the personal recollections of his brother Gary and some of his colleagues and friends....... honor in the Higher-Order and Symbolic Computation Journal in the years 2003 and 2005. Among them there are two papers by Bob: (i) a retrospective view of his research lines, and (ii) a proposal for future studies in the area of the automatic program derivation. The book also includes some papers...

  18. Automaticity or active control

    DEFF Research Database (Denmark)

    Tudoran, Ana Alina; Olsen, Svein Ottar

    This study addresses the quasi-moderating role of habit strength in explaining action loyalty. A model of loyalty behaviour is proposed that extends the traditional satisfaction–intention–action loyalty network. Habit strength is conceptualised as a cognitive construct to refer to the psychological...... aspects of the construct, such as routine, inertia, automaticity, or very little conscious deliberation. The data consist of 2962 consumers participating in a large European survey. The results show that habit strength significantly moderates the association between satisfaction and action loyalty, and......, respectively, between intended loyalty and action loyalty. At high levels of habit strength, consumers are more likely to free up cognitive resources and incline the balance from controlled to routine and automatic-like responses....

  19. Automatic food decisions

    DEFF Research Database (Denmark)

    Mueller Loose, Simone

    Consumers' food decisions are to a large extent shaped by automatic processes, which are either internally directed through learned habits and routines or externally influenced by context factors and visual information triggers. Innovative research methods such as eye tracking, choice experiments...... and food diaries allow us to better understand the impact of unconscious processes on consumers' food choices. Simone Mueller Loose will provide an overview of recent research insights into the effects of habit and context on consumers' food choices....

  20. Automatic Language Identification

    Science.gov (United States)

    2000-08-01

    hundreds guish one language from another. The reader is referred of input languages would need to be supported , the cost of to the linguistics literature...eventually obtained bet- 108 TRAINING FRENCH GERMAN ITRAIING FRENCH M- ALGORITHM - __ GERMAN NHSPANISH TRAINING SPEECH SET OF MODELS: UTTERANCES ONE MODEL...i.e. vowels ) for each speech utterance are located malized to be insensitive to overall amplitude, pitch and automatically. Next, feature vectors

  1. On-line coupling of molecularly imprinted solid phase extraction with liquid chromatography for the fast determination of coumarins from complex samples.

    Science.gov (United States)

    Machyňáková, Andrea; Lhotská, Ivona; Hroboňová, Katarína; Šatínský, Dalibor

    2017-10-25

    In this work, an on-line SPE-HPLC method with spectrophotometric detection was developed for the determination of coumarins in complex samples. For the on-line cleanup of samples, a molecularly imprinted polymer was packed into the column cartridge and coupled directly with HPLC (MISPE-HPLC) using a column switching system. The separation of coumarins was performed on a C18 core-shell column (100×4.6mm, 5μm) with a mobile phase consisting of 0.3% acetic acid/acetonitrile with gradient elution at a flow-rate of 1mLmin -1 . The total time of the whole analytical run, including the extraction step, was 13.25min. The on-line MISPE-HPLC method was optimized and validated. The results showed good linearity (0.10-100μgmL -1 ) with correlation coefficients higher than 0.99. The LOD values were from 0.03 to 0.15μgmL -1 . The proposed method was successfully applied for analysis of real samples (Cassia cinnamon, chamomile tea, and Tokaj specialty wines) and obtained recoveries varied from 78.7% to 112.2% with an RSD less than 9%. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Extraction of Gd3+and UO22+Ions Using Polystyrene Grafted Dibenzo Crown Ether (DB18C6) with Octanol and Nitrobenzene: A Molecular Dynamics Study.

    Science.gov (United States)

    Sappidi, Praveenkumar; Namsani, Sadanandam; Ali, Sk Musharaf; Singh, Jayant Kumar

    2018-01-25

    Atomistic molecular dynamics (MD) simulations are performed in order to derive thermodynamic properties important to understand the extraction of gadolinium (Gd 3+ ) and uranium dioxide (UO 2 ) with dibenzo crown ether (DBCE) in nitrobenzene (NB) and octanol (OCT) solvents. The effect of polystyrene graft length, on DBCE, on the binding behavior of Gd 3+ and UO 2 2+ is investigated for the first time. Our simulation results demonstrate that the binding of Gd 3+ and UO 2 2+ onto the oxygens of crown ethers is favorable for polystyrene grafted crown ether in the organic solvents OCT and NB. The metal ion binding free energy (ΔG Binding ) in different solvent environments is calculated using the thermodynamic integration (TI) method. ΔG Binding becomes more favorable in both solvents, NB and OCT, with an increase in the polystyrene monomer length. The metal ion transferability from an aqueous phase to an organic phase is estimated by calculating transfer free-energy calculations (ΔG Transfer ). ΔG Transfer is significantly favorable for both Gd 3+ and UO 2 2+ for the transfer from the aqueous phase to the organic phase (i.e., NB and OCT) via ion-complexation to DBCE with an increase in polystyrene length. The partition coefficient (log P) values for Gd 3+ and UO 2 2+ show a 5-fold increase in separation capacity with polystyrene grafted DBCE. We corroborate the observed behavior by further analyzing the structural and dynamical properties of the ions in different phases.

  3. A Preclinical Evaluation of Antrodia camphorata Alcohol Extracts in the Treatment of Non-Small Cell Lung Cancer Using Non-Invasive Molecular Imaging

    Directory of Open Access Journals (Sweden)

    Jeng-Feng Chiou

    2011-01-01

    Full Text Available This study was carried out to provide a platform for the pre-clinical evaluation of anti-cancer properties of a unique CAM (complementary and alternative medicine agent, Antrodia camphorata alcohol extract (ACAE, in a mouse model with the advantageous non-invasive in vivo bioluminescence molecular imaging technology. In vitro analyses on the proliferation, migration/invasion, cell cycle and apoptosis were performed on ACAE-treated non-small cell lung cancer cells, H441GL and control CGL1 cells. In vivo, immune-deficient mice were inoculated subcutaneously with H441GL followed by oral gavages of ACAE. The effect of ACAE on tumor progression was monitored by non-invasive bioluminescence imaging. The proliferation and migration/invasion of H441GL cells were inhibited by ACAE in a dose-dependent manner. In addition, ACAE induced cell cycle arrest at G0/G1 phase and apoptosis in H441GL cells as shown by flow cytometric analysis, Annexin-V immunoflourescence and DNA fragmentation. In vivo bioluminescence imaging revealed that tumorigenesis was significantly retarded by oral treatment of ACAE in a dose-dependent fashion. Based on our experimental data, ACAE contains anti-cancer properties and could be considered as a potential CAM agent in future clinical evaluation.

  4. High molecular weight components containing N-linked oligosaccharides of Ascaris suum extract inhibit the dendritic cells activation through DC-SIGN and MR.

    Science.gov (United States)

    Favoretto, Bruna C; Casabuono, Adriana A C; Portes-Junior, José A; Jacysyn, Jacqueline F; Couto, Alicia S; Faquim-Mauro, Eliana L

    2017-07-01

    Helminths, as well as their secretory/excretory products, induce a tolerogenic immune microenvironment. High molecular weight components (PI) from Ascaris suum extract down-modulate the immune response against ovalbumin (OVA). The PI exerts direct effect on dendritic cells (DCs) independent of TLR 2, 4 and MyD88 molecule and, thus, decreases the T lymphocytes response. Here, we studied the glycoconjugates in PI and the role of C-type lectin receptors (CLRs), DC-SIGN and MR, in the modulation of DCs activity. Our data showed the presence of glycoconjugates with high mannose- and complex-type N-linked oligosaccharide chains and phosphorylcholine residues on PI. In addition, these N-linked glycoconjugates inhibited the DCs maturation induced by LPS. The binding and internalization of PI-Alexa were decreased on DCs previously incubated with mannan, anti-DC-SIGN and/or anti-MR antibodies. In agreement with this, the incubation of DCs with mannan, anti-DC-SIGN and/or anti-MR antibodies abolished the down-modulatory effect of PI on these cells. It was also observed that the blockage of CLRs, DC-SIGN and MR on DCs reverted the inhibitory effect of PI in in vitro T cells proliferation. Therefore, our data show the involvement of DC-SIGN and MR in the recognition and consequent modulatory effect of N-glycosylated components of PI on DCs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Synthesis and properties of magnetic molecularly imprinted polymers based on multiwalled carbon nanotubes for magnetic extraction of bisphenol A from water.

    Science.gov (United States)

    Zhang, Zhaohui; Chen, Xing; Rao, Wei; Chen, Hongjun; Cai, Rong

    2014-08-15

    Novel magnetic molecularly imprinted polymers based on multiwalled carbon nanotubes (MWNTs@MMIPs) with specific selectivity toward bisphenol A were synthesized using bisphenol A as the template molecule, methacrylic acid, and β-cyclodextrin as binary functional monomers and ethylene glycol dimethacrylate as the cross-linker. The MWNTs@MMIPs were characterized by Fourier transform infrared, vibrating sample magnetometer, and transmission electron microscopy. Batch mode adsorption experiment was carried out to investigate the specific adsorption equilibrium and kinetics of the MWNTs@MMIPs. The MWNTs@MMIPs exhibited good affinity with a maximum adsorption capacity of 49.26 μmol g(-1) and excellent selectivity toward bisphenol A. Combined with high-performance liquid chromatography analysis, the MWNTs@MMIPs were employed to extract bisphenol A in tap water, rain water, and lake water successfully with the recoveries of 89.8-95.4, 89.9-93.4, and 87.3-94.1%, respectively. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Fernblock (Polypodium leucotomos Extract: Molecular Mechanisms and Pleiotropic Effects in Light-Related Skin Conditions, Photoaging and Skin Cancers, a Review

    Directory of Open Access Journals (Sweden)

    Concepcion Parrado

    2016-06-01

    Full Text Available Healthier life styles include increased outdoors time practicing sports and walking. This means increased exposure to the sun, leading to higher risk of sunburn, photoaging and skin cancer. In addition to topical barrier products, oral supplementations of various botanicals endowed with antioxidant activity are emerging as novel method of photoprotection. Polypodium leucotomos extract (PL, commercial name Fernblock®, IFC Group, Spain is a powerful antioxidant due to its high content of phenolic compounds. PL is administered orally, with proven safety, and it can also be used topically. Its mechanisms include inhibition of the generation and release of reactive oxygen species (ROS by ultraviolet (UV light. It also prevents UV- and ROS-induced DNA damage with inhibition of AP1 and NF-κB and protection of natural antioxidant enzyme systems. At the cellular level, PL decreases cellular apoptosis and necrosis mediated UV and inhibits abnormal extracellular matrix remodeling. PL reduces inflammation, prevents immunosuppression, activates tumor suppressor p53 and inhibits UV-induced cyclooxygenase-2 (COX-2 enzyme expression. In agreement with increased p53 activity, PL decreased UV radiation-induced cell proliferation. PL also prevents common deletions mitochondrial DNA damage induced by UVA, and MMP-1 expression induced Visible Light and Infrared Radiation. These cellular and molecular effects are reflected in inhibitions of carcinogenesis and photoaging.

  7. Sensitive, automatic method for the determination of diazepam and its five metabolites in human oral fluid by online solid-phase extraction and liquid chromatography with tandem mass spectrometry

    DEFF Research Database (Denmark)

    Jiang, Fengli; Rao, Yulan; Wang, Rong

    2016-01-01

    A novel and simple online solid-phase extraction liquid chromatography-tandem mass spectrometry method was developed and validated for the simultaneous determination of diazepam and its five metabolites including nordazepam, oxazepam, temazepam, oxazepam glucuronide, and temazepam glucuronide...... in human oral fluid. Human oral fluid was obtained using the Salivette(®) collection device, and 100 μL of oral fluid samples were loaded onto HySphere Resin GP cartridge for extraction. Analytes were separated on a Waters Xterra C18 column and quantified by liquid chromatography with tandem mass....... Intraday and interday precision for all analytes was 0.6-12.8 and 1.0-9.2%, respectively. Accuracy ranged from 95.6 to 114.7%. Method recoveries were in the range of 65.1-80.8%. This method was fully automated, simple, and sensitive. Authentic oral fluid samples collected from two volunteers after...

  8. Automatic quantitative renal scintigraphy

    International Nuclear Information System (INIS)

    Valeyre, J.; Deltour, G.; Delisle, M.J.; Bouchard, A.

    1976-01-01

    Renal scintigraphy data may be analyzed automatically by the use of a processing system coupled to an Anger camera (TRIDAC-MULTI 8 or CINE 200). The computing sequence is as follows: normalization of the images; background noise subtraction on both images; evaluation of mercury 197 uptake by the liver and spleen; calculation of the activity fractions on each kidney with respect to the injected dose, taking into account the kidney depth and the results referred to normal values; edition of the results. Automation minimizes the scattering parameters and by its simplification is a great asset in routine work [fr

  9. Automatic Construction of Hypotheses for Linear Objects in Digital and Laser Scanning Images

    Directory of Open Access Journals (Sweden)

    Quintino Dalmolin

    2004-12-01

    Full Text Available This paper presents an automatic road hypotheses approach using digital image and laser scanning image combining various Digital Image Processing techniques. The semantic objects, in this work, are linear features, such as, roads and streets. The aim of this paper is extract automatically road hypotheses on image space and object space for use the information in automatic absolute orientation process. The results show that methodology is efficiency and the roads hypotheses are generate and validate.

  10. Automatic Visualization of Software Requirements: Reactive Systems

    International Nuclear Information System (INIS)

    Castello, R.; Mili, R.; Tollis, I.G.; Winter, V.

    1999-01-01

    In this paper we present an approach that facilitates the validation of high consequence system requirements. This approach consists of automatically generating a graphical representation from an informal document. Our choice of a graphical notation is statecharts. We proceed in two steps: we first extract a hierarchical decomposition tree from a textual description, then we draw a graph that models the statechart in a hierarchical fashion. The resulting drawing is an effective requirements assessment tool that allows the end user to easily pinpoint inconsistencies and incompleteness

  11. Automatic readout micrometer

    Science.gov (United States)

    Lauritzen, T.

    A measuring system is described for surveying and very accurately positioning objects with respect to a reference line. A principle use of this surveying system is for accurately aligning the electromagnets which direct a particle beam emitted from a particle accelerator. Prior art surveying systems require highly skilled surveyors. Prior art systems include, for example, optical surveying systems which are susceptible to operator reading errors, and celestial navigation-type surveying systems, with their inherent complexities. The present invention provides an automatic readout micrometer which can very accurately measure distances. The invention has a simplicity of operation which practically eliminates the possibilities of operator optical reading error, owning to the elimination of traditional optical alignments for making measurements. The invention has an extendable arm which carries a laser surveying target. The extendable arm can be continuously positioned over its entire length of travel by either a coarse of fine adjustment without having the fine adjustment outrun the coarse adjustment until a reference laser beam is centered on the target as indicated by a digital readout. The length of the micrometer can then be accurately and automatically read by a computer and compared with a standardized set of alignment measurements. Due to its construction, the micrometer eliminates any errors due to temperature changes when the system is operated within a standard operating temperature range.

  12. Automatic personnel contamination monitor

    International Nuclear Information System (INIS)

    Lattin, Kenneth R.

    1978-01-01

    United Nuclear Industries, Inc. (UNI) has developed an automatic personnel contamination monitor (APCM), which uniquely combines the design features of both portal and hand and shoe monitors. In addition, this prototype system also has a number of new features, including: micro computer control and readout, nineteen large area gas flow detectors, real-time background compensation, self-checking for system failures, and card reader identification and control. UNI's experience in operating the Hanford N Reactor, located in Richland, Washington, has shown the necessity of automatically monitoring plant personnel for contamination after they have passed through the procedurally controlled radiation zones. This final check ensures that each radiation zone worker has been properly checked before leaving company controlled boundaries. Investigation of the commercially available portal and hand and shoe monitors indicated that they did not have the sensitivity or sophistication required for UNI's application, therefore, a development program was initiated, resulting in the subject monitor. Field testing shows good sensitivity to personnel contamination with the majority of alarms showing contaminants on clothing, face and head areas. In general, the APCM has sensitivity comparable to portal survey instrumentation. The inherit stand-in, walk-on feature of the APCM not only makes it easy to use, but makes it difficult to bypass. (author)

  13. Automatic detection of typical dust devils from Mars landscape images

    Science.gov (United States)

    Ogohara, Kazunori; Watanabe, Takeru; Okumura, Susumu; Hatanaka, Yuji

    2018-02-01

    This paper presents an improved algorithm for automatic detection of Martian dust devils that successfully extracts tiny bright dust devils and obscured large dust devils from two subtracted landscape images. These dust devils are frequently observed using visible cameras onboard landers or rovers. Nevertheless, previous research on automated detection of dust devils has not focused on these common types of dust devils, but on dust devils that appear on images to be irregularly bright and large. In this study, we detect these common dust devils automatically using two kinds of parameter sets for thresholding when binarizing subtracted images. We automatically extract dust devils from 266 images taken by the Spirit rover to evaluate our algorithm. Taking dust devils detected by visual inspection to be ground truth, the precision, recall and F-measure values are 0.77, 0.86, and 0.81, respectively.

  14. Extracting historical time periods from the Web

    NARCIS (Netherlands)

    de Boer, V.; van Someren, M.; Wielinga, B.J.

    2010-01-01

    In this work we present an automatic method for the extraction of time periods related to ontological concepts from the Web. The method consists of two parts: an Information Extraction phase and a Semantic Representation phase. In the Information Extraction phase, temporal information about events

  15. Reachability Games on Automatic Graphs

    Science.gov (United States)

    Neider, Daniel

    In this work we study two-person reachability games on finite and infinite automatic graphs. For the finite case we empirically show that automatic game encodings are competitive to well-known symbolic techniques such as BDDs, SAT and QBF formulas. For the infinite case we present a novel algorithm utilizing algorithmic learning techniques, which allows to solve huge classes of automatic reachability games.

  16. Automatic reactor protection system tester

    International Nuclear Information System (INIS)

    Deliant, J.D.; Jahnke, S.; Raimondo, E.

    1988-01-01

    The object of this paper is to present the automatic tester of reactor protection systems designed and developed by EDF and Framatome. In order, the following points are discussed: . The necessity for reactor protection system testing, . The drawbacks of manual testing, . The description and use of the Framatome automatic tester, . On-site installation of this system, . The positive results obtained using the Framatome automatic tester in France

  17. A simple QuEChERS-like extraction approach for molecular chemical characterization of organic aerosols: application to nitrated and oxygenated PAH derivatives (NPAH and OPAH) quantified by GC-NICIMS.

    Science.gov (United States)

    Albinet, A; Nalin, F; Tomaz, S; Beaumont, J; Lestremau, F

    2014-05-01

    An extraction procedure based on the Quick Easy Cheap Effective Rugged and Safe (QuEChERS) approach has been developed and used for analysis of particle-bound nitrated and oxygenated PAH derivatives (NPAH and OPAH, respectively). Several analytical conditions, for example GC injection temperature and MS detection settings, were optimized. This analytical procedure enabled simultaneous GC-NICIMS quantification of 32 NPAH and 32 OPAH (or other oxygenated compounds), including typical components of secondary organic aerosol (SOA) formed by photooxidation of PAH (e.g. 2-formyl-trans-cinnamaldehyde and 6H-dibenzo[b,d]pyran-6-one). The QuEChERS-like approach was optimized, including the nature of the extraction solvent, the sorbent used for clean-up, and extraction time. The final extraction procedure was based on brief mechanical agitation (vortex mixing for 1.5 min), with 7 mL acetonitrile as solvent. Because dispersive solid-phase extraction (d-SPE) did not provide satisfactory results, SPE using SiO2 was selected for sample purification. Identical results were obtained when the QuEChERS-like and traditional pressurised solvent extraction (PLE) procedures were compared for analysis of fortified ambient air particle samples. The procedure was validated by analysis of two aerosol standard reference materials (NIST SRM 1649b (urban dust) and SRM 2787 (fine particulate matter, extraction methods, including PLE, the QuEChERS-like procedure resulted in increased productivity and reduced extraction cost. This paper shows that QuEChERS-like extraction procedures can be suitably adapted for molecular chemical characterization of aerosol samples and could be extended to other categories of compound.

  18. Automatic sets and Delone sets

    International Nuclear Information System (INIS)

    Barbe, A; Haeseler, F von

    2004-01-01

    Automatic sets D part of Z m are characterized by having a finite number of decimations. They are equivalently generated by fixed points of certain substitution systems, or by certain finite automata. As examples, two-dimensional versions of the Thue-Morse, Baum-Sweet, Rudin-Shapiro and paperfolding sequences are presented. We give a necessary and sufficient condition for an automatic set D part of Z m to be a Delone set in R m . The result is then extended to automatic sets that are defined as fixed points of certain substitutions. The morphology of automatic sets is discussed by means of examples

  19. Automatically Creating Bilingual Lexicons for Machine Translation from Bilingual Text

    OpenAIRE

    Turcato, Davide

    1998-01-01

    A method is presented for automatically augmenting the bilingual lexicon of an existing Machine Translation system, by extracting bilingual entries from aligned bilingual text. The proposed method only relies on the resources already available in the MT system itself. It is based on the use of bilingual lexical templates to match the terminal symbols in the parses of the aligned sentences.

  20. Automatic selective feature retention in patient specific elastic surface registration

    CSIR Research Space (South Africa)

    Jansen van Rensburg, GJ

    2011-01-01

    Full Text Available . An intelligent mesh morphing strategy where dissimilar feature surfaces can be extracted automatically also greatly reduces the amount of user input required. REFERENCES [1] R. Bryan, P.S. Mohan, A. Hopkins, F. Galloway, M. Taylor and P. Nair, Statitical...

  1. Building an Image-Based System to automatically Score psoriasis

    DEFF Research Database (Denmark)

    G{'o}mez, D. Delgado; Carstensen, Jens Michael; Ersbøll, Bjarne Kjær

    2003-01-01

    the images. The system is tested on patients with the dermatological disease psoriasis. Temporal series of images are taken for each patient and the lesions are automatically extracted. Results indicate that to the images obtained are a good source for obtaining derived variables to track the lesion....

  2. Magnetic molecularly imprinted polymers based on silica modified by deep eutectic solvents for the rapid simultaneous magnetic-based solid-phase extraction of Salvia miltiorrhiza bunge, Glycine max (Linn.) Merr and green tea.

    Science.gov (United States)

    Li, Guizhen; Wang, Xiaoqin; Row, Kyung Ho

    2018-01-19

    Novel magnetic molecularly imprinted polymers (MMIPs) with multiple-template based on silica were modified by four types of deep eutectic solvents (DESs) for the rapid simultaneous magnetic solid-phase extraction (MSPE) of tanshinone Ⅰ, tanshinone ⅡA, and cryptotanshinone from Salvia miltiorrhiza bunge; glycitein, genistein, and daidzein from Glycine max (Linn.) Merr; and epicatechin, epigallocatechin gallate, and epicatechin gallate from green tea, respectively. The synthesized materials were characterized by Fourier transform infrared spectroscopy and field emission scanning electron microscopy. Single factor experiments were to explore the relationship between the extraction efficiency and four factors (the sample solution pH, amount of DESs for modification, amount of adsorbent, and extraction time). It was showed that the DES4-MMIPs have better extraction ability than the MMIPs without DESs and the other three DESs-modified MMIPs. The best extraction recoveries with DES4-MMIP were tanshinone Ⅰ (85.57%), tanshinone ⅡA (80.58%), cryptotanshinone (92.12%), glycitein (81.65%), genistein (87.72%), daidzein (92.24%), epicatechin (86.43%), epigallocatechin gallate (80.92%), and epicatechin gallate (93.64%), respectively. The novel multiple-template MMIPs materials modified by DES for the rapid simultaneous MSPE of active compounds were proved to reduce the experimental steps than single-template technique, and increase the extraction efficiency. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Automatic quantitative metallography

    International Nuclear Information System (INIS)

    Barcelos, E.J.B.V.; Ambrozio Filho, F.; Cunha, R.C.

    1976-01-01

    The quantitative determination of metallographic parameters is analysed through the description of Micro-Videomat automatic image analysis system and volumetric percentage of perlite in nodular cast irons, porosity and average grain size in high-density sintered pellets of UO 2 , and grain size of ferritic steel. Techniques adopted are described and results obtained are compared with the corresponding ones by the direct counting process: counting of systematic points (grid) to measure volume and intersections method, by utilizing a circunference of known radius for the average grain size. The adopted technique for nodular cast iron resulted from the small difference of optical reflectivity of graphite and perlite. Porosity evaluation of sintered UO 2 pellets is also analyzed [pt

  4. Semi-automatic fluoroscope

    International Nuclear Information System (INIS)

    Tarpley, M.W.

    1976-10-01

    Extruded aluminum-clad uranium-aluminum alloy fuel tubes must pass many quality control tests before irradiation in Savannah River Plant nuclear reactors. Nondestructive test equipment has been built to automatically detect high and low density areas in the fuel tubes using x-ray absorption techniques with a video analysis system. The equipment detects areas as small as 0.060-in. dia with 2 percent penetrameter sensitivity. These areas are graded as to size and density by an operator using electronic gages. Video image enhancement techniques permit inspection of ribbed cylindrical tubes and make possible the testing of areas under the ribs. Operation of the testing machine, the special low light level television camera, and analysis and enhancement techniques are discussed

  5. AUTOMATIC ARCHITECTURAL STYLE RECOGNITION

    Directory of Open Access Journals (Sweden)

    M. Mathias

    2012-09-01

    Full Text Available Procedural modeling has proven to be a very valuable tool in the field of architecture. In the last few years, research has soared to automatically create procedural models from images. However, current algorithms for this process of inverse procedural modeling rely on the assumption that the building style is known. So far, the determination of the building style has remained a manual task. In this paper, we propose an algorithm which automates this process through classification of architectural styles from facade images. Our classifier first identifies the images containing buildings, then separates individual facades within an image and determines the building style. This information could then be used to initialize the building reconstruction process. We have trained our classifier to distinguish between several distinct architectural styles, namely Flemish Renaissance, Haussmannian and Neoclassical. Finally, we demonstrate our approach on various street-side images.

  6. Automatic surveying techniques

    International Nuclear Information System (INIS)

    Sah, R.

    1976-01-01

    In order to investigate the feasibility of automatic surveying methods in a more systematic manner, the PEP organization signed a contract in late 1975 for TRW Systems Group to undertake a feasibility study. The completion of this study resulted in TRW Report 6452.10-75-101, dated December 29, 1975, which was largely devoted to an analysis of a survey system based on an Inertial Navigation System. This PEP note is a review and, in some instances, an extension of that TRW report. A second survey system which employed an ''Image Processing System'' was also considered by TRW, and it will be reviewed in the last section of this note. 5 refs., 5 figs., 3 tabs

  7. Automatic alkaloid removal system.

    Science.gov (United States)

    Yahaya, Muhammad Rizuwan; Hj Razali, Mohd Hudzari; Abu Bakar, Che Abdullah; Ismail, Wan Ishak Wan; Muda, Wan Musa Wan; Mat, Nashriyah; Zakaria, Abd

    2014-01-01

    This alkaloid automated removal machine was developed at Instrumentation Laboratory, Universiti Sultan Zainal Abidin Malaysia that purposely for removing the alkaloid toxicity from Dioscorea hispida (DH) tuber. It is a poisonous plant where scientific study has shown that its tubers contain toxic alkaloid constituents, dioscorine. The tubers can only be consumed after it poisonous is removed. In this experiment, the tubers are needed to blend as powder form before inserting into machine basket. The user is need to push the START button on machine controller for switching the water pump ON by then creating turbulence wave of water in machine tank. The water will stop automatically by triggering the outlet solenoid valve. The powders of tubers are washed for 10 minutes while 1 liter of contaminated water due toxin mixture is flowing out. At this time, the controller will automatically triggered inlet solenoid valve and the new water will flow in machine tank until achieve the desire level that which determined by ultra sonic sensor. This process will repeated for 7 h and the positive result is achieved and shows it significant according to the several parameters of biological character ofpH, temperature, dissolve oxygen, turbidity, conductivity and fish survival rate or time. From that parameter, it also shows the positive result which is near or same with control water and assuming was made that the toxin is fully removed when the pH of DH powder is near with control water. For control water, the pH is about 5.3 while water from this experiment process is 6.0 and before run the machine the pH of contaminated water is about 3.8 which are too acid. This automated machine can save time for removing toxicity from DH compared with a traditional method while less observation of the user.

  8. Automatic seamless image mosaic method based on SIFT features

    Science.gov (United States)

    Liu, Meiying; Wen, Desheng

    2017-02-01

    An automatic seamless image mosaic method based on SIFT features is proposed. First a scale-invariant feature extracting algorithm SIFT is used for feature extraction and matching, which gains sub-pixel precision for features extraction. Then, the transforming matrix H is computed with improved PROSAC algorithm , compared with RANSAC algorithm, the calculate efficiency is advanced, and the number of the inliers are more. Then the transforming matrix H is purify with LM algorithm. And finally image mosaic is completed with smoothing algorithm. The method implements automatically and avoids the disadvantages of traditional image mosaic method under different scale and illumination conditions. Experimental results show the image mosaic effect is wonderful and the algorithm is stable very much. It is high valuable in practice.

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