WorldWideScience

Sample records for automatically extracting molecular

  1. Challenges for automatically extracting molecular interactions from full-text articles

    Directory of Open Access Journals (Sweden)

    Curran James R

    2009-09-01

    Full Text Available Abstract Background The increasing availability of full-text biomedical articles will allow more biomedical knowledge to be extracted automatically with greater reliability. However, most Information Retrieval (IR and Extraction (IE tools currently process only abstracts. The lack of corpora has limited the development of tools that are capable of exploiting the knowledge in full-text articles. As a result, there has been little investigation into the advantages of full-text document structure, and the challenges developers will face in processing full-text articles. Results We manually annotated passages from full-text articles that describe interactions summarised in a Molecular Interaction Map (MIM. Our corpus tracks the process of identifying facts to form the MIM summaries and captures any factual dependencies that must be resolved to extract the fact completely. For example, a fact in the results section may require a synonym defined in the introduction. The passages are also annotated with negated and coreference expressions that must be resolved. We describe the guidelines for identifying relevant passages and possible dependencies. The corpus includes 2162 sentences from 78 full-text articles. Our corpus analysis demonstrates the necessity of full-text processing; identifies the article sections where interactions are most commonly stated; and quantifies the proportion of interaction statements requiring coherent dependencies. Further, it allows us to report on the relative importance of identifying synonyms and resolving negated expressions. We also experiment with an oracle sentence retrieval system using the corpus as a gold-standard evaluation set. Conclusion We introduce the MIM corpus, a unique resource that maps interaction facts in a MIM to annotated passages within full-text articles. It is an invaluable case study providing guidance to developers of biomedical IR and IE systems, and can be used as a gold-standard evaluation

  2. Automatic Keyword Extraction from Individual Documents

    Energy Technology Data Exchange (ETDEWEB)

    Rose, Stuart J.; Engel, David W.; Cramer, Nicholas O.; Cowley, Wendy E.

    2010-05-03

    This paper introduces a novel and domain-independent method for automatically extracting keywords, as sequences of one or more words, from individual documents. We describe the method’s configuration parameters and algorithm, and present an evaluation on a benchmark corpus of technical abstracts. We also present a method for generating lists of stop words for specific corpora and domains, and evaluate its ability to improve keyword extraction on the benchmark corpus. Finally, we apply our method of automatic keyword extraction to a corpus of news articles and define metrics for characterizing the exclusivity, essentiality, and generality of extracted keywords within a corpus.

  3. 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.

  4. Automatic extraction of legal concepts and definitions

    NARCIS (Netherlands)

    R. Winkels; R. Hoekstra

    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.

  5. 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 under

  6. Automatic Extraction of JPF Options and Documentation

    Science.gov (United States)

    Luks, Wojciech; Tkachuk, Oksana; Buschnell, David

    2011-01-01

    Documenting existing Java PathFinder (JPF) projects or developing new extensions is a challenging task. JPF provides a platform for creating new extensions and relies on key-value properties for their configuration. Keeping track of all possible options and extension mechanisms in JPF can be difficult. This paper presents jpf-autodoc-options, a tool that automatically extracts JPF projects options and other documentation-related information, which can greatly help both JPF users and developers of JPF extensions.

  7. 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.

  8. Automatic Extraction of Planetary Image Features

    Science.gov (United States)

    Troglio, G.; LeMoigne, J.; Moser, G.; Serpico, S. B.; Benediktsson, J. A.

    2009-01-01

    With the launch of several Lunar missions such as the Lunar Reconnaissance Orbiter (LRO) and Chandrayaan-1, a large amount of Lunar images will be acquired and will need to be analyzed. Although many automatic feature extraction methods have been proposed and utilized for Earth remote sensing images, these methods are not always applicable to Lunar data that often present low contrast and uneven illumination characteristics. In this paper, we propose a new method for the extraction of Lunar features (that can be generalized to other planetary images), based on the combination of several image processing techniques, a watershed segmentation and the generalized Hough Transform. This feature extraction has many applications, among which image registration.

  9. 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.

  10. Automatic Extraction of Metadata from Scientific Publications for CRIS Systems

    Science.gov (United States)

    Kovacevic, Aleksandar; Ivanovic, Dragan; Milosavljevic, Branko; Konjovic, Zora; Surla, Dusan

    2011-01-01

    Purpose: The aim of this paper is to develop a system for automatic extraction of metadata from scientific papers in PDF format for the information system for monitoring the scientific research activity of the University of Novi Sad (CRIS UNS). Design/methodology/approach: The system is based on machine learning and performs automatic extraction…

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

    OpenAIRE

    Haijian Chen; Dongmei Han; Yonghui Dai; Lina Zhao

    2015-01-01

    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 ...

  12. Image feature meaning for automatic key-frame extraction

    Science.gov (United States)

    Di Lecce, Vincenzo; Guerriero, Andrea

    2003-12-01

    Video abstraction and summarization, being request in several applications, has address a number of researches to automatic video analysis techniques. The processes for automatic video analysis are based on the recognition of short sequences of contiguous frames that describe the same scene, shots, and key frames representing the salient content of the shot. Since effective shot boundary detection techniques exist in the literature, in this paper we will focus our attention on key frames extraction techniques to identify the low level visual features of the frames that better represent the shot content. To evaluate the features performance, key frame automatically extracted using these features, are compared to human operator video annotations.

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

    International Nuclear Information System (INIS)

    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)

  14. 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.

  15. Automatic Extraction of Protein Interaction in Literature

    OpenAIRE

    Liu, Peilei; Wang, Ting

    2014-01-01

    Protein-protein interaction extraction is the key precondition of the construction of protein knowledge network, and it is very important for the research in the biomedicine. This paper extracted directional protein-protein interaction from the biological text, using the SVM-based method. Experiments were evaluated on the LLL05 corpus with good results. The results show that dependency features are import for the protein-protein interaction extraction and features related to the interaction w...

  16. 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 rea

  17. Automatic Eye Extraction in Human Face Images

    Institute of Scientific and Technical Information of China (English)

    LIU Rujie; YUAN Baozong

    2001-01-01

    This paper presents a fuzzy-basedmethod to locate the position and the size of irises ina head-shoulder image with plain background. Thismethod is composed of two stages: the face region es-timation stage and the eye feature extraction stage.In the first stage, a region growing method is adoptedto estimate the face region. In the second stage, thecoarse eye area is firstly extracted based on the loca-tion of the nasion, and the deformable template al-gorithm is then applied to eye area to determine theposition and the size of irises. Experimental resultsshow the efficiency and robustness of this method.

  18. Fast Hough transform for automatic bridge extraction

    Science.gov (United States)

    Hao, Qiwei; Chen, Xiaomei; Ni, Guoqiang; Zhang, Huaili

    2008-03-01

    In this paper, a new method to recognize bridge in the complicated background is presented. The algorithm takes full advantages of the characteristics of the bridge image. Firstly, the image is preprocessed and the object edges are extracted. Then according to the limitations of traditional Hough transform (HT), the extraction method of the image line segment characteristic of HT is improved, which eliminates spurious peaks on the basis of global and local thresholds, discriminates the position relation between two straight line segments, and merges segments with near endpoints, etc. Experiments show that this algorithm is more precise and efficient than traditional HT, moreover it can provide a complete description of the bridge in a complicated background.

  19. Automatic Road Centerline Extraction from Imagery Using Road GPS Data

    OpenAIRE

    Chuqing Cao; Ying Sun

    2014-01-01

    Road centerline extraction from imagery constitutes a key element in numerous geospatial applications, which has been addressed through a variety of approaches. However, most of the existing methods are not capable of dealing with challenges such as different road shapes, complex scenes, and variable resolutions. This paper presents a novel method for road centerline extraction from imagery in a fully automatic approach that addresses the aforementioned challenges by exploiting road GPS data....

  20. Automatically extracting translation links using a wide coverage semantic taxonomy

    OpenAIRE

    Rigau Claramunt, German; Rodríguez Hontoria, Horacio; Turmo Borras, Jorge

    1995-01-01

    TGE (Tlink Generator Environment) is a system for semi-automatically extracting translation links. The system was developed within the ACQUILEX II project as a tool for supporting the construction of a multi-lingual lexical knowledge base containing detailed syntactic and semantic information from MRD resources. A drawback of the original system was the need of human intervention for selecting the more appropriate translation links in the case where more than one were extracted and proposed b...

  1. Document Exploration and Automatic Knowledge Extraction for Unstructured Biomedical Text

    Science.gov (United States)

    Chu, S.; Totaro, G.; Doshi, N.; Thapar, S.; Mattmann, C. A.; Ramirez, P.

    2015-12-01

    We describe our work on building a web-browser based document reader with built-in exploration tool and automatic concept extraction of medical entities for biomedical text. Vast amounts of biomedical information are offered in unstructured text form through scientific publications and R&D reports. Utilizing text mining can help us to mine information and extract relevant knowledge from a plethora of biomedical text. The ability to employ such technologies to aid researchers in coping with information overload is greatly desirable. In recent years, there has been an increased interest in automatic biomedical concept extraction [1, 2] and intelligent PDF reader tools with the ability to search on content and find related articles [3]. Such reader tools are typically desktop applications and are limited to specific platforms. Our goal is to provide researchers with a simple tool to aid them in finding, reading, and exploring documents. Thus, we propose a web-based document explorer, which we called Shangri-Docs, which combines a document reader with automatic concept extraction and highlighting of relevant terms. Shangri-Docsalso provides the ability to evaluate a wide variety of document formats (e.g. PDF, Words, PPT, text, etc.) and to exploit the linked nature of the Web and personal content by performing searches on content from public sites (e.g. Wikipedia, PubMed) and private cataloged databases simultaneously. Shangri-Docsutilizes Apache cTAKES (clinical Text Analysis and Knowledge Extraction System) [4] and Unified Medical Language System (UMLS) to automatically identify and highlight terms and concepts, such as specific symptoms, diseases, drugs, and anatomical sites, mentioned in the text. cTAKES was originally designed specially to extract information from clinical medical records. Our investigation leads us to extend the automatic knowledge extraction process of cTAKES for biomedical research domain by improving the ontology guided information extraction

  2. Development of Automatic Extraction Weld for Industrial Radiographic Negative Inspection

    Institute of Scientific and Technical Information of China (English)

    张晓光; 林家骏; 李浴; 卢印举

    2003-01-01

    In industrial X-ray inspection, in order to identify weld defects automatically, raise the identification ratio, and avoid processing of complex background, it is an important step for sequent processing to extract weld from the image. According to the characteristics of weld radiograph image, median filter is adopted to reduce the noise with high frequency, then relative gray-scale of image is chosen as fuzzy characteristic, and image gray-scale fuzzy matrix is constructed and suitable membership function is selected to describe edge characteristic. A fuzzy algorithm is adopted for enhancing radiograph image processing. Based on the intensity distribution characteristic in weld, methodology of weld extraction is then designed. This paper describes the methodology of all the weld extraction, including reducing noise, fuzzy enhancement and weld extraction process. To prove its effectiveness, this methodology was tested with 64 weld negative images available for this study. The experimental results show that this methodology is very effective for extracting linear weld.

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

    Science.gov (United States)

    Chen, Haijian; Han, Dongmei; Dai, Yonghui; Zhao, Lina

    2015-01-01

    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. PMID:26448738

  4. 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.

  5. Automatically extracting sheet-metal features from solid model

    Institute of Scientific and Technical Information of China (English)

    刘志坚; 李建军; 王义林; 李材元; 肖祥芷

    2004-01-01

    With the development of modern industry,sheet-metal parts in mass production have been widely applied in mechanical,communication,electronics,and light industries in recent decades; but the advances in sheet-metal part design and manufacturing remain too slow compared with the increasing importance of sheet-metal parts in modern industry. This paper proposes a method for automatically extracting features from an arbitrary solid model of sheet-metal parts; whose characteristics are used for classification and graph-based representation of the sheet-metal features to extract the features embodied in a sheet-metal part. The extracting feature process can be divided for valid checking of the model geometry,feature matching,and feature relationship. Since the extracted features include abundant geometry and engineering information,they will be effective for downstream application such as feature rebuilding and stamping process planning.

  6. Automatic Railway Power Line Extraction Using Mobile Laser Scanning Data

    Science.gov (United States)

    Zhang, Shanxin; Wang, Cheng; Yang, Zhuang; Chen, Yiping; Li, Jonathan

    2016-06-01

    Research on power line extraction technology using mobile laser point clouds has important practical significance on railway power lines patrol work. In this paper, we presents a new method for automatic extracting railway power line from MLS (Mobile Laser Scanning) data. Firstly, according to the spatial structure characteristics of power-line and trajectory, the significant data is segmented piecewise. Then, use the self-adaptive space region growing method to extract power lines parallel with rails. Finally use PCA (Principal Components Analysis) combine with information entropy theory method to judge a section of the power line whether is junction or not and which type of junction it belongs to. The least squares fitting algorithm is introduced to model the power line. An evaluation of the proposed method over a complicated railway point clouds acquired by a RIEGL VMX450 MLS system shows that the proposed method is promising.

  7. Automatic local Gabor Features extraction for face recognition

    CERN Document Server

    Jemaa, Yousra Ben

    2009-01-01

    We present in this paper a biometric system of face detection and recognition in color images. The face detection technique is based on skin color information and fuzzy classification. A new algorithm is proposed in order to detect automatically face features (eyes, mouth and nose) and extract their correspondent geometrical points. These fiducial points are described by sets of wavelet components which are used for recognition. To achieve the face recognition, we use neural networks and we study its performances for different inputs. We compare the two types of features used for recognition: geometric distances and Gabor coefficients which can be used either independently or jointly. This comparison shows that Gabor coefficients are more powerful than geometric distances. We show with experimental results how the importance recognition ratio makes our system an effective tool for automatic face detection and recognition.

  8. 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.

  9. Automatic Extraction of Building Outline from High Resolution Aerial Imagery

    Science.gov (United States)

    Wang, Yandong

    2016-06-01

    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.

  10. Automatic object extraction over multiscale edge field for multimedia retrieval.

    Science.gov (United States)

    Kiranyaz, Serkan; Ferreira, Miguel; Gabbouj, Moncef

    2006-12-01

    In this work, we focus on automatic extraction of object boundaries from Canny edge field for the purpose of content-based indexing and retrieval over image and video databases. A multiscale approach is adopted where each successive scale provides further simplification of the image by removing more details, such as texture and noise, while keeping major edges. At each stage of the simplification, edges are extracted from the image and gathered in a scale-map, over which a perceptual subsegment analysis is performed in order to extract true object boundaries. The analysis is mainly motivated by Gestalt laws and our experimental results suggest a promising performance for main objects extraction, even for images with crowded textural edges and objects with color, texture, and illumination variations. Finally, integrating the whole process as feature extraction module into MUVIS framework allows us to test the mutual performance of the proposed object extraction method and subsequent shape description in the context of multimedia indexing and retrieval. A promising retrieval performance is achieved, and especially in some particular examples, the experimental results show that the proposed method presents such a retrieval performance that cannot be achieved by using other features such as color or texture. PMID:17153949

  11. 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.

  12. Automatic segmentation of brain images: selection of region extraction methods

    Science.gov (United States)

    Gong, Leiguang; Kulikowski, Casimir A.; Mezrich, Reuben S.

    1991-07-01

    In automatically analyzing brain structures from a MR image, the choice of low level region extraction methods depends on the characteristics of both the target object and the surrounding anatomical structures in the image. The authors have experimented with local thresholding, global thresholding, and other techniques, using various types of MR images for extracting the major brian landmarks and different types of lesions. This paper describes specifically a local- binary thresholding method and a new global-multiple thresholding technique developed for MR image segmentation and analysis. The initial testing results on their segmentation performance are presented, followed by a comparative analysis of the two methods and their ability to extract different types of normal and abnormal brain structures -- the brain matter itself, tumors, regions of edema surrounding lesions, multiple sclerosis lesions, and the ventricles of the brain. The analysis and experimental results show that the global multiple thresholding techniques are more than adequate for extracting regions that correspond to the major brian structures, while local binary thresholding is helpful for more accurate delineation of small lesions such as those produced by MS, and for the precise refinement of lesion boundaries. The detection of other landmarks, such as the interhemispheric fissure, may require other techniques, such as line-fitting. These experiments have led to the formulation of a set of generic computer-based rules for selecting the appropriate segmentation packages for particular types of problems, based on which further development of an innovative knowledge- based, goal directed biomedical image analysis framework is being made. The system will carry out the selection automatically for a given specific analysis task.

  13. Automatic extraction of candidate nomenclature terms using the doublet method

    Directory of Open Access Journals (Sweden)

    Berman Jules J

    2005-10-01

    nomenclature. Results A 31+ Megabyte corpus of pathology journal abstracts was parsed using the doublet extraction method. This corpus consisted of 4,289 records, each containing an abstract title. The total number of words included in the abstract titles was 50,547. New candidate terms for the nomenclature were automatically extracted from the titles of abstracts in the corpus. Total execution time on a desktop computer with CPU speed of 2.79 GHz was 2 seconds. The resulting output consisted of 313 new candidate terms, each consisting of concatenated doublets found in the reference nomenclature. Human review of the 313 candidate terms yielded a list of 285 terms approved by a curator. A final automatic extraction of duplicate terms yielded a final list of 222 new terms (71% of the original 313 extracted candidate terms that could be added to the reference nomenclature. Conclusion The doublet method for automatically extracting candidate nomenclature terms can be used to quickly find new terms from vast amounts of text. The method can be immediately adapted for virtually any text and any nomenclature. An implementation of the algorithm, in the Perl programming language, is provided with this article.

  14. 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

  15. Automatic moving object extraction toward compact video representation

    Science.gov (United States)

    Fan, Jianping; Fujita, Gen; Furuie, Makoto; Onoye, Takao; Shirakawa, Isao; Wu, Lide

    2000-02-01

    An automatic object-oriented video segmentation and representation algorithm is proposed, where the local variance contrast and the frame differences contrast are jointly exploited for meaningful moving object extinction because these two visual features can indicate the spatial homogeneity of the gray levels and the temporal coherence of the motion fields efficiently. The 2D entropic thresholding technique and the watershed transformation method are further developed to determine the global feature thresholds adaptively according to the variation of the video components. The obtained video components are first represented by a group of 4 X 4 blocks coarsely, and then the meaningful moving objects are generated by an iterative region-merging procedure according to the spatiotemporal similarity measure. The temporal tracking procedure is further proposed to obtain more semantic moving objects among frames. Therefore, the proposed automatic moving object extraction algorithm can detect the appearance of new objects as well as the disappearance of existing objects efficiently because the correspondence of the video objects among frames is also established. Moreover, an object- oriented video representation and indexing approach is suggested, where both the operation of the camera (i.e., change of the viewpoint) and the birth or death of the individual objects are exploited to detect the breakpoints of the video data and to select the key frames adaptively.

  16. 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.

  17. 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 ...

  18. Automatic Contour Extraction from 2D Neuron Images

    CERN Document Server

    Leandro, J J G; Costa, L da F

    2008-01-01

    The current work describes a novel system devised for automatic contour extraction of 2D branching structures images obtained from 3D neurons. Most contour-based methods for neuronal cell shape analysis fall short of suitable representation of such cells because overlaps between neuronal processes prevent traditional contour following algorithms from entering the innermost cell regions. The herein-proposed framework is specifically aimed at the problem of contour following even in presence of multiple overlaps. First, the input image is preprocessed in order to obtain an 8-connected skeleton with one-pixel-wide branches, as well as a set of subtree seed pixels and critical regions (i.e., bifurcations and crossings). Next, for each subtree, the tracking algorithm iteratively labels all valid pixel branches, up to a critical region, where the algorithm determines the suitable direction to proceed. Our algorithm has been found to exhibit robustness even for images with close parallel segments. Experimental resul...

  19. 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.

  20. Definition extraction for glossary creation : a study on extracting definitions for semi-automatic glossary creation in Dutch

    NARCIS (Netherlands)

    Westerhout, E.N.

    2010-01-01

    The central topic of this thesis is the automatic extraction of definitions from text. Definition extraction can play a role in various applications including the semi-automatic development of glossaries in an eLearning context, which constitutes the main focus of this dissertation. A glossary provi

  1. Methods and Prospects of Road and Linear Structure Automatic Extraction from Remote Sensing Images

    Institute of Scientific and Technical Information of China (English)

    LIU Zhengrong

    2003-01-01

    Automatic extraction of road and linear structure from remote sensing images is a very important problem. This paper analyses several existing methods of the automatic road and linear structure extraction by using some multi-spectral remote sensing images acquired from different spatial resolutions, districts and road characteristics. Their advantages and disadvantages have been generalized.

  2. Automatic Building Extraction From LIDAR Data Covering Complex Urban Scenes

    Science.gov (United States)

    Awrangjeb, M.; Lu, G.; Fraser, C.

    2014-08-01

    This paper presents a new method for segmentation of LIDAR point cloud data for automatic building extraction. Using the ground height from a DEM (Digital Elevation Model), the non-ground points (mainly buildings and trees) are separated from the ground points. Points on walls are removed from the set of non-ground points by applying the following two approaches: If a plane fitted at a point and its neighbourhood is perpendicular to a fictitious horizontal plane, then this point is designated as a wall point. When LIDAR points are projected on a dense grid, points within a narrow area close to an imaginary vertical line on the wall should fall into the same grid cell. If three or more points fall into the same cell, then the intermediate points are removed as wall points. The remaining non-ground points are then divided into clusters based on height and local neighbourhood. One or more clusters are initialised based on the maximum height of the points and then each cluster is extended by applying height and neighbourhood constraints. Planar roof segments are extracted from each cluster of points following a region-growing technique. Planes are initialised using coplanar points as seed points and then grown using plane compatibility tests. If the estimated height of a point is similar to its LIDAR generated height, or if its normal distance to a plane is within a predefined limit, then the point is added to the plane. Once all the planar segments are extracted, the common points between the neghbouring planes are assigned to the appropriate planes based on the plane intersection line, locality and the angle between the normal at a common point and the corresponding plane. A rule-based procedure is applied to remove tree planes which are small in size and randomly oriented. The neighbouring planes are then merged to obtain individual building boundaries, which are regularised based on long line segments. Experimental results on ISPRS benchmark data sets show that the

  3. Automatic Extraction of Mangrove Vegetation from Optical Satellite Data

    Science.gov (United States)

    Agrawal, Mayank; Sushma Reddy, Devireddy; Prasad, Ram Chandra

    2016-06-01

    Mangrove, the intertidal halophytic vegetation, are one of the most significant and diverse ecosystem in the world. They protect the coast from sea erosion and other natural disasters like tsunami and cyclone. In view of their increased destruction and degradation in the current scenario, mapping of this vegetation is at priority. Globally researchers mapped mangrove vegetation using visual interpretation method or digital classification approaches or a combination of both (hybrid) approaches using varied spatial and spectral data sets. In the recent past techniques have been developed to extract these coastal vegetation automatically using varied algorithms. In the current study we tried to delineate mangrove vegetation using LISS III and Landsat 8 data sets for selected locations of Andaman and Nicobar islands. Towards this we made an attempt to use segmentation method, that characterize the mangrove vegetation based on their tone and the texture and the pixel based classification method, where the mangroves are identified based on their pixel values. The results obtained from the both approaches are validated using maps available for the region selected and obtained better accuracy with respect to their delineation. The main focus of this paper is simplicity of the methods and the availability of the data on which these methods are applied as these data (Landsat) are readily available for many regions. Our methods are very flexible and can be applied on any region.

  4. 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....

  5. 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.

  6. Automatic molecular structure perception for the universal force field.

    Science.gov (United States)

    Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane

    2016-05-15

    The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (http://www.samson-connect.net). We validate both the automatic perception method and the UFF implementation on a series of benchmarks. PMID:26927616

  7. 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

  8. Unsupervised segmentation of cardiac PET transmission images for automatic heart volume extraction.

    Science.gov (United States)

    Juslin, Anu; Tohka, Jussi

    2006-01-01

    In this study, we propose an automatic method to extract the heart volume from the cardiac positron emission tomography (PET) transmission images. The method combines the automatic 3D segmentation of the transmission image using Markov random fields (MRFs) to surface extraction using deformable models. Deformable models were automatically initialized using the MRFs segmentation result. The extraction of the heart region is needed e.g. in independent component analysis (ICA). The volume of the heart can be used to mask the emission image corresponding to the transmission image, so that only the cardiac region is used for the analysis. The masking restricts the number of independent components and reduces the computation time. In addition, the MRF segmentation result could be used for attenuation correction. The method was tested with 25 patient images. The MRF segmentation results were of good quality in all cases and we were able to extract the heart volume from all the images. PMID:17946020

  9. Physiologically Motivated Feature Extraction for Robust Automatic Speech Recognition

    OpenAIRE

    Ibrahim Missaoui; Zied Lachiri

    2016-01-01

    In this paper, a new method is presented to extract robust speech features in the presence of the external noise. The proposed method based on two-dimensional Gabor filters takes in account the spectro-temporal modulation frequencies and also limits the redundancy on the feature level. The performance of the proposed feature extraction method was evaluated on isolated speech words which are extracted from TIMIT corpus and corrupted by background noise. The evaluation results demonstrate that ...

  10. Physiologically Motivated Feature Extraction for Robust Automatic Speech Recognition

    Directory of Open Access Journals (Sweden)

    Ibrahim Missaoui

    2016-04-01

    Full Text Available In this paper, a new method is presented to extract robust speech features in the presence of the external noise. The proposed method based on two-dimensional Gabor filters takes in account the spectro-temporal modulation frequencies and also limits the redundancy on the feature level. The performance of the proposed feature extraction method was evaluated on isolated speech words which are extracted from TIMIT corpus and corrupted by background noise. The evaluation results demonstrate that the proposed feature extraction method outperforms the classic methods such as Perceptual Linear Prediction, Linear Predictive Coding, Linear Prediction Cepstral coefficients and Mel Frequency Cepstral Coefficients.

  11. A Semi-automatic Method Based on Statistic for Mandarin Semantic Structures Extraction in Specific Domains

    Institute of Scientific and Technical Information of China (English)

    熊英; 朱杰; 孙静

    2004-01-01

    This paper proposed a new method of semi-automatic extraction for semantic structures from unlabelled corpora in specific domains. The approach is statistical in nature. The extracted structures can be used for shallow parsing and semantic labeling. By iteratively extracting new words and clustering words, we get an inital semantic lexicon that groups words of the same semantic meaning together as a class. After that, a bootstrapping algorithm is adopted to extract semantic structures. Then the semantic structures are used to extract new key words and augment the semantic lexicon. The resultant semantic structures are interpreted by persons and are amenable to hand-editing for refinement. In this experiment, the semi-automatically extracted structures SSA provide recall rate of 84.5%.

  12. Automatic Segmentation of Raw LIDAR Data for Extraction of Building Roofs

    OpenAIRE

    Mohammad Awrangjeb; Fraser, Clive S.

    2014-01-01

    Automatic extraction of building roofs from remote sensing data is important for many applications, including 3D city modeling. This paper proposes a new method for automatic segmentation of raw LIDAR (light detection and ranging) data. Using the ground height from a DEM (digital elevation model), the raw LIDAR points are separated into two groups. The first group contains the ground points that form a “building mask”. The second group contains non-ground points that are clustered using the b...

  13. An automatic abrupt information extraction method based on singular value decomposition and higher-order statistics

    International Nuclear Information System (INIS)

    One key aspect of local fault diagnosis is how to effectively extract abrupt features from the vibration signals. This paper proposes a method to automatically extract abrupt information based on singular value decomposition and higher-order statistics. In order to observe the distribution law of singular values, a numerical analysis to simulate the noise, periodic signal, abrupt signal and singular value distribution is conducted. Based on higher-order statistics and spectrum analysis, a method to automatically choose the upper and lower borders of the singular value interval reflecting the abrupt information is built. And the selected singular values derived from this method are used to reconstruct abrupt signals. It is proven that the method is able to obtain accurate results by processing the rub-impact fault signal measured from the experiments. The analytical and experimental results indicate that the proposed method is feasible for automatically extracting abrupt information caused by faults like the rotor–stator rub-impact. (paper)

  14. Automatic Key-Frame Extraction from Optical Motion Capture Data

    Institute of Scientific and Technical Information of China (English)

    ZHANG Qiang; YU Shao-pei; ZHOU Dong-sheng; WEI Xiao-peng

    2013-01-01

    Optical motion capture is an increasingly popular animation technique. In the last few years, plenty of methods have been proposed for key-frame extraction of motion capture data, and it is a common method to extract key-frame using quaternion. Here, one main difficulty is due to the fact that previous algorithms often need to manually set various parameters. In addition, it is problematic to predefine the appropriate threshold without knowing the data content. In this paper, we present a novel adaptive threshold-based extraction method. Key-frame can be found according to quaternion distance. We propose a simple and efficient algorithm to extract key-frame from a motion sequence based on adaptive threshold. It is convenient with no need to predefine parameters to meet certain compression ratio. Experimental results of many motion captures with different traits demonstrate good performance of the proposed algorithm. Our experiments show that one can typically cut down the process of extraction from several minutes to a couple of seconds.

  15. Automatic Data Extraction from Websites for Generating Aquatic Product Market Information

    Institute of Scientific and Technical Information of China (English)

    YUAN Hong-chun; CHEN Ying; SUN Yue-fu

    2006-01-01

    The massive web-based information resources have led to an increasing demand for effective automatic retrieval of target information for web applications. This paper introduces a web-based data extraction tool that deploys various algorithms to locate, extract and filter tabular data from HTML pages and to transform them into new web-based representations. The tool has been applied in an aquaculture web application platform for extracting and generating aquatic product market information.Results prove that this tool is very effective in extracting the required data from web pages.

  16. Automatic Extraction of Leaf Characters from Herbarium Specimens

    OpenAIRE

    Corney, DPA; Clark, JY; Tang, HL; Wilkin, P

    2012-01-01

    Herbarium specimens are a vital resource in botanical taxonomy. Many herbaria are undertaking large-scale digitization projects to improve access and to preserve delicate specimens, and in doing so are creating large sets of images. Leaf characters are important for describing taxa and distinguishing between them and they can be measured from herbarium specimens. Here, we demonstrate that herbarium images can be analysed using suitable software and that leaf characters can be extracted automa...

  17. Fully automatic extraction of salient objects from videos in near real-time

    CERN Document Server

    Kazuma, Akamine; Kimura, Akisato; Takagi, Shigeru

    2010-01-01

    Automatic video segmentation plays an important role in a wide range of computer vision and image processing applications. Recently, various methods have been proposed for this purpose. The problem is that most of these methods are far from real-time processing even for low-resolution videos due to the complex procedures. To this end, we propose a new and quite fast method for automatic video segmentation with the help of 1) efficient optimization of Markov random fields with polynomial time of number of pixels by introducing graph cuts, 2) automatic, computationally efficient but stable derivation of segmentation priors using visual saliency and sequential update mechanism, and 3) an implementation strategy in the principle of stream processing with graphics processor units (GPUs). Test results indicates that our method extracts appropriate regions from videos as precisely as and much faster than previous semi-automatic methods even though any supervisions have not been incorporated.

  18. 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...

  19. Automatic extraction of gene and protein synonyms from MEDLINE and journal articles.

    OpenAIRE

    Hong YU; Hatzivassiloglou, Vasileios; Friedman, Carol; Rzhetsky, Andrey; Wilbur, W. John

    2002-01-01

    Genes and proteins are often associated with multiple names, and more names are added as new functional or structural information is discovered. Because authors often alternate between these synonyms, information retrieval and extraction benefits from identifying these synonymous names. We have developed a method to extract automatically synonymous gene and protein names from MEDLINE and journal articles. We first identified patterns authors use to list synonymous gene and protein names. We d...

  20. Automatic Extraction of Document Keyphrases for Use in Digital Libraries: Evaluation and Applications.

    Science.gov (United States)

    Jones, Steve; Paynter, Gordon W.

    2002-01-01

    Discussion of finding relevant documents in electronic document collections focuses on an evaluation of the Kea automatic keyphrase extraction algorithm which was developed by members of the New Zealand Digital Library Project. Results are based on evaluations by human assessors of the quality and appropriateness of Kea keyphrases. (Author/LRW)

  1. An automatic and fast centerline extraction algorithm for virtual colonoscopy.

    Science.gov (United States)

    Jiang, Guangxiang; Gu, Lixu

    2005-01-01

    This paper introduces a new refined centerline extraction algorithm, which is based on and significantly improved from distance mapping algorithms. The new approach include three major parts: employing a colon segmentation method; designing and realizing a fast Euclidean Transform algorithm and inducting boundary voxels cutting (BVC) approach. The main contribution is the BVC processing, which greatly speeds up the Dijkstra algorithm and improves the whole performance of the new algorithm. Experimental results demonstrate that the new centerline algorithm was more efficient and accurate comparing with existing algorithms. PMID:17281406

  2. 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.

  3. Automatic extraction of discontinuity orientation from rock mass surface 3D point cloud

    Science.gov (United States)

    Chen, Jianqin; Zhu, Hehua; Li, Xiaojun

    2016-10-01

    This paper presents a new method for extracting discontinuity orientation automatically from rock mass surface 3D point cloud. The proposed method consists of four steps: (1) automatic grouping of discontinuity sets using an improved K-means clustering method, (2) discontinuity segmentation and optimization, (3) discontinuity plane fitting using Random Sample Consensus (RANSAC) method, and (4) coordinate transformation of discontinuity plane. The method is first validated by the point cloud of a small piece of a rock slope acquired by photogrammetry. The extracted discontinuity orientations are compared with measured ones in the field. Then it is applied to a publicly available LiDAR data of a road cut rock slope at Rockbench repository. The extracted discontinuity orientations are compared with the method proposed by Riquelme et al. (2014). The results show that the presented method is reliable and of high accuracy, and can meet the engineering needs.

  4. Automatic centerline extraction of coronary arteries in coronary computed tomographic angiography.

    Science.gov (United States)

    Yang, Guanyu; Kitslaar, Pieter; Frenay, Michel; Broersen, Alexander; Boogers, Mark J; Bax, Jeroen J; Reiber, Johan H C; Dijkstra, Jouke

    2012-04-01

    Coronary computed tomographic angiography (CCTA) is a non-invasive imaging modality for the visualization of the heart and coronary arteries. To fully exploit the potential of the CCTA datasets and apply it in clinical practice, an automated coronary artery extraction approach is needed. The purpose of this paper is to present and validate a fully automatic centerline extraction algorithm for coronary arteries in CCTA images. The algorithm is based on an improved version of Frangi's vesselness filter which removes unwanted step-edge responses at the boundaries of the cardiac chambers. Building upon this new vesselness filter, the coronary artery extraction pipeline extracts the centerlines of main branches as well as side-branches automatically. This algorithm was first evaluated with a standardized evaluation framework named Rotterdam Coronary Artery Algorithm Evaluation Framework used in the MICCAI Coronary Artery Tracking challenge 2008 (CAT08). It includes 128 reference centerlines which were manually delineated. The average overlap and accuracy measures of our method were 93.7% and 0.30 mm, respectively, which ranked at the 1st and 3rd place compared to five other automatic methods presented in the CAT08. Secondly, in 50 clinical datasets, a total of 100 reference centerlines were generated from lumen contours in the transversal planes which were manually corrected by an expert from the cardiology department. In this evaluation, the average overlap and accuracy were 96.1% and 0.33 mm, respectively. The entire processing time for one dataset is less than 2 min on a standard desktop computer. In conclusion, our newly developed automatic approach can extract coronary arteries in CCTA images with excellent performances in extraction ability and accuracy. PMID:21637981

  5. Towards Automatic Music Transcription: Extraction of MIDI-Data out of Polyphonic Piano Music

    Directory of Open Access Journals (Sweden)

    Jens Wellhausen

    2005-06-01

    Full Text Available Driven by the increasing amount of music available electronically the need of automatic search and retrieval systems for music becomes more and more important. In this paper an algorithm for automatic transcription of polyphonic piano music into MIDI data is presented, which is a very interesting basis for database applications and music analysis. The first part of the algorithm performs a note accurate temporal audio segmentation. The resulting segments are examined to extract the notes played in the second part. An algorithm for chord separation based on Independent Subspace Analysis is presented. Finally, the results are used to build a MIDI file.

  6. Automatic Extraction of Femur Contours from Calibrated X-Ray Images using Statistical Information

    Directory of Open Access Journals (Sweden)

    Xiao Dong

    2007-09-01

    Full Text Available Automatic identification and extraction of bone contours from x-ray images is an essential first step task for further medical image analysis. In this paper we propose a 3D statistical model based framework for the proximal femur contour extraction from calibrated x-ray images. The automatic initialization to align the 3D model with the x-ray images is solved by an Estimation of Bayesian Network Algorithm to fit a simplified multiple component geometrical model of the proximal femur to the x-ray data. Landmarks can be extracted from the geometrical model for the initialization of the 3D statistical model. The contour extraction is then accomplished by a joint registration and segmentation procedure. We iteratively updates the extracted bone contours and an instanced 3D model to fit the x-ray images. Taking the projected silhouettes of the instanced 3D model on the registered x-ray images as templates, bone contours can be extracted by a graphical model based Bayesian inference. The 3D model can then be updated by a non-rigid 2D/3D registration between the 3D statistical model and the extracted bone contours. Preliminary experiments on clinical data sets verified its validity.

  7. Automatic landmark extraction from image data using modified growing neural gas network.

    Science.gov (United States)

    Fatemizadeh, Emad; Lucas, Caro; Soltanian-Zadeh, Hamid

    2003-06-01

    A new method for automatic landmark extraction from MR brain images is presented. In this method, landmark extraction is accomplished by modifying growing neural gas (GNG), which is a neural-network-based cluster-seeking algorithm. Using modified GNG (MGNG) corresponding dominant points of contours extracted from two corresponding images are found. These contours are borders of segmented anatomical regions from brain images. The presented method is compared to: 1) the node splitting-merging Kohonen model and 2) the Teh-Chin algorithm (a well-known approach for dominant points extraction of ordered curves). It is shown that the proposed algorithm has lower distortion error, ability of extracting landmarks from two corresponding curves simultaneously, and also generates the best match according to five medical experts. PMID:12834162

  8. 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...

  9. Motion states extraction with optical flow for rat-robot automatic navigation.

    Science.gov (United States)

    Zhang, Xinlu; Sun, Chao; Zheng, Nenggan; Chen, Weidong; Zheng, Xiaoxiang

    2012-01-01

    The real-time acquisition of precise motion states is significant and difficult for bio-robot automatic navigation. In this paper, we propose a real-time video-tracking algorithm to extract motion states of rat-robots in complex environment using optical flow. The rat-robot's motion states, including location, speed and motion trend, are acquired accurately in real time. Compared with the traditional methods based on single frame image, our algorithm using consecutive frames provides more exact and rich motion information for the automatic navigation of bio-robots. The video of the manual navigation experiments on rat-robots in eight-arm maze is applied to test this algorithm. The average computation time is 25.76 ms which is less than the speed of image acquisition. The results show that our method could extract the motion states with good performance of accuracy and time consumption.

  10. AUTOMATIC ROAD EXTRACTION BASED ON INTEGRATION OF HIGH RESOLUTION LIDAR AND AERIAL IMAGERY

    OpenAIRE

    Rahimi, S.; H. Arefi; Bahmanyar, R.

    2015-01-01

    In recent years, the rapid increase in the demand for road information together with the availability of large volumes of high resolution Earth Observation (EO) images, have drawn remarkable interest to the use of EO images for road extraction. Among the proposed methods, the unsupervised fully-automatic ones are more efficient since they do not require human effort. Considering the proposed methods, the focus is usually to improve the road network detection, while the roads’ precise...

  11. Automatic facial feature extraction and expression recognition based on neural network

    OpenAIRE

    Khandait, S. P.; Dr. R.C.Thool; P.D.Khandait

    2012-01-01

    In this paper, an approach to the problem of automatic facial feature extraction from a still frontal posed image and classification and recognition of facial expression and hence emotion and mood of a person is presented. Feed forward back propagation neural network is used as a classifier for classifying the expressions of supplied face into seven basic categories like surprise, neutral, sad, disgust, fear, happy and angry. For face portion segmentation and localization, morphological image...

  12. 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.

  13. Automatic Authorship Detection Using Textual Patterns Extracted from Integrated Syntactic Graphs

    Science.gov (United States)

    Gómez-Adorno, Helena; Sidorov, Grigori; Pinto, David; Vilariño, Darnes; Gelbukh, Alexander

    2016-01-01

    We apply the integrated syntactic graph feature extraction methodology to the task of automatic authorship detection. This graph-based representation allows integrating different levels of language description into a single structure. We extract textual patterns based on features obtained from shortest path walks over integrated syntactic graphs and apply them to determine the authors of documents. On average, our method outperforms the state of the art approaches and gives consistently high results across different corpora, unlike existing methods. Our results show that our textual patterns are useful for the task of authorship attribution. PMID:27589740

  14. Automatic facial expression recognition based on features extracted from tracking of facial landmarks

    Science.gov (United States)

    Ghimire, Deepak; Lee, Joonwhoan

    2014-01-01

    In this paper, we present a fully automatic facial expression recognition system using support vector machines, with geometric features extracted from the tracking of facial landmarks. Facial landmark initialization and tracking is performed by using an elastic bunch graph matching algorithm. The facial expression recognition is performed based on the features extracted from the tracking of not only individual landmarks, but also pair of landmarks. The recognition accuracy on the Extended Kohn-Kanade (CK+) database shows that our proposed set of features produces better results, because it utilizes time-varying graph information, as well as the motion of individual facial landmarks.

  15. Semi-Automatically Extracting FAQs to Improve Accessibility of Software Development Knowledge

    CERN Document Server

    Henß, Stefan; Mezini, Mira

    2012-01-01

    Frequently asked questions (FAQs) are a popular way to document software development knowledge. As creating such documents is expensive, this paper presents an approach for automatically extracting FAQs from sources of software development discussion, such as mailing lists and Internet forums, by combining techniques of text mining and natural language processing. We apply the approach to popular mailing lists and carry out a survey among software developers to show that it is able to extract high-quality FAQs that may be further improved by experts.

  16. Automatic Identification and Data Extraction from 2-Dimensional Plots in Digital Documents

    CERN Document Server

    Brouwer, William; Das, Sujatha; Mitra, Prasenjit; Giles, C L

    2008-01-01

    Most search engines index the textual content of documents in digital libraries. However, scholarly articles frequently report important findings in figures for visual impact and the contents of these figures are not indexed. These contents are often invaluable to the researcher in various fields, for the purposes of direct comparison with their own work. Therefore, searching for figures and extracting figure data are important problems. To the best of our knowledge, there exists no tool to automatically extract data from figures in digital documents. If we can extract data from these images automatically and store them in a database, an end-user can query and combine data from multiple digital documents simultaneously and efficiently. We propose a framework based on image analysis and machine learning to extract information from 2-D plot images and store them in a database. The proposed algorithm identifies a 2-D plot and extracts the axis labels, legend and the data points from the 2-D plot. We also segrega...

  17. Sequential Clustering based Facial Feature Extraction Method for Automatic Creation of Facial Models from Orthogonal Views

    CERN Document Server

    Ghahari, Alireza

    2009-01-01

    Multiview 3D face modeling has attracted increasing attention recently and has become one of the potential avenues in future video systems. We aim to make more reliable and robust automatic feature extraction and natural 3D feature construction from 2D features detected on a pair of frontal and profile view face images. We propose several heuristic algorithms to minimize possible errors introduced by prevalent nonperfect orthogonal condition and noncoherent luminance. In our approach, we first extract the 2D features that are visible to both cameras in both views. Then, we estimate the coordinates of the features in the hidden profile view based on the visible features extracted in the two orthogonal views. Finally, based on the coordinates of the extracted features, we deform a 3D generic model to perform the desired 3D clone modeling. Present study proves the scope of resulted facial models for practical applications like face recognition and facial animation.

  18. Automatic Extraction and Size Distribution of Landslides in Kurdistan Region, NE Iraq

    Directory of Open Access Journals (Sweden)

    Arsalan A. Othman

    2013-05-01

    Full Text Available This study aims to assess the localization and size distribution of landslides using automatic remote sensing techniques in (semi- arid, non-vegetated, mountainous environments. The study area is located in the Kurdistan region (NE Iraq, within the Zagros orogenic belt, which is characterized by the High Folded Zone (HFZ, the Imbricated Zone and the Zagros Suture Zone (ZSZ. The available reference inventory includes 3,190 landslides mapped from sixty QuickBird scenes using manual delineation. The landslide types involve rock falls, translational slides and slumps, which occurred in different lithological units. Two hundred and ninety of these landslides lie within the ZSZ, representing a cumulated surface of 32 km2. The HFZ implicates 2,900 landslides with an overall coverage of about 26 km2. We first analyzed cumulative landslide number-size distributions using the inventory map. We then proposed a very simple and robust algorithm for automatic landslide extraction using specific band ratios selected upon the spectral signatures of bare surfaces as well as posteriori slope and the normalized difference vegetation index (NDVI thresholds. The index is based on the contrast between landslides and their background, whereas the landslides have high reflections in the green and red bands. We applied the slope threshold map to remove low slope areas, which have high reflectance in red and green bands. The algorithm was able to detect ~96% of the recent landslides known from the reference inventory on a test site. The cumulative landslide number-size distribution of automatically extracted landslide is very similar to the one based on visual mapping. The automatic extraction is therefore adapted for the quantitative analysis of landslides and thus can contribute to the assessment of hazards in similar regions.

  19. 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...

  20. Automatic Road Extraction Based on Integration of High Resolution LIDAR and Aerial Imagery

    Science.gov (United States)

    Rahimi, S.; Arefi, H.; Bahmanyar, R.

    2015-12-01

    In recent years, the rapid increase in the demand for road information together with the availability of large volumes of high resolution Earth Observation (EO) images, have drawn remarkable interest to the use of EO images for road extraction. Among the proposed methods, the unsupervised fully-automatic ones are more efficient since they do not require human effort. Considering the proposed methods, the focus is usually to improve the road network detection, while the roads' precise delineation has been less attended to. In this paper, we propose a new unsupervised fully-automatic road extraction method, based on the integration of the high resolution LiDAR and aerial images of a scene using Principal Component Analysis (PCA). This method discriminates the existing roads in a scene; and then precisely delineates them. Hough transform is then applied to the integrated information to extract straight lines; which are further used to segment the scene and discriminate the existing roads. The roads' edges are then precisely localized using a projection-based technique, and the round corners are further refined. Experimental results demonstrate that our proposed method extracts and delineates the roads with a high accuracy.

  1. Automatic extraction of building boundaries using aerial LiDAR data

    Science.gov (United States)

    Wang, Ruisheng; Hu, Yong; Wu, Huayi; Wang, Jian

    2016-01-01

    Building extraction is one of the main research topics of the photogrammetry community. This paper presents automatic algorithms for building boundary extractions from aerial LiDAR data. First, segmenting height information generated from LiDAR data, the outer boundaries of aboveground objects are expressed as closed chains of oriented edge pixels. Then, building boundaries are distinguished from nonbuilding ones by evaluating their shapes. The candidate building boundaries are reconstructed as rectangles or regular polygons by applying new algorithms, following the hypothesis verification paradigm. These algorithms include constrained searching in Hough space, enhanced Hough transformation, and the sequential linking technique. The experimental results show that the proposed algorithms successfully extract building boundaries at rates of 97%, 85%, and 92% for three LiDAR datasets with varying scene complexities.

  2. Template Guided Live Wire and Its Application on Automatic Extraction of Tongue in Digital Image

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yuan-jie; YANG Jie; ZHOU Yue

    2005-01-01

    In this paper, we propose a novel automatic object extraction algorithm, named the Template Guided Live Wire, based on the popularly used livewire techniques. We discuss in details the novel method's applications on tongue extraction in digital images. With the guides of a given template curve which approximates the tongue's shape, our method can finish the extraction of tongue without any human intervention. In the paper, we also discussed in details how the template guides the live wire, and why our method functions more effectively than other boundary based segmentation methods especially the snake algorithm. Experimental results on some tongue images areas well provided to show our method's better accuracy and robustness than the snake algorithm.

  3. 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.

  4. Automatic Segmentation of Raw LIDAR Data for Extraction of Building Roofs

    Directory of Open Access Journals (Sweden)

    Mohammad Awrangjeb

    2014-04-01

    Full Text Available Automatic extraction of building roofs from remote sensing data is important for many applications, including 3D city modeling. This paper proposes a new method for automatic segmentation of raw LIDAR (light detection and ranging data. Using the ground height from a DEM (digital elevation model, the raw LIDAR points are separated into two groups. The first group contains the ground points that form a “building mask”. The second group contains non-ground points that are clustered using the building mask. A cluster of points usually represents an individual building or tree. During segmentation, the planar roof segments are extracted from each cluster of points and refined using rules, such as the coplanarity of points and their locality. Planes on trees are removed using information, such as area and point height difference. Experimental results on nine areas of six different data sets show that the proposed method can successfully remove vegetation and, so, offers a high success rate for building detection (about 90% correctness and completeness and roof plane extraction (about 80% correctness and completeness, when LIDAR point density is as low as four points/m2. Thus, the proposed method can be exploited in various applications.

  5. Semi-Automatic Mapping Generation for the DBpedia Information Extraction Framework

    Directory of Open Access Journals (Sweden)

    Arup Sarkar, Ujjal Marjit, Utpal Biswas

    2013-03-01

    Full Text Available DBpedia is one of the very well known live projectsfrom the Semantic Web. It is likeamirror version ofthe Wikipedia site in Semantic Web. Initially itpublishes the information collected from theWikipedia, but only that part which is relevant tothe Semantic Web.Collecting information forSemantic Web from the Wikipedia is demonstratedas the extraction of structured data. DBpedianormally do this by using a specially designedframework called DBpedia Information ExtractionFramework. This extraction framework do itsworks thorough the evaluation of the similarproperties from the DBpedia Ontology and theWikipedia template. This step is known as DBpediamapping.At present mostof the mapping jobs aredone complete manually.In this paper a newframework is introduced considering the issuesrelated to the template to ontology mapping. A semi-automatic mapping tool for the DBpedia projectisproposedwith the capability of automaticsuggestion generation for the end usersso thatusers can identify the similar Ontology and templateproperties.Proposed framework is useful since afterselection of similar properties, the necessary code tomaintain the mapping between Ontology andtemplate is generated automatically.

  6. AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.

    Science.gov (United States)

    Lounnas, V; Vriend, G

    2012-02-27

    Coordinates describing the chemical structures of small molecules that are potential ligands for pharmaceutical targets are used at many stages of the drug design process. The coordinates of the vast majority of ligands can be obtained from either publicly accessible or commercial databases. However, interesting ligands sometimes are only available from the scientific literature, in which case their coordinates need to be reconstructed manually--a process that consists of a series of time-consuming steps. We present a Web server that helps reconstruct the three-dimensional (3D) coordinates of ligands for which a two-dimensional (2D) picture is available in a PDF file. The software, called AsteriX, analyses every picture contained in the PDF file and attempts to determine automatically whether or not it contains ligands. Areas in pictures that may contain molecular structures are processed to extract connectivity and atom type information that allow coordinates to be subsequently reconstructed. The AsteriX Web server was tested on a series of articles containing a large diversity in graphical representations. In total, 88% of 3249 ligand structures present in the test set were identified as chemical diagrams. Of these, about half were interpreted correctly as 3D structures, and a further one-third required only minor manual corrections. It is principally impossible to always correctly reconstruct 3D coordinates from pictures because there are many different protocols for drawing a 2D image of a ligand, but more importantly a wide variety of semantic annotations are possible. The AsteriX Web server therefore includes facilities that allow the users to augment partial or partially correct 3D reconstructions. All 3D reconstructions are submitted, checked, and corrected by the users domain at the server and are freely available for everybody. The coordinates of the reconstructed ligands are made available in a series of formats commonly used in drug design research. The

  7. Extracting Noun Phrases from Large-Scale Texts A Hybrid Approach and Its Automatic Evaluation

    CERN Document Server

    Chen, K; Chen, Kuang-hua; Chen, Hsin-Hsi

    1994-01-01

    To acquire noun phrases from running texts is useful for many applications, such as word grouping,terminology indexing, etc. The reported literatures adopt pure probabilistic approach, or pure rule-based noun phrases grammar to tackle this problem. In this paper, we apply a probabilistic chunker to deciding the implicit boundaries of constituents and utilize the linguistic knowledge to extract the noun phrases by a finite state mechanism. The test texts are SUSANNE Corpus and the results are evaluated by comparing the parse field of SUSANNE Corpus automatically. The results of this preliminary experiment are encouraging.

  8. An Efficient Method for Automatic Road Extraction Based on Multiple Features from LiDAR Data

    Science.gov (United States)

    Li, Y.; Hu, X.; Guan, H.; Liu, P.

    2016-06-01

    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. Hydrophilic solutes in modified carbon dioxide extraction-prediction of the extractability using molecular dynamic simulation.

    Science.gov (United States)

    Günther, Martina; Maus, Martin; Wagner, Karl Gerhard; Schmidt, Peter Christian

    2005-06-01

    Super- and subcritical carbon dioxide (CO2) extractions of crude drugs were simulated by molecular modelling to predict the extractability of different hydrophilic plant constituents under various extraction conditions. The CO2 extraction fluids were simulated either with pure CO2 or with solvent modified CO2 at different pressures and temperatures. Molecular modelling resulted in three different solubility parameters: the total solubility parameter delta and the partial solubility parameters delta(d) for the van der Waals and delta(EL) for the polar forces. Thus, delta(EL) enabled the estimation of the polarity of the extraction fluids and the solute molecules. If the value of delta(EL) of the extraction fluid reached the value of the solute molecule in the crude drug, i.e. minimum extraction value, the compound was soluble at the distinct extraction conditions. For a further increase in yield of the hydrophilic solutes, the polarity of the extraction fluid had to be increased, too. That means delta(EL) of the fluid exceeded the minimum extraction value. All simulations were verified by CO2 extractions of the secondary roots of Harpagophytum procumbens (harpagoside, stachyose) and the seeds of Aesculus hippocastanum (aescin). CO2 extractions of the flowers of Matricaria recutita ((-)-alpha-bisabolol) were obtained from literature data. These four constituents with different properties, like molecular size and the allocation of polar functional groups were extracted, analysed, simulated and the extract content was correlated with the extraction fluid used, respectively. PMID:15911229

  10. Automatic facial feature extraction and expression recognition based on neural network

    CERN Document Server

    Khandait, S P; Khandait, P D

    2012-01-01

    In this paper, an approach to the problem of automatic facial feature extraction from a still frontal posed image and classification and recognition of facial expression and hence emotion and mood of a person is presented. Feed forward back propagation neural network is used as a classifier for classifying the expressions of supplied face into seven basic categories like surprise, neutral, sad, disgust, fear, happy and angry. For face portion segmentation and localization, morphological image processing operations are used. Permanent facial features like eyebrows, eyes, mouth and nose are extracted using SUSAN edge detection operator, facial geometry, edge projection analysis. Experiments are carried out on JAFFE facial expression database and gives better performance in terms of 100% accuracy for training set and 95.26% accuracy for test set.

  11. 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.

  12. Template-based automatic extraction of the joint space of foot bones from CT scan

    Science.gov (United States)

    Park, Eunbi; Kim, Taeho; Park, Jinah

    2016-03-01

    Clean bone segmentation is critical in studying the joint anatomy for measuring the spacing between the bones. However, separation of the coupled bones in CT images is sometimes difficult due to ambiguous gray values coming from the noise and the heterogeneity of bone materials as well as narrowing of the joint space. For fine reconstruction of the individual local boundaries, manual operation is a common practice where the segmentation remains to be a bottleneck. In this paper, we present an automatic method for extracting the joint space by applying graph cut on Markov random field model to the region of interest (ROI) which is identified by a template of 3D bone structures. The template includes encoded articular surface which identifies the tight region of the high-intensity bone boundaries together with the fuzzy joint area of interest. The localized shape information from the template model within the ROI effectively separates the bones nearby. By narrowing the ROI down to the region including two types of tissue, the object extraction problem was reduced to binary segmentation and solved via graph cut. Based on the shape of a joint space marked by the template, the hard constraint was set by the initial seeds which were automatically generated from thresholding and morphological operations. The performance and the robustness of the proposed method are evaluated on 12 volumes of ankle CT data, where each volume includes a set of 4 tarsal bones (calcaneus, talus, navicular and cuboid).

  13. Automatic Extraction and Regularization of Building Outlines from Airborne LIDAR Point Clouds

    Science.gov (United States)

    Albers, Bastian; Kada, Martin; Wichmann, Andreas

    2016-06-01

    Building outlines are needed for various applications like urban planning, 3D city modelling and updating cadaster. Their automatic reconstruction, e.g. from airborne laser scanning data, as regularized shapes is therefore of high relevance. Today's airborne laser scanning technology can produce dense 3D point clouds with high accuracy, which makes it an eligible data source to reconstruct 2D building outlines or even 3D building models. In this paper, we propose an automatic building outline extraction and regularization method that implements a trade-off between enforcing strict shape restriction and allowing flexible angles using an energy minimization approach. The proposed procedure can be summarized for each building as follows: (1) an initial building outline is created from a given set of building points with the alpha shape algorithm; (2) a Hough transform is used to determine the main directions of the building and to extract line segments which are oriented accordingly; (3) the alpha shape boundary points are then repositioned to both follow these segments, but also to respect their original location, favoring long line segments and certain angles. The energy function that guides this trade-off is evaluated with the Viterbi algorithm.

  14. 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. PMID:25019134

  15. Automatic Extraction of Tide-Coordinated Shoreline Using Open Source Software and Landsat Imagery

    Science.gov (United States)

    Goncalves, G.; Duro, N.; Sousa, E.; Figueiredo, I.

    2015-04-01

    Due to both natural and anthropogenic causes, the coastal lines keeps changing dynamically and continuously their shape, position and extend over time. In this paper we propose an approach to derive a tide-coordinate shoreline from two extracted instantaneous shorelines corresponding to a nearly low tide and high tide events. First, all the multispectral images are panshaperned to meet the 15 meters spatial resolution of the panchromatic images. Second, by using the Modification of Normalized Difference Water Index (MNDWI) and the kmeans clustering method we extract the raster shoreline for each image acquisition time. Third, each raster shoreline is smoothed and vectorized using a penalized least square method. Fourth, a 2D constrained Delaunay triangulation is built from the two extracted instantaneous shorelines with their respective heights interpolated from a Tidal gauche station. Finally, the desired tide-coordinate shoreline is interpolated from the previous triangular intertidal surface. The results show that an automatic tide-coordinated extraction method can be efficiently implemented using free available remote sensing imagery data (Landsat 8) and open source software (QGIS and Orfeo toolbox) and python scripting for task automation and software integration.

  16. 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

  17. Framework for automatic information extraction from research papers on nanocrystal devices

    Directory of Open Access Journals (Sweden)

    Thaer M. Dieb

    2015-09-01

    Full Text Available To support nanocrystal device development, we have been working on a computational framework to utilize information in research papers on nanocrystal devices. We developed an annotated corpus called “ NaDev” (Nanocrystal Device Development for this purpose. We also proposed an automatic information extraction system called “NaDevEx” (Nanocrystal Device Automatic Information Extraction Framework. NaDevEx aims at extracting information from research papers on nanocrystal devices using the NaDev corpus and machine-learning techniques. However, the characteristics of NaDevEx were not examined in detail. In this paper, we conduct system evaluation experiments for NaDevEx using the NaDev corpus. We discuss three main issues: system performance, compared with human annotators; the effect of paper type (synthesis or characterization on system performance; and the effects of domain knowledge features (e.g., a chemical named entity recognition system and list of names of physical quantities on system performance. We found that overall system performance was 89% in precision and 69% in recall. If we consider identification of terms that intersect with correct terms for the same information category as the correct identification, i.e., loose agreement (in many cases, we can find that appropriate head nouns such as temperature or pressure loosely match between two terms, the overall performance is 95% in precision and 74% in recall. The system performance is almost comparable with results of human annotators for information categories with rich domain knowledge information (source material. However, for other information categories, given the relatively large number of terms that exist only in one paper, recall of individual information categories is not high (39–73%; however, precision is better (75–97%. The average performance for synthesis papers is better than that for characterization papers because of the lack of training examples for

  18. Framework for automatic information extraction from research papers on nanocrystal devices.

    Science.gov (United States)

    Dieb, Thaer M; Yoshioka, Masaharu; Hara, Shinjiro; Newton, Marcus C

    2015-01-01

    To support nanocrystal device development, we have been working on a computational framework to utilize information in research papers on nanocrystal devices. We developed an annotated corpus called " NaDev" (Nanocrystal Device Development) for this purpose. We also proposed an automatic information extraction system called "NaDevEx" (Nanocrystal Device Automatic Information Extraction Framework). NaDevEx aims at extracting information from research papers on nanocrystal devices using the NaDev corpus and machine-learning techniques. However, the characteristics of NaDevEx were not examined in detail. In this paper, we conduct system evaluation experiments for NaDevEx using the NaDev corpus. We discuss three main issues: system performance, compared with human annotators; the effect of paper type (synthesis or characterization) on system performance; and the effects of domain knowledge features (e.g., a chemical named entity recognition system and list of names of physical quantities) on system performance. We found that overall system performance was 89% in precision and 69% in recall. If we consider identification of terms that intersect with correct terms for the same information category as the correct identification, i.e., loose agreement (in many cases, we can find that appropriate head nouns such as temperature or pressure loosely match between two terms), the overall performance is 95% in precision and 74% in recall. The system performance is almost comparable with results of human annotators for information categories with rich domain knowledge information (source material). However, for other information categories, given the relatively large number of terms that exist only in one paper, recall of individual information categories is not high (39-73%); however, precision is better (75-97%). The average performance for synthesis papers is better than that for characterization papers because of the lack of training examples for characterization papers

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

    Science.gov (United States)

    Yu, Kun; Ji, Guangrong; Zheng, Haiyong

    2016-05-01

    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 eff ectively 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 eff ects.

  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. 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.

  2. 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.

  3. 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.

  4. 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. PMID:22412336

  5. Visual content highlighting via automatic extraction of embedded captions on MPEG compressed video

    Science.gov (United States)

    Yeo, Boon-Lock; Liu, Bede

    1996-03-01

    Embedded captions in TV programs such as news broadcasts, documentaries and coverage of sports events provide important information on the underlying events. In digital video libraries, such captions represent a highly condensed form of key information on the contents of the video. In this paper we propose a scheme to automatically detect the presence of captions embedded in video frames. The proposed method operates on reduced image sequences which are efficiently reconstructed from compressed MPEG video and thus does not require full frame decompression. The detection, extraction and analysis of embedded captions help to capture the highlights of visual contents in video documents for better organization of video, to present succinctly the important messages embedded in the images, and to facilitate browsing, searching and retrieval of relevant clips.

  6. Feasibility of Automatic Extraction of Electronic Health Data to Evaluate a Status Epilepticus Clinical Protocol.

    Science.gov (United States)

    Hafeez, Baria; Paolicchi, Juliann; Pon, Steven; Howell, Joy D; Grinspan, Zachary M

    2016-05-01

    Status epilepticus is a common neurologic emergency in children. Pediatric medical centers often develop protocols to standardize care. Widespread adoption of electronic health records by hospitals affords the opportunity for clinicians to rapidly, and electronically evaluate protocol adherence. We reviewed the clinical data of a small sample of 7 children with status epilepticus, in order to (1) qualitatively determine the feasibility of automated data extraction and (2) demonstrate a timeline-style visualization of each patient's first 24 hours of care. Qualitatively, our observations indicate that most clinical data are well labeled in structured fields within the electronic health record, though some important information, particularly electroencephalography (EEG) data, may require manual abstraction. We conclude that a visualization that clarifies a patient's clinical course can be automatically created using the patient's electronic clinical data, supplemented with some manually abstracted data. Future work could use this timeline to evaluate adherence to status epilepticus clinical protocols. PMID:26518205

  7. Automatic layout feature extraction for lithography hotspot detection based on deep neural network

    Science.gov (United States)

    Matsunawa, Tetsuaki; Nojima, Shigeki; Kotani, Toshiya

    2016-03-01

    Lithography hotspot detection in the physical verification phase is one of the most important techniques in today's optical lithography based manufacturing process. Although lithography simulation based hotspot detection is widely used, it is also known to be time-consuming. To detect hotspots in a short runtime, several machine learning based methods have been proposed. However, it is difficult to realize highly accurate detection without an increase in false alarms because an appropriate layout feature is undefined. This paper proposes a new method to automatically extract a proper layout feature from a given layout for improvement in detection performance of machine learning based methods. Experimental results show that using a deep neural network can achieve better performance than other frameworks using manually selected layout features and detection algorithms, such as conventional logistic regression or artificial neural network.

  8. 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.

  9. Automatic Extraction of Open Space Area from High Resolution Urban Satellite Imagery

    Directory of Open Access Journals (Sweden)

    Hiremath P S & Kodge B G

    2010-06-01

    Full Text Available In the 21st century, Aerial and satellite images are information rich. They are alsocomplex to analyze. For GIS systems, many features require fast and reliableextraction of open space area from high resolution satellite imagery. In this paperwe will study efficient and reliable automatic extraction algorithm to find out theopen space area from the high resolution urban satellite imagery. This automaticextraction algorithm uses some filters and segmentations and grouping isapplying on satellite images. And the result images may use to calculate the totalavailable open space area and the built up area. It may also use to compare thedifference between present and past open space area using historical urbansatellite images of that same projection.

  10. Feasibility of Automatic Extraction of Electronic Health Data to Evaluate a Status Epilepticus Clinical Protocol.

    Science.gov (United States)

    Hafeez, Baria; Paolicchi, Juliann; Pon, Steven; Howell, Joy D; Grinspan, Zachary M

    2016-05-01

    Status epilepticus is a common neurologic emergency in children. Pediatric medical centers often develop protocols to standardize care. Widespread adoption of electronic health records by hospitals affords the opportunity for clinicians to rapidly, and electronically evaluate protocol adherence. We reviewed the clinical data of a small sample of 7 children with status epilepticus, in order to (1) qualitatively determine the feasibility of automated data extraction and (2) demonstrate a timeline-style visualization of each patient's first 24 hours of care. Qualitatively, our observations indicate that most clinical data are well labeled in structured fields within the electronic health record, though some important information, particularly electroencephalography (EEG) data, may require manual abstraction. We conclude that a visualization that clarifies a patient's clinical course can be automatically created using the patient's electronic clinical data, supplemented with some manually abstracted data. Future work could use this timeline to evaluate adherence to status epilepticus clinical protocols.

  11. DEM automatic extraction on Rio de Janeiro from WV2 stereo pair images

    International Nuclear Information System (INIS)

    The use of three-dimensional data has become, for a lot of mapping applications, very important. DEM are applied for modelling purposes, i.e. the 3D city model generation, but principally for imagery orthorectification. In aerial photogrammetry is well known the suitable use of stereo imagery to produce an accurate DEM, but the limits of the process (cost, schedule of data collection, highly technical staff) and the new advanced digital image processing algorithms have open the work scenario to the remote sensing data. This research has wanted to investigate the possibility to obtain accurate DEMs by means of automatic terrain extraction algorithms implemented in Leica Photogrammetry Suite (LPS) from stereoscopic remote sensing images collected by DigitalGlobe's WorldView-2 (WV2) satellite. The DEM of Rio de Janeiro (Brazil) and the correspondent digital orthoimages have been the results

  12. Feature-point-extracting-based automatically mosaic for composite microscopic images

    Institute of Scientific and Technical Information of China (English)

    YIN YanSheng; ZHAO XiuYang; TIAN XiaoFeng; LI Jia

    2007-01-01

    Image mosaic is a crucial step in the three-dimensional reconstruction of composite materials to align the serial images. A novel method is adopted to mosaic two SiC/Al microscopic images with an amplification coefficient of 1000. The two images are denoised by Gaussian model, and feature points are then extracted by using Harris corner detector. The feature points are filtered through Canny edge detector. A 40x40 feature template is chosen by sowing a seed in an overlapped area of the reference image, and the homologous region in floating image is acquired automatically by the way of correlation analysis. The feature points in matched templates are used as feature point-sets. Using the transformational parameters acquired by SVD-ICP method, the two images are transformed into the universal coordinates and merged to the final mosaic image.

  13. Automatic extraction of insulators from 3D LiDAR data of an electrical substation

    Science.gov (United States)

    Arastounia, M.; Lichti, D. D.

    2013-10-01

    A considerable percentage of power outages are caused by animals that come into contact with conductive elements of electrical substations. These can be prevented by insulating conductive electrical objects, for which a 3D as-built plan of the substation is crucial. This research aims to create such a 3D as-built plan using terrestrial LiDAR data while in this paper the aim is to extract insulators, which are key objects in electrical substations. This paper proposes a segmentation method based on a new approach of finding the principle direction of points' distribution. This is done by forming and analysing the distribution matrix whose elements are the range of points in 9 different directions in 3D space. Comparison of the computational performance of our method with PCA (principal component analysis) shows that our approach is 25% faster since it utilizes zero-order moments while PCA computes the first- and second-order moments, which is more time-consuming. A knowledge-based approach has been developed to automatically recognize points on insulators. The method utilizes known insulator properties such as diameter and the number and the spacing of their rings. The results achieved indicate that 24 out of 27 insulators could be recognized while the 3 un-recognized ones were highly occluded. Check point analysis was performed by manually cropping all points on insulators. The results of check point analysis show that the accuracy, precision and recall of insulator recognition are 98%, 86% and 81%, respectively. It is concluded that automatic object extraction from electrical substations using only LiDAR data is not only possible but also promising. Moreover, our developed approach to determine the directional distribution of points is computationally more efficient for segmentation of objects in electrical substations compared to PCA. Finally our knowledge-based method is promising to recognize points on electrical objects as it was successfully applied for

  14. Comparison of edge detection techniques for the automatic information extraction of Lidar data

    Science.gov (United States)

    Li, H.; di, L.; Huang, X.; Li, D.

    2008-05-01

    In recent years, there has been much interest in information extraction from Lidar point cloud data. Many automatic edge detection algorithms have been applied to extracting information from Lidar data. Generally they can be divided as three major categories: early vision gradient operators, optimal detectors and operators using parametric fitting models. Lidar point cloud includes the intensity information and the geographic information. Thus, traditional edge detectors used in remote sensed images can take advantage with the coordination information provided by point data. However, derivation of complex terrain features from Lidar data points depends on the intensity properties and topographic relief of each scene. Take road for example, in some urban area, road has the alike intensity as buildings, but the topographic relationship of road is distinct. The edge detector for road in urban area is different from the detector for buildings. Therefore, in Lidar extraction, each kind of scene has its own suitable edge detector. This paper compares application of the different edge detectors from the previous paragraph to various terrain areas, in order to figure out the proper algorithm for respective terrain type. The Canny, EDISON and SUSAN algorithms were applied to data points with the intensity character and topographic relationship of Lidar data. The Lidar data for test are over different terrain areas, such as an urban area with a mass of buildings, a rural area with vegetation, an area with slope, or an area with a bridge, etc. Results using these edge detectors are compared to determine which algorithm is suitable for a specific terrain area. Key words: Edge detector, Extraction, Lidar, Point data

  15. [DNA extraction methods of compost for molecular ecology analysis].

    Science.gov (United States)

    Yang, Zhao-Hui; Xiao, Yong; Zeng, Guang-Ming; Liu, Yun-Guo; Deng, Jiu-Hua

    2006-08-01

    Molecular ecology provides new techniques for studying compost microbes, and the DNA extraction is the basis of molecular techniques. Because of the contamination of humic acids, it turns to be more difficult for compost microbial DNA extraction. Three different approaches, named as lysozyme lysis, ultrasonic lysis and proteinase K lysis with CTAB, were used to extract the total DNA from compost. The detection performed on a nucleic acids and protein analyzer showed that all the three approaches produced high DNA yields. The agarose gel electrophoresis showed that the DNA fragments extracted from compost had a length of about 23 kb. A eubacterial 16S rRNA gene targeted primer pair (27F and 1 495R) was used for PCR amplification, and all the samples got almost the full length 16S rDNA sequence (about 1.5 kb). After digested by restriction endonucleases (Hae Ill and Alu I), the restriction map showed relatively identical microbial diversity in the DNA, which was extracted by the three different approaches. All the compost microbial DNA extracted by the three different approaches could be used for molecular ecological study, and researchers should choose the right approach for extracting microbial DNA from compost based on the facts.

  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 Spatio-Temporal Information from Arabic Text Documents

    Directory of Open Access Journals (Sweden)

    Abdelkoui Feriel

    2015-10-01

    Full Text Available Unstructured Arabic text documents are an important source of geographical and temporal information. The possibility of automatically tracking spatio-temporal information, capturing changes relating to events from text documents, is a new challenge in the fields of geographic information retrieval (GIR, temporal information retrieval (TIR and natural language processing (NLP. There was a lot of work on the extraction of information in other languages that use Latin alphabet, such as English,, French, or Spanish, by against the Arabic language is still not well supported in GIR and TIR and it needs to conduct more researches. In this paper, we present an approach that support automated exploration and extraction of spatio-temporal information from Arabic text documents in order to capture and model such information before it can be utilized in search and exploration tasks. The system has been successfully tested on 50 documents that include a mixture of types of Spatial/temporal information. The result achieved 91.01% of recall and of 80% precision. This illustrates that our approach is effective and its performance is satisfactory.

  18. Automatic Extraction of DTM from Low Resolution Dsm by Twosteps Semi-Global Filtering

    Science.gov (United States)

    Zhang, Yanfeng; Zhang, Yongjun; Zhang, Yi; Li, Xin

    2016-06-01

    Automatically extracting DTM from DSM or LiDAR data by distinguishing non-ground points from ground points is an important issue. Many algorithms for this issue are developed, however, most of them are targeted at processing dense LiDAR data, and lack the ability of getting DTM from low resolution DSM. This is caused by the decrease of distinction on elevation variation between steep terrains and surface objects. In this paper, a method called two-steps semi-global filtering (TSGF) is proposed to extract DTM from low resolution DSM. Firstly, the DSM slope map is calculated and smoothed by SGF (semi-global filtering), which is then binarized and used as the mask of flat terrains. Secondly, the DSM is segmented with the restriction of the flat terrains mask. Lastly, each segment is filtered with semi-global algorithm in order to remove non-ground points, which will produce the final DTM. The first SGF is based on global distribution characteristic of large slope, which distinguishes steep terrains and flat terrains. The second SGF is used to filter non-ground points on DSM within flat terrain segments. Therefore, by two steps SGF non-ground points are removed robustly, while shape of steep terrains is kept. Experiments on DSM generated by ZY3 imagery with resolution of 10-30m demonstrate the effectiveness of the proposed method.

  19. AUTOMATIC ROAD EXTRACTION FROM SATELLITE IMAGES USING EXTENDED KALMAN FILTERING AND EFFICIENT PARTICLE FILTERING

    Directory of Open Access Journals (Sweden)

    Jenita Subash

    2011-12-01

    Full Text Available Users of geospatial data in government, military, industry, research, and other sectors have need foraccurate display of roads and other terrain information in areas where there are ongoing operations orlocations of interest. Hence, road extraction that is significantly more automated than the employment ofcostly and scarce human resources has become a challenging technical issue for the geospatialcommunity. An automatic road extraction based on Extended Kalman Filtering (EKF and variablestructured multiple model particle filter (VS-MMPF from satellite images is addressed. EKF traces themedian axis of a single road segment while VS-MMPF traces all road branches initializing at theintersection. In case of Local Linearization Particle filter (LLPF, a large number of particles are usedand therefore high computational expense is usually required in order to attain certain accuracy androbustness. The basic idea is to reduce the whole sampling space of the multiple model system to the modesubspace by marginalization over the target subspace and choose better importance function for modestate sampling. The core of the system is based on profile matching. During the estimation, new referenceprofiles were generated and stored in the road template memory for future correlation analysis, thuscovering the space of road profiles. .

  20. Uncertain Training Data Edition for Automatic Object-Based Change Map Extraction

    Science.gov (United States)

    Hajahmadi, S.; Mokhtarzadeh, M.; Mohammadzadeh, A.; Valadanzouj, M. J.

    2013-09-01

    Due to the rapid transformation of the societies, and the consequent growth of the cities, it is necessary to study these changes in order to achieve better control and management of urban areas and assist the decision-makers. Change detection involves the ability to quantify temporal effects using multi-temporal data sets. The available maps of the under study area is one of the most important sources for this reason. Although old data bases and maps are a great resource, it is more than likely that the training data extracted from them might contain errors, which affects the procedure of the classification; and as a result the process of the training sample editing is an essential matter. Due to the urban nature of the area studied and the problems caused in the pixel base methods, object-based classification is applied. To reach this, the image is segmented into 4 scale levels using a multi-resolution segmentation procedure. After obtaining the segments in required levels, training samples are extracted automatically using the existing old map. Due to the old nature of the map, these samples are uncertain containing wrong data. To handle this issue, an editing process is proposed according to K-nearest neighbour and k-means algorithms. Next, the image is classified in a multi-resolution object-based manner and the effects of training sample refinement are evaluated. As a final step this classified image is compared with the existing map and the changed areas are detected.

  1. 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. PMID:24707316

  2. AUTOMATIC EXTRACTION OF ROAD SURFACE AND CURBSTONE EDGES FROM MOBILE LASER SCANNING DATA

    Directory of Open Access Journals (Sweden)

    A. Miraliakbari

    2015-05-01

    Full Text Available 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.

  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. 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

  5. Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy

    Science.gov (United States)

    Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo

    2015-05-01

    We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file at input optional; (3) The package provides fast calculation of the total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented in C and Fortran programming languages, with the Cilk Plus extension to harness the computing power of both multicore and vector processing. Computational experiments demonstrate the successful application of PAFMPB to the calculation of the PB potential on a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles.

  6. Extraction of High Molecular Weight DNA from Microbial Mats

    OpenAIRE

    Bey, Benjamin S.; Fichot, Erin B.; Norman, R. Sean

    2011-01-01

    Successful and accurate analysis and interpretation of metagenomic data is dependent upon the efficient extraction of high-quality, high molecular weight (HMW) community DNA. However, environmental mat samples often pose difficulties to obtaining large concentrations of high-quality, HMW DNA. Hypersaline microbial mats contain high amounts of extracellular polymeric substances (EPS)1 and salts that may inhibit downstream applications of extracted DNA. Direct and harsh methods are often used i...

  7. Solvent extraction of molybdophosphoric acid with high-molecular alkylamines

    International Nuclear Information System (INIS)

    Extraction of dodecamolibdophosphoric acid H3PMo12O40 by nitrates of some high molecular amines (di-(2-ethylene-hexyl)-amine, diponylamine, diisoamyloctylamine) dichlorthane solution has been studied. The composition of associates in the organic phase may be presented as (BH3)PMo12O40, where BH+ is the protonized form of the amine. The overall conventional equilibrium constant of complex formation and extraction equals (1.51+-0.35)x1011

  8. Molecular imprinted polymer for solid-phase extraction of flavonol aglycones from Moringa oleifera extracts.

    Science.gov (United States)

    Pakade, Vusumzi; Cukrowska, Ewa; Lindahl, Sofia; Turner, Charlotta; Chimuka, Luke

    2013-02-01

    Molecular imprinted polymer produced using quercetin as the imprinting compound was applied for the extraction of flavonol aglycones (quercetin and kaempferol) from Moringa oleifera methanolic extracts obtained using heated reflux extraction method. Identification and quantification of these flavonols in the Moringa extracts was achieved using high performance liquid chromatography with ultra violet detection. Breakthrough volume and retention capacity of molecular imprinted polymer SPE was investigated using a mixture of myricetin, quercetin and kaempferol. The calculated theoretical number of plates was found to be 14, 50 and 8 for myricetin, quercetin and kaempferol, respectively. Calculated adsorption capacities were 2.0, 3.4 and 3.7 μmol/g for myricetin, quercetin and kaempferol, respectively. No myricetin was observed in Moringa methanol extracts. Recoveries of quercetin and kaempferol from Moringa methanol extracts of leaves and flowers ranged from 77 to 85% and 75 to 86%, respectively, demonstrating the feasibility of using the developed molecularly imprinted SPE method for quantitative clean-up of both of these flavonoids. Using heated reflux extraction combined with molecularly imprinted SPE, quercetin concentrations of 975 ± 58 and 845 ± 32 mg/kg were determined in Moringa leaves and flowers, respectively. However, the concentrations of kaempferol found in leaves and flowers were 2100 ± 176 and 2802 ± 157 mg/kg, respectively. PMID:23255435

  9. Automatic dynamic mask extraction for PIV images containing an unsteady interface, bubbles, and a moving structure

    Science.gov (United States)

    Dussol, David; Druault, Philippe; Mallat, Bachar; Delacroix, Sylvain; Germain, Grégory

    2016-07-01

    When performing Particle Image Velocimetry (PIV) measurements in complex fluid flows with moving interfaces and a two-phase flow, it is necessary to develop a mask to remove non-physical measurements. This is the case when studying, for example, the complex bubble sweep-down phenomenon observed in oceanographic research vessels. Indeed, in such a configuration, the presence of an unsteady free surface, of a solid-liquid interface and of bubbles in the PIV frame, leads to generate numerous laser reflections and therefore spurious velocity vectors. In this note, an image masking process is developed to successively identify the boundaries of the ship and the free surface interface. As the presence of the solid hull surface induces laser reflections, the hull edge contours are simply detected in the first PIV frame and dynamically estimated for consecutive ones. As for the unsteady surface determination, a specific process is implemented like the following: i) the edge detection of the gradient magnitude in the PIV frame, ii) the extraction of the particles by filtering high-intensity large areas related to the bubbles and/or hull reflections, iii) the extraction of the rough region containing these particles and their reflections, iv) the removal of these reflections. The unsteady surface is finally obtained with a fifth-order polynomial interpolation. The resulted free surface is successfully validated from the Fourier analysis and by visualizing selected PIV images containing numerous spurious high intensity areas. This paper demonstrates how this data analysis process leads to PIV images database without reflections and an automatic detection of both the free surface and the rigid body. An application of this new mask is finally detailed, allowing a preliminary analysis of the hydrodynamic flow.

  10. An Automatic Building Extraction and Regularisation Technique Using LiDAR Point Cloud Data and Orthoimage

    Directory of Open Access Journals (Sweden)

    Syed Ali Naqi Gilani

    2016-03-01

    Full Text Available The development of robust and accurate methods for automatic building detection and regularisation using multisource data continues to be a challenge due to point cloud sparsity, high spectral variability, urban objects differences, surrounding complexity, and data misalignment. To address these challenges, constraints on object’s size, height, area, and orientation are generally benefited which adversely affect the detection performance. Often the buildings either small in size, under shadows or partly occluded are ousted during elimination of superfluous objects. To overcome the limitations, a methodology is developed to extract and regularise the buildings using features from point cloud and orthoimagery. The building delineation process is carried out by identifying the candidate building regions and segmenting them into grids. Vegetation elimination, building detection and extraction of their partially occluded parts are achieved by synthesising the point cloud and image data. Finally, the detected buildings are regularised by exploiting the image lines in the building regularisation process. Detection and regularisation processes have been evaluated using the ISPRS benchmark and four Australian data sets which differ in point density (1 to 29 points/m2, building sizes, shadows, terrain, and vegetation. Results indicate that there is 83% to 93% per-area completeness with the correctness of above 95%, demonstrating the robustness of the approach. The absence of over- and many-to-many segmentation errors in the ISPRS data set indicate that the technique has higher per-object accuracy. While compared with six existing similar methods, the proposed detection and regularisation approach performs significantly better on more complex data sets (Australian in contrast to the ISPRS benchmark, where it does better or equal to the counterparts.

  11. ANTIOXIDATIVE LOW MOLECULAR WEIGHT EXTRACTIVES FROM TRIPLOID POPULUS TOMENTOSA XYLEM

    Directory of Open Access Journals (Sweden)

    Yong-Hao Ni

    2011-02-01

    Full Text Available Triploid Populus tomentosa Carr. (Salicaceae is a good alternative to meet the increasing need of the global pulp and paper industry. Meanwhile, the xylem of this species could be a useful bioresource to develop low molecular extractives with significant bioactive potential. In the present work, a phytochemical investigation on aqueous EtOH extractives of Triploid P. tomentosa xylem, by systematical performance of Sephadex LH-20 open column chromatography and Thin Layer Chromatography (TLC, resulted in the isolation of two phenolic acids (ρ-coumaric acid (I and caffeic acid (II, two flavonoids (apigenin (III and luteolin (IV, and three phenolic glucosides (salicortin (V, salireposide (VI and populoside (VII. The structure elucidation and determination of the isolated extractives were based on their spectroscopical data and physiochemical evidences. This was the first time to report the low molecular weight extractives of Triploid P. tomentosa. Various low molecular weight extractives from Triploid P. tomentosa xylem exhibited significant antioxidative activities by DPPH and hydroxyl radical scavenging assays.

  12. Semantic Gap in CBIR: Automatic Objects Spatial Relationships Semantic Extraction and Representation

    Directory of Open Access Journals (Sweden)

    Hui Hui Wang, Dzulkifli Mohamad & N.A. Ismail

    2010-08-01

    Full Text Available The explosive growth of image data leads to the need of research anddevelopment of Image retrieval. Image retrieval researches are moving fromkeyword, to low level features and to semantic features. Drive towards semanticfeatures is due to the problem of the keywords which can be very subjective andtime consuming while low level features cannot always describe high levelconcepts in the users’ mind. This paper is proposed a novel technique for objectsspatial relationships semantics extraction and representation among objectsexists in images. All objects are identified based on low level features extractionintegrated with proposed line detection techniques. Objects are representedusing a Minimum Bound Region (MBR with a reference coordinate. Thereference coordinate is used to compute the spatial relation among objects.There are 8 spatial relationship concepts are determined: “Front”, “Back”, “Right”,“Left”, “Right-Front”, “Left-Front”, “Right-Back”, “Left-Back” concept. The userquery in text form is automatically translated to semantic meaning andrepresentation. Besides, the image similarity of objects spatial relationshipssemantic has been proposed.

  13. Automatic indicator dilution curve extraction in dynamic-contrast enhanced imaging using spectral clustering

    Science.gov (United States)

    Saporito, Salvatore; Herold, Ingeborg HF; Houthuizen, Patrick; van den Bosch, Harrie CM; Korsten, Hendrikus HM; van Assen, Hans C.; Mischi, Massimo

    2015-07-01

    Indicator dilution theory provides a framework for the measurement of several cardiovascular parameters. Recently, dynamic imaging and contrast agents have been proposed to apply the method in a minimally invasive way. However, the use of contrast-enhanced sequences requires the definition of regions of interest (ROIs) in the dynamic image series; a time-consuming and operator dependent task, commonly performed manually. In this work, we propose a method for the automatic extraction of indicator dilution curves, exploiting the time domain correlation between pixels belonging to the same region. Individual time intensity curves were projected into a low dimensional subspace using principal component analysis; subsequently, clustering was performed to identify the different ROIs. The method was assessed on clinically available DCE-MRI and DCE-US recordings, comparing the derived IDCs with those obtained manually. The robustness to noise of the proposed approach was shown on simulated data. The tracer kinetic parameters derived on real images were in agreement with those obtained from manual annotation. The presented method is a clinically useful preprocessing step prior to further ROI-based cardiac quantifications.

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

    International Nuclear Information System (INIS)

    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 Sleep Staging using Multi-dimensional Feature Extraction and Multi-kernel Fuzzy Support Vector Machine

    OpenAIRE

    Yanjun Zhang; Xiangmin Zhang; Wenhui Liu; Yuxi Luo; Enjia Yu; Keju Zou; Xiaoliang Liu

    2014-01-01

    This paper employed the clinical Polysomnographic (PSG) data, mainly including all-night Electroencephalogram (EEG), Electrooculogram (EOG) and Electromyogram (EMG) signals of subjects, and adopted the American Academy of Sleep Medicine (AASM) clinical staging manual as standards to realize automatic sleep staging. Authors extracted eighteen different features of EEG, EOG and EMG in time domains and frequency domains to construct the vectors according to the existing literatures as well as cl...

  16. Automatic segmentation of the bone and extraction of the bone cartilage interface from magnetic resonance images of the knee

    Science.gov (United States)

    Fripp, Jurgen; Crozier, Stuart; Warfield, Simon K.; Ourselin, Sébastien

    2007-03-01

    The accurate segmentation of the articular cartilages from magnetic resonance (MR) images of the knee is important for clinical studies and drug trials into conditions like osteoarthritis. Currently, segmentations are obtained using time-consuming manual or semi-automatic algorithms which have high inter- and intra-observer variabilities. This paper presents an important step towards obtaining automatic and accurate segmentations of the cartilages, namely an approach to automatically segment the bones and extract the bone-cartilage interfaces (BCI) in the knee. The segmentation is performed using three-dimensional active shape models, which are initialized using an affine registration to an atlas. The BCI are then extracted using image information and prior knowledge about the likelihood of each point belonging to the interface. The accuracy and robustness of the approach was experimentally validated using an MR database of fat suppressed spoiled gradient recall images. The (femur, tibia, patella) bone segmentation had a median Dice similarity coefficient of (0.96, 0.96, 0.89) and an average point-to-surface error of 0.16 mm on the BCI. The extracted BCI had a median surface overlap of 0.94 with the real interface, demonstrating its usefulness for subsequent cartilage segmentation or quantitative analysis.

  17. Automatic extraction of lunar impact craters from Chang'E images based on Hough transform and RANSAC

    Science.gov (United States)

    Luo, Zhongfei; Kang, Zhizhong

    2016-03-01

    This article proposed an algorithm combining Hough transform and RANSAC algorithm for automatic extraction of lunar craters. (1) In order to suppress noise, the images were filtered; (2) The edge of image were extracted, subsequently, eliminate false edge points by qualifying the gradient direction and the area of connected domain; (3) The edge images were segmented through Hough transform, gathering the same crater edge points together; (4) The edge images after segmentation were fitted using RANSAC algorithm, getting the high precision parameter. High precision of the algorithm was verified by the experiments of images acquired by the Chang'E-1 satellites.

  18. Automatic extraction of road seeds from high-resolution aerial images

    Directory of Open Access Journals (Sweden)

    Aluir P. Dal-Poz

    2005-09-01

    Full Text Available This article presents an automatic methodology for extraction of road seeds from high-resolution aerial images. The method is based on a set of four road objects and another set of connection rules among road objects. Each road object is a local representation of an approximately straight road fragment and its construction is based on a combination of polygons describing all relevant image edges, according to some rules embodying road knowledge. Each one of the road seeds is composed by a sequence of connected road objects, in which each sequence of this type can be geometrically structured as a chain of contiguous quadrilaterals. Experiments carried out with high-resolution aerial images showed that the proposed methodology is very promising in extracting road seeds. This article presents the fundamentals of the method and the experimental results, as well.Este artigo apresenta uma metodologia automática para extração de sementes de rodovia a partir de imagens aéreas de alta resolução. O método se baseia em um conjunto de quatro objetos de rodovia e em um conjunto de regras de conexão entre tais objetos. Cada objeto de rodovia é uma representação local de um fragmento de rodovia aproximadamente reto e sua construção é baseada na combinação de polígonos que descrevem todas as bordas relevantes da imagem, de acordo com algumas regras que incorporam conhecimento sobre a feição rodovia. Cada uma das sementes de rodovia é composta por uma sucessão de objetos de rodovia conectados, sendo que cada sucessão deste tipo pode ser geometricamente estruturada como uma cadeia de quadriláteros contíguos. Os experimentos realizados com imagens aéreas de alta resolução mostraram que a metodologia proposta é muito promissora na extração de sementes de rodovia. Este artigo apresenta os fundamentos do método, bem como os resultados experimentais.

  19. Automatic Extraction of Optimal Endmembers from Airborne Hyperspectral Imagery Using Iterative Error Analysis (IEA and Spectral Discrimination Measurements

    Directory of Open Access Journals (Sweden)

    Ahram Song

    2015-01-01

    Full Text Available Pure surface materials denoted by endmembers play an important role in hyperspectral processing in various fields. Many endmember extraction algorithms (EEAs have been proposed to find appropriate endmember sets. Most studies involving the automatic extraction of appropriate endmembers without a priori information have focused on N-FINDR. Although there are many different versions of N-FINDR algorithms, computational complexity issues still remain and these algorithms cannot consider the case where spectrally mixed materials are extracted as final endmembers. A sequential endmember extraction-based algorithm may be more effective when the number of endmembers to be extracted is unknown. In this study, we propose a simple but accurate method to automatically determine the optimal endmembers using such a method. The proposed method consists of three steps for determining the proper number of endmembers and for removing endmembers that are repeated or contain mixed signatures using the Root Mean Square Error (RMSE images obtained from Iterative Error Analysis (IEA and spectral discrimination measurements. A synthetic hyperpsectral image and two different airborne images such as Airborne Imaging Spectrometer for Application (AISA and Compact Airborne Spectrographic Imager (CASI data were tested using the proposed method, and our experimental results indicate that the final endmember set contained all of the distinct signatures without redundant endmembers and errors from mixed materials.

  20. A microfluidic approach for high efficiency extraction of low molecular weight RNA.

    Science.gov (United States)

    Vulto, Paul; Dame, Gregory; Maier, Urban; Makohliso, Solomzi; Podszun, Susann; Zahn, Peter; Urban, Gerald A

    2010-03-01

    The lack of sample pre-treatment concepts that are easily automatable, miniaturized and highly efficient for both small volumes and low target concentrations, is one of the key issues that block the road towards effective miniaturized diagnostic instruments. This paper presents a novel, highly efficient and simple method for low-molecular weight RNA extraction using electricity only. Cells are lysed by thermo-electric lysis and RNA is purified using a gel-electrophoretic purification step. The combination of the two steps in one integrated cartridge reduces the time frame between the two steps, thus protecting RNA from enzymatic degradation. A disposable chip solution is proposed using a novel dry film resist laminate technology that allows cheap, large-scale fabrication. The chip contains crucial microfluidic innovations that allow for a simple user interface, reproducible functioning and precise quantification. Phaseguides are invented that allow controlled spatial injection of gel, injection of sample and recovery of extracted RNA. A precise sample volume can be defined by integrating electrophoretic actuation electrodes in the microfluidic chamber. Electrolytic gas bubbles that are the result of constant-current actuation are driven out from the chip by the novel introduction of capillary bubble-expulsion techniques. The extraction approach and the functionality of the chip are demonstrated for Escherichia coli and Streptococcus thermophilus bacteria. Linear extraction behavior is obtained for transfer-messenger RNA down to one colony-forming unit per microlitre, or five colony-forming units per chip. The latter is an increase in extraction efficiency of a factor of 1000 with respect to the commercial extraction kit Ambion Ribopure. The chip shows particularly good performance for extraction of low-molecular weight RNA, thereby eliminating the need for large ribosomal RNA and DNA removal. RNA can be extracted in less than 11 min, being a speed-up of more than a

  1. Computer Vision Based Automatic Extraction and Thickness Measurement of Deep Cervical Flexor from Ultrasonic Images

    OpenAIRE

    Kwang Baek Kim; Doo Heon Song; Hyun Jun Park

    2016-01-01

    Deep Cervical Flexor (DCF) muscles are important in monitoring and controlling neck pain. While ultrasonographic analysis is useful in this area, it has intrinsic subjectivity problem. In this paper, we propose automatic DCF extractor/analyzer software based on computer vision. One of the major difficulties in developing such an automatic analyzer is to detect important organs and their boundaries under very low brightness contrast environment. Our fuzzy sigma binarization process is one of t...

  2. Automatic Vehicle Extraction from Airborne LiDAR Data Using an Object-Based Point Cloud Analysis Method

    Directory of Open Access Journals (Sweden)

    Jixian Zhang

    2014-09-01

    Full Text Available Automatic vehicle extraction from an airborne laser scanning (ALS point cloud is very useful for many applications, such as digital elevation model generation and 3D building reconstruction. In this article, an object-based point cloud analysis (OBPCA method is proposed for vehicle extraction from an ALS point cloud. First, a segmentation-based progressive TIN (triangular irregular network densification is employed to detect the ground points, and the potential vehicle points are detected based on the normalized heights of the non-ground points. Second, 3D connected component analysis is performed to group the potential vehicle points into segments. At last, vehicle segments are detected based on three features, including area, rectangularity and elongatedness. Experiments suggest that the proposed method is capable of achieving higher accuracy than the exiting mean-shift-based method for vehicle extraction from an ALS point cloud. Moreover, the larger the point density is, the higher the achieved accuracy is.

  3. Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.

    Directory of Open Access Journals (Sweden)

    Leandro Martínez

    Full Text Available The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD and Root Mean Square Fluctuations (RMSF of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.

  4. Automatic ECG wave extraction in long-term recordings using Gaussian mesa function models and nonlinear probability estimators.

    Science.gov (United States)

    Dubois, Rémi; Maison-Blanche, Pierre; Quenet, Brigitte; Dreyfus, Gérard

    2007-12-01

    This paper describes the automatic extraction of the P, Q, R, S and T waves of electrocardiographic recordings (ECGs), through the combined use of a new machine-learning algorithm termed generalized orthogonal forward regression (GOFR) and of a specific parameterized function termed Gaussian mesa function (GMF). GOFR breaks up the heartbeat signal into Gaussian mesa functions, in such a way that each wave is modeled by a single GMF; the model thus generated is easily interpretable by the physician. GOFR is an essential ingredient in a global procedure that locates the R wave after some simple pre-processing, extracts the characteristic shape of each heart beat, assigns P, Q, R, S and T labels through automatic classification, discriminates normal beats (NB) from abnormal beats (AB), and extracts features for diagnosis. The efficiency of the detection of the QRS complex, and of the discrimination of NB from AB, is assessed on the MIT and AHA databases; the labeling of the P and T wave is validated on the QTDB database. PMID:17997186

  5. A multi-scale method for automatically extracting the dominant features of cervical vertebrae in CT images

    Directory of Open Access Journals (Sweden)

    Tung-Ying Wu

    2013-07-01

    Full Text Available Localization of the dominant points of cervical spines in medical images is important for improving the medical automation in clinical head and neck applications. In order to automatically identify the dominant points of cervical vertebrae in neck CT images with precision, we propose a method based on multi-scale contour analysis to analyzing the deformable shape of spines. To extract the spine contour, we introduce a method to automatically generate the initial contour of the spine shape, and the distance field for level set active contour iterations can also be deduced. In the shape analysis stage, we at first coarsely segment the extracted contour with zero-crossing points of the curvature based on the analysis with curvature scale space, and the spine shape is modeled with the analysis of curvature scale space. Then, each segmented curve is analyzed geometrically based on the turning angle property at different scales, and the local extreme points are extracted and verified as the dominant feature points. The vertices of the shape contour are approximately derived with the analysis at coarse scale, and then adjusted precisely at fine scale. Consequently, the results of experiment show that we approach a success rate of 93.4% and accuracy of 0.37mm by comparing with the manual results.

  6. 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. PMID:25618718

  7. Automatic extraction analysis of the anatomical functional area for normal brain 18F-FDG PET imaging

    International Nuclear Information System (INIS)

    Using self-designed automatic extraction software of brain functional area, the grey scale distribution of 18F-FDG imaging and the relationship between the 18F-FDG accumulation of brain anatomic function area and the 18F-FDG injected dose, the level of glucose, the age, etc., were studied. According to the Talairach coordinate system, after rotation, drift and plastic deformation, the 18F-FDG PET imaging was registered into the Talairach coordinate atlas, and then the average gray value scale ratios between individual brain anatomic functional area and whole brain area was calculated. Further more the statistics of the relationship between the 18F-FDG accumulation of every brain anatomic function area and the 18F-FDG injected dose, the level of glucose and the age were tested by using multiple stepwise regression model. After images' registration, smoothing and extraction, main cerebral cortex of the 18F-FDG PET brain imaging can be successfully localized and extracted, such as frontal lobe, parietal lobe, occipital lobe, temporal lobe, cerebellum, brain ventricle, thalamus and hippocampus. The average ratios to the inner reference of every brain anatomic functional area were 1.01 ± 0.15. By multiple stepwise regression with the exception of thalamus and hippocampus, the grey scale of all the brain functional area was negatively correlated to the ages, but with no correlation to blood sugar and dose in all areas. To the 18F-FDG PET imaging, the brain functional area extraction program could automatically delineate most of the cerebral cortical area, and also successfully reflect the brain blood and metabolic study, but extraction of the more detailed area needs further investigation

  8. BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction

    CERN Document Server

    Jonnalagadda, Siddhartha

    2011-01-01

    BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification for improving human readability). The model is based on a "shot-gun" approach that produces many different (simpler) versions of the original sentence by combining variants of its constituent elements. This tool is optimized for processing biomedical scientific literature such as the abstracts indexed in PubMed. We tested our tool on its impact to the task of PPI extraction and it improved the f-score of the PPI tool by around 7%, with an improvement in recall of around 20%. The BioSimplify tool and test corpus can be downloaded from https://biosimplify.sourceforge.net.

  9. Automatic Extraction of Building Roof Planes from Airborne LIDAR Data Applying AN Extended 3d Randomized Hough Transform

    Science.gov (United States)

    Maltezos, Evangelos; Ioannidis, Charalabos

    2016-06-01

    This study aims to extract automatically building roof planes from airborne LIDAR data applying an extended 3D Randomized Hough Transform (RHT). The proposed methodology consists of three main steps, namely detection of building points, plane detection and refinement. For the detection of the building points, the vegetative areas are first segmented from the scene content and the bare earth is extracted afterwards. The automatic plane detection of each building is performed applying extensions of the RHT associated with additional constraint criteria during the random selection of the 3 points aiming at the optimum adaptation to the building rooftops as well as using a simple design of the accumulator that efficiently detects the prominent planes. The refinement of the plane detection is conducted based on the relationship between neighbouring planes, the locality of the point and the use of additional information. An indicative experimental comparison to verify the advantages of the extended RHT compared to the 3D Standard Hough Transform (SHT) is implemented as well as the sensitivity of the proposed extensions and accumulator design is examined in the view of quality and computational time compared to the default RHT. Further, a comparison between the extended RHT and the RANSAC is carried out. The plane detection results illustrate the potential of the proposed extended RHT in terms of robustness and efficiency for several applications.

  10. [An automatic extraction algorithm for individual tree crown projection area and volume based on 3D point cloud data].

    Science.gov (United States)

    Xu, Wei-Heng; Feng, Zhong-Ke; Su, Zhi-Fang; Xu, Hui; Jiao, You-Quan; Deng, Ou

    2014-02-01

    Tree crown projection area and crown volume are the important parameters for the estimation of biomass, tridimensional green biomass and other forestry science applications. Using conventional measurements of tree crown projection area and crown volume will produce a large area of errors in the view of practical situations referring to complicated tree crown structures or different morphological characteristics. However, it is difficult to measure and validate their accuracy through conventional measurement methods. In view of practical problems which include complicated tree crown structure, different morphological characteristics, so as to implement the objective that tree crown projection and crown volume can be extracted by computer program automatically. This paper proposes an automatic untouched measurement based on terrestrial three-dimensional laser scanner named FARO Photon120 using plane scattered data point convex hull algorithm and slice segmentation and accumulation algorithm to calculate the tree crown projection area. It is exploited on VC+6.0 and Matlab7.0. The experiments are exploited on 22 common tree species of Beijing, China. The results show that the correlation coefficient of the crown projection between Av calculated by new method and conventional method A4 reaches 0.964 (ppoint or sixteen-point projection with fixed angles to estimate crown projections, and (2) different regular volume formula to simulate crown volume according to the tree crown shapes. Based on the high-resolution 3D LIDAR point cloud data of individual tree, tree crown structure was reconstructed at a high rate of speed with high accuracy, and crown projection and volume of individual tree were extracted by this automatical untouched method, which can provide a reference for tree crown structure studies and be worth to popularize in the field of precision forestry.

  11. Combining contour detection algorithms for the automatic extraction of the preparation line from a dental 3D measurement

    Science.gov (United States)

    Ahlers, Volker; Weigl, Paul; Schachtzabel, Hartmut

    2005-04-01

    Due to the increasing demand for high-quality ceramic crowns and bridges, the CAD/CAM-based production of dental restorations has been a subject of intensive research during the last fifteen years. A prerequisite for the efficient processing of the 3D measurement of prepared teeth with a minimal amount of user interaction is the automatic determination of the preparation line, which defines the sealing margin between the restoration and the prepared tooth. Current dental CAD/CAM systems mostly require the interactive definition of the preparation line by the user, at least by means of giving a number of start points. Previous approaches to the automatic extraction of the preparation line rely on single contour detection algorithms. In contrast, we use a combination of different contour detection algorithms to find several independent potential preparation lines from a height profile of the measured data. The different algorithms (gradient-based, contour-based, and region-based) show their strengths and weaknesses in different clinical situations. A classifier consisting of three stages (range check, decision tree, support vector machine), which is trained by human experts with real-world data, finally decides which is the correct preparation line. In a test with 101 clinical preparations, a success rate of 92.0% has been achieved. Thus the combination of different contour detection algorithms yields a reliable method for the automatic extraction of the preparation line, which enables the setup of a turn-key dental CAD/CAM process chain with a minimal amount of interactive screen work.

  12. The Automatic Generation of Chinese Outline Font Based on Stroke Extraction

    Institute of Scientific and Technical Information of China (English)

    1995-01-01

    A new method to obtain spline outline description of Chinese font based on stroke extraction is presented.It has two primary advantages:(1)the quality of Chinese output is greatly improved;(2)the memory requirement is reduced.The method for stroke extraction is discussed in detail and experimental results are presented.

  13. An automatic countercurrent liquid-liquid micro-extraction system coupled with atomic absorption spectrometry for metal determination.

    Science.gov (United States)

    Mitani, Constantina; Anthemidis, Aristidis N

    2015-02-01

    A novel and versatile automatic sequential injection countercurrent liquid-liquid microextraction (SI-CC-LLME) system coupled with atomic absorption spectrometry (FAAS) is presented for metal determination. The extraction procedure was based on the countercurrent flow of aqueous and organic phases which takes place into a newly designed lab made microextraction chamber. A noteworthy feature of the extraction chamber is that it can be utilized for organic solvents heavier or lighter than water. The proposed method was successfully demonstrated for on-line lead determination and applied in environmental water samples using an amount of 120 μL of chloroform as extractant and ammonium diethyldithiophosphate as chelating reagent. The effect of the major experimental parameters including the volume of extractant, as well as the flow rate of aqueous and organic phases were studied and optimized. Under the optimum conditions for 6 mL sample consumption an enhancement factor of 130 was obtained. The detection limit was 1.5 μg L(-1) and the precision of the method, expressed as relative standard deviation (RSD) was 2.7% at 40.0 μg L(-1) Pb(II) concentration level. The proposed method was evaluated by analyzing certified reference materials and spiked environmental water samples. PMID:25435230

  14. 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.

  15. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.

    Science.gov (United States)

    Mugnai, Mauro L; Elber, Ron

    2015-01-01

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system-the diffusion along the backbone torsions of a solvated alanine dipeptide. PMID:25573551

  16. 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

    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...

  17. Automatic segmentation of coronary artery tree based on multiscale Gabor filtering and transition region extraction

    Science.gov (United States)

    Wang, Fang; Wang, Guozhu; Kang, Lie; Wang, Juan

    2011-11-01

    This paper presents a novel segmentation method for extracting coronary artery tree from angiogram, which is based on multiscale Gabor filtering and transition region extraction. Firstly the enhanced image is obtained after multiscale Gabor filtering, then the transition region of the enhanced image is extracted using the local complexity algorithm, and the final segmentation threshold is calculated, finally the image segmentation is achieved. To evaluate the performance of the proposed approach, we carried out experiments on various sets of angiographic images, and compared its effects with those of the improved top-hat segmentation method. The experiments indicate that the proposed method outperforms the latter method about better extraction of small vessels, more background elimination, better visualized coronary artery tree and continuity of the vessels.

  18. Automatic Extraction of Tongue Coatings from Digital Images: A Traditional Chinese Medicine Diagnostic Tool

    Institute of Scientific and Technical Information of China (English)

    Linda Yunlu BAI; SHI Yundi; WU Jia; ZHANG Yonghong; WONG Weiliang; WU Yu; BAI Jing

    2009-01-01

    In traditional Chinese medicine, the coating on the tongue is considered to be a reflection of various pathologic factors. However, the conventional method to examine the tongue lacks an acceptable standard and does not provide the means for sharing information. This paper describes a segmentation method to extract tongue coatings. First, the tongue body was extracted from the original image using the watershed transform. Then, a threshold method was applied to the image to eliminate the light from the camera flash.Finally, a threshold method using the Otsu model in combination with a splitting-merging method was used in the red, green, and blue (RGB) space to extract the thin coating. The combination of the above two methods is applied in the hue, saturation, and value (HSV) space to extract the thick coating. The feasibility of this method is tested by experiments, and the accuracy of segmentation is 95.9%.

  19. Free Model of Sentence Classifier for Automatic Extraction of Topic Sentences

    OpenAIRE

    M.L. Khodra; D.H. Widyantoro; E.A. Aziz; B.R. Trilaksono

    2011-01-01

    This research employs free model that uses only sentential features without paragraph context to extract topic sentences of a paragraph. For finding optimal combination of features, corpus-based classification is used for constructing a sentence classifier as the model. The sentence classifier is trained by using Support Vector Machine (SVM). The experiment shows that position and meta-discourse features are more important than syntactic features to extract topic sentence, and the best perfor...

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

    OpenAIRE

    Ben Abacha Asma; Zweigenbaum Pierre

    2011-01-01

    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) r...

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

    OpenAIRE

    Li, Y.; Hu, X.; H. Guan; Liu, P.

    2016-01-01

    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...

  2. Semi-automatic building extraction in informal settlements from high-resolution satellite imagery

    Science.gov (United States)

    Mayunga, Selassie David

    The extraction of man-made features from digital remotely sensed images is considered as an important step underpinning management of human settlements in any country. Man-made features and buildings in particular are required for varieties of applications such as urban planning, creation of geographical information systems (GIS) databases and Urban City models. The traditional man-made feature extraction methods are very expensive in terms of equipment, labour intensive, need well-trained personnel and cannot cope with changing environments, particularly in dense urban settlement areas. This research presents an approach for extracting buildings in dense informal settlement areas using high-resolution satellite imagery. The proposed system uses a novel strategy of extracting building by measuring a single point at the approximate centre of the building. The fine measurement of the building outlines is then effected using a modified snake model. The original snake model on which this framework is based, incorporates an external constraint energy term which is tailored to preserving the convergence properties of the snake model; its use to unstructured objects will negatively affect their actual shapes. The external constrained energy term was removed from the original snake model formulation, thereby, giving ability to cope with high variability of building shapes in informal settlement areas. The proposed building extraction system was tested on two areas, which have different situations. The first area was Tungi in Dar Es Salaam, Tanzania where three sites were tested. This area is characterized by informal settlements, which are illegally formulated within the city boundaries. The second area was Oromocto in New Brunswick, Canada where two sites were tested. Oromocto area is mostly flat and the buildings are constructed using similar materials. Qualitative and quantitative measures were employed to evaluate the accuracy of the results as well as the performance

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    Sophie Crommelinck

    2016-08-01

    Full Text Available 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 could increase the pace of current mapping procedures. This review introduces a workflow considered applicable for automated boundary delineation from UAV data. This is done by reviewing approaches for feature extraction from various application fields and synthesizing these into a hypothetical generalized cadastral workflow. The workflow consists of preprocessing, image segmentation, line extraction, contour generation and postprocessing. The review lists example methods per workflow step—including a description, trialed implementation, and a list of case studies applying individual methods. Furthermore, accuracy assessment methods are outlined. Advantages and drawbacks of each approach are discussed in terms of their applicability on UAV data. This review can serve as a basis for future work on the implementation of most suitable methods in a UAV-based cadastral mapping workflow.

  5. Automatic extraction of myocardial mass and volumes using parametric images from dynamic non-gated PET

    DEFF Research Database (Denmark)

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

    2016-01-01

    -gated dynamic cardiac PET. METHODS: Thirty-five patients with aortic-valve stenosis and 10 healthy controls (HC) underwent a 27-min 11C-acetate PET/CT scan and cardiac magnetic resonance imaging (CMR). HC were scanned twice to assess repeatability. Parametric images of uptake rate K1 and the blood pool were......LV and WT only and an overestimation for LVEF at lower values. Intra- and inter-observer correlations were >0.95 for all PET measurements. PET repeatability accuracy in HC was comparable to CMR. CONCLUSION: LV mass and volumes are accurately and automatically generated from dynamic 11C-acetate PET without...... ECG-gating. This method can be incorporated in a standard routine without any additional workload and can, in theory, be extended to other PET tracers....

  6. Automatic extraction of mandibular bone geometry for anatomy-based synthetization of radiographs.

    Science.gov (United States)

    Antila, Kari; Lilja, Mikko; Kalke, Martti; Lötjönen, Jyrki

    2008-01-01

    We present an automatic method for segmenting Cone-Beam Computerized Tomography (CBCT) volumes and synthetizing orthopantomographic, anatomically aligned views of the mandibular bone. The model-based segmentation method was developed having the characteristics of dental CBCT, severe metal artefacts, relatively high noise and high variability of the mandibular bone shape, in mind. First, we applied the segmentation method to delineate the bone. Second, we aligned a model resembling the geometry of orthopantomographic imaging according to the segmented surface. Third, we estimated the tooth orientations based on the local shape of the segmented surface. These results were used in determining the geometry of the synthetized radiograph. Segmentation was done with excellent results: with 14 samples we reached 0.57+/-0.16 mm mean distance from hand drawn reference. The estimation of tooth orientations was accurate with error of 0.65+/-8.0 degrees. An example of these results used in synthetizing panoramic radiographs is presented.

  7. Free Model of Sentence Classifier for Automatic Extraction of Topic Sentences

    Directory of Open Access Journals (Sweden)

    M.L. Khodra

    2011-04-01

    Full Text Available This research employs free model that uses only sentential features without paragraph context to extract topic sentences of a paragraph. For finding optimal combination of features, corpus-based classification is used for constructing a sentence classifier as the model. The sentence classifier is trained by using Support Vector Machine (SVM. The experiment shows that position and meta-discourse features are more important than syntactic features to extract topic sentence, and the best performer (80.68% is SVM classifier with all features.

  8. Automatic Extraction of Three Dimensional Prismatic Machining Features from CAD Model

    Directory of Open Access Journals (Sweden)

    B.V. Sudheer Kumar

    2011-12-01

    Full Text Available Machining features recognition provides the necessary platform for the computer aided process planning (CAPP and plays a key role in the integration of computer aided design (CAD and computer aided manufacturing (CAM. This paper presents a new methodology for extracting features from the geometrical data of the CAD Model present in the form of Virtual Reality Modeling Language (VRML files. First, the point cloud is separated into the available number of horizontal cross sections. Each cross section consists of a 2D point cloud. Then, a collection of points represented by a set of feature points is derived for each slice, describing the cross section accurately, and providing the basis for a feature-extraction. These extracted manufacturing features, gives the necessary information regarding the manufacturing activities tomanufacture the part. Software in Microsoft Visual C++ environment is developed to recognize the features, where geometric information of the part isextracted from the CAD model. By using this data, anoutput file i.e., text file is generated, which gives all the machinable features present in the part. This process has been tested on various parts and successfully extracted all the features

  9. GDRMS: a system for automatic extraction of the disease-centre relation

    Science.gov (United States)

    Yang, Ronggen; Zhang, Yue; Gong, Lejun

    2012-01-01

    With the rapidly increasing of biomedical literature, the deluge of new articles is leading to information overload. Extracting the available knowledge from the huge amount of biomedical literature has become a major challenge. GDRMS is developed as a tool that extracts the relationship between disease and gene, gene and gene from biomedical literatures using text mining technology. It is a ruled-based system which also provides disease-centre network visualization, constructs the disease-gene database, and represents a gene engine for understanding the function of the gene. The main focus of GDRMS is to provide a valuable opportunity to explore the relationship between disease and gene for the research community about etiology of disease.

  10. Automatic Shape-Based Target Extraction for Close-Range Photogrammetry

    Science.gov (United States)

    Guo, X.; Chen, Y.; Wang, C.; Cheng, M.; Wen, C.; Yu, J.

    2016-06-01

    In order to perform precise identification and location of artificial coded targets in natural scenes, a novel design of circle-based coded target and the corresponding coarse-fine extraction algorithm are presented. The designed target separates the target box and coding box totally and owns an advantage of rotation invariance. Based on the original target, templates are prepared by three geometric transformations and are used as the input of shape-based template matching. Finally, region growing and parity check methods are used to extract the coded targets as final results. No human involvement is required except for the preparation of templates and adjustment of thresholds in the beginning, which is conducive to the automation of close-range photogrammetry. The experimental results show that the proposed recognition method for the designed coded target is robust and accurate.

  11. Automatic extraction of PIOPED interpretations from ventilation/perfusion lung scan reports.

    OpenAIRE

    Fiszman, M.; Haug, P. J.; Frederick, P. R.

    1998-01-01

    Free-text documents are the main type of data produced by a radiology department in a hospital information system. While this type of data is readily accessible for clinical data review it can not be accessed by other applications to perform medical decision support, quality assurance, and outcome studies. In an attempt to solve this problem, natural language processing systems have been developed and tested against chest x-rays reports to extract relevant clinical information and make it acc...

  12. 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.

  13. 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.

  14. 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......,on-line SPE assays performed in permanent mode lack sufficient reliability as a consequence of progressively tighter packing of the bead reactor, contamination of the solid surfaces and potential leakage of functional moieties. This article overviews the current state-of-the-art of an appealing tool...

  15. Terrain-driven unstructured mesh development through semi-automatic vertical feature extraction

    Science.gov (United States)

    Bilskie, Matthew V.; Coggin, David; Hagen, Scott C.; Medeiros, Stephen C.

    2015-12-01

    A semi-automated vertical feature terrain extraction algorithm is described and applied to a two-dimensional, depth-integrated, shallow water equation inundation model. The extracted features describe what are commonly sub-mesh scale elevation details (ridge and valleys), which may be ignored in standard practice because adequate mesh resolution cannot be afforded. The extraction algorithm is semi-automated, requires minimal human intervention, and is reproducible. A lidar-derived digital elevation model (DEM) of coastal Mississippi and Alabama serves as the source data for the vertical feature extraction. Unstructured mesh nodes and element edges are aligned to the vertical features and an interpolation algorithm aimed at minimizing topographic elevation error assigns elevations to mesh nodes via the DEM. The end result is a mesh that accurately represents the bare earth surface as derived from lidar with element resolution in the floodplain ranging from 15 m to 200 m. To examine the influence of the inclusion of vertical features on overland flooding, two additional meshes were developed, one without crest elevations of the features and another with vertical features withheld. All three meshes were incorporated into a SWAN+ADCIRC model simulation of Hurricane Katrina. Each of the three models resulted in similar validation statistics when compared to observed time-series water levels at gages and post-storm collected high water marks. Simulated water level peaks yielded an R2 of 0.97 and upper and lower 95% confidence interval of ∼ ± 0.60 m. From the validation at the gages and HWM locations, it was not clear which of the three model experiments performed best in terms of accuracy. Examination of inundation extent among the three model results were compared to debris lines derived from NOAA post-event aerial imagery, and the mesh including vertical features showed higher accuracy. The comparison of model results to debris lines demonstrates that additional

  16. An automatic procedure to extract galaxy clusters from CRoNaRio catalogues

    CERN Document Server

    Puddu, E; Longo, G; Paolillo, M; Scaramella, R; Testa, V; Gal, R R; De Carvalho, R R; Djorgovski, S G

    1999-01-01

    We present preliminary results of a simple peak finding algorithm applied to catalogues of galaxies, extracted from the Second Palomar Sky Survey in the framework of the CRoNaRio project. All previously known Abell and Zwicky clusters in a test region of 5x5 sq. deg. are recovered and new candidate clusters are also detected. This algorithm represents an alternative way of searching for galaxy clusters with respect to that implemented and tested at Caltech on the same type of data (Gal et al. 1998).

  17. Automatic Building Extraction and Roof Reconstruction in 3k Imagery Based on Line Segments

    Science.gov (United States)

    Köhn, A.; Tian, J.; Kurz, F.

    2016-06-01

    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.

  18. Automatic molecular collection and detection by using fuel-powered microengines

    Science.gov (United States)

    Han, Di; Fang, Yangfu; Du, Deyang; Huang, Gaoshan; Qiu, Teng; Mei, Yongfeng

    2016-04-01

    We design and fabricate a simple self-powered system to collect analyte molecules in fluids for surface-enhanced Raman scattering (SERS) detection. The system is based on catalytic Au/SiO/Ti/Ag-layered microengines by employing rolled-up nanotechnology. Pronounced SERS signals are observed on microengines with more carrier molecules compared with the same structure without automatic motions.We design and fabricate a simple self-powered system to collect analyte molecules in fluids for surface-enhanced Raman scattering (SERS) detection. The system is based on catalytic Au/SiO/Ti/Ag-layered microengines by employing rolled-up nanotechnology. Pronounced SERS signals are observed on microengines with more carrier molecules compared with the same structure without automatic motions. Electronic supplementary information (ESI) available: Experimental procedures, characterization, SERS enhancement factor calculation and videos. See DOI: 10.1039/c6nr00117c

  19. Histogram of Intensity Feature Extraction for Automatic Plastic Bottle Recycling System Using Machine Vision

    Directory of Open Access Journals (Sweden)

    Suzaimah Ramli

    2008-01-01

    Full Text Available Currently, many recycling activities adopt manual sorting for plastic recycling that relies on plant personnel who visually identify and pick plastic bottles as they travel along the conveyor belt. These bottles are then sorted into the respective containers. Manual sorting may not be a suitable option for recycling facilities of high throughput. It has also been noted that the high turnover among sorting line workers had caused difficulties in achieving consistency in the plastic separation process. As a result, an intelligent system for automated sorting is greatly needed to replace manual sorting system. The core components of machine vision for this intelligent sorting system is the image recognition and classification. In this research, the overall plastic bottle sorting system is described. Additionally, the feature extraction algorithm used is discussed in detail since it is the core component of the overall system that determines the success rate. The performance of the proposed feature extractions were evaluated in terms of classification accuracy and result obtained showed an accuracy of more than 80%.

  20. Design of automatic control system for the precipitation of bromelain from the extract of pineapple wastes

    Directory of Open Access Journals (Sweden)

    Flavio Vasconcelos da Silva

    2010-12-01

    Full Text Available In this work, bromelain was recovered from ground pineapple stem and rind by means of precipitation with alcohol at low temperature. Bromelain is the name of a group of powerful protein-digesting, or proteolytic, enzymes that are particularly useful for reducing muscle and tissue inflammation and as a digestive aid. Temperature control is crucial to avoid irreversible protein denaturation and consequently to improve the quality of the enzyme recovered. The process was carried out alternatively in two fed-batch pilot tanks: a glass tank and a stainless steel tank. Aliquots containing 100 mL of pineapple aqueous extract were fed into the tank. Inside the jacketed tank, the protein was exposed to unsteady operating conditions during the addition of the precipitating agent (ethanol 99.5% because the dilution ratio "aqueous extract to ethanol" and heat transfer area changed. The coolant flow rate was manipulated through a variable speed pump. Fine tuned conventional and adaptive PID controllers were on-line implemented using a fieldbus digital control system. The processing performance efficiency was enhanced and so was the quality (enzyme activity of the product.

  1. Hierarchical Algorithm in DTM Generation and Automatic Extraction of Road from LIDAR Data

    Science.gov (United States)

    Hui-ying, L.; Yu-jun, X.; Zhi, W.; Yi-nan, L.

    2012-07-01

    Growing demand for an efficient land use above and below the ground is motivating cadastre and land management systems to move from traditional 2D systems toward three dimensional ones. Airborne laser technology offers direct acquisition of dense and accurate 3D data. In order to get 3D road this paper proposes a hierarchical algorithm to extract terrain point from LIDAR data. We stratify the raw LiDAR data according to the height, judge terrain points and non-terrain points by the connectivity. In the case of road network, it indicates the morphological characteristics of network structure with a certain length continuous strip and small difference in intensity. All these information, including elevation information, the intensity information, the morphological characteristics and other local features, are used for extracting the road network from DTM. Local morphological filtering method is implementing for finding clear boundaries and rich details of the road profile. Following the presentation of the algorithm results for this approach are shown and evaluated

  2. 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

  3. Automatic extraction of the mid-sagittal plane using an ICP variant

    Science.gov (United States)

    Fieten, Lorenz; Eschweiler, Jörg; de la Fuente, Matías; Gravius, Sascha; Radermacher, Klaus

    2008-03-01

    Precise knowledge of the mid-sagittal plane is important for the assessment and correction of several deformities. Furthermore, the mid-sagittal plane can be used for the definition of standardized coordinate systems such as pelvis or skull coordinate systems. A popular approach for mid-sagittal plane computation is based on the selection of anatomical landmarks located either directly on the plane or symmetrically to it. However, the manual selection of landmarks is a tedious, time-consuming and error-prone task, which requires great care. In order to overcome this drawback, previously it was suggested to use the iterative closest point (ICP) algorithm: After an initial mirroring of the data points on a default mirror plane, the mirrored data points should be registered iteratively to the model points using rigid transforms. Finally, a reflection transform approximating the cumulative transform could be extracted. In this work, we present an ICP variant for the iterative optimization of the reflection parameters. It is based on a closed-form solution to the least-squares problem of matching data points to model points using a reflection. In experiments on CT pelvis and skull datasets our method showed a better ability to match homologous areas.

  4. A simple multi-scale Gaussian smoothing-based strategy for automatic chromatographic peak extraction.

    Science.gov (United States)

    Fu, Hai-Yan; Guo, Jun-Wei; Yu, Yong-Jie; Li, He-Dong; Cui, Hua-Peng; Liu, Ping-Ping; Wang, Bing; Wang, Sheng; Lu, Peng

    2016-06-24

    Peak detection is a critical step in chromatographic data analysis. In the present work, we developed a multi-scale Gaussian smoothing-based strategy for accurate peak extraction. The strategy consisted of three stages: background drift correction, peak detection, and peak filtration. Background drift correction was implemented using a moving window strategy. The new peak detection method is a variant of the system used by the well-known MassSpecWavelet, i.e., chromatographic peaks are found at local maximum values under various smoothing window scales. Therefore, peaks can be detected through the ridge lines of maximum values under these window scales, and signals that are monotonously increased/decreased around the peak position could be treated as part of the peak. Instrumental noise was estimated after peak elimination, and a peak filtration strategy was performed to remove peaks with signal-to-noise ratios smaller than 3. The performance of our method was evaluated using two complex datasets. These datasets include essential oil samples for quality control obtained from gas chromatography and tobacco plant samples for metabolic profiling analysis obtained from gas chromatography coupled with mass spectrometry. Results confirmed the reasonability of the developed method.

  5. 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.

  6. How does the preparation of rye porridge affect molecular weight distribution of extractable dietary fibers?

    Science.gov (United States)

    Rakha, Allah; Aman, Per; Andersson, Roger

    2011-01-01

    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.

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

    Science.gov (United States)

    Qiao, Jixin; Xu, Yihong; Hou, Xiaolin; Miró, Manuel

    2014-10-01

    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-concentration approaches afford dissimilar method performances and care should be taken for specific experimental parameters for improving chemical yields. The best analytical performances in terms of turnaround time (6h) and chemical yields for plutonium (88.7 ± 11.6%) and neptunium (94.2 ± 2.0%) were achieved by manganese dioxide co-precipitation. The need of drying ashing (≥ 7h) for calcium phosphate co-precipitation and long-term aging (5d) for iron hydroxide co-precipitation, respectively, rendered time-consuming analytical protocols. Despite the fact that evaporation is also somewhat time-consuming (1.5d), it endows urinalysis methods with better reliability and repeatability compared with co-precipitation techniques. In view of the applicability of different pre-concentration techniques proposed previously in the literature, the main challenge behind relevant method development is pointed to be the release of plutonium and neptunium associated with organic compounds in real urine assays. In this work, different protocols for decomposing organic matter in urine were investigated, of which potassium persulfate (K2S2O8) treatment provided the highest chemical yield of neptunium in the iron hydroxide co-precipitation step, yet, the occurrence of sulfur compounds in the processed sample deteriorated the analytical performance of the ensuing extraction chromatographic separation with chemical

  8. Noncontact optical imaging in mice with full angular coverage and automatic surface extraction

    Science.gov (United States)

    Meyer, Heiko; Garofalakis, Anikitos; Zacharakis, Giannis; Psycharakis, Stylianos; Mamalaki, Clio; Kioussis, Dimitris; Economou, Eleftherios N.; Ntziachristos, Vasilis; Ripoll, Jorge

    2007-06-01

    During the past decade, optical imaging combined with tomographic approaches has proved its potential in offering quantitative three-dimensional spatial maps of chromophore or fluorophore concentration in vivo. Due to its direct application in biology and biomedicine, diffuse optical tomography (DOT) and its fluorescence counterpart, fluorescence molecular tomography (FMT), have benefited from an increase in devoted research and new experimental and theoretical developments, giving rise to a new imaging modality. The most recent advances in FMT and DOT are based on the capability of collecting large data sets by using CCDs as detectors, and on the ability to include multiple projections through recently developed noncontact approaches. For these to be implemented, we have developed an imaging setup that enables three-dimensional imaging of arbitrary shapes in fluorescence or absorption mode that is appropriate for small animal imaging. This is achieved by implementing a noncontact approach both for sources and detectors and coregistering surface geometry measurements using the same CCD camera. A thresholded shadowgrammetry approach is applied to the geometry measurements to retrieve the surface mesh. We present the evaluation of the system and method in recovering three-dimensional surfaces from phantom data and live mice. The approach is used to map the measured in vivo fluorescence data onto the tissue surface by making use of the free-space propagation equations, as well as to reconstruct fluorescence concentrations inside highly scattering tissuelike phantom samples. Finally, the potential use of this setup for in vivo small animal imaging and its impact on biomedical research is discussed.

  9. Linking attentional processes and conceptual problem solving: visual cues facilitate the automaticity of extracting relevant information from diagrams.

    Science.gov (United States)

    Rouinfar, Amy; Agra, Elise; Larson, Adam M; Rebello, N Sanjay; Loschky, Lester C

    2014-01-01

    This study investigated links between visual attention processes and conceptual problem solving. This was done by overlaying visual cues on conceptual physics problem diagrams to direct participants' attention to relevant areas to facilitate problem solving. Participants (N = 80) individually worked through four problem sets, each containing a diagram, while their eye movements were recorded. Each diagram contained regions that were relevant to solving the problem correctly and separate regions related to common incorrect responses. Problem sets contained an initial problem, six isomorphic training problems, and a transfer problem. The cued condition saw visual cues overlaid on the training problems. Participants' verbal responses were used to determine their accuracy. This study produced two major findings. First, short duration visual cues which draw attention to solution-relevant information and aid in the organizing and integrating of it, facilitate both immediate problem solving and generalization of that ability to new problems. Thus, visual cues can facilitate re-representing a problem and overcoming impasse, enabling a correct solution. Importantly, these cueing effects on problem solving did not involve the solvers' attention necessarily embodying the solution to the problem, but were instead caused by solvers attending to and integrating relevant information in the problems into a solution path. Second, this study demonstrates that when such cues are used across multiple problems, solvers can automatize the extraction of problem-relevant information extraction. These results suggest that low-level attentional selection processes provide a necessary gateway for relevant information to be used in problem solving, but are generally not sufficient for correct problem solving. Instead, factors that lead a solver to an impasse and to organize and integrate problem information also greatly facilitate arriving at correct solutions.

  10. Linking attentional processes and conceptual problem solving: Visual cues facilitate the automaticity of extracting relevant information from diagrams

    Directory of Open Access Journals (Sweden)

    Amy eRouinfar

    2014-09-01

    Full Text Available This study investigated links between lower-level visual attention processes and higher-level problem solving. This was done by overlaying visual cues on conceptual physics problem diagrams to direct participants’ attention to relevant areas to facilitate problem solving. Participants (N = 80 individually worked through four problem sets, each containing a diagram, while their eye movements were recorded. Each diagram contained regions that were relevant to solving the problem correctly and separate regions related to common incorrect responses. Problem sets contained an initial problem, six isomorphic training problems, and a transfer problem. The cued condition saw visual cues overlaid on the training problems. Participants’ verbal responses were used to determine their accuracy. The study produced two major findings. First, short duration visual cues can improve problem solving performance on a variety of insight physics problems, including transfer problems not sharing the surface features of the training problems, but instead sharing the underlying solution path. Thus, visual cues can facilitate re-representing a problem and overcoming impasse, enabling a correct solution. Importantly, these cueing effects on problem solving did not involve the solvers’ attention necessarily embodying the solution to the problem. Instead, the cueing effects were caused by solvers attending to and integrating relevant information in the problems into a solution path. Second, these short duration visual cues when administered repeatedly over multiple training problems resulted in participants becoming more efficient at extracting the relevant information on the transfer problem, showing that such cues can improve the automaticity with which solvers extract relevant information from a problem. Both of these results converge on the conclusion that lower-order visual processes driven by attentional cues can influence higher-order cognitive processes

  11. Identifying Structures in Social Conversations in NSCLC Patients through the Semi-Automatic extraction of Topical Taxonomies

    Directory of Open Access Journals (Sweden)

    Giancarlo Crocetti

    2016-01-01

    Full Text Available The exploration of social conversations for addressing patient’s needs is an important analytical task in which many scholarly publications are contributing to fill the knowledge gap in this area. The main difficulty remains the inability to turn such contributions into pragmatic processes the pharmaceutical industry can leverage in order to generate insight from social media data, which can be considered as one of the most challenging source of information available today due to its sheer volume and noise. This study is based on the work by Scott Spangler and Jeffrey Kreulen and applies it to identify structure in social media through the extraction of a topical taxonomy able to capture the latent knowledge in social conversations in health-related sites. The mechanism for automatically identifying and generating a taxonomy from social conversations is developed and pressured tested using public data from media sites focused on the needs of cancer patients and their families. Moreover, a novel method for generating the category’s label and the determination of an optimal number of categories is presented which extends Scott and Jeffrey’s research in a meaningful way. We assume the reader is familiar with taxonomies, what they are and how they are used.

  12. Automatic Sleep Staging using Multi-dimensional Feature Extraction and Multi-kernel Fuzzy Support Vector Machine

    Directory of Open Access Journals (Sweden)

    Yanjun Zhang

    2014-01-01

    Full Text Available This paper employed the clinical Polysomnographic (PSG data, mainly including all-night Electroencephalogram (EEG, Electrooculogram (EOG and Electromyogram (EMG signals of subjects, and adopted the American Academy of Sleep Medicine (AASM clinical staging manual as standards to realize automatic sleep staging. Authors extracted eighteen different features of EEG, EOG and EMG in time domains and frequency domains to construct the vectors according to the existing literatures as well as clinical experience. By adopting sleep samples self-learning, the linear combination of weights and parameters of multiple kernels of the fuzzy support vector machine (FSVM were learned and the multi-kernel FSVM (MK-FSVM was constructed. The overall agreement between the experts' scores and the results presented was 82.53%. Compared with previous results, the accuracy of N1 was improved to some extent while the accuracies of other stages were approximate, which well reflected the sleep structure. The staging algorithm proposed in this paper is transparent, and worth further investigation.

  13. Automatic fault feature extraction of mechanical anomaly on induction motor bearing using ensemble super-wavelet transform

    Science.gov (United States)

    He, Wangpeng; Zi, Yanyang; Chen, Binqiang; Wu, Feng; He, Zhengjia

    2015-03-01

    Mechanical anomaly is a major failure type of induction motor. It is of great value to detect the resulting fault feature automatically. In this paper, an ensemble super-wavelet transform (ESW) is proposed for investigating vibration features of motor bearing faults. The ESW is put forward based on the combination of tunable Q-factor wavelet transform (TQWT) and Hilbert transform such that fault feature adaptability is enabled. Within ESW, a parametric optimization is performed on the measured signal to obtain a quality TQWT basis that best demonstrate the hidden fault feature. TQWT is introduced as it provides a vast wavelet dictionary with time-frequency localization ability. The parametric optimization is guided according to the maximization of fault feature ratio, which is a new quantitative measure of periodic fault signatures. The fault feature ratio is derived from the digital Hilbert demodulation analysis with an insightful quantitative interpretation. The output of ESW on the measured signal is a selected wavelet scale with indicated fault features. It is verified via numerical simulations that ESW can match the oscillatory behavior of signals without artificially specified. The proposed method is applied to two engineering cases, signals of which were collected from wind turbine and steel temper mill, to verify its effectiveness. The processed results demonstrate that the proposed method is more effective in extracting weak fault features of induction motor bearings compared with Fourier transform, direct Hilbert envelope spectrum, different wavelet transforms and spectral kurtosis.

  14. Semi-automatic template matching based extraction of hyperbolic signatures in ground-penetrating radar images

    Science.gov (United States)

    Sagnard, Florence; Tarel, Jean-Philippe

    2015-04-01

    In civil engineering applications, ground-penetrating radar (GPR) is one of the main non destructive technique based on the refraction and reflection of electromagnetic waves to probe the underground and particularly detect damages (cracks, delaminations, texture changes…) and buried objects (utilities, rebars…). An UWB ground-coupled radar operating in the frequency band [0.46;4] GHz and made of bowtie slot antennas has been used because, comparing to a air-launched radar, it increases energy transfer of electromagnetic radiation in the sub-surface and penetration depth. This paper proposes an original adaptation of the generic template matching algorithm to GPR images to recognize, localize and characterize with parameters a specific pattern associated with a hyperbola signature in the two main polarizations. The processing of a radargram (Bscan) is based on four main steps. The first step consists in pre-processing and scaling. The second step uses template matching to isolate and localize individual hyperbola signatures in an environment containing unwanted reflections, noise and overlapping signatures. The algorithm supposes to generate and collect a set of reference hyperbola templates made of a small reflection pattern in the vicinity of the apex in order to further analyze multiple time signals of embedded targets in an image. The standard Euclidian distance between the template shifted and a local zone in the radargram allows to obtain a map of distances. A user-defined threshold allows to select a reduced number of zones having a high similarity measure. In a third step, each zone is analyzed to detect minimum or maximum discrete amplitudes belonging to the first arrival times of a hyperbola signature. In the fourth step, the extracted discrete data (i,j) are fitted by a parametric hyperbola modeling based on the straight ray path hypothesis and using a constraint least square criterion associated with parameter ranges, that are the position, the

  15. Design of molecularly imprinted polymers for sensors and solid phase extraction

    OpenAIRE

    Subrahmanyam, Sreenath

    2002-01-01

    This thesis presents broadly the applications of molecularly imprinted polymers in sensors and solid phase extraction. Sensors for creatine and creatinine have been reported using a novel method of rational design of molecularly imprinted polymers (MIPs), and solid phase extraction of aflatoxin-B 1 has also been described in the thesis. A method for the selective detection of creataine and creatinine is reported in this thesis, which is based on the reaction between polymeri...

  16. Preparation of molecularly imprinted polymers based on magnetic nanoparticles for the selective extraction of protocatechuic acid from plant extracts.

    Science.gov (United States)

    Xie, Xiaoyu; Wei, Fen; Chen, Liang; Wang, Sicen

    2015-03-01

    In this study, highly selective core-shell molecularly imprinted polymers on the surface of magnetic nanoparticles were prepared using protocatechuic acid as the template molecule. The resulting magnetic molecularly imprinted polymers were characterized by transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray diffraction, and vibrating sample magnetometry. The binding performances of the prepared materials were evaluated by static and selective adsorption. The binding isotherms were obtained for protocatechuic acid and fitted by the Langmuir isotherm model and Freundlich isotherm model. Furthermore, the resulting materials were used as the solid-phase extraction materials coupled to high-performance liquid chromatography for the selective extraction and detection of protocatechuic acid from the extracts of Homalomena occulta and Cynomorium songaricum with the recoveries in the range 86.3-102.2%. PMID:25641806

  17. Multiple Features Based Approach to Extract Bio-molecular Event Triggers Using Conditional Random Field

    Directory of Open Access Journals (Sweden)

    Amit Majumder

    2012-11-01

    Full Text Available The purpose of Biomedical Natural Language Processing (BioNLP is to capture biomedical phenomena from textual data by extracting relevant entities, information and relations between biomedical entities (i.e. proteins and genes. In general, in most of the published papers, only binary relations were extracted. In a recent past, the focus is shifted towards extracting more complex relations in the form of bio-molecular events that may include several entities or other relations. In this paper we propose an approach that enables event trigger extraction of relatively complex bio-molecular events. We approach this problem as a detection of bio-molecular event trigger using the well-known algorithm, namely Conditional Random Field (CRF. We apply our experiments on development set. It shows the overall average recall, precision and F-measure values of 64.27504%, 69.97559% and 67.00429%, respectively for the event detection.

  18. 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.

  19. 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.

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

    OpenAIRE

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

    2013-01-01

    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...

  1. 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.

  2. Computer Domain Term Automatic Extraction and Hierarchical Structure Building%计算机领域术语的自动获取与层次构建

    Institute of Scientific and Technical Information of China (English)

    林源; 陈志泊; 孙俏

    2011-01-01

    This paper presents a computer domain term automatic extraction method based on roles and statistics.It uses computer book titles from Amazon.com website as corpus, data are preprocessed by words splitting, stop words and special characters filtering.Terms are extracted by a set of rules and frequency statistics and inserted into a word tree from ODP to build the hierarchical structure.Experimental results show high precision and recall of the automatically extracted results compared with manual tagged terms.%设计一种能够自动获取计算机领域术语的方案,提出基于规则与统计相结合的抽取方法,使用亚马逊网站的计算机类图书作为语料库,通过分词、去停止词预处理以及词频统计的方法提取出计算机类领域术语,并插入到由ODP构建的树中,形成计算机领域术语的层次结构.实验结果表明,与人工标注结果相比,使用该方法自动获取的术语有很高的准确率与召回率.

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

    OpenAIRE

    Shah Parantu K; Wattarujeekrit Tuangthong; Collier Nigel

    2004-01-01

    Abstract 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 sen...

  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 microspheres for solid-phase extraction of protocatechuic acid in Rhizoma homalomenae.

    Science.gov (United States)

    Chen, Fang-Fang; Wang, Guo-Ying; Shi, Yan-Ping

    2011-10-01

    Molecularly imprinted polymers (MIPs) had been prepared by precipitation polymerization method using acrylamide as the functional monomer, ethylene glycol dimethacrylate as the cross-linker, acetonitrile as the porogen solvent and protocatechuic acid (PA), one of phenolic acids, as the template molecule. The MIPs were characterized by scanning electron microscopy and Fourier transform infrared, and their performance relative to non-imprinted polymers was assessed by equilibrium binding experiments. Six structurally similar phenolic acids, including p-hydroxybenzoic acid, gallic acid, salicylic acid, syringic acid, vanillic acid, ferulic acid were selected to assess the selectivity and recognition capability of the MIPs. The MIPs were applied to extract PA from the traditional Chinese medicines as a solid-phase extraction sorbent. The resultant cartridge showed that the MIPs have a good extraction performance and were able to selectively extract almost 82% of PA from the extract of Rhizoma homalomenae. Thus, the proposed molecularly imprinted-solid phase extraction-high performance liquid chromatography method can be successfully used to extract and analyse PA in traditional Chinese medicines. PMID:21809445

  6. Molecular diversity of riverine alkaline-extractable sediment organic matter and its linkages with spectral indicators and molecular size distributions.

    Science.gov (United States)

    He, Wei; Chen, Meilian; Park, Jae-Eun; Hur, Jin

    2016-09-01

    Few studies have been conducted to examine the spatial heterogeneity of riverine sediment organic matter (SOM) at the molecular level. The present study explored the chemical and molecular heterogeneity of alkaline-extractable SOM from riverine sediments via multiple analytical tools including molecular composition, absorption and fluorescence spectra, and molecular size distributions. The riverine SOM revealed complex and diverse characteristics, exhibiting a great number of non-redundant formulas and high spatial variations. The molecular diversity was more pronounced for the sediments affected by a higher degree of anthropogenic activities. Unlike the cases of aquatic dissolved organic matter, highly-unsaturated structures with oxygen (HUSO) of SOM were more associated with the spectral and size features of humic-like (or terrestrial) substances than aromatic molecules were, cautioning the interpretation of the SOM molecules responsible for apparent indicators. Noting that a higher detection rate (DR) produces fewer common molecules, the common molecules of 23 different SOMs were determined at a reasonable DR value of 0.35, which accounted for a small portion (5.8%) of all detected molecules. They were mainly CHO compounds (>98%), which positively correlated with spectral indicators of biological production. Despite the low abundance, however, the ratios of aromatic to aliphatic substances could be indexed to classify the common molecules into several geochemical molecular groups with different degrees of the associations with the apparent spectral and size indicators. PMID:27192357

  7. Unsupervised Threshold for Automatic Extraction of Dolphin Dorsal Fin Outlines from Digital Photographs in DARWIN (Digital Analysis and Recognition of Whale Images on a Network)

    CERN Document Server

    Hale, Scott A

    2012-01-01

    At least two software packages---DARWIN, Eckerd College, and FinScan, Texas A&M---exist to facilitate the identification of cetaceans---whales, dolphins, porpoises---based upon the naturally occurring features along the edges of their dorsal fins. Such identification is useful for biological studies of population, social interaction, migration, etc. The process whereby fin outlines are extracted in current fin-recognition software packages is manually intensive and represents a major user input bottleneck: it is both time consuming and visually fatiguing. This research aims to develop automated methods (employing unsupervised thresholding and morphological processing techniques) to extract cetacean dorsal fin outlines from digital photographs thereby reducing manual user input. Ideally, automatic outline generation will improve the overall user experience and improve the ability of the software to correctly identify cetaceans. Various transformations from color to gray space were examined to determine whi...

  8. Automated extraction improves multiplex molecular detection of infection in septic patients.

    Directory of Open Access Journals (Sweden)

    Benito J Regueiro

    Full Text Available Sepsis is one of the leading causes of morbidity and mortality in hospitalized patients worldwide. Molecular technologies for rapid detection of microorganisms in patients with sepsis have only recently become available. LightCycler SeptiFast test M(grade (Roche Diagnostics GmbH is a multiplex PCR analysis able to detect DNA of the 25 most frequent pathogens in bloodstream infections. The time and labor saved while avoiding excessive laboratory manipulation is the rationale for selecting the automated MagNA Pure compact nucleic acid isolation kit-I (Roche Applied Science, GmbH as an alternative to conventional SeptiFast extraction. For the purposes of this study, we evaluate extraction in order to demonstrate the feasibility of automation. Finally, a prospective observational study was done using 106 clinical samples obtained from 76 patients in our ICU. Both extraction methods were used in parallel to test the samples. When molecular detection test results using both manual and automated extraction were compared with the data from blood cultures obtained at the same time, the results show that SeptiFast with the alternative MagNA Pure compact extraction not only shortens the complete workflow to 3.57 hrs., but also increases sensitivity of the molecular assay for detecting infection as defined by positive blood culture confirmation.

  9. 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)

    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)

  10. Molecular events underlying maggot extract promoted rat in vivo and human in vitro skin wound healing.

    Science.gov (United States)

    Li, Pei-Nan; Li, Hong; Zhong, Li-Xia; Sun, Yuan; Yu, Li-Jun; Wu, Mo-Li; Zhang, Lin-Lin; Kong, Qing-You; Wang, Shou-Yu; Lv, De-Cheng

    2015-01-01

    Maggot extracts promote wound healing, but their bioactive part(s) and molecular effects on the regenerating tissues/cells remain largely unclear. These issues are addressed here by treating rat skin wounds, human keratinocyte line/HaCat and fibroblasts with maggot secretion/excretion, and the extracts of maggots without and with secretion/excretion. The wound closure rates, cell proliferation activities, and statuses of wound healing-related signaling pathways (STAT3, Notch1, Wnt2, NF-κB, and TGF-beta/Smad3) and their downstream gene expression (c-Myc, cyclin D1, and VEGF) are evaluated by multiple approaches. The results reveal that the maggot extracts, especially the one from the maggots without secretion/excretion, show the best wound healing-promoting effects in terms of quicker wound closure rates and more rapid growth of keratinocytes and fibroblasts. Of the five signaling pathways checked, the ones mediated by TGF-beta/Smad3, and STAT3 are activated in the untreated wounds and become further enhanced by the maggot extracts, accompanied with c-Myc, VEGF, and cyclin D1 up-regulation. Our results thus show (1) that both body extract and secretion/excretion of maggots contain favorable wound healing elements and (2) that the enhancement of TGF-beta/Smad3 and STAT3 signaling activities may be the main molecular effects of maggot extracts on the wound tissues.

  11. A method for automatic extraction of key fames%一种关键帧的自动提取方法

    Institute of Scientific and Technical Information of China (English)

    刘善磊; 赵银娣; 王光辉; 李英成; 薛艳丽; 李建军

    2012-01-01

    In the paper, first, two main lens distortions and camera calibration were introduced* Then the formula of key frames forward overlap was developed within intrinsic parameters of the camera and video frame rate. Then key frames were automatically extracted from the file or real time source. Automatic extraction of timing from real time source was processed and key frame positioning method was used for extracting key frames from file source. Finally key frames were corrected with the calibration parameters. Real data was used to test the developed method, and results showed that the technique was efficient and exact*%本文首先介绍了2种主要透镜畸变及摄像机标定方法;然后结合摄像机内部参数和视频帧率推导出关键帧航向重叠度计算公式;在此基础上实现了指定航向重叠度关键帧从文件源或实时源中的自动提取,文件源中采用定位关键帧自动提取算法,实时源中采用定时自动提取算法;最后利用得到的标定参数完成关键帧影像矫正.实验结果表明本文采用的算法能够高效、准确地得到矫正好的指定航向重叠度关键帧.

  12. 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

    2014-11-01

    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

  13. The molecular mechanisms of Curcuma Wenyujin extract-mediated inhibitory effects on human esophageal carcinoma cells in Vitro

    Institute of Scientific and Technical Information of China (English)

    景钊

    2012-01-01

    Objective To study the molecular mechanisms of Curcuma Wenyujin extract-mediated inhibitory effects on human esophageal carcinoma cells. Methods The Curcuma Wenyujin extract was obtained by supercritical carbon dioxide extraction. TE-1 cells were divided into 4 groups after adherence.

  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. Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases

    OpenAIRE

    Jeddi, Fakhri; Piarroux, Renaud; Mary, Charles

    2013-01-01

    During the last 20 years, molecular biology techniques have propelled the diagnosis of parasitic diseases into a new era, as regards assay speed, sensitivity, and parasite characterization. However, DNA extraction remains a critical step and should be adapted for diagnostic and epidemiological studies. The aim of this report was to document the constraints associated with DNA extraction for the diagnosis of parasitic diseases and illustrate the adaptation of an automated extraction system, Nu...

  16. Molecular Characteristics of Kraft-AQ Pulping Lignin Fractionated by Sequential Organic Solvent Extraction

    Directory of Open Access Journals (Sweden)

    Kun Wang

    2010-08-01

    Full Text Available Kraft-AQ pulping lignin was sequentially fractionated by organic solvent extractions and the molecular properties of each fraction were characterized by chemical degradation, GPC, UV, FT-IR, 13C-NMR and thermal analysis. The average molecular weight and polydispersity of each lignin fraction increased with its hydrogen-bonding capacity (Hildebrand solubility parameter. In addition, the ratio of the non-condensed guaiacyl/syringyl units and the content of β-O-4 linkages increased with the increment of the lignin fractions extracted successively with hexane, diethylether, methylene chloride, methanol, and dioxane. Furthermore, the presence of the condensation reaction products was contributed to the higher thermal stability of the larger molecules.

  17. A New Molecularly Imprinted Polymer for Solid-phase Extraction of Cotinine from Human Urine

    Institute of Scientific and Technical Information of China (English)

    Jun YANG; Xiao Lan ZHU; Ji Bao CAI; Qing De SU; Yun GAO; Liang ZHANG

    2005-01-01

    A molecularly imprinted polymer (MIP), prepared around a cotinine template, has been synthesized. The feasibility of using the polymer for solid-phase extraction (SPE) of cotinine from biological samples has been investigated. The results show that cotinine can be quantitatively retained and eluted from the polymer. Experiments with human urine samples indicate that clean target analyte is obtained for HPLC with UV detection using the protocol.

  18. Extraction from Natural Planktonic Microorganisms of DNA Suitable for Molecular Biological Studies

    OpenAIRE

    Jed A. Fuhrman; Comeau, Dorothy E.; Hagström, Åke; Chan, Amy M.

    1988-01-01

    We developed a simple technique for the high-yield extraction of purified DNA from mixed populations of natural planktonic marine microbes (primarily bacteria). This is a necessary step for several molecular biological approaches to the study of microbial communities in nature. The microorganisms from near-shore marine and brackish water samples, ranging in volume from 8 to 40 liters, were collected on 0.22-μm-pore-size fluorocarbon-based filters, after prefiltration through glass fiber filte...

  19. 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.

  20. Automatic Extraction and Recognition of Nmnbers in Topographic Maps%地形图数字注记的自动提取与识别

    Institute of Scientific and Technical Information of China (English)

    徐战武; 张涛; 刘肖琳

    2001-01-01

    地形图的自动扫描矢量化是GIS领域亟待解决的一个重要难题。地形图中包含了大量的字体丰富的数字注记,用以表示地物地貌的属性等特征,正确提取并识别这些数字是图纸处理中的重要组成部分。本文分析了现有的提取方法的不足,提出了一种新的数字注记自动提取与识别算法,首先根据先验的尺寸大小确定候选数字,再采用OCON结构的BP神经网络识别出真正的数字,然后利用近邻关系提取出扩展数字。实验表明,该算法是快速、高效、可靠的。%Automatic vectorization of scanned topographic maps is an important and difficult problem that needs to be solved urgently. Atopographic map includes plenty of numbers with various fonts which indicate properties and other features of general configuration. Extracting and recognizing these numbers correctly is an important part in map disposal. Many present methods of extraction are analyzed on their disadvantages and a new extraction and recognition algorithm of numbers is presented in this paper. The algorithm first fixes on candidates according to transcendental sizes, and then recognizes real numbers with BP neural network of OCON structure. At last, it extracts extended numbers using relation of neighborhood. Experiments have proved it is fast, efficient and reliable.

  1. 挖掘专利知识实现关键词自动抽取%Mining Patent Knowledge for Automatic Keyword Extraction

    Institute of Scientific and Technical Information of China (English)

    陈忆群; 周如旗; 朱蔚恒; 李梦婷; 印鉴

    2016-01-01

    关键词是人们快速判断是否要详细阅读文件内容的重要线索,关键词自动抽取在信息检索、自然语言处理等研究领域均有重要应用。设计了一种新的关键词自动抽取方法,使计算机能够像人类专家一样,利用知识库对目标文本进行学习和理解,最终自动抽取出关键词。专利数据因其数据量庞大、内容丰富、表达准确、专业权威而被选中作为知识库来源。详细讨论了专利数据的特性,挖掘不同专利间的知识关联,针对某一知识领域构造背景知识库,在此基础上进行目标文本的关键词自动抽取。与目标文本相关的专利文集中每个专利的专利发明人、权利人、专利引用和分类信息都被用于在不同的专利文档之间发现关联性,利用关联信息扩充背景知识库,获得目标文档在各个相关知识领域的背景知识库。基于背景知识库设计了词知识特征值,以反映词在目标文本背景知识中的重要程度。最后,把关键词抽取问题转化为分类问题,利用支持向量机(support vector machine ,SVM )抽取出目标文本的关键词。在专利数据集和开放数据集的实验结果证明明显优于现有算法。%Keywords are important clues that can help a user quickly decide whether to skip ,to scan , or to read the article .Keyword extraction plays an increasingly crucial role in information retrieval , natural language processing and other several text related researches . This paper addresses the problem of automatic keyword extraction and designs a novel automatic keyword extraction approach making use of patent knowledge . This approach can help computer to learn and understand the document as human being according to its background knowledge , finally pick out keywords automatically .The patent data set is chosen as external knowledge repository because of its huge amount of data ,rich content ,accurate

  2. Application of a molecularly imprinted polymer for the extraction of kukoamine a from potato peels.

    Science.gov (United States)

    Piletska, Elena V; Burns, Rosemary; Terry, Leon A; Piletsky, Sergey A

    2012-01-11

    A molecularly imprinted polymer (MIP) for the purification of N(1),N(12)-bis(dihydrocaffeoyl)spermine (kukoamine A) was computationally designed and tested. The properties of the polymer were characterized. The protocol of the solid phase extraction (SPE) of kukoamine A from potato peels was optimized. A HPLC-MS method for the quantification of kukoamine A was developed and used for all optimization studies. The capacity of the MIP in relation to kukoamine A from the potato peels extract was estimated at 54 mg/g of the polymer. The kukoamine A purified from potato extract using MIP was exceptionally pure (≈ 90%). Although the corresponding blank polymer was less selective than the MIP for the extraction of kukoamine A from the potato extract, it was shown that the blank polymer could be effectively used for the purification of the crude synthetic kukoamine (polymer capacity = 80 mg of kukoamine A/g of the adsorbent, kukoamine A purity ≈ 86%). Therefore, selective adsorbents could be computationally designed for other plant products, allowing their purification in quantities that would be sufficient for more detailed studies and potential practical applications. PMID:22142260

  3. 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.

  4. Automatic labeling of molecular biomarkers on a cell-by-cell basis in immunohistochemistry images using convolutional neural networks

    Science.gov (United States)

    Sheikhzadeh, Fahime; Carraro, Anita; Korbelik, Jagoda; MacAulay, Calum; Guillaud, Martial; Ward, Rabab K.

    2016-03-01

    This paper addresses the problem of classifying cells expressing different biomarkers. A deep learning based method that can automatically localize and count the cells expressing each of the different biomarkers is proposed. To classify the cells, a Convolutional Neural Network (CNN) was employed. Images of Immunohistochemistry (IHC) stained slides that contain these cells were digitally scanned. The images were taken from digital scans of IHC stained cervical tissues, acquired for a clinical trial. More than 4,500 RGB images of cells were used to train the CNN. To evaluate our method, the cells were first manually labeled based on the expressing biomarkers. Then we performed the classification on 156 randomly selected images of cells that were not used in training the CNN. The accuracy of the classification was 92% in this preliminary data set. The results have shown that this method has a good potential in developing an automatic method for immunohistochemical analysis.

  5. 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.

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

    Science.gov (United States)

    Grazzini, Jacopo; Dillard, Scott; Soille, Pierre

    2010-10-01

    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.

  7. 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.

  8. 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.

  9. Computer-Aided Molecular Design of Bis-phosphine Oxide Lanthanide Extractants.

    Science.gov (United States)

    McCann, Billy W; Silva, Nuwan De; Windus, Theresa L; Gordon, Mark S; Moyer, Bruce A; Bryantsev, Vyacheslav S; Hay, Benjamin P

    2016-06-20

    Computer-aided molecular design and high-throughput screening of viable host architectures can significantly reduce the efforts in the design of novel ligands for efficient extraction of rare earth elements. This paper presents a computational approach to the deliberate design of bis-phosphine oxide host architectures that are structurally organized for complexation of trivalent lanthanides. Molecule building software, HostDesigner, was interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential R2(O)P-link-P(O)R2 ligand geometries. The molecular mechanics ranking of ligand structures is consistent with both the solution-phase free energies of complexation obtained with density functional theory and the performance of known bis-phosphine oxide extractants. For the case where the link is -CH2-, evaluation of the ligand geometry provides the first characterization of a steric origin for the "anomalous aryl strengthening" effect. The design approach has identified a number of novel bis-phosphine oxide ligands that are better organized for lanthanide complexation than previously studied examples.

  10. Computer-Aided Molecular Design of Bis-phosphine Oxide Lanthanide Extractants.

    Science.gov (United States)

    McCann, Billy W; Silva, Nuwan De; Windus, Theresa L; Gordon, Mark S; Moyer, Bruce A; Bryantsev, Vyacheslav S; Hay, Benjamin P

    2016-06-20

    Computer-aided molecular design and high-throughput screening of viable host architectures can significantly reduce the efforts in the design of novel ligands for efficient extraction of rare earth elements. This paper presents a computational approach to the deliberate design of bis-phosphine oxide host architectures that are structurally organized for complexation of trivalent lanthanides. Molecule building software, HostDesigner, was interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential R2(O)P-link-P(O)R2 ligand geometries. The molecular mechanics ranking of ligand structures is consistent with both the solution-phase free energies of complexation obtained with density functional theory and the performance of known bis-phosphine oxide extractants. For the case where the link is -CH2-, evaluation of the ligand geometry provides the first characterization of a steric origin for the "anomalous aryl strengthening" effect. The design approach has identified a number of novel bis-phosphine oxide ligands that are better organized for lanthanide complexation than previously studied examples. PMID:26883005

  11. 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.

  12. 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.

  13. Magnetic molecular imprint-based extraction of sulfonylurea herbicides and their determination by capillary liquid chromatography

    International Nuclear Information System (INIS)

    We have developed a simple method for the extraction of sulfonylurea herbicides (SUHs) from environmental water samples. It is based on a magnetic molecular imprint (MMIP) as a sorbent. The MMIP was prepared using metsulfuron-methyl as the template molecule, methacrylic acid as the functional monomer, trimethylolpropane trimethacrylate as the cross-linking agent, and magnetite as the magnetic component. Extraction can be carried out by blending and stirring water sample, extraction solvent and MMIP. Once the extraction is completed, the MMIP containing the SUHs can be separated from the sample matrix with a magnet. The SUHs desorbed from the polymers were then quantified by capillary liquid chromatography with diode array detection. The limits of quantification are in the range of 0.08 to 0.1 ng mL-1. Repeatabilities of peak areas and retention times range from 2.9 % to 4.0 % and from 0.1 % to 0.3 %, respectively. The method was successfully applied to the determination of the SUHs bensulfuron-methyl, metsulfuronmethyl, pyrazosulfuron-methyl, thifensulfuron-methyl, and triasulfuron in waste water samples. Recoveries range from 94.3 % to 102.3 %. (author)

  14. Semi-automatic methods for landslide features and channel network extraction in a complex mountainous terrain: new opportunities but also challenges from high resolution topography

    Science.gov (United States)

    Tarolli, Paolo; Sofia, Giulia; Pirotti, Francesco; Dalla Fontana, Giancarlo

    2010-05-01

    In recent years, remotely sensed technologies such as airborne and terrestrial laser scanner have improved the detail of analysis providing high-resolution and high-quality topographic data over large areas better than other technologies. A new generation of high resolution (~ 1m) Digital Terrain Models (DTMs) are now available for different landscapes. These data call for the development of the new generation of methodologies for objective extraction of geomorphic features, such as channel heads, channel networks, bank geometry, landslide scars, service roads, etc. The most important benefit of a high resolution DTM is the detailed recognition of surface features. It is possible to recognize in detail divergent-convex landforms, associated with the dominance of hillslope processes, and convergent-concave landforms, associated with fluvial-dominated erosion. In this work, we test the performance of new methodologies for objective extraction of geomorphic features related to landsliding and channelized processes in order to provide a semi-automatic method for channel network and landslide features recognition in a complex mountainous terrain. The methodologies are based on the detection of thresholds derived by statistical analysis of variability of surface curvature. We considered a study area located in the eastern Italian Alps where a high-quality set of LiDAR data is available and where channel heads, related channel network, and landslides have been mapped in the field by DGPS. In the analysis we derived 1 m DTMs from bare ground LiDAR points, and we used different smoothing factors for the curvature calculation in order to set the more suitable curvature maps for the recognition of selected features. Our analyses suggest that: i) the scale for curvature calculations has to be a function of the scale of the features to be detected, (ii) rougher curvature maps are not optimal as they do not explore a sufficient range at which features occur, while smoother

  15. A NEW APPROACH BASED ON THE DETECTION OF OPINION BY SENTIWORDNET FOR AUTOMATIC TEXT SUMMARIES BY EXTRACTION

    Directory of Open Access Journals (Sweden)

    Reda Mohamed HAMOU

    2015-11-01

    Full Text Available In this paper, we propose a new approach based on the detection of opinion by the SentiWordNet for the production of text summarization by using the scoring extraction technique adapted to detecting of opinion. The texts are decomposed into sentences then represented by a vector of scores of opinion of this sentences. The summary will be done by elimination of sentences whose opinion is different from the original text. This difference is expressed by a threshold opinion. The following hypothesis: "textual units that do not share the same opinion of the text are ideas used for the development or comparison and their absences have no vocation to reach the semantics of the abstract" Has been verified by the statistical measure of Chi_2 which we used it to calculate a dependence between the unit textual and the text. Finally we found an opinion threshold interval which generate the optimal assessments.

  16. A semi-automatic method to extract canal pathways in 3D micro-CT images of Octocorals.

    Directory of Open Access Journals (Sweden)

    Alfredo Morales Pinzón

    Full Text Available The long-term goal of our study is to understand the internal organization of the octocoral stem canals, as well as their physiological and functional role in the growth of the colonies, and finally to assess the influence of climatic changes on this species. Here we focus on imaging tools, namely acquisition and processing of three-dimensional high-resolution images, with emphasis on automated extraction of canal pathways. Our aim was to evaluate the feasibility of the whole process, to point out and solve - if possible - technical problems related to the specimen conditioning, to determine the best acquisition parameters and to develop necessary image-processing algorithms. The pathways extracted are expected to facilitate the structural analysis of the colonies, namely to help observing the distribution, formation and number of canals along the colony. Five volumetric images of Muricea muricata specimens were successfully acquired by X-ray computed tomography with spatial resolution ranging from 4.5 to 25 micrometers. The success mainly depended on specimen immobilization. More than [Formula: see text] of the canals were successfully detected and tracked by the image-processing method developed. Thus obtained three-dimensional representation of the canal network was generated for the first time without the need of histological or other destructive methods. Several canal patterns were observed. Although most of them were simple, i.e. only followed the main branch or "turned" into a secondary branch, many others bifurcated or fused. A majority of bifurcations were observed at branching points. However, some canals appeared and/or ended anywhere along a branch. At the tip of a branch, all canals fused into a unique chamber. Three-dimensional high-resolution tomographic imaging gives a non-destructive insight to the coral ultrastructure and helps understanding the organization of the canal network. Advanced image-processing techniques greatly

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

    Directory of Open Access Journals (Sweden)

    Xiao Yu

    2015-11-01

    Full Text Available 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

  18. 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.

  19. Application of molecular sieves in the fractionation of lemongrass oil from high-pressure carbon dioxide extraction

    Directory of Open Access Journals (Sweden)

    L. Paviani

    2006-06-01

    Full Text Available The aim of this work was to study the feasibility of simultaneous process of high-pressure extraction and fractionation of lemongrass essential oil using molecular sieves. For this purpose, a high-pressure laboratory-scale extraction unit coupled with a column with four different stationary phases for fractionation: ZSM5 zeolite, MCM-41 mesoporous material, alumina and silica was employed. Additionally, the effect of carbon dioxide extraction variables on the global yield and chemical composition of the essential oil was also studied in a temperature range of 293 to 313 K and a pressure range of 100 to 200 bar. The volatile organic compounds of the extracts were identified by a gas chromatograph coupled with a mass spectrometer detector (GC/MS. The results indicated that the extraction process variables and the stationary phase exerted an effect on both the extraction yield and the chemical composition of the extracts.

  20. 高校学生信息自动提取与分析系统研究%Research and analysis of college students information automatic extraction

    Institute of Scientific and Technical Information of China (English)

    聂明辉

    2013-01-01

    Digital campus construction to the third stage, started system integration and large-scale data sharing. Through the mutual sharing of data platform, data extraction and clean-up technologies, particularly get the information we need, but also enables us to understand and evaluate students more comprehensive and objective in the university campus life, learning situation. This paper is based on ODI technology, MapReduce technology and data warehouse technology as the foundation, proposed and constructed a university student in school, life information automatic extraction and analysis system model, for the university informatization environment more intelligent management students provides a feasible technical scheme.%高校数字化校园建设到第三阶段,开始了大规模的系统整合以及数据共享。通过互通共享的数据平台,利用数据抽取和清理技术,有所侧重的获取我们需要的信息,也使我们能够更全面更客观的了解和评价学生在大学校园内的生活、学习情况。本文就此以ODI技术、MapReduce技术以及数据仓库技术为基础,提出并构筑了一套高校学生在校学习、生活信息自动提取与分析系统模型,为信息化大环境下高校更加智慧的管理学生提供了一种可行的技术方案。

  1. Etna_NETVIS: A dedicated tool for automatically pre-processing high frequency data useful to extract geometrical parameters and track the evolution of the lava field

    Science.gov (United States)

    Marsella, Maria; Junior Valentino D'Aranno, Peppe; De Bonis, Roberto; Nardinocchi, Carla; Scifoni, Silvia; Scutti, Marianna; Sonnessa, Alberico; Wahbeh, Wissam; Biale, Emilio; Coltelli, Mauro; Pecora, Emilio; Prestifilippo, Michele; Proietti, Cristina

    2016-04-01

    In volcanic areas, where it could be difficult to gain access to the most critical zones for carrying out direct surveys, digital photogrammetry techniques are rarely experimented, although in many cases they proved to have remarkable potentialities, as the possibility to follow the evolution of volcanic (fracturing, vent positions, lava fields, lava front positions) and deformation processes (inflation/deflation and instability phenomena induced by volcanic activity). These results can be obtained, in the framework of standard surveillance activities, by acquiring multi-temporal datasets including Digital Orthophotos (DO) and Digital Elevation Models (DEM) to be used for implementing a quantitative and comparative analysis. The frequency of the surveys can be intensified during emergency phases to implement a quasi real-time monitoring for supporting civil protection actions. The high level of accuracy and the short time required for image processing make digital photogrammetry a suitable tool for controlling the evolution of volcanic processes which are usually characterized by large and rapid mass displacements. In order to optimize and extend the existing permanent ground NEtwork of Thermal and VIsible Sensors located on Mt. Etna (Etna_NETVIS) and to improve the observation of the most active areas, an approach for monitoring surface sin-eruptive processes was implemented. A dedicated tool for automatically pre-processing high frequency data, useful to extract geometrical parameters as well as to track the evolution of the lava field, was developed and tested both in simulated and real scenarios. The tool allows to extract a coherent multi-temporal dataset of orthophotos useful to evaluate active flow area and to estimate effusion rates. Furthermore, Etna_NETVIS data were used to downscale the information derived from satellite data and/or to integrate the satellite datasets in case of incomplete coverage or missing acquisitions. This work was developed in the

  2. 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.

  3. An automatic face contour extracting method%一种自动的人脸轮廓定位方法

    Institute of Scientific and Technical Information of China (English)

    李昕昕; 龚勋; 夏冉

    2013-01-01

    人脸分割对人脸识别、人脸三维建模等人脸图像处理问题具有重要意义,而人脸图像往往轮廓边缘模糊、梯度不明显,常规无边缘几何活动轮廓模型通常无法获得理想的分割效果且计算量较大.为实现快速、准确的人脸轮廓定位及分割,将无边缘几何活动轮廓模型和稀疏场数值算法相结合提出了一个改进的算法,并结合人脸检测和数学形态学算子提出一个基于曲线演化的人脸分割方案.实验结果表明,该算法不仅提高了计算效率,还可以有效地检测出局部模糊或分断边界,进化曲线不会断裂,能够获得较好的人脸分割效果.%Images containing faces are essential to intelligent vision-based human computer interaction,and research efforts in face processing include face recognition, face tracking, and expression recognition. Many applications assume that the faces in an image or an image sequence have been identified and localized. To build fully automated systems that analyze the information contained in face images, robust and efficient face detection algorithms are required. However,such a problem is challenging because faces are non-rigid and have a high degree of variability in size,shape,color,and texture. The purpose of this paper is to provide a relative robust method for face segmentation in images based on curve evolution methodology. Since the face image always has a blur boundary and little gradient changes,the region segmentations obtained by the original Chan-Vese model are generally unsatisfactory and need large amount of calculations. To achieve more accurate facial contour extraction and face segmentation, a new face segmentation scheme based on curve evolution model is proposed which is a combination of Chan-Vese model, sparse-field algorithm, face detection and mathematical morphology operators. Experimental results show that the improved algorithm can effectively detect the local blur and breaking

  4. Use of neuropathological tissue for molecular genetic studies: parameters affecting DNA extraction and polymerase chain reaction.

    Science.gov (United States)

    Kösel, S; Graeber, M B

    1994-01-01

    Nuclear and mitochondrial DNA were extracted from gray matter of human cerebral cortex which had either been formalin-fixed and embedded into paraffin or stored in formalin for up to 26 years. Extraction conditions were optimized for proteinase K digestion, i.e., enzyme concentration, digestion temperature and incubation time. Using the polymerase chain reaction (PCR), DNA was successfully amplified from archival material and sequenced employing a direct nonradioactive cycle sequencing protocol. In general, tissue embedded into paraffin following brief fixation in formalin gave good quantitative results, i.e., up to 1 microgram DNA/mg tissue were extracted. This yield was at least one order of magnitude higher than that obtained with tissue stored in formalin. However, paraffin-embedded neuropathological material was found to contain an as-yet-unidentified PCR inhibitor, and a deleterious effect of long-term fixation in unbuffered low-grade formalin was clearly detectable. Importantly, both paraffin-embedded tissue blocks and human brain that had been stored in formalin for many years yielded DNA sufficient for qualitative analysis. The implications of these findings for the use of neuropathological material in molecular genetic studies are discussed.

  5. 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. PMID:26851451

  6. 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.

  7. Ball milling improves extractability and affects molecular properties of psyllium (Plantago ovata Forsk) seed husk arabinoxylan.

    Science.gov (United States)

    Van Craeyveld, Valerie; Delcour, Jan A; Courtin, Christophe M

    2008-12-10

    Psyllium (Plantago ovata Forsk) seed husk (PSH) is very rich in arabinoxylan (AX). However, its high gelling capacity and the complex nature of the AX make it difficult to process. In this study, ball milling was investigated as a tool for enhancing PSH AX water extractability and molecular mass (MM). A 48 h laboratory-scale ball mill treatment under standardized optimal conditions reduced the PSH average particle size from 161 microm for the untreated sample to 6 microm. Concurrently, it increased the water-extractable AX (WE-AX) level from 13 (untreated PSH) to 90% of the total PSH AX. While the WE-AX of the untreated PSH had a peak MM of 216 kDa and an arabinose to xylose (A/X) ratio of 0.20, WE-AX fragments from ball mill-pretreated PSH had a peak MM of 22 kDa and an A/X ratio of 0.31. Ball milling further drastically reduced the intrinsic viscosity of PSH extracts and their water-holding capacity. Prolonged treatment brought almost all AX (98%) in solution and yielded WE-AX fragments with an even higher A/X ratio (0.42) and a lower peak MM (11 kDa). While impact and jet milling of PSH equally led to significant reductions in particle size, these technologies only marginally affected the water extractability of PSH AX. This implies that ball milling affects PSH particles and their constituent molecules differently than impact and jet milling. PMID:19007123

  8. EXTRACT

    DEFF Research Database (Denmark)

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

    2016-01-01

    therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment...... and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed.Database URL: https://extract.hcmr.gr/....

  9. Poder Antioxidante de Extractos de Romero Concentrados por Destilación Molecular Antioxidant Potential of Rosemary Extracts Concentrated by Molecular Distillation

    Directory of Open Access Journals (Sweden)

    M.A. Martinello

    2005-01-01

    Full Text Available Se ha estudiado el poder antioxidativo de extractos de romero concentrados por destilación molecular. Las hojas de romero fueron molidas y secadas previamente a la extracción, la cual fue llevada a cabo en un equipo de lixiviación de lecho fijo utilizando alcohol isopropílico como solvente. El solvente fue separado del extracto mediante destilación bajo vacío. El rendimiento promedio de extracción fue del 15,5%. El extracto resultante, verde y altamente viscoso, fue sometido a concentración por destilación molecular. La corriente de destilado consistió en un líquido levemente coloreado de verde, mientras que el residuo mantuvo un aspecto más parecido a la alimentación. El poder antioxidativo de ambos extractos fue medido sobre aceite de uva crudo, aceite de uva blanqueado y aceite de uva desodorizado, agregando el destilado y el residuo y determinando la estabilidad oxidativa por medio del Test de Schaal. En los tres tipos de aceites, el extracto obtenido como residuo de la destilación molecular mostró mayor poder antioxidante que el extracto obtenido como destilado. Por otra parte, ambos extractos probaron su potencial antioxidante al ser contrastados con muestras de control, sin agregado de extractos.A study was made of the antioxidant potential of rosemary extracts concentrated by molecular distillation. The rosemary leaves were milled and dried prior to extraction, and the extraction was carried out in fixed bed leaching equipment using isopropyl alcohol as solvent. The solvent was separated from the extract by vacuum distillation. The average yield of the extraction was 15.5%. The resulting extract, green and highly viscous, was concentrated by molecular distillation. The distillate stream consisted of a lightly colored green liquid, while the residue maintained an aspect similar to the feed stream, producing a thicker green fluid, darker than the feed stream. The antioxidant potential of both extracts was measured on crude

  10. FieldChopper, a new tool for automatic model generation and virtual screening based on molecular fields.

    Science.gov (United States)

    Kalliokoski, Tuomo; Ronkko, Toni; Poso, Antti

    2008-06-01

    Algorithms were developed for ligand-based virtual screening of molecular databases. FieldChopper (FC) is based on the discretization of the electrostatic and van der Waals field into three classes. A model is built from a set of superimposed active molecules. The similarity of the compounds in the database to the model is then calculated using matrices that define scores for comparing field values of different categories. The method was validated using 12 publicly available data sets by comparing the method to the electrostatic similarity comparison program EON. The results suggest that FC is competitive with more complex descriptors and could be used as a molecular sieve in virtual screening experiments when multiple active ligands are known. PMID:18489083

  11. A novel reliable method of DNA extraction from olive oil suitable for molecular traceability.

    Science.gov (United States)

    Raieta, Katia; Muccillo, Livio; Colantuoni, Vittorio

    2015-04-01

    Extra virgin olive oil production has a worldwide economic impact. The use of this brand, however, is of great concern to Institutions and private industries because of the increasing number of fraud and adulteration attempts to the market products. Here, we present a novel, reliable and not expensive method for extracting the DNA from commercial virgin and extra virgin olive oils. The DNA is stable overtime and amenable for molecular analyses; in fact, by carrying out simple sequence repeats (SSRs) markers analysis, we characterise the genetic profile of monovarietal olive oils. By comparing the oil-derived pattern with that of the corresponding tree, we can unambiguously identify four cultivars from Samnium, a region of Southern Italy, and distinguish them from reference and more widely used varieties. Through a parentage statistical analysis, we also identify the putative pollinators, establishing an unprecedented and powerful tool for olive oil traceability.

  12. 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.

  13. Novel restricted access materials combined to molecularly imprinted polymers for selective solid-phase extraction of organophosphorus pesticides from honey.

    Science.gov (United States)

    He, Juan; Song, Lixin; Chen, Si; Li, Yuanyuan; Wei, Hongliang; Zhao, Dongxin; Gu, Keren; Zhang, Shusheng

    2015-11-15

    A novel restricted access materials (RAM) combined to molecularly imprinted polymers (MIPs), using malathion as template molecule and glycidilmethacrylate (GMA) as pro-hydrophilic co-monomer, were prepared for the first time. RAM-MIPs with hydrophilic external layer were characterized by scanning electron microscopy and recognition and selectivity properties were compared with the restricted access materials-non-molecularly imprinted polymers (RAM-NIPs) and unmodified MIPs. RAM-MIPs were used as the adsorbent enclosed in solid phase extraction column and several important extraction parameters were comprehensively optimized to evaluate the extraction performance. Under the optimum extraction conditions, RAM-MIPs exhibited comparable or even higher selectivity with greater extraction capacity toward six kinds of organophosphorus pesticides (including malathion, ethoprophos, phorate, terbufos, dimethoate, and fenamiphos) compared with the MIPs and commercial solid phase extraction columns. The RAM-MIPs solid phase extraction coupled with gas chromatography was successfully applied to simultaneously determine six kinds of organophosphorus pesticides from honey sample. The new established method showed good linearity in the range of 0.01-1.0 μg mL(-1), low limits of detection (0.0005-0.0019 μg mL(-1)), acceptable reproducibility (RSD, 2.26-4.81%, n = 6), and satisfactory relative recoveries (90.9-97.6%). It was demonstrated that RAM-MIPs solid phase extraction with excellent selectivity and restricted access function was a simple, rapid, selective, and effective sample pretreatment method.

  14. Separation of phenolic acids from natural plant extracts using molecularly imprinted anion-exchange polymer confined ionic liquids.

    Science.gov (United States)

    Bi, Wentao; Tian, Minglei; Row, Kyung Ho

    2012-04-01

    Polymer-confined ionic liquids were used for the separation of phenolic acids from natural plant extract by utilizing an anion-exchange mechanism. They were synthesized using molecular imprinting technique to reduce non-directional ion-ion interactions during anion-exchange and other interactions with interference substances that could decrease selectivity. A suitable sorbent for phenolic acid separation could be identified based on the adsorption behaviors of phenolic acids on different polymer-confined ionic liquids. Thus, the developed ionic liquid-based molecularly imprinted anion-exchange polymer (IMAP) achieved high recovery rates by solid-phase extraction of phenolic acids from Salicornia herbacea L. extract: 90.1% for protocatechuic acid, 95.5% for ferulic acid and 96.6% for caffeic acid. Moreover, the phenolic acids were separable from each other by repeated solid phase extraction cycles. The proposed method could be used to separate other phenolic acids or organic acids from complex samples. PMID:21903215

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

    International Nuclear Information System (INIS)

    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.

  16. Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases.

    Science.gov (United States)

    Jeddi, Fakhri; Piarroux, Renaud; Mary, Charles

    2013-01-01

    During the last 20 years, molecular biology techniques have propelled the diagnosis of parasitic diseases into a new era, as regards assay speed, sensitivity, and parasite characterization. However, DNA extraction remains a critical step and should be adapted for diagnostic and epidemiological studies. The aim of this report was to document the constraints associated with DNA extraction for the diagnosis of parasitic diseases and illustrate the adaptation of an automated extraction system, NucliSENS easyMAG, to these constraints, with a critical analysis of system performance. Proteinase K digestion of samples is unnecessary with the exception of solid tissue preparation. Mechanically grinding samples prior to cell lysis enhances the DNA extraction rate of fungal cells. The effect of host-derived nucleic acids on the extraction efficiency of parasite DNA varies with sample host cell density. The optimal cell number for precise parasite quantification ranges from 10 to 100,000 cells. Using the NucliSENS easyMAG technique, the co-extraction of inhibitors is reduced, with an exception for whole blood, which requires supplementary extraction steps to eliminate inhibitors.

  17. Determination of Three Tanshinones from Radix Salvia Miltiorrhiza by Molecularly Imprinted Solid-phase Extraction

    Institute of Scientific and Technical Information of China (English)

    YAN, Hongyuan; TIAN, Minglei; ROW, Kyung Ho

    2009-01-01

    A selective molecularly imprinted solid-phase extraction procedure was developed for the selective separation of tanshinone Ⅰ, tanshinone ⅡA, and cryptotanshinone from Radix Salvia Miltiorrhiza samples. Tanshinone ⅡA imprinted polymers (MIP) synthesized in ethanol-dodecanol system show high affinity to tanshinone ⅡA and its structure analogs in aqueous environment and the affinity can be controlled by adjusting the intensity of the eluents. By using 60% water-40% methanol (volume ratio) and 99.5% methanol-0.5% trifluoroacetic acid (volume ratio) as washing and eluting solvents, most interferences originating from the salvia matrix were eliminated. The extracts were sufficiently clean enough to be directly injected into HPLC for further chromatographic analysis. Good linearity was obtained from 0.4 to 500.0 mg·L~(-1) (r~2=0.999) with the relative standard deviations less than 4.2%. The mean recoveries of tanshinone ⅡA in Radix Salvia Miltiorrhiza were more than 85.6% at three different concentrations and the limits of detection were 0.06-0.09 mg·L~(-1). This method is a viable alternative tool to the existing HPLC methods for analyzing the content of the three tanshinones in Radix Salvia Miltiorrhiza samples.

  18. From the Cover: Cooperative extraction of membrane nanotubes by molecular motors

    Science.gov (United States)

    Leduc, Cécile; Campàs, Otger; Zeldovich, Konstantin B.; Roux, Aurélien; Jolimaitre, Pascale; Bourel-Bonnet, Line; Goud, Bruno; Joanny, Jean-François; Bassereau, Patricia; Prost, Jacques

    2004-12-01

    In eukaryotic cells, nanotubes represent a substantial fraction of transport intermediates between organelles. They are extracted from membranes by molecular motors walking along microtubules. We previously showed that kinesins fixed on giant unilamellar vesicles in contact with microtubules are sufficient to form nanotubes in vitro. Motors were attached to the membrane through beads, thus facilitating cooperative effects. Koster et al. [Koster, G., VanDuijn, M., Hofs, B. & Dogterom, M. (2003) Proc. Natl. Acad. Sci. USA 100, 15583-15588] proposed that motors could dynamically cluster at the tip of tubes when they are individually attached to the membrane. We demonstrate, in a recently designed experimental system, the existence of an accumulation of motors allowing tube extraction. We determine the motor density along a tube by using fluorescence intensity measurements. We also perform a theoretical analysis describing the dynamics of motors and tube growth. The only adjustable parameter is the motor binding rate onto microtubules, which we measure to be 4.7 ± 2.4 s-1. In addition, we quantitatively determine, for a given membrane tension, the existence of a threshold in motor density on the vesicle above which nanotubes can be formed. We find that the number of motors pulling a tube can range from four at threshold to a few tens away from it. The threshold in motor density (or in membrane tension at constant motor density) could be important for the understanding of membrane traffic regulation in cells. giant unilamellar vesicle | intracellular transport | kinesin | membrane tubule | traffic jam

  19. Molecular Characterization Of Hair Cuticle And Its Extracted Proteins In Seven Mammalian Species

    Directory of Open Access Journals (Sweden)

    S. K. Areida, M. F. Ismail, E. K. Abdel Hady, and A. O. Osman

    2006-06-01

    Full Text Available Hair is an of the epidermis in mammals and consists of two large groups of human hair proteins. One is hard -keratins and the other is matrix proteins. The present investigation aimed to compare the ultrastructural of the hair scale using the scanning electron microscope, and the proteins and amino acids content of the keratin in seven mammalian species. The values of the hair thickness, x/y feret and hair pattern of the species in the present study confirm the presence of species-specific characteristics and ultra structural variation. The situation in man differs from the wild mammals due to damage of hair cuticle caused by mechanical abuse, exposure to ultraviolet radiation and chemical over processing. The maximum amount of extracted proteins from hair keratin was analyzed by SDS-PAGE. The electrophoretic patterns showed an overall degree of similarity. However, differences exist between species in the intensity of stain. Quantitatively, the electrophoretic patterns scanned and analyzed using gel protein analyzer. The results showed no difference between the molecular mass of some species, but different in molecular mass distribution. Amino acid composition of keratin of mammalian hair species of the present study showed some variation, especially for methionine, isoleucine, lysine and arginine. The other amino acids studied are significantly present in most hair. One of the later amino acid is cysteine. Cysteine is a very important due to the presence of disulfate cross-links.

  20. Automatic knowledge extraction from EHRs

    OpenAIRE

    Vasiljeva, Ieva; Arandelovic, Ognjen

    2016-01-01

    Increasing efforts in the collection, standardization, and maintenance of large scale longitudinal elec- tronic health care records (EHRs) across the world provide a promising source of real world medical data with the potential of providing major novel insights of benefit both to specific individuals in the context of personalized medicine, as well as on the level of population-wide health care and policy. The present paper builds upon the existing and intensifying efforts at using machine l...

  1. Liquid/liquid metal extraction: Phase diagram topology resulting from molecular interactions between extractant, ion, oil and water

    Science.gov (United States)

    Bauer, C.; Bauduin, P.; Dufrêche, J. F.; Zemb, T.; Diat, O.

    2012-11-01

    We consider the class of surfactants called "extractants" since they specifically interact with some cations and are used in liquid-liquid separation processes. We review here features of water-poor reverse micelles in water/oil/ extractant systems as determined by combined structural studies including small angle scattering techniques on absolute scale. Origins of instabilities, liquid-liquid separation as well as emulsification failure are detected. Phase diagrams contain the same multi-phase domains as classical microemulsions, but special unusual features appear due to the high spontaneous curvature directed towards the polar cores of aggregates as well as rigidity of the film made by extracting molecules.

  2. 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.

  3. Inter-watershed and Its Automatic Extraction Based on DEMs%域间流域及自动提取方法研究

    Institute of Scientific and Technical Information of China (English)

    孙建伟; 汤国安

    2013-01-01

    目前,基于DEM及常规GIS软件进行的流域自动分割方法,往往忽视了一般流域与域间流域的差异性,并且未在属性上区分二者。本文强调流域划分必须充分,明确域间流域的概念与基本特征(包括域间流域的数量与面积、空间分布及空间形态特征)。鉴此,本文提出了基于DEM的域间流域自动提取方法,并以陕北黄土高原丘陵沟壑地区为实证。结果显示:通过对汇流阈值、地形特征、数据边界效应等因素的影响分析,可实现对域间流域的快速准确提取。另外,本文还对此分析了域间流域与一般流域在水文、空间形态及空间分布方面的特征差异。%Watershed delineation based on DEMs in the GIS environment is a fundamental work for hydrological analysis. But the feature difference between normal and inter-watershed watershed has long been ignored. This text believes that existence of inter-watershed must be taken into account during watershed delineation and analy-sis. In this paper, an overall explanation of basic concepts and characteristics of inter-watershed is presented, and a method of extracting inter-watershed automatically based on DEMs is introduced. Experimental results in the Loess Plateau region show that inter-watershed could be extracted accurately and quickly after a comprehensive consideration of water accumulation threshold, terrain feature and the boundary of data. Generally speaking, flat topography may lead to the wrong position of outlets of watersheds, which can be corrected with help of rivers’ DLG data. And if boundary of the data is not the dividing crest, it’s difficult to determine whether a watershed whose dividing line consists of data’s boundary is inter-watershed or not. Comparison of inter-watershed and normal watershed in terms of spatial form, spatial distribution and hydrological characteristics based on experi-mental results show that inter-watershed performs

  4. 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 imprint

  5. Molecularly imprinted solid-phase extraction of glutathione from urine samples

    Energy Technology Data Exchange (ETDEWEB)

    Song, Renyuan, E-mail: songrenyuan0726@163.com; Hu, Xiaoling; Guan, Ping; Li, Ji; Zhao, Na; Wang, Qiaoli

    2014-11-01

    Molecularly imprinted polymer (MIP) particles for glutathione were synthesized through iniferter-controlled living radical precipitation polymerization (IRPP) under ultraviolet radiation at ambient temperature. Static adsorption, solid-phase extraction, and high-performance liquid chromatography were carried out to evaluate the adsorption properties and selective recognition characteristics of the polymers for glutathione and its structural analogs. The obtained IRPP-MIP particles exhibited a regularly spherical shape, rapid binding kinetics, high imprinting factor, and high selectivity compared with the MIP particles prepared using traditional free-radical precipitation polymerization. The selective separation and enrichment of glutathione from the mixture of glycyl-glycine and glutathione disulfide could be achieved on the IRPP-MIP cartridge. The recoveries of glutathione, glycyl-glycine, and glutathione disulfide were 95.6% ± 3.65%, 29.5% ± 1.26%, and 49.9% ± 1.71%, respectively. The detection limit (S/N = 3) of glutathione was 0.5 mg·L{sup −1}. The relative standard deviations (RSDs) for 10 replicate detections of 50 mg·L{sup −1} of glutathione were 5.76%, and the linear range of the calibration curve was 0.5 mg·L{sup −1} to 200 mg·L{sup −1} under optimized conditions. The proposed approach was successfully applied to determine glutathione in spiked human urine samples with recoveries of 90.24% to 96.20% and RSDs of 0.48% to 5.67%. - Highlights: • Imprinted polymer particles were prepared by IRPP at ambient temperature. • High imprinting factor, high selectivity, and rapid binding kinetics were achieved. • Selective solid-phase extraction of glutathione from human urine samples.

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

    Directory of Open Access Journals (Sweden)

    Shah Parantu K

    2004-10-01

    Full Text Available Abstract 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

  7. Investigation of Molecular Marker Lipids in Alpine Ice Cores Via Stir Bar Sorptive Extraction

    Science.gov (United States)

    Makou, M. C.; Eglinton, T. I.; Thompson, L. G.; Hughen, K. A.

    2005-12-01

    Recently developed analytical techniques were employed to identify and quantify organic molecular markers trapped in high-altitude ice. While various compounds represent potentially useful proxies for biomass burning, vegetation type, atmospheric circulation, and anthropogenic activity, prior attempts to measure organic compounds in ice cores have typically required large volumes of sample material that are incompatible with generation of high-resolution paleoclimate records. We employed stir bar sorptive extraction (SBSE) and thermal desorption (TD), coupled with gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS), to examine the organic content of small quantities (≤ 30 ml) of ice. To test the utility of the approach, post-industrial ice core samples from the Huascarán and Sajama sites (Andes), the Dasuopu and Puruogangri sites (Tibetan Plateau), and Mt. Kilimanjaro (east Africa) were tested. n-Alkanes, n-alkanoic acids, n-alkyl amides and nitriles, polycyclic aromatic hydrocarbons (PAHs), and various diterpenoids were identified in this suite of cores. These marker compounds suggest inputs from biomass burning, fresh vascular plant material, and anthropogenic activities such as fossil fuel combustion. Differences in distributions of the alkyl amide and nitrile homologues between the different sites suggest a predominantly local or regional supply of organic matter. Pre-industrial samples from the Sajama and Puruogangri ice cores were also analyzed in order to assess the character of biomarker assemblages in the absence of anthropogenic contributions and investigate changes in inputs over time. PAHs and diterpenoids, which may result from biomass burning and were observed in the modern Sajama samples, occurred in two Holocene Sajama samples, but not in a last glacial sample. Enhanced inputs of terrestrial vegetation combustion biomarkers were consistent with periods of enhanced aridity in both cores. This study demonstrates the utility of SBSE, TD

  8. Cellular biopolymers and molecular structure of a secondary pulp and paper mill sludge verified by spectroscopy and chemical extraction techniques.

    Science.gov (United States)

    Edalatmanesh, Maryam; Sain, Mohini; Liss, Steven N

    2010-01-01

    For proper treatment, recycling, or disposal of the pulp and paper mill secondary sludge qualitative and quantitative determination of its characteristics are necessary. Chemical extraction, quantitative characterization, and spectroscopic experiments have been performed to determine the molecular composition and chemical functionality of a pulp and paper mill secondary sludge. In order to extract the low-molecular-weight substances, soxhlet extraction with polar and non-polar solvents was performed where most of the target substances (17±1.3%.) were extracted after 2 hours. Over time, this extraction followed a first-order kinetics. Fiber analyses have shown 12±3% lignin, 28±3% cellulose, and 12±4% hemicelluloses content. The ash content was about 17±0.5%. In this work, 7 and 16% intra- and extracellular polymeric substances, respectively, were extracted from the secondary sludge. EPS and mixture of intra- and extracellular biopolymers have shown similar chemical functionalities. These analyses confirmed that the paper secondary sludge consisted mainly of wood fiber, i.e. lignocellulosic substances, along with proteins and polysaccharides originated from microorganisms. PMID:21123914

  9. Preparation and evaluation of molecularly imprinted solid-phase micro-extraction fibers for selective extraction of phthalates in an aqueous sample

    Energy Technology Data Exchange (ETDEWEB)

    He Juan, E-mail: juanhe@haut.edu.cn [School of Chemistry and Chemical Engineering, Henan University of, Technology, LianHua Road, Zhengzhou 450051 (China); Lv Ruihe; Zhan Haijun; Wang Huizhi; Cheng Jie; Lu Kui; Wang Fengcheng [School of Chemistry and Chemical Engineering, Henan University of, Technology, LianHua Road, Zhengzhou 450051 (China)

    2010-07-26

    A novel molecularly imprinted polymer (MIP) that was applied to a solid-phase micro-extraction (SPME) device, which could be coupled directly to gas chromatograph and mass spectrometer (GC/MS), was prepared using dibutyl phthalate (DBP) as the template molecule. The characteristics and application of this fiber were investigated. Electron microscope images indicated that the MIP-coated solid-phase micro-extraction (MI-SPME) fibers were homogeneous and porous. The extraction yield of DBP with the MI-SPME fibers was higher than that of the non-imprinted polymer (NIP)-coated SPME (NI-SPME) fibers. The MI-SPME fibers had a higher selectivity to other phthalates that had similar structures as DBP. A method was developed for the determination of phthalates using MI-SPME fibers coupled with GC/MS. The extraction conditions were optimized. Detection limits for the phthalate samples were within the range of 2.17-20.84 ng L{sup -1}. The method was applied to five kinds of phthalates dissolved in spiked aqueous samples and resulted in recoveries of up to 94.54-105.34%, respectively. Thus, the MI-SPME fibers are suitable for the extraction of trace phthalates in complicated samples.

  10. 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.

  11. Comparative analysis of four methods to extract DNA from paraffin-embedded tissues: effect on downstream molecular applications

    Directory of Open Access Journals (Sweden)

    Savelkoul Paul HM

    2010-09-01

    Full Text Available Abstract Background A large portion of tissues stored worldwide for diagnostic purposes is formalin-fixed and paraffin-embedded (FFPE. These FFPE-archived tissues are an extremely valuable source for retrospective (genetic studies. These include mutation screening in cancer-critical genes as well as pathogen detection. In this study we evaluated the impact of several widely used DNA extraction methods on the quality of molecular diagnostics on FFPE tissues. Findings We compared 4 DNA extraction methods from 4 identically processed FFPE mammary-, prostate-, colon- and lung tissues with regard to PCR inhibition, real time SNP detection and amplifiable fragment size. The extraction methods, with and without proteinase K pre-treatment, tested were: 1 heat-treatment, 2 QIAamp DNA-blood-mini-kit, 3 EasyMAG NucliSens and 4 Gentra Capture-Column-kit. Amplifiable DNA fragment size was assessed by multiplexed 200-400-600 bp PCR and appeared highly influenced by the extraction method used. Proteinase K pre-treatment was a prerequisite for proper purification of DNA from FFPE. Extractions with QIAamp, EasyMAG and heat-treatment were found suitable for amplification of fragments up to 400 bp from all tissues, 600 bp amplification was marginally successful (best was QIAamp. QIAamp and EasyMAG extracts were found suitable for downstream real time SNP detection. Gentra extraction was unsuitable. Hands-on time was lowest for heat-treatment, followed by EasyMAG. Conclusions We conclude that the extraction method plays an important role with regard to performance in downstream molecular applications.

  12. LDFF, the large molecular weight DNA fragmentation factor, is responsible for the large molecular weight DNA degradation during apoptosis in Xenopus egg extracts

    Institute of Scientific and Technical Information of China (English)

    Zhi Gang LU; Chuan Mao ZHANG; Zhong He ZHAI

    2004-01-01

    DNA degradation is a biochemical hallmark in apoptosis. It has been demonstrated in many cell types that there are two stages of DNA fragmentation during the apoptotic execution. In the early stage, chromatin DNA is cut into large molecular weight DNA fragments, although the responsible nuclease(s) has not been recognized. In the late stage, the chromatin DNA is cleaved further into short oligonucleosomal fragments by a well-characterized nuclease in apoptosis,the caspase-activated DNase (CAD/DFF40). In this study, we demonstrate that large molecular weight DNA fragmentation also occurs in Xenopus egg extracts in apoptosis. We show that the large molecular weight DNA fragmentation factor (LDFF) is not the Xenopus CAD homolog XCAD. LDFF is activated by caspase-3. The large molecular weight DNA fragmentation activity of LDFF is Mg2+-dependent and Ca2+-independent, can occur in both acidic and neutral pH conditions and can tolerate 45℃ treatment. These results indicate that LDFF in Xenopus egg extracts might be a new DNase (or DNases) responsible for the large DNA fragmentation.

  13. 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. PMID:26399155

  14. Selective extraction of derivates of p-hydroxy-benzoic acid from plant material by using a molecularly imprinted polymer.

    Science.gov (United States)

    Karasová, Gabriela; Lehotay, Jozef; Sádecká, Jana; Skacáni, Ivan; Lachová, Miroslava

    2005-12-01

    Selective SPE of derivates of p-hydroxybenzoic acid (pHBA) from plant extract of Melissa officinalis is presented using a molecularly imprinted polymer (MIP) made with protocatechuic acid (PA) as template molecule. MIP was prepared with acrylamide as functional monomer, ethylene glycol dimethacrylate as crosslinking monomer and ACN as porogen. MIP was evaluated towards six phenolic acids: PA, gallic acid, pHBA, vanillic acid (VA), gentisic acid (GeA) and syringic acid (SyrA), and then steps of molecularly imprinted SPE (MISPE) procedure were optimized. The best specific binding capacity of MIP was obtained for PA in ACN (34.7 microg/g of MIP). Other tested acids were also bound on MIP if they were dissolved in this solvent. ACN was chosen as solvent for sample application. M. officinalis was extracted into methanol/water (4:1, v/v), the extract was then evaporated to dryness and dissolved in ACN before application on MIP. Water and ACN were used as washing solvents and elution of benzoic acids was performed by means of a mixture methanol/acetic acid (9:1, v/v). pHBA, GA, PA and VA were extracted with recoveries of 56.3-82.1% using this MISPE method. GeA was not determined in plant extract. PMID:16405176

  15. 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

  16. DNA Extraction from Bronchial Aspirates for Molecular Cytology: Which Method to Take?

    OpenAIRE

    Grote, Hans Jürgen; Schmiemann, Viola; Sarbia, Mario; Böcking, Alfred

    2003-01-01

    Objective: To date, there are only few systematic reports on the quality of DNA extracted from routine diagnostic cytologic specimens. It was the aim of the present study to evaluate the ability of 50% ethanol/2% carbowax (Saccomanno fixative) to preserve bronchial secretions with high quality genomic DNA as well as to compare different DNA extraction methods. Methods: DNA was extracted from 45 bronchial aspirates by four different extraction protocols. Beside DNA yield, DNA quality with rega...

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

    OpenAIRE

    Pinto S.M.; Fernandes-Matioli F.M.C.; Schlenz E.

    2000-01-01

    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 in...

  18. 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.

  19. Molecular characterization of antitumor effects of the rhizome extract from Curcuma zedoaria on human esophageal carcinoma cells.

    Science.gov (United States)

    Hadisaputri, Yuni Elsa; Miyazaki, Tatsuya; Suzuki, Shigemasa; Kubo, Norio; Zuhrotun, Ade; Yokobori, Takehiko; Abdulah, Rizky; Yazawa, Shin; Kuwano, Hiroyuki

    2015-12-01

    Curcuma zedoaria has been used as a traditional agent against malignant diseases. To elucidate detailed mechanisms producing such an activity, characterization and determination of molecular mechanisms of its antitumor effects was conducted. Inhibiting activities against cell proliferation, invasion and colony formation, and expression levels of corresponding molecules were investigated using human esophageal cancer TE-8 cells treated with the rhizome extract from C. zedoaria. Antitumor effect of the extract administered orally was also examined in tumor-bearing mice. The extract possessed strong anti-proliferation and invasion activities against TE-8 cells. Further, upregulated PTEN and downregulated phosphorylated Akt, mTOR and STAT3 expressions in the cells were induced shortly after treatment with the extract, followed by attenuation of FGFR1 and MMP-2, activation of caspase-9, caspase-3 and PARP, and suppression of Bcl-2 expressions, which led the cells to apoptotic cell death. Furthermore, tumor formation in mice was significantly suppressed through the oral administration of the extract. Taken together, these results suggest that the C. zedoaria extract could be a promising agent against esophageal cancer.

  20. Removal and destruction of endocrine disrupting contaminants by adsorption with molecularly imprinted polymers followed by simultaneous extraction and phototreatment

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez-Alvarez, Paula [Department of Biotechnology, Lund University, P.O. Box 124, 22100 Lund (Sweden); University of Santiago de Compostela, Department of Chemical Engineering, Instituto de Investigaciones Tecnologicas, C/Constantino Candeira, s/n. E-15782 Santiago de Compostela (Spain); Le Noir, Mathieu [Department of Biotechnology, Lund University, P.O. Box 124, 22100 Lund (Sweden); Guieysse, Benoit [Department of Biotechnology, Lund University, P.O. Box 124, 22100 Lund (Sweden); School of Civil and Environmental Engineering, Nanyang Technological University, Block N1, Nanyang Avenue, Singapore 639798 (Singapore)], E-mail: bjguieysse@ntu.edu.sg

    2009-04-30

    This study presents a method to regenerate molecularly imprinted polymers (MIPs) used for the selective removal of endocrine disrupting compounds from aqueous effluents. Regeneration was based on solvent extraction under UV irradiation to regenerate the polymer and the solvent while destroying the contaminants. Acetone was selected as the best solvent for irradiation of estrone (E1), 17{beta}-estradiol (E2) and ethinylestradiol (EE2) using either UVC (254 nm) or UV-vis. A MIP synthesized with E2 as template was then tested for the extraction of this compound from a 2 {mu}g/L loaded aqueous solution. E2 was recovered by 73 {+-} 11% and 46 {+-} 13% from the MIPs and a non-imprinted control polymer synthesized under the same conditions, respectively, after a single step elution with acetone. The irradiated polymers and acetone were reused for an additional extraction-regeneration cycle and showed no capacity decrease.

  1. Automatic Reading

    Institute of Scientific and Technical Information of China (English)

    胡迪

    2007-01-01

    <正>Reading is the key to school success and,like any skill,it takes practice.A child learns to walk by practising until he no longer has to think about how to put one foot in front of the other.The great athlete practises until he can play quickly,accurately and without thinking.Ed- ucators call it automaticity.

  2. 基于主动轮廓模型的肺纹理自动提取新方法%A Novel Automatic Extraction Method of Lung Texture Tree from HRCT Images

    Institute of Scientific and Technical Information of China (English)

    刘军伟; 冯焕清; 周颖玥; 李传富

    2009-01-01

    Computed tomography (CT) is the primary imaging modality for investigation of lung function and lung diseases. High resolution CT slice images of chest contain lots of texture information, which provides powerful datasets to research computer aid-diagnosis (CAD) system. But the extraction of lung tissue textures is a challenge task. In this paper, we introduce a novel method based on level set to extract lung tissue texture tree, which is automatic and effectual. Firstly, we propose an improved implicit active contour model driven by local binary fitting energy, and the parameters are dynamic and modulated by image gradient information. Secondly, a new technique of painting background based on intensity nonlinear mapping is brought forward to remove the influence of background during the evolution of single level set function. At last, a number of contrast experiments are performed, and the results of 3D surface reconstruction show our method is efficient and powerful for the segmentation of fine lung tree texture structures.

  3. 基于自适应图像分割自动提取道路中心线%The automatic road centerline extraction based on adaptive image segmentation

    Institute of Scientific and Technical Information of China (English)

    汤瑞华

    2015-01-01

    道路是城区地理空间信息中最重要的基础设施之一,从高分辨影像中自动、快速的提取道路特征,是快速更新城市道路网信息的重要途径。文中在分析道路基本特征的基础上,选择基于自适应结构元素的形态分析算法提取初始道路区域;引入面积和长宽比等形状指数,得到较精确的道路信息;最后,采用Hilditch细化算法,并进行优化处理。实验证明,该道路提取过程中无需人工设置参数,且能够得到具有较高完整性和正确性的道路中心线。%The road is one of the most important infrastructures in urban geospatial information .Automatic and fast road extraction from high resolution image is an important way of updating the urban road network fast .Thus a new automatic method is proposed to extract the road feature .First ,the adaptive structure element is adopted in the image segmentation .And then ,the precise road features can be extracted under the constrains of area and length‐breadth ratio (referred to as L/B) .Final ,the road line is obtained by using Hilditch algorithm and optimizing process .The experiments indicate that the road extraction without artificial set parameters in the process can get the centerline of the road with high completeness and correctness .

  4. 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.

  5. 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...

  6. Molecularly Imprinted Polymers for Selective Extraction of Crystal Violet from Natural Seawater coupled with High- Performance Liquid Chromatographic Determination

    Institute of Scientific and Technical Information of China (English)

    LIAN Ziru; WANG Jiangtao

    2014-01-01

    Molecularly imprinted polymers (MIPs) were prepared by the bulk polymerization using crystal violet as the template molecule, and the methacrylic acid and ethylene glycol dimetheacrylate as functional monomer and cross-linker, respectively. Sys-tematic investigations of synthetic conditions were conducted. The surface morphology and recognition mechanism of the obtained polymers were studied using scanning electron microscope and spectrophotometric analysis. MIPs showed high affinity to template molecule and were successfully applied as special solid-phase extraction sorbent for selective extraction of crystal violet from natural seawater. An off-line molecularly imprinted solid-phase extraction (MISPE) method followed by high-performance liquid chroma-tography with diodearray detection for the analysis of crystal violet was also established. MISPE columns have good recoveries for crystal violet standard solutions and good linearity was obtained over the concentration range of 0-200μg L-1 (R2>0.99). Finally, two natural seawater samples were investigated. The recoveries of spiked seawater on the MISPE columns were from 44.47% to 62.34%, the relative standard deviation (n=3) being in the range of 2.89%-5.96%.

  7. Comparing an ionic liquid to a molecular solvent in the cesium cation extraction by a calixarene: a molecular dynamics study of the aqueous interfaces.

    Science.gov (United States)

    Sieffert, Nicolas; Wipff, Georges

    2006-10-01

    We report a molecular dynamics (MD) study of the interfacial behavior of key partners involved in the Cs(+) cation extraction by a calix[4]arene-crown-6 host (L), comparing an ionic liquid (IL) to a classical molecular solvent (chloroform) as receiving "oil" phase. The IL is composed of hydrophobic 1-butyl-3-methylimidazolium cations (BMI(+)) and bis(trifluoromethylsulfonyl)imide anions (Tf(2)N(-)) and forms a biphasic system with water. The simulations reveal similarities but also interesting differences between the two types of interfaces. Much longer times are needed to "equilibrate" IL systems, compared to classical liquid mixtures, and there is more intersolvent mixing with the IL than with chloroform, especially concerning the water-in-oil content. There is also some excess of the BMI(+) cations over the Tf(2)N(-) anions in the aqueous phase. Simulations on the Na(+)NO(3)(-) and Cs(+)NO(3)(-) ions show that they sometimes interact at the interface with the IL ions, forming hydrated intimate ion pairs, whereas they are "repelled" by the classical interface. The LCs(+) complex and L ligand also behave differently, depending on the "oil phase". They are better solvated by the IL than by chloroform and thus poorly attracted at the IL interface, whereas they adsorb at the chloroform interface, adopting well-defined amphiphilic orientations. The results are discussed in the context of assisted ion transfer and provide a number of arguments explaining the specificity and efficiency of IL based, compared to classical extraction systems.

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

    OpenAIRE

    Gea Guerriero; Lauralie Mangeot-Peter; Jean-Francois Hausman; Sylvain Legay

    2016-01-01

    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 ...

  9. Separation and determination of citrinin in corn using HPLC fluorescence detection assisted by molecularly imprinted solid phase extraction clean-up

    Science.gov (United States)

    A liquid chromatography based method to detect citrinin in corn was developed using molecularly imprinted solid phase extraction (MISPE) sample clean-up. Molecularly imprinted polymers were synthesized using 1,4-dihydroxy-2-naphthoic acid as the template and an amine functional monomer. Density func...

  10. 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.

  11. Evaluation of molecular chaperons Hsp72 and neuropeptide Y as characteristic markers of adaptogenic activity of plant extracts.

    Science.gov (United States)

    Asea, Alexzander; Kaur, Punit; Panossian, Alexander; Wikman, Karl Georg

    2013-11-15

    We have previously demonstrated that ADAPT-232, a fixed combination of adaptogenic substances derived from Eleutherococcus senticosus root extract, Schisandra chinensis berry extract, Rhodiola rosea root extract stimulated the expression and release of neuropeptide Y (NPY) and molecular chaperone Hsp72 from isolated human neurolgia cells. Both of these mediators of stress response are known to play an important role in regulation of neuroendocrine system and immune response. We further demonstrated that ADAPT-232 induced release of Hsp70 is mediated by NPY, suggesting an existence of NPY-mediated pathway of activation of Hsp72 release into the blood circulation system. The objective of this study was to determine whether this pathway is common for adaptogens and whether NPY and/or Hsp72 can be considered as necessary specific biomarkers for adaptogenic activity. The release of NPY and Hsp72 from neuroglia cells in response to treatment with various plant extracts (n=23) including selected validated adaptogens, partly validated adaptogens, claimed but negligibly validated adaptogens and some other plant extracts affecting neuroendocrine and immune systems but never considered as adaptogens was measured using high throughput ELISA techniques. We demonstrated that adaptogens, e.g. R. rosea, S. chinensis and E. senticosus stimulate both NPY and Hsp70 release from neuroblastoma cells, while tonics and stimulants have no significant effect on NPY in this in vitro test. In the groups of partly validated adaptogens the effect of Panax ginseng and Withania somnifera was not statistically significant both on NPY and Hsp70 release, while the activating effect of Bryonia alba and Rhaponticum cartamoides was significant only on Hsp70. In contrast, all tested non-adaptogens, such as antiinflammatoty plant extracts Matricaria recutita, Pelargonium sidoides, Hedera helix and Vitis vinifera significantly inhibit Hsp70 release and have no influence on NPY release from neuroblastoma

  12. Molecularly imprinted pipette-tip solid phase extraction for selective determination of fluoroquinolones in human urine using HPLC-DAD.

    Science.gov (United States)

    de Oliveira, Hanna Leijoto; da Silva Anacleto, Sara; da Silva, Anny Talita Maria; Pereira, Arnaldo César; de Souza Borges, Warley; Figueiredo, Eduardo Costa; Borges, Keyller Bastos

    2016-10-15

    A simple method using HPLC-DAD was developed for the determination of fluoroquinolones in human urine including ciprofloxacin (CIPRO), enrofloxacino (ENRO), marbofloxacino (MARBO) and norfloxacin (NOR). In addition, it was studied the extraction of fluoroquinolones in human urine samples using pipette tip-based molecularly imprinted polymers solid phase extraction (PT-MIPs-SPE). With the goal of finding the best procedure for extraction of four fluoroquinolones in human urine, several parameters that are likely to affect the efficiency of extraction during sample preparation, including the washing solvent, type and volume of eluent, amount of material, the volume of the sample, pH and the ionic strength were systematically optimized. Chromatographic separations of fluoroquinolones were hit within 10min using a Synergi(®) C18 (250×4.6mm, 4μm) column and mobile phase consisting of water (10mM of phosphoric acid, the pH adjusted at 3.29 with triethylamine) : acetonitrile (85.7: 14.3, v/v) at a flow rate of 1.5mLmin(-1). Detection was performed at 290nm. The average extraction recoveries/standard deviation relative to ENRO, CIPRO, NOR and MARBO were 96.40±5.51%, 42.47±4.81%, 41.82±7.99% and 87.49±4.70, respectively. The method was liner from 39 to 1260ngmL(-1) for each fluoroquinolone with correlation coefficient of 0.9904, 0.9910, 0.9914 and 0.9919, to ENRO, CIPRO, NOR and MARBO, respectively. The assays of within-day and between-day precision and accuracy for all analytes were studied at three concentration levels and were lower than 15%. The method was successfully employed in a preliminary cumulative urinary excretion study after administration of CIPRO to a healthy volunteer.

  13. Synthesis of molecularly imprinted polymers for the application of selective clean-up vinblastine from Catharanthus roseus extract

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Molecularly imprinted polymers (MIPs) are synthetic tailor-made polymers with high selectivity towards a particular substance (template).An MIP using vinblastine (VLB) as the template molecule was synthesized and characterized.The presence of monomer-template complexes in a non-covalent way was confirmed by UV-vis spectrometry analysis.The polymerization was performed using methacrylic acid (MAA) as the functional monomer,ethylene glycol dimethacrylate (EGDMA) as the cross-linking agent,and toluene as the porogenic solvent by a thermo-polymerization method.The characterization of the obtained MIP was evaluated by scanning electron microscopy (SEM) and Brunauer-Emmett-Teller (BET) analysis.It was observed that the morphology of the MIP was more porous and rough,and the surface area had a significant increase compared with that of the non-imprinted polymer (NIP).This MIP was used as the sorbents of solid-phase extraction (SPE) to assess the selectivity of the MIP after optimization of the SPE protocol.VLB was specifically adsorbed on the MIP cartridge,while to vincristine (VCR),the chemical analog of VLB,almost no selective binding appeared.On the basis of the results,Catharanthus roseus extract was applied to the MIP cartridge for investigating its capability to extract VLB from the plant extract,and the capacity of the MIP cartridge was also evaluated.It was shown that the MIP could effectively enrich VLB from C.roseus extract and the recovery amounted to 93.8%.The solvents dissolving the samples had significant influence on the capacity of the MIP cartridge;it was 750 μg/g in toluene,625 μg/g in chloroform,and 250 μg/g in methanol.

  14. 移动车载激光点云的道路标线自动识别与提取%Automatic Road Marking Detection and Extraction Based on LiDAR Point Clouds from Vehicle- Borne MMS

    Institute of Scientific and Technical Information of China (English)

    邹晓亮; 缪剑; 郭锐增; 李星全; 赵桂华

    2012-01-01

    The research focuses on LiDAR point clouds of road surface acquired from vehicle - borne mobile mapping system - Land- Mark. An automatic road marking detection and extraction method is proposed. Combining LiDAR features of retro, angle and distance with the properties of traffic marking, point clouds of road marking is extracted. The road marking is best fitted in a least squares poly- nomial fitting method and CAD map is generated for automatic detection. Based on the experimental data from Sick laser scanner mounted on LandMark system, the experimental results show the method is feasible and available.%对移动车载激光测量LandMark系统获取的路面激光点云数据进行研究,结合激光点云的回波反射率、扫描角,以及量测距离等特征信息与道路标线的属性信息,提出了一种基于车载激光点云的道路标线自动识别与提取算法。从点云中提取道路标线,采用最小二乘线性最优拟合算法对提取的标线点云进行拟合,生成道路标线的CAD轮廓线,实现道路标线的自动化识别。以移动车载LandMark系统的Sick激光扫描仪获取的路面激光点云为例进行实验,实验结果表明该方法的可行性和有效性。

  15. Automatic generation of time resolved motion vector fields of coronary arteries and 4D surface extraction using rotational x-ray angiography

    Science.gov (United States)

    Jandt, Uwe; Schäfer, Dirk; Grass, Michael; Rasche, Volker

    2009-01-01

    Rotational coronary angiography provides a multitude of x-ray projections of the contrast agent enhanced coronary arteries along a given trajectory with parallel ECG recording. These data can be used to derive motion information of the coronary arteries including vessel displacement and pulsation. In this paper, a fully automated algorithm to generate 4D motion vector fields for coronary arteries from multi-phase 3D centerline data is presented. The algorithm computes similarity measures of centerline segments at different cardiac phases and defines corresponding centerline segments as those with highest similarity. In order to achieve an excellent matching accuracy, an increasing number of bifurcations is included as reference points in an iterative manner. Based on the motion data, time-dependent vessel surface extraction is performed on the projections without the need of prior reconstruction. The algorithm accuracy is evaluated quantitatively on phantom data. The magnitude of longitudinal errors (parallel to the centerline) reaches approx. 0.50 mm and is thus more than twice as large as the transversal 3D extraction errors of the underlying multi-phase 3D centerline data. It is shown that the algorithm can extract asymmetric stenoses accurately. The feasibility on clinical data is demonstrated on five different cases. The ability of the algorithm to extract time-dependent surface data, e.g. for quantification of pulsating stenosis is demonstrated.

  16. Automatic generation of time resolved motion vector fields of coronary arteries and 4D surface extraction using rotational x-ray angiography

    Energy Technology Data Exchange (ETDEWEB)

    Jandt, Uwe; Schaefer, Dirk; Grass, Michael [Philips Research Europe-Hamburg, Roentgenstr. 24, 22335 Hamburg (Germany); Rasche, Volker [University of Ulm, Department of Internal Medicine II, Robert-Koch-Strasse 8, 89081 Ulm (Germany)], E-mail: ujandt@gmx.de

    2009-01-07

    Rotational coronary angiography provides a multitude of x-ray projections of the contrast agent enhanced coronary arteries along a given trajectory with parallel ECG recording. These data can be used to derive motion information of the coronary arteries including vessel displacement and pulsation. In this paper, a fully automated algorithm to generate 4D motion vector fields for coronary arteries from multi-phase 3D centerline data is presented. The algorithm computes similarity measures of centerline segments at different cardiac phases and defines corresponding centerline segments as those with highest similarity. In order to achieve an excellent matching accuracy, an increasing number of bifurcations is included as reference points in an iterative manner. Based on the motion data, time-dependent vessel surface extraction is performed on the projections without the need of prior reconstruction. The algorithm accuracy is evaluated quantitatively on phantom data. The magnitude of longitudinal errors (parallel to the centerline) reaches approx. 0.50 mm and is thus more than twice as large as the transversal 3D extraction errors of the underlying multi-phase 3D centerline data. It is shown that the algorithm can extract asymmetric stenoses accurately. The feasibility on clinical data is demonstrated on five different cases. The ability of the algorithm to extract time-dependent surface data, e.g. for quantification of pulsating stenosis is demonstrated.

  17. 面向导航型网页关键词自动抽取的视觉模型与算法%Visual representation model and automatic keywords extraction algorithm for hub Web pages

    Institute of Scientific and Technical Information of China (English)

    彭浩; 蔡美玲; 陈继锋; 刘炽; 余炳锐

    2012-01-01

    导航型网页中往往包含了大量的噪声信息,为自动提取网页中的关键词带来了较大的困难.为此,提出一个新的网页表示模型PIX-PAGE和导航型网页关键词自动抽取算法P-KEA.PIX-PAGE模型利用提出的区域合并算法,将一张网页分割为适当粒度的区域;然后,依据人类视觉特点,对各区域进行视觉“奇异性”量化,同时利用奇异性传递规则进一步强化关键词相关区域的视觉“奇异性”.P-KEA根据PIX-PAGE模型模型的视觉量化结果,能够较准确地找到视觉突出区域中的关键词.实验结果表明,与基于DocView模型的算法DVM相比,P-KEA的准确率平均提高了20.9%.%It is very hard to exactly extract keywords from hub Web pages because of its topic noise. To resolve this problem, a new sub Web page representation model and its automatic keywords extraction algorithm were proposed in this paper. At first, the new model segmented Web page into some blocks by using the block composition algorithm. Secondly, according to the visual recognition method of humanity, the new model computed the visual measurement of these blocks. At the same time, the transmission rule of visual measurement made blocks special where keywords were contained more specially. The automatic keywords extraction algorithm could exactly fmd these keywords in the most special hlocks. The experimental results show that the proposed algorithm has bumped up by 20. 9% on average in accuracy compared with keywords extraction algorithm based on DocView model.

  18. 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.

  19. Abbreviation definition identification based on automatic precision estimates

    OpenAIRE

    Kim Won; Comeau Donald C; Sohn Sunghwan; Wilbur W John

    2008-01-01

    Abstract Background The rapid growth of biomedical literature presents challenges for automatic text processing, and one of the challenges is abbreviation identification. The presence of unrecognized abbreviations in text hinders indexing algorithms and adversely affects information retrieval and extraction. Automatic abbreviation definition identification can help resolve these issues. However, abbreviations and their definitions identified by an automatic process are of uncertain validity. ...

  20. Selective mixed-bed solid phase extraction of atrazine herbicide from environmental water samples using molecularly imprinted polymer.

    Science.gov (United States)

    Zarejousheghani, Mashaalah; Fiedler, Petra; Möder, Monika; Borsdorf, Helko

    2014-11-01

    A novel approach for the selective extraction of organic target compounds from water samples has been developed using a mixed-bed solid phase extraction (mixed-bed SPE) technique. The molecularly imprinted polymer (MIP) particles are embedded in a network of silica gel to form a stable uniform porous bed. The capabilities of this method are demonstrated using atrazine as a model compound. In comparison to conventional molecularly imprinted-solid phase extraction (MISPE), the proposed mixed-bed MISPE method in combination with gas chromatography-mass spectrometry (GC-MS) analysis enables more reproducible and efficient extraction performance. After optimization of operational parameters (polymerization conditions, bed matrix ingredients, polymer to silica gel ratio, pH of the sample solution, breakthrough volume plus washing and elution conditions), improved LODs (1.34 µg L(-1) in comparison to 2.25 µg L(-1) obtained using MISPE) and limits of quantification (4.5 µg L(-1) for mixed-bed MISPE and 7.5 µg L(-1) for MISPE) were observed for the analysis of atrazine. Furthermore, the relative standard deviations (RSDs) for atrazine at concentrations between 5 and 200 µg L(-1) ranged between 1.8% and 6.3% compared to MISPE (3.5-12.1%). Additionally, the column-to-column reproducibility for the mixed-bed MISPE was significantly improved to 16.1%, compared with 53% that was observed for MISPE. Due to the reduced bed-mass sorbent and at optimized conditions, the total amount of organic solvents required for conditioning, washing and elution steps reduced from more than 25 mL for conventional MISPE to less than 2 mL for mixed-bed MISPE. Besides reduced organic solvent consumption, total sample preparation time of the mixed-bed MISPE method relative to the conventional MISPE was reduced from more than 20 min to less than 10 min. The amount of organic solvent required for complete elution diminished from 3 mL (conventional MISPE) to less than 0.4 mL with the mixed

  1. 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.

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

    Science.gov (United States)

    Díaz-Bao, Mónica; Barreiro, Rocío; Miranda, José Manuel; Cepeda, Alberto; Regal, Patricia

    2015-01-01

    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. PMID:25785233

  3. Molecularly imprinted polymer for the selective extraction of luteolin from Chrysanthemum morifolium Ramat.

    Science.gov (United States)

    Gao, Die; Yang, Fengqing; Xia, Zhining; Zhang, Qihui

    2016-08-01

    In this work, luteolin-imprinted polymers were prepared by noncovalent precipitation polymerization for the first time. Their structural features and morphologies were analyzed by using Fourier transform infrared spectroscopy and scanning electron microscopy, respectively. The adsorption experiments revealed that the luteolin-imprinted polymers presented high selective recognition property to luteolin. The selectivity experiment showed that the adsorption capacity and selectivity of polymers to luteolin was higher than that of three structural analogs, including quercetin, isorhamnetin, and ombuin. Furthermore, an efficient method based on luteolin-imprinted polymers coupled with solid-phase extraction was developed for the pretreatment of luteolin from Chrysanthemum morifolium Ramat. The results demonstrated that the luteolin-imprinted polymers coupled with solid phase extraction method was proven to be a potentially competitive technique for the separation and enrichment of luteolin in complex samples such as Chinese patent medicines and biological samples. PMID:27288270

  4. French Maritime Pine Bark Extract (Pycnogenol®) Effects on Human Skin: Clinical and Molecular Evidence.

    Science.gov (United States)

    Grether-Beck, Susanne; Marini, Alessandra; Jaenicke, Thomas; Krutmann, Jean

    2016-01-01

    Nutritional strategies to benefit skin health are of growing importance. Current approaches mainly involve nutritional supplements containing antioxidants which were initially designed to protect human skin against ultraviolet radiation-induced damage. Within recent years, however, a growing number of studies suggests that the beneficial effects of these products clearly extend beyond photoprotection. In this review we take the nutritional supplement Pycnogenol®, which is based on an extract prepared from French marine pine bark extract, as an example to illustrate this development. Accordingly, the existing data provide compelling evidence that Pycnogenol® intake does not only provide photoprotection, but may be used to (i) reduce hyperpigmentation of human skin and (ii) improve skin barrier function and extracellular matrix homeostasis. PMID:26492562

  5. Molecular design of Calix[4]arene derivatives for uranyl ion extraction from aqueous media

    International Nuclear Information System (INIS)

    Uranyl ion extraction is an important part of nuclear waste reprocessing. Use of organic ligands having chelating property with uranyl ions is a promising tool in this area, because of the possibility to improve the selectivity and the affinity of the ligands towards uranyl ions. In this study, Calix[4]arene derivatives containing B, Al, C, Si, N, P, O and S elements in bridging positions were designed and their chelating energetics with uranyl cation are calculated by means of DFT methods.

  6. 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.

  7. 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.

  8. 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)

    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

  9. 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

    Sequential injection microcolumn extraction (SI-MCE) based on the implementation of a soil containing microcartridge as external reactor in a sequential injection network is, for the first time, proposed for dynamic fractionation of macronutrients in environmental solids, as exemplified by the pa......Sequential injection microcolumn extraction (SI-MCE) based on the implementation of a soil containing microcartridge as external reactor in a sequential injection network is, for the first time, proposed for dynamic fractionation of macronutrients in environmental solids, as exemplified...... by the partitioning of inorganic phosphorous in agricultural soils. The on-line fractionation method capitalises on the accurate metering and sequential exposure of the various extractants to the solid sample by application of programmable flow as precisely coordinated by a syringe pump. Three different soil phase...... 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...

  10. How molecular motors extract order from chaos (a key issues review)

    Science.gov (United States)

    Hoffmann, Peter M.

    2016-03-01

    Molecular motors are the workhorses of living cells. Seemingly by ‘magic’, these molecules are able to complete purposeful tasks while being immersed in a sea of thermal chaos. Here, we review the current understanding of how these machines work, present simple models based on thermal ratchets, discuss implications for statistical physics, and provide an overview of ongoing research in this important and fascinating field of study.

  11. How molecular motors extract order from chaos (a key issues review).

    Science.gov (United States)

    Hoffmann, Peter M

    2016-03-01

    Molecular motors are the workhorses of living cells. Seemingly by 'magic', these molecules are able to complete purposeful tasks while being immersed in a sea of thermal chaos. Here, we review the current understanding of how these machines work, present simple models based on thermal ratchets, discuss implications for statistical physics, and provide an overview of ongoing research in this important and fascinating field of study. PMID:26863000

  12. Aqueous two phase extraction of proteins: From molecular understanding to process development

    OpenAIRE

    Oelmeier, Stefan A

    2012-01-01

    A high throughput screening method was implemented and applied to an industrial separation task. Previously reported correlations between protein descriptors and distribution were evaluated. A new approach to screen ATPS for their industrial application was devised and put to use for the selection of ATPSs used in centrifugal partitioning chromatography. A new modeling approach based on molecular dynamics was set up. This approach was validated using single PEG molecules in solution.

  13. 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

  14. 基于厦门岛的海岸线自动提取方法研究%The Method of Coastline Automatic Extraction in Xiamen Island

    Institute of Scientific and Technical Information of China (English)

    齐宇; 任航科

    2012-01-01

    应用遥感的方法监测海岸线变化、提取海岸线、进行景观分析具有范围广、精度高、可动态监测的特点。提取海岸线由于海岸带类型的不同,选取的提取方法不同,会得出不同的结果。本文以厦门岛海岸线为例,使用TM和遥感影像,利用两种提取海岸线方法,得到计算机自动提取的两种海岸线位置,并通过实地调查确认海岸类型和叠加高空间分辨率的SPOT影像进行精度分析。探讨了根据不同海岸带类型,如何选取海岸线自动提取方法的问题。%In terms of supervising the change of coastline, extracting the coastline, and analyzing the landscape, re- mote sensing has many advantages: it is wider, more precise and dynamic. Owing to different types of coastal zone and different extracting methods,the results of coastline auto-extraction may differ significantly. Taking the coastal zone a- round Xiamen island as an example, this paper uses TM image and two different methods of computer coastline auto-ex- traction to extract its coastline,which are of two types: sandy-beach and artificial beach coasts. Based on the result of field research around the Xiamen island, the paper also precisely analyzes the result of the fusion with its high spatial res- olution SPOT image. Finally, the paper discusses how to select the methods of computer coastline auto-extraction subject to different coastal zones

  15. 一种新型自动深冷及活化分子筛的吸附泵设计%Design of a new adsorption pump with cryogenically refrigerated and automatically activated molecular sieve

    Institute of Scientific and Technical Information of China (English)

    邓云伟; 李军格; 杜卫星

    2012-01-01

    设计实现了一种新型自动深冷及活化分子筛的吸附泵.进行了吸附能力设计,采用基于PLC(可编程逻辑控制器)软硬件为核心的电气系统,方便地实现了对分子筛吸附泵的液氮自动输送以维持液氮量及分子筛活化的远程控制,有利于操作者操作和安全保障.验证实验结果表明,该分子筛吸附泵能快速吸附泄漏到密封容器里的有害气体,且吸附效果良好.%A new adsorption pump was designed and manufactured by applying the design technique of adsorption ability of molecular sieve. The hardware and software of the PLC (programmable logic controller) were used as the kernel of the electric system, which was applied to refrigerate cryogenically the molecular sieve by supplying and automatic -maintaining of the volume of the liquid nitrogen and activate the molecular sieve by heating the heater in the pump. The electric system made the pump operation easier and safer for operators. Further experiments demonstrated effectively rapid adsorption ability of the molecular sieve pump to deleterious gas leaked into the sealed box.

  16. Quenching of singlet molecular oxygen by Commiphora myrrha extracts and menthofuran.

    Science.gov (United States)

    Racine, P; Auffray, B

    2005-06-01

    The quenching activity against singlet oxygen, an actor of lipid peroxidation and DNA degradation, of the essential oil and resinoid of Commiphora myrrha from Somalia has been studied and compared to DL-alpha-tocopherol using 1,3-diphenylisobenzofuran (DPBF) as a probe. To insure that the furan ring was the site of the reaction, experiments were conducted with menthofuran. The essential oil and menthofuran show a higher activity than DL-alpha-tocopherol, suggesting their potential usefulness to neutralise this deleterious form of molecular oxygen.

  17. Relationship of molecular weight distribution profile of unreduced gluten protein extracts with quality characteristics of bread.

    Science.gov (United States)

    Chaudhary, Nisha; Dangi, Priya; Khatkar, B S

    2016-11-01

    A statistical correlation was established among the molecular weight distribution patterns of unreduced gluten proteins and physicochemical, rheological and bread-making quality characteristics of wheat varieties. Size exclusion chromatography fractionated the gluten proteins apparently into five peaks. Peak I signified glutenins (30-130kDa), peak II as gliadins (20-55kDa), peak III as very low molecular weight monomeric gliadins (10-28kDa), peak IV and V, collectively, as albumins and globulins (gluten index (r=0.959(∗∗)), and gliadin/glutenin ratio (r=-0.952(∗∗)), while peak II influenced inversely as expected. Peak I exhibited positive statistical significance with bread loaf volume (r=0.848(∗∗)); however, peak II had negative (r=-0.818(∗∗)) impact. Bread firmness increased with increment in peak II (r=0.625(∗∗)), and decreased with accretion in peak I (r=-0.623(∗∗)). PMID:27211654

  18. Analysis of testosterone in human urine using molecularly imprinted solid-phase extraction and corona discharge ion mobility spectrometry.

    Science.gov (United States)

    Mirmahdieh, Shiva; Mardihallaj, Azam; Hashemian, Zahra; Razavizadeh, Jalal; Ghaziaskar, Hassan; Khayamian, Taghi

    2011-01-01

    Analysis of testosterone was accomplished using corona discharge ion mobility spectrometry. Molecular imprinted polymer was used for the extraction and pre-concentration of testosterone. Analytical parameters including precision, dynamic range and detection limit were obtained. The linear dynamic range was from 10 to 250 ng/mL and the limit of detection was 0.9 ng/mL. The proposed method was used for analysis of testosterone in urine samples. A urine sample from a 3-year-old girl was used as the blank. The RSD was below 10%. The obtained results from the method were also compared with the standard method for analysis of testosterone using SPE-HPLC analysis. The results demonstrate the accuracy of the method. PMID:21171183

  19. New Advance of Studies on Molecularly Imprinted Solid-phase Extraction%分子印迹固相萃取技术研究新进展

    Institute of Scientific and Technical Information of China (English)

    刘祺文; 熊远福; 王锦; 文祝友; 熊海蓉; 胡红远

    2015-01-01

    随着人们对环境污染和食品安全的关注,分子印迹固相萃取技术在各领域的应用有了进一步发展.在介绍分子印迹固相萃取技术的基础上,对近年来分子印迹固相萃取技术在环境样品中农药残留的检测,食品及饲料中药物残留的检测,功能药物成分提纯及药物检测,水土环境中的其它污染物检测等4大方面的研究现状进行了综述. 同时,指出了分子印迹固相萃取技术目前存在的问题,探讨了分子印迹固相萃取技术未来的发展方向.%With attention to environmental pollution and food safety, molecular imprinted solid phase extraction technique in various fields has been further developed. Therefore, molecular imprinted solid phase extraction were briefly described in this article. Molecular imprinted solid phase extraction enrichment and detection of pesticide residues, drug residues in food and feed, other contaminants in water and soil, and also molecular imprinted solid phase extraction of drug testing and purification of functional pharmaceutical ingredient in recent years were reviewed. In this paper, the problem molecular imprinted solid phase extraction technique encountered in recent years was analyzed, and the trend of molecular imprinted solid phase extraction technique was also discussed.

  20. 分子印迹固相萃取技术研究新进展%New Advance of Studies on Molecularly Imprinted Solid-phase Extraction

    Institute of Scientific and Technical Information of China (English)

    刘祺文; 熊远福; 王锦; 文祝友; 熊海蓉; 胡红远

    2015-01-01

    With attention to environmental pollution and food safety, molecular imprinted solid phase extraction technique in various fields has been further developed. Therefore, molecular imprinted solid phase extraction were briefly described in this article. Molecular imprinted solid phase extraction enrichment and detection of pesticide residues, drug residues in food and feed, other contaminants in water and soil, and also molecular imprinted solid phase extraction of drug testing and purification of functional pharmaceutical ingredient in recent years were reviewed. In this paper, the problem molecular imprinted solid phase extraction technique encountered in recent years was analyzed, and the trend of molecular imprinted solid phase extraction technique was also discussed.%随着人们对环境污染和食品安全的关注,分子印迹固相萃取技术在各领域的应用有了进一步发展.在介绍分子印迹固相萃取技术的基础上,对近年来分子印迹固相萃取技术在环境样品中农药残留的检测,食品及饲料中药物残留的检测,功能药物成分提纯及药物检测,水土环境中的其它污染物检测等4大方面的研究现状进行了综述. 同时,指出了分子印迹固相萃取技术目前存在的问题,探讨了分子印迹固相萃取技术未来的发展方向.

  1. 采用CRF技术的军事情报术语自动抽取研究%Research on automatic military intelligence term extraction using CRF model

    Institute of Scientific and Technical Information of China (English)

    贾美英; 杨炳儒; 郑德权; 杨靖

    2009-01-01

    针对军事情报领域,提出了一种基于条件随机场的术语抽取方法,该方法将领域术语抽取看作一个序列标注问题,将领域术语分布的特征量化作为训练的特征.利用CRF工具包训练出一个领域术语特征模板,然后利用该模板进行领域术语抽取.实验采用的训练语料来自"搜狐网络军事频道"的新闻数据,测试语料选取杂志2007年第1-8期的所有文章.实验取得了良好的结果,准确率为73.24%,召回率为69.57%,F-测度为71.36%,表明该方法简单易行,且具有领域通用性.%This paper introduces a Conditional Random Fields(CRF) based method for term extraction,which intends to be used in military intelligent process.This method takes the field term extraction as an issue of sequence marking,quantitates the characters of field term distribution and takes it as the training chaxacters,leverages the CRF toolkit to generate a field term character template and uses the template for field term extraction.In the experiment,the materials for training are the news data from the military channel of Sohu Networks,the materials for testing axe all of the articles from magazine of Modern Military 2007,issues 1 to 8.The experimental result is positive with precision rate of 73.24%,recall rate of 69.75%,and F-measure of 71.36%.h turns out that this method is simple and feasible,and can be used on other fields.

  2. 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.

  3. Molecular Mechanisms by Which a Fucus vesiculosus Extract Mediates Cell Cycle Inhibition and Cell Death in Pancreatic Cancer Cells

    Directory of Open Access Journals (Sweden)

    Ulf Geisen

    2015-07-01

    Full Text Available Pancreatic cancer is one of the most aggressive cancer entities, with an extremely poor 5-year survival rate. Therefore, novel therapeutic agents with specific modes of action are urgently needed. Marine organisms represent a promising source to identify new pharmacologically active substances. Secondary metabolites derived from marine algae are of particular interest. The present work describes cellular and molecular mechanisms induced by an HPLC-fractionated, hydrophilic extract derived from the Baltic brown seaweed Fucus vesiculosus (Fv1. Treatment with Fv1 resulted in a strong inhibition of viability in various pancreatic cancer cell lines. This extract inhibited the cell cycle of proliferating cells due to the up-regulation of cell cycle inhibitors, shown on the mRNA (microarray data and protein level. As a result, cells were dying in a caspase-independent manner. Experiments with non-dividing cells showed that proliferation is a prerequisite for the effectiveness of Fv1. Importantly, Fv1 showed low cytotoxic activity against non-malignant resting T cells and terminally differentiated cells like erythrocytes. Interestingly, accelerated killing effects were observed in combination with inhibitors of autophagy. Our in vitro data suggest that Fv1 may represent a promising new agent that deserves further development towards clinical application.

  4. Molecularly imprinted polymers combination with deep eutectic solvents for solid-phase extraction of caffeic acid from hawthorn.

    Science.gov (United States)

    Li, Guizhen; Tang, Weiyang; Cao, Weimin; Wang, Qian; Zhu, Tao

    2015-08-01

    Molecularly imprinted polymers (MIPs) with caffeic acid as template and non-imprinted polymers (NIPs) materials were prepared in the same procedure. Field emission scanning electron microscopy (FE-SEM) and adsorption capacity test were used to evaluate characteristic of the new materials. MIPs, NIPs and C18 were used for rapid purification of caffeic acid from hawthorn with solid-phase extraction ( SPE) , and extract yields of caffeic acid with the proposed materials were 3.46 µg/g, 1.01 µg/g and 1.17 µg/g, respectively. To optimize the MIPs-SPE procedures, different kinds of elution solutions were studied. Deep eutectic solvents (DESs) were prepared by choline chloride (ChCl)-glycerol (1/2, n/n) and choline chloride-urea (1/ 2, n/n). Methanol was mixed with the two kinds of DESs (glycerol-based DESs, urea-based DESs) in different ratios (0.5:1, 1:1, 2:1, 3:1, 4:1, 5:1, v/v), and they were used to investigated as elution solutions in the above MIPs-SPE procedures. The results showed that MIPs were potential SPE materials, and methanol/ glycerol-based DESs (3 :1, v/v) had the best elution capability with the recovery of 82.32%. PMID:26749853

  5. Automatic extracting topic page links from Hub page%中心网页中主题网页链接的自动抽取

    Institute of Scientific and Technical Information of China (English)

    夏天

    2012-01-01

    基于扩展标记树,提出了一种从中心网页中自动抽取主题网页链接的方法。首先构建链接有序表,利用链接前缀树发现主题网页链接拒绝规则,实现对网页链接类型的预判定;其次,通过分组分割和相似分组重新合并,把页面中的链接归入到不同分组之中,进而识别分组的类型和核心区域所在的分组,最终把链接归入三类链接集合之中。实验结果表明该方法无需训练即可实现中心网页中主题网页链接的高精度抽取。%A topic link extraction method from Hub page based on extended label tree was proposed.Firs,a topic link sorted list was build and deny rules were learned by prefix tree,then,the link type was pre-determined.Second,by group splitting and re-merging,each candidate link was classified into different groups.The group type and the group which represented the hub page's core region were identified,and finally all links were put into three different collections.Experimental results show that this method can achieve high-precision for topic link extraction without training.

  6. Preparation, characterization and usage of molecularly imprinted polymer for the isolation of quercetin from hydrolyzed nettle extract.

    Science.gov (United States)

    Karaman Ersoy, Şeyda; Tütem, Esma; Sözgen Başkan, Kevser; Apak, Reşat; Nergiz, Cevdet

    2016-04-01

    Quercetin (3,3',4',5,7-pentahydroxyflavone, QC) is a health-beneficial flavonoid, widely occurring in leaves, fruits, and flowers of various plants. In this work aiming isolation, purification and pre-concentration of QC, QC imprinted polymers (QC-MIPs) in different molar ratios {template:monomer:cross-linker (1:4:20, 1:5:30, 1:8:40, 1:10:50)} were prepared thermally through bulk polymerization by using QC as the template molecule, 4-vinylpyridine (4-VP), methacrylic acid (MAA), acrylamide (AA) as the functional monomers, ethylene glycol dimethacrylate (EDMA) as the cross-linker and 2,2'-azobisisobutyronitrile (AIBN) as initiator in the porogens of acetone and tetrahydrofuran. Their recognition and selectivity properties were investigated in solutions containing QC and other similar-structure phenolics by equilibrium binding experiments using different proportions of acetonitrile (ACN)-dimethylsulfoxide (DMSO) mixtures and methanol (MeOH) as solvents. The MIP with 1:4:20 molar ratio of QC:4-VP:EDMA was established as the most suitable for recognition of QC. Sorption parameters of the MIP and the NIP (non-imprinted polymer) were calculated by using Freundlich and Langmuir isotherms with QC solutions in ACN:DMSO (98:2, v/v). The mentioned MIP was found to be highly selective for quercetin over other phenolic compounds (rutin, catechin, etc.). Thus, molecularly imprinted solid-phase extraction (MISPE) procedures were applied for selective pre-concentration and purification of QC from synthetic mixtures of phenolic compounds and nettle extract, known as a source of official and folk medicine. The results demonstrated the possibility of direct extraction of certain pharmacophoric constituents such as QC and QC derivatives from nettle by MIP separation. PMID:26953839

  7. Extracting Farmland Shelterbelt Automatically Based on ZY-3 Remote Sensing Images%基于ZY-3影像的农田防护林自动提取

    Institute of Scientific and Technical Information of China (English)

    幸泽峰; 李颖; 邓荣鑫; 朱红雷; 付波霖

    2016-01-01

    理提供技术支持。%Objective] This paper was to explore a high precision automatic extraction method of farmland shelterbelt in northeast China based on analyzing its spectral and spatial geometric characteristics. And the results will provide basic data support for a wide range of farmland shelterbelt extraction and remote sensing monitoring.[Method]In this paper, part zones of Dehui City and Nong’an County of Jilin Province were took as the study area. We analyzed the vegetation index and spatial geometric features of the farmland shelterbelt based on ZY-3 multi-spectral image. The residential boundary was extracted from Landsat8 OLI data. Then we put forward using the object-oriented method to deal with binary image data. The vector results of farmland shelterbelt were extracted in combination with the mathematical morphology and the GIS technology.[Result]The total length of farmland shelterbelt is 304. 46 km within the 50 km × 50 km study area. The correct extraction of farmland shelterbelt is 286. 42 km,the excess extraction of 18. 05 km and missing extraction is 14. 19 km. In this study,we used the region verification,filed verification and high resolution images verification based on existing outcome data,filed observation data,GeoEye image and ZY-3 image. As for reqion verification,the extraction accuracy is 89. 89%,the redundancy error is 5. 66% and the missing error is 4. 45%. All 22 belts collected in field were extracted correctly and the extraction accuracy of length is 93. 93%.[Conclusion]The ratio vegetation index( RVI) is better than the normalized difference vegetation index( NDVI) when extracting the farmland shelterbelts in high vegetation coverage. Mathematical morphology method and object-oriented method have their unique advantages in processing linear characteristic features which has a certain gap,especially for the farmland shelterbelt. It should be given full consideration to the phenology information,spectral information and spatial geometry information of farmland

  8. Molecular mechanisms underlying the cholesterol-lowering effect of Ginkgo biloba extract in hepatocytes: a comparative study with Iovastatin

    Institute of Scientific and Technical Information of China (English)

    Zuo-quan XIE; Gai LIANG; Lu ZHANG; Qi WANG; Yi QU; Yang GAO; Li-bo LIN; Sai YE; Ji ZHANG; Hui WANG; Guo-ping ZHAO; Qing-hua ZHANG

    2009-01-01

    Aim: To explore the molecular mechanisms underlying the cholesterol-lowering effect of a Ginkgo biloba extract (GBE). Methods: Enzyme activity, cholesterol flux and changes in gene expression levels were assessed in cultured hepatocytes treated with GBE or Iovastatin. Results: GBE decreased the total cholesterol content in cultured hepatocytes and inhibited the activity of HMG-CoA reductase, as determined by an in vitro enzyme activity assay. In addition, GBE decreased cholesterol influx, whereas Iovastatin increased choles-terol influx. GBE treatment induced significant increases in the expression of cholesterogenic genes and genes involved in cholesterol metabolism, such as SREBF2, as determined by cDNA microarray and real-time RT-PCR. Furthermore, INSIG2, LDLR, LRP1, and LRP10 were differentially regulated by GBE and Iovastatin. The data imply that the two compounds modulate cholesterol metabolism through distinct mechanisms. Conclusion: By using a gene expression profiling approach, we were able to broaden the understanding of the molecular mechanisms by which GBE lowers cellular cholesterol levels. Specifically, we demonstrated that GBE exhibited dual effects on the cellular choles-terol pool by modulating both HMG-CoA reductase activity and inhibiting cholesterol influx.

  9. 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.

  10. Research on Automatic Extraction of Web Sentiment Words%网络情感词自动识别方法研究

    Institute of Scientific and Technical Information of China (English)

    张清亮; 徐健

    2011-01-01

    To improve the efficiency of extracting sentiment words and building sentiment lexicon, the authors propose a method to extract a set of basic sentiment words, and then to calculate both the PMI - IR value between candidate word and the positive basic sentiment word set and the PMI - IR value between candidate words and the negative basic sentiment word set, to judge the orientation of a candidate word. Taking account of frequency, orientation, intensity and definiteness of words, computers are able to finish most of the work. It improves the efficiency and reduces cost of building sentiment lexicon. Experiment is processed on the dataset constituted with 71 061 reviews from 360buy and 1 736 reviews from Joyo. With the dataset, the method achieves a recall rate of 76. 36% , a precision of 76.94% ,and the precision of sentiment orientation is 62.70%.%针对情感词识别及情感词库构建效率不高的问题,提出一种自动提取基准情感词集的方法,从词频、词的领域性情感倾向和词的情感强度三方面进行基准词筛选,再凭借目标词与正、负基准词集的不同语义相似度进行情感词的识别和情感倾向的判断,使机器能够自动完成大部分工作,提高效率,降低构建不同领域情感词库的成本。以京东商城71061条评论和卓越网1736条评论为数据集进行实验,获得的召回率为76.36%,准确率为76.94%,情感倾向判断的准确率为62.70%。

  11. High-capacity magnetic hollow porous molecularly imprinted polymers for specific extraction of protocatechuic acid.

    Science.gov (United States)

    Li, Hui; Hu, Xin; Zhang, Yuping; Shi, Shuyun; Jiang, Xinyu; Chen, Xiaoqin

    2015-07-24

    Magnetic hollow porous molecularly imprinted polymers (HPMIPs) with high binding capacity, fast mass transfer, and easy magnetic separation have been fabricated for the first time. In this method, HPMIPs was firstly synthesized using protocatechuic acid (PCA) as template, 4-vinylpyridine (4-VP) as functional monomer, glycidilmethacrylate (GMA) as co-monomer, and MCM-48 as sacrificial support. After that, epoxide ring of GMA was opened for chemisorbing Fe3O4 nanoparticles to prepare magnetic HPMIPs. The results of characterization indicated that magnetic HPMIPs exhibited large surface area (548m(2)/g) with hollow porous structure and magnetic sensitivity (magnetic saturation at 2.9emu/g). The following adsorption characteristics investigation exhibited surprisingly higher adsorption capacity (37.7mg/g), and faster kinetic binding (25min) than any previously reported PCA imprinted MIPs by traditional or surface imprinting technology. The equilibrium data fitted well to Langmuir equation and the adsorption process could be described by pseudo-second order model. The selective recognition experiments also demonstrated the high selectivity of magnetic HPMIPs towards PCA over analogues. The results of the real sample analysis confirmed the superiority of the proposed magnetic HPMIPs for selective and efficient enrichment of trace PCA from complex matrices. PMID:26044378

  12. Hypoglycemic effect of Octomeles sumatrana aqueous extract in streptozotocin-induced diabetic rats and its molecular mechanisms

    Institute of Scientific and Technical Information of China (English)

    Mohd Aidil Azahar; Ghanya Al-Naqeb; Mizaton Hasan; Aishah Adam

    2012-01-01

    Objective:To investigate the hypoglycemic effect of the aqueous extract of Octomeles sumatrana (O. sumatrana) (OS) in streptozotocin-induced diabetic rats (STZ) and its molecular mechanisms. Methods: Diabetes was induced by intraperitoneal (i.p.) injection of streptozotocin (55 mg/kg) in to male Sprague-Dawley rats. Rats were divided into six different groups;normal control rats were not induced with STZ and served as reference, STZ diabetic control rats were given normal saline. Three groups were treated with OS aqueous extract at 0.2, 0.3 and 0.5 g/kg, orally twice daily continuously for 21 d. The fifth group was treated with glibenclamide (6 mg/kg) in aqueous solution orally continuously for 21 d. After completion of the treatment period, biochemical parameters and expression levels of glucose transporter 2 (Slc2a2), glucose-6-phosphatase (G6Pase) and phosphoenolpyruvate carboxykinase (PCK1) were determined in liver by quantitative real time PCR. Results: Administration of OS at different doses to STZ induced diabetic rats, resulted in significant decrease (P<0.05) in blood glucose level in a dose dependent manner by 36%, 48%, and 64%at doses of 0.2, 0.3 and 0.5 g/kg, respectively, in comparison to the STZ control values. Treatment with OS elicited an increase in the expression level of Slc2a2 gene but reduced the expression of G6Pase and PCK1 genes. Morefore, OS treated rats, showed significantly lower levels of serum alanine transaminase (ALT), aspartate aminotransferase (AST) and urea levels compared to STZ untreated rats. The extract at different doses elicited signs of recovery in body weight gain when compared to STZ diabetic controls although food and water consumption were significantly lower in treated groups compared to STZ diabetic control group. Conclusions:O. sumatrana aqueous extract is beneficial for improvement of hyperglycemia by increasing gene expression of liver Slc2a2 and reducing expression of G6Pase and PCK1 genes in streptozotocin

  13. Molecular and Biochemical Effects of a Kola Nut Extract on Androgen Receptor-Mediated Pathways

    International Nuclear Information System (INIS)

    The low incidence of prostate cancer in Asians has been attributed to chemo preventative properties of certain chemicals found in their diet. This study characterized the androgenic and chemo preventative 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 pro apoptotic 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.

  14. 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.

  15. 全自动固相萃取/超高压液相色谱测定食品中合成色素%Determination of Synthetic Colorants in Food by Automatic Solid Phase Extraction/UPLC

    Institute of Scientific and Technical Information of China (English)

    吴丽容

    2014-01-01

    建立了全自动固相萃取/超高压液相色谱法同时测定食品中10种人工合成色素柠檬黄、苋菜红、胭脂红、日落黄、亮蓝、诱惑红、靛蓝、赤藓红、新红、酸性红的方法。液体样品经加热驱除二氧化碳和酒精,固体或半固体样品经乙醇-水-氨水(70+29+1)溶液提取,所得待净化液采用全自动固相萃取仪经Strata X-AW SPE小柱净化,采用超高压液相色谱进行分析。用甲醇和0.02 mol/L乙酸铵溶液作为流动相进行梯度洗脱,流速0.3 mL/min,在4 min内实现10种合成色素的良好分离。10种色素在1~50μg/mL的范围内线性良好。10种色素的方法最低检出限是0.004 mg/kg,加标回收率在83.8%~111.2%之间,相对标准偏差在1.24%~4.18%之间(n=6)。本方法操作简单,灵敏度高,干扰少,能满足食品中多种合成色素同时分析测定要求。%An automatic solid phase extraction/ultra high pressure liquid chromatographic method was established for the simultaneous determination of 10 synthetic colorants tartrazine, amaranth, ponceau 4R, sunset yellow, brilliant blue, allura red, indigotine, erythrosine, new red, and carmoisine in food.Liquid samples were removed carbon dioxide and alcohol by heating , solid or semi-solid samples were extracted with alcohol -water-ammonia ( 70+29+1 ) solution , and the extract was purified on Strata X -AW SPE column by automatic solid phase extraction apparatus , than analyzed by UPLC.The mobile phase was methanol and 0.02 mol/L ammonium acetate solution in gradient condition.The flow rate was 0.3 mL/min.Using the best gradient condition , ten synthetic colorants achieved the grate separation in 4 min.All the ten synthetic colorants had a good linearity in a concentration range of 1 ~50 μg/mL.The detect limit of the method was 0.004 mg/kg.The spiked recoveries of ten colorants ranged from 83.8% to 111.2%, with the RSDs of 1.24%~4.18%( n =6 ).This method

  16. UMLS-based automatic image indexing.

    Science.gov (United States)

    Sneiderman, C; Sneiderman, Charles Alan; Demner-Fushman, D; Demner-Fushman, Dina; Fung, K W; Fung, Kin Wah; Bray, B; Bray, Bruce

    2008-01-01

    To date, most accurate image retrieval techniques rely on textual descriptions of images. Our goal is to automatically generate indexing terms for an image extracted from a biomedical article by identifying Unified Medical Language System (UMLS) concepts in image caption and its discussion in the text. In a pilot evaluation of the suggested image indexing method by five physicians, a third of the automatically identified index terms were found suitable for indexing.

  17. 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...

  18. A New Color Facial Identification Feature Extraction Method' and Automatic Identification%一种改进的彩色人脸鉴别特征抽取方法及自动识别

    Institute of Scientific and Technical Information of China (English)

    高燕; 明曙军; 刘永俊

    2011-01-01

    Currently face recognition has made some success, algorithms are constantly being improved. According to the common needs of the average sample solution in traditional linear analysis methods, this paper proposes the face recognition based on intermediate samples. This method can remove the influence of average samples to interference samples. Combined with the color of face recognition, the paper proposes color facial identification feature extraction and automatic identification based on the middle samples. Finally, extensive experiments performed on the international and universal AR standard color face database verify the effectiveness of the proposed method.%针对传统的线性分析方法中都需要的平均样本的共性,提出了基于中间样本的人脸识别.这种方法有效去除了干扰样本对平均样本的影响,并结合彩色人脸识别,提出了基于中间样本的彩色人脸鉴别特征抽取及自动识别方法.最后,在国际通用的AR标准彩色人脸库中进行了大量实验,验证了算法的有效性.

  19. Kavain, the Major Constituent of the Anxiolytic Kava Extract, Potentiates GABAA Receptors: Functional Characteristics and Molecular Mechanism

    Science.gov (United States)

    Chua, Han Chow; Christensen, Emilie T. H.; Hoestgaard-Jensen, Kirsten; Hartiadi, Leonny Y.; Ramzan, Iqbal; Jensen, Anders A.; Absalom, Nathan L.; Chebib, Mary

    2016-01-01

    Extracts of the pepper plant kava (Piper methysticum) are effective in alleviating anxiety in clinical trials. Despite the long-standing therapeutic interest in kava, the molecular target(s) of the pharmacologically active constituents, kavalactones have not been established. γ-Aminobutyric acid type A receptors (GABAARs) are assumed to be the in vivo molecular target of kavalactones based on data from binding assays, but evidence in support of a direct interaction between kavalactones and GABAARs is scarce and equivocal. In this study, we characterised the functional properties of the major anxiolytic kavalactone, kavain at human recombinant α1β2, β2γ2L, αxβ2γ2L (x = 1, 2, 3 and 5), α1βxγ2L (x = 1, 2 and 3) and α4β2δ GABAARs expressed in Xenopus oocytes using the two-electrode voltage clamp technique. We found that kavain positively modulated all receptors regardless of the subunit composition, but the degree of enhancement was greater at α4β2δ than at α1β2γ2L GABAARs. The modulatory effect of kavain was unaffected by flumazenil, indicating that kavain did not enhance GABAARs via the classical benzodiazepine binding site. The β3N265M point mutation which has been previously shown to profoundly decrease anaesthetic sensitivity, also diminished kavain-mediated potentiation. To our knowledge, this study is the first report of the functional characteristics of a single kavalactone at distinct GABAAR subtypes, and presents the first experimental evidence in support of a direct interaction between a kavalactone and GABAARs. PMID:27332705

  20. Development of sample preparation method for auxin analysis in plants by vacuum microwave-assisted extraction combined with molecularly imprinted clean-up procedure.

    Science.gov (United States)

    Hu, Yuling; Li, Yuanwen; Zhang, Yi; Li, Gongke; Chen, Yueqin

    2011-04-01

    A novel sample preparation method for auxin analysis in plant samples was developed by vacuum microwave-assisted extraction (VMAE) followed by molecularly imprinted clean-up procedure. The method was based on two steps. In the first one, conventional solvent extraction was replaced by VMAE for extraction of auxins from plant tissues. This step provided efficient extraction of 3-indole acetic acid (IAA) from plant with dramatically decreased extraction time, furthermore prevented auxins from degradation by creating a reduced oxygen environment under vacuum condition. In the second step, the raw extract of VMAE was further subjected to a clean-up procedure by magnetic molecularly imprinted polymer (MIP) beads. Owing to the high molecular recognition ability of the magnetic MIP beads for IAA and 3-indole-butyric acid (IBA), the two target auxins in plants can be selectively enriched and the interfering substance can be eliminated by dealing with a magnetic separation procedure. Both the VMAE and the molecularly imprinted clean-up conditions were investigated. The proposed sample preparation method was coupled with high-performance liquid chromatogram and fluorescence detection for determination of IAA and IBA in peas and rice. The detection limits obtained for IAA and IBA were 0.47 and 1.6 ng/mL and the relative standard deviation were 2.3% and 2.1%, respectively. The IAA contents in pea seeds, pea embryo, pea roots and rice seeds were determined. The recoveries were ranged from 70.0% to 85.6%. The proposed method was also applied to investigate the developmental profiles of IAA concentration in pea seeds and rice seeds during seed germination. PMID:20953778

  1. Synthesis and characterization of molecularly imprinted polymer nanoparticles for coenzyme Q10 dispersive micro solid phase extraction.

    Science.gov (United States)

    Contin, Mario; Bonelli, Pablo; Lucangioli, Silvia; Cukierman, Ana; Tripodi, Valeria

    2016-07-22

    Molecularly imprinted polymer nanoparticles (MIPNPs) with the ability to recognize coenzyme Q10 (CoQ10) were synthesised in order to be employed as sorbent in a dispersive micro-solid phase extraction (DMSPE) for the determination of CoQ10 in a liver extract. CoQ10 is a redox-active, lipophilic substance integrated in the mitochondrial respiratory chain which acts as an electron carrier, shuttling electrons from complex I (NADH-ubiquinone oxidoreductase) and II (succinate-ubiquinone oxidoreductase) to complex III (ubiquinol-cytochrome c reductase), for the production of cellular energy. The MIPNPs were synthesised by precipitation polymerization using coenzyme Q0 as the dummy template, methacrylic acid as the functional monomer, an acetonitrile: water mixture as the porogen, ethylene glycol dimethacrylate as the crosslinker and potassium persulfate as initiator. The nanoparticles were characterized by microscopy, capillary electrophoresis, dynamic light scattering, N2 adsorption-desorption isotherms, and infrared spectroscopy. The MIPNPs demonstrated the presence of selective cavities complementary to the quinone nucleus of CoQ10, leading to a specific recognition of CoQ10 compared with related compounds. In the liver extract the relative CoQ10 peak area (CoQ10 area/total peak area) increased from 4.6% to 25.4% after the DMSPE procedure. The recovery percentage of CoQ10 from the liver matrix was between 70.5% and 83.7% quantified against CoQ10 standard processed under the same conditions. The DMSPE procedure allows the elution of almost all the CoQ10 retained (99.4%) in a small volume (200μL), allowing the sample to be concentrated 2.5 times (LOD: 1.1μgg(-1) and LOQ: 3.7μgg(-1) of tissue). The resulted clean up of the sample, the improvement in peak shape and baseline and the reduction of interferences, evidence that the MIPNPs could potentially be applied as sorbent in a DMSPE with satisfactory results and with a minimum amount of sorbent (1mg). PMID:27317007

  2. Selective extraction of Bactrocera oleae sexual pheromone from olive oil by dispersive magnetic microsolid phase extraction using a molecularly imprinted nanocomposite.

    Science.gov (United States)

    Del Carmen Alcudia-León, María; Lucena, Rafael; Cárdenas, Soledad; Valcárcel, Miguel

    2016-07-15

    Bactrocera oleae Gmelin, also known as olive fruit fly, is the main olive tree pest. It produces a severe effect not only on the productivity but also on the quality of the olive-related products. In fact, the oil obtained from infected olives has a lower antioxidant power. In addition, an increase of the oil acidity, peroxide index and UV-absorbance can also be observed. 1,7-dioxaspiro-[5,5]-undecane (DSU), is the main component of the sexual pheromone of this pest and may be used as marker of the pest incidence. In this context, the development of new methods able to detect the pheromones in several samples, including agri-food or environmental ones, is interesting. In this work, we synthesized a molecularly imprinted polymer (MIPS) layer over magnetic nanoparticles (Fe3O4@SiO2@MIP) for the selective recognition of DSU. They were prepared using DSU as template and 3-aminopropyltriethoxysilane (APTES) to associate the target analyte on the surface of the magnetic substrate and the later polymerization of ethylene glycol dimethacrylate (EGDMA) in presence of 2,2-azobisisobutyonnitrile (AIBN). The resulting Fe3O4@SiO2@MIP composite was characterized by different techniques. The maximum adsorption capacity of DSU on Fe3O4@SiO2@MIP in hexane was 32mg/g (5.3 times than that obtained for the non-imprinted composite). In addition, Fe3O4@SiO2@MIP showed a short equilibrium time (45min) and potential reusability. The combination of dispersive magnetic microsolid phase extraction and gas chromatography with mass spectrometric detection allows the determination of DSU in real samples at concentrations as low as 10μg/L with precision better than 7.5% (expressed as relative standard deviation). The relative recoveries are in the range between 95 and 99%, which indicates the potential of the methodology. Finally, it has been applied to real olive oil samples being the presence of the pest detected is some of them. PMID:27295964

  3. An Automatic Extraction Approach to Fractional Vegetation Cover of Saline Land with Digital Images%吉林西部盐碱地数字图像植被覆盖度的自动提取

    Institute of Scientific and Technical Information of China (English)

    丁艳玲; 赵凯; 李晓峰; 郑兴明

    2013-01-01

      植被覆盖度是生态环境变化的重要指标,也是遥感反演的关键参数。盐碱地植被覆盖度的准确测量对研究地表植被蒸腾、土壤水分蒸发及土壤退化、盐碱化等具有重要意义。过绿指数(Excess Green index,ExG)对绿色植被比较敏感,能突显植被信息,去除土壤、阴影的干扰。通过对吉林西部盐碱地玉米、高粱、绿豆、杂草、土壤数字图像特征分析,利用改进过绿指数(Modified Excess Green index,MExG)算法计算植被和土壤的MExG值;并确定区分植被和土壤的MExG阈值为40,进而计算植被覆盖度。本文采用监督分类的最大似然法对比验证MExG自动提取结果,并对两种方法计算的玉米、高粱、绿豆和杂草的覆盖度,分别进行目视判读和t检验。研究表明,MExG自动提取方法具有客观性强,处理时间短,分类精度高等优点,是计算不同植被类型覆盖度的有效方法。%Fractional vegetation cover is an important variable in ecological environment and a key parameter in remote sensing estimation, which is needed in the modeling of the land-atmosphere exchanges of momentum, en-ergy, water, and trace gases. Determination of fractional vegetation cover exactly is necessary for studies on plant transpiration, ground surface evaporation, soil degradation and salinization. Excess green, highlighting veg-etation and inhibiting the interference of soil and shadow, was used as a contrast enhancement for identifying plants from soil regions. This study uses modified excess green index to extract fractional vegetation cover by an-alyzing RGB color features of corn, sorghum, mung beans and weeds growing in saline land in western Jilin Province. The digital images are geometrically corrected in order to eliminate distortion. The automatic extrac-tion approach using modified excess green indexes which is about 40 for vegetation growing on the saline land of western

  4. Text-mining and information-retrieval services for molecular biology

    OpenAIRE

    Krallinger, Martin; Valencia, Alfonso

    2005-01-01

    Text-mining in molecular biology - defined as the automatic extraction of information about genes, proteins and their functional relationships from text documents - has emerged as a hybrid discipline on the edges of the fields of information science, bioinformatics and computational linguistics. A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators.

  5. 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. PMID:27283627

  6. Molecular detection and in vitro antioxidant activity of S-allyl-L-cysteine (SAC) extracted from Allium sativum.

    Science.gov (United States)

    Sun, Y-E; Wang, W-D

    2016-01-01

    It is well known that Allium sativum has potential applications to clinical treatment of various cancers due to its remarkable ability in eliminating free radicals and increasing metabolism. An allyl-substituted cysteine derivative - S-allyl-L-cysteine (SAC) was separated and identified from Allium sativum. The extracted SAC was reacted with 1-pyrenemethanol to obtain pyrene-labelled SAC (Py-SAC) to give SAC fluorescence properties. Molecular detection of Py-SAC was conducted by steady-state fluorescence spectroscopy and time-resolved fluorescence method to quantitatively measure concentrations of Py-SAC solutions. The ability of removing 1,1-diphenyl-2-picrylhydrazyl (DPPH) and hydroxyl radical using Py-SAC was determined through oxygen radical absorbance capacity (ORAC). Results showed the activity of Py-SAC and Vitamin C (VC) with ORAC as index, the concentrations of Py-SAC and VC were 58.43 mg/L and 5.72 mg/L respectively to scavenge DPPH, and 8.16 mg/L and 1.67 mg/L to scavenge •OH respectively. Compared with VC, the clearance rates of Py-SAC to scavenge DPPH were much higher, Py-SAC could inhibit hydroxyl radical. The ability of removing radical showed a dose-dependent relationship within the scope of the drug concentration. PMID:27453278

  7. 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.

  8. Introducing meta-services for biomedical information extraction

    OpenAIRE

    Leitner, Florian; Krallinger, Martin; Johnson, Calvin A.; Saetre, Rune; Yoshida, Kazuhiro; Chen, Yan Hua; Kim, Sun; Shin, Soo-Yong; Zhang, Byoung-Tak; Baumgartner, William A.; Hunter, Lawrence; Haddow, Barry; Rodriguez-Penagos, Carlos; Matthews, Michael; Wang, Xinglong

    2008-01-01

    We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This servi...

  9. Development of magnetic molecularly imprinted polymers for selective extraction: determination of citrinin in rice samples by liquid chromatography with UV diode array detection.

    Science.gov (United States)

    Urraca, Javier L; Huertas-Pérez, José F; Cazorla, Guillermo Aragoneses; Gracia-Mora, Jesus; García-Campaña, Ana M; Moreno-Bondi, María Cruz

    2016-04-01

    In this work, we report the synthesis of novel magnetic molecularly imprinted polymers (m-MIPs) and their application to the selective extraction of the mycotoxin citrinin (CIT) from food samples. The polymers were prepared by surface imprinting of Fe3O4 nanoparticles, using 2-naphtholic acid (2-NA) as template molecule, N-3,5-bis(trifluoromethyl)phenyl-N'-4-vinylphenyl urea and methacrylamide as functional monomers and ethyleneglycol dimethacrylate as cross-linker. The resulting material was characterized by transmission electron microscopy (TEM), and X-ray diffraction (XRD) and Fourier transform infrared spectroscopies (FT-IR). The polymers were used to develop a solid-phase extraction method (m-MISPE) for the selective recovery of CIT from rice extracts prior to its determination by HPLC with UV diode array detection. The method involves ultrasound-assisted extraction of the mycotoxin from rice samples with (7:3, v/v) methanol/water, followed by sample cleanup and preconcentration with m-MIP. The extraction (washing and elution) conditions were optimized and their optimal values found to provide CIT recoveries of 94-98 % with relative standard deviations (RSD) less than 3.4 % (n = 3) for preconcentrated sample extracts (5 mL) fortified with the analyte at concentrations over the range 25-100 μg kg(-1). Based on the results, the application of the m-MIPs facilitates the accurate and efficient determination of CIT in rice extracts. Graphical Abstract Novel magnetic molecularly imprinted polymers (m-MIPs) for citrinin (CIT) have been obtained and applied to the selective extraction of the mycotoxin from rice samples. PMID:26873195

  10. 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.

  11. Automatic brain tissue extraction approach of serial magnetic resonance head images%序列磁共振颅脑影像的脑组织自动提取方法

    Institute of Scientific and Technical Information of China (English)

    贾迪; 杨金柱; 张一飞; 赵大哲; 于戈

    2011-01-01

    To extract brain tissue from cerebral MR image automatically, a novel brain tissue extraction algorithm is proposed. Based on level set and morphology, this algorithm can cut off the tissue adhesion of non-brain tissue more accurately. The C-V model is firstly used to segment the input image. Because the gray scale of some brain tissues is the same as that of visual nerve and other organs, and the C-V model is based on the regional average grayscale, so, after segmentation accurately extracting brain tissue is impossible. To solve the problem, a morphology method of corrosion expansion algorithm is adopted, which circularly corrodes the border to get the image of the separated adhe-sion tissue, then expands the border to the position before corrosion and the brain tissue is extracted correctly. In or-der to improve the practicability, improved level set algorithm is used for solving, which greatly improves the speed of segmentation and ensures the correctness of the result. The algorithm can be applied to 2D and 3D brain tissue ex-traction. Experiment results prove the accuracy, commonality and practicality of the proposed method.%为自动从MR脑影像中提取脑组织,提出一种新颖的脑组织提取算法.该算法在水平集算法的基础上,通过结合形态学方法,可以较为准确地截断脑组织与非脑组织粘连的部分.首先采用C-V模型对输入的影像进行预分割,由于某些脑组织会与视觉神经等部位的灰度相同,而C-V模型是基于区域平均灰度的分割,因此导致分割后无法提取脑组织.为了解决这一问题,采用一种形态学的腐蚀膨胀算法,通过循环腐蚀边界,得到粘连组织分离时刻的影像,再通过膨胀算法,使分离后的影像膨胀到腐蚀前的位置,与水平集算法结果取交集,从而完成脑组织的正确提取.为了提高实用性,采用改进后的水平集算法进行求解,在确保结果正确的基础上极大地提高了分割速度.算法适

  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. 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

  14. 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.

  15. Automatic generation of a view to geographical database

    OpenAIRE

    Dunkars, Mats

    2001-01-01

    This thesis concerns object oriented modelling and automatic generalisation of geographic information. The focus however is not on traditional paper maps, but on screen maps that are automatically generated from a geographical database. Object oriented modelling is used to design screen maps that are equipped with methods that automatically extracts information from a geographical database, generalises the information and displays it on a screen. The thesis consists of three parts: a theoreti...

  16. Effect of gamma-irradiation on rice seed DNA. Pt. 1. Yield and molecular size of DNA extracted from irradiated rice seeds

    International Nuclear Information System (INIS)

    The effect of gamma-irradiation on the DNA of hulled rice seeds was investigated. The cetyltrimethylammonium bromide (CTAB) method was preferred for the extraction of DNA from rice seeds because of its high quality and good yield. The yield of DNA that was determined by gel electrophoresis, decreased as the irradiation dose increased from 1 kGy. DNA extracted from rice seeds irradiated with a 30 kGy dose showed a molecular size of less than 20 kb, while that from unirradiated rice showed more than 100 kb in electrophoretic profiles. It can be assumed that the decrease in yield was mainly induced by the crosslinking between protein and DNA, and the reduction in molecular size was induced by double-strand breaks. (J.P.N.)

  17. Automatic transcription of polyphonic singing

    OpenAIRE

    Paščinski, Uroš

    2015-01-01

    In this work we focus on automatic transcription of polyphonic singing. In particular we do the multiple fundamental frequency (F0) estimation. From the terrain recordings a test set of Slovenian folk songs with polyphonic singing is extracted and manually transcribed. On the test set we try the general algorithm for multiple F0 detection. An interactive visualization of the main parts of the algorithm is made to analyse how it works and try to detect possible issues. As the data set is ne...

  18. Automatic Discovery of Word Semantic Relations

    OpenAIRE

    Dias, Gael; Moraliyski, Rumen; Cordeiro, Joao; Doucet, Antoine; Ahonen-Myka, Helena

    2010-01-01

    In this paper, we propose an unsupervised methodology to automatically discover pairs of semantically related words by highlighting their local environment and evaluating their semantic similarity in local and global semantic spaces. This proposal di®ers from previous research as it tries to take the best of two different methodologies i.e. semantic space models and information extraction models. It can be applied to extract close semantic relations, it limits the search space and...

  19. Induction of apoptosis by pistachio (Pistacia vera L.) hull extract and its molecular mechanisms of action in human hepatoma cell line HepG2.

    Science.gov (United States)

    Fathalizadeh, J; Bagheri, V; Khorramdelazad, H; Kazemi Arababadi, M; Jafarzadeh, A; Mirzaei, M R; Shamsizadeh, A; Hajizadeh, M R

    2015-11-30

    Several important Pistacia species such as P. vera have been traditionally used for treating a wide range of diseases (for instance, liver-related disorders). There is a relative lack of research into pharmacological aspects of pistachio hull. Hence, this study was aimed at investigating whether pistachio rosy hull (PRH) extract exerts apoptotic impacts on HepG2 liver cancer cell line. In order to evaluate cell viability and apoptosis in response to treatment with the extract, MTT assay and Annexin-V-fluorescein/propidium iodide (PI) double staining were performed, respectively. Moreover, molecular mechanism of apoptosis induced by the extract was determined using human apoptosis PCR array. Our findings showed that PRH extract treatment reduced cell viability (IC50 ~ 0.3 mg/ml) in a dose-dependent manner. Flow cytometric analysis revealed that the extract significantly induced apoptosis in HepG2 cells. In addition, quantitative PCR array results demonstrated the regulation of a considerable number of apoptosis-related genes belonging to the TNF, BCL2, IAP, TRAF, and caspase families. We observed altered expression of both pro-apoptotic and anti-apoptotic genes associated with the extrinsic and intrinsic apoptosis signaling pathways. These results suggest that the aqueous extract of PRH possesses apoptotic activity through cytotoxic and apoptosis-inducing effects on HepG2 cells.

  20. Metsulfuron-methyl Molecularly Imprinted Stir Bar Sorptive Extraction Coupled with High Performance Liquid Chromatography for Trace Sulfonylurea Herbicides Analysis in Complex Samples

    Institute of Scientific and Technical Information of China (English)

    XU Zhi-gang; DU Zhuo; LIAN Hai-xian; HU Yu-ling; LI Gong-ke

    2012-01-01

    Metsulfuron-methyl molecularly imprinted polymer(MIP)-coated stir bar was prepared for sorptive extraction of sulfonylurea herbicides in complex samples.The MIP-coating was about 21.3 μm thickness with the relative standard deviation(RSD) of 4.4%(n=10).It was homogeneous and porous with good thermal stability and chemical stability.The extraction capability of the MIP-coating was 2.8 timcs over that of the non-imprinted polymer (NIP)-coating in hexane.The MIP-coating exhibited selective adsorption ability to the template and its analogues.The extraction conditions,including extraction solvent,desorption solvent,extraction time,desorption time and stirring speed,were optimized.A method for the determination of six sulfonylurea herbicides by MIP-coated stir bar sorptive extraction coupled with high performance liquid chromatography(HPLC) was developed.The linear range was 10-200 μg/L and the detection limits were within a range of 2.0-3.3 μg/L.It was also applied to the analysis of sulfonylurea herbicides in spiked river water,soil and rice samples.

  1. Induction of apoptosis by pistachio (Pistacia vera L.) hull extract and its molecular mechanisms of action in human hepatoma cell line HepG2.

    Science.gov (United States)

    Fathalizadeh, J; Bagheri, V; Khorramdelazad, H; Kazemi Arababadi, M; Jafarzadeh, A; Mirzaei, M R; Shamsizadeh, A; Hajizadeh, M R

    2015-01-01

    Several important Pistacia species such as P. vera have been traditionally used for treating a wide range of diseases (for instance, liver-related disorders). There is a relative lack of research into pharmacological aspects of pistachio hull. Hence, this study was aimed at investigating whether pistachio rosy hull (PRH) extract exerts apoptotic impacts on HepG2 liver cancer cell line. In order to evaluate cell viability and apoptosis in response to treatment with the extract, MTT assay and Annexin-V-fluorescein/propidium iodide (PI) double staining were performed, respectively. Moreover, molecular mechanism of apoptosis induced by the extract was determined using human apoptosis PCR array. Our findings showed that PRH extract treatment reduced cell viability (IC50 ~ 0.3 mg/ml) in a dose-dependent manner. Flow cytometric analysis revealed that the extract significantly induced apoptosis in HepG2 cells. In addition, quantitative PCR array results demonstrated the regulation of a considerable number of apoptosis-related genes belonging to the TNF, BCL2, IAP, TRAF, and caspase families. We observed altered expression of both pro-apoptotic and anti-apoptotic genes associated with the extrinsic and intrinsic apoptosis signaling pathways. These results suggest that the aqueous extract of PRH possesses apoptotic activity through cytotoxic and apoptosis-inducing effects on HepG2 cells. PMID:26638894

  2. 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.

  3. Selective tools for the solid-phase extraction of Ochratoxin A from various complex samples: immunosorbents, oligosorbents, and molecularly imprinted polymers.

    Science.gov (United States)

    Pichon, Valérie; Combès, Audrey

    2016-10-01

    The evolution of instrumentation in terms of separation and detection has allowed a real improvement of the sensitivity and the analysis time. However, the analysis of ultra-traces of toxins such as ochratoxin A (OTA) from complex samples (foodstuffs, biological fluids…) still requires a step of purification and of preconcentration before chromatographic determination. In this context, extraction sorbents leading to a molecular recognition mechanism appear as powerful tools for the selective extraction of OTA and of its structural analogs in order to obtain more reliable and sensitive quantitative analyses of these compounds in complex media. Indeed, immunosorbents and oligosorbents that are based on the use of immobilized antibodies and of aptamers, respectively, and that are specific to OTA allow its selective clean-up from complex samples with high enrichment factors. Similar molecular recognition mechanisms can also be obtained by developing molecularly imprinted polymers, the synthesis of which leads to the formation of cavities that are specific to OTA, thus mimicking the recognition site of the biomolecules. Therefore, the principle, the advantages, the limits of these different types of extraction tools, and their complementary behaviors will be presented. The introduction of these selective tools in miniaturized devices will also be discussed. PMID:27585915

  4. Automatic thematic mapping in the EROS program

    Science.gov (United States)

    Edson, D. T.

    1972-01-01

    A specified approach to the automatic extraction and catographic presentation of thematic data contained in multispectral photographic images is presented. Experimental efforts were directed toward the mapping of open waters, snow and ice, infrared reflective vegetation, and massed works of man. The system must also be able to process data from a wide variety of sources.

  5. 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...

  6. 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.

  7. Automatic input rectification

    OpenAIRE

    Long, Fan; Ganesh, Vijay; Carbin, Michael James; Sidiroglou, Stelios; Rinard, Martin

    2012-01-01

    We present a novel technique, automatic input rectification, and a prototype implementation, SOAP. SOAP learns a set of constraints characterizing typical inputs that an application is highly likely to process correctly. When given an atypical input that does not satisfy these constraints, SOAP automatically rectifies the input (i.e., changes the input so that it satisfies the learned constraints). The goal is to automatically convert potentially dangerous inputs into typical inputs that the ...

  8. 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

    2015-12-01

    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.

  9. 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.

  10. Development of a group selective molecularly imprinted polymers based solid phase extraction of malachite green from fish water and fish feed samples

    Energy Technology Data Exchange (ETDEWEB)

    Li Yahui; Yang Tao; Qi Xiaoling; Qiao Yuwei [College of Chemistry, Sichuan University, Wangjiang Road 29, Chengdu 610064 (China); Deng Anping [College of Chemistry, Sichuan University, Wangjiang Road 29, Chengdu 610064 (China)], E-mail: denganping6119@yahoo.com.cn

    2008-08-29

    A group selective molecularly imprinted solid phase extraction (MISPE) for malachite green (MG) from fish water and fish feed samples was developed. Using MG as template molecule, methacrylic acid as functional monomer, ethylene glycoldimethacrylate as linking agent and bulk polymerization as synthetic method, the molecularly imprinted polymers (MIPs) were synthesized and characterized with rebinding experiment. The Scatchard polt's analysis revealed that the template-polymer system showed the two-site binding behavior with dissociation constants of 0.3194 {mu}mol L{sup -1} and 15.70 {mu}mol L{sup -1}, respectively. MG and two structurally related compounds, leucomalachite green (LMG) and crystal violet (CV) were employed for selectivity test. The MIPs exhibited the highest selective rebinding to MG, but also displayed 83.0% and 87.5% of cross-reactivity with LMG and CV, demonstrating that MIPs could be used as group recognition sorbents in solid phase extraction. The extraction conditions of MISPE column for MG were optimized. Tap water samples spiked with MG at concentration of 0.5-10 ng mL{sup -1} were extracted by MISPE column and analyzed by high performance liquid chromatography. The recoveries of MISPE column for MG extraction were found to be 76.8-93.7% with the relative standard deviations of 2.12-10.09%, indicating the feasibility of the prepared MIPs for MG extraction. No detectable MG was observed in one fish farming water sample and two fish feed samples; while the MG concentrations in two pet fishpond water samples were found at 1.50 ng mL{sup -1} and 0.67 ng mL{sup -1}, respectively.

  11. 基于语序位置特征的汉英术语对自动抽取研究%Research on automatic Chinese-English term extraction based on order and position feature of words

    Institute of Scientific and Technical Information of China (English)

    张莉; 刘昱显

    2015-01-01

    With the explosion of information and in current society,knowledge is spreading among information in various areas and also in different languages.The characteristic of knowledge spreading brings people tremendous obstacles in understanding,retrieving and exchanging their thinking.Bilingual terminology is an important language resource for natural language processing tasks such as machine translation,data mining and bilingual information re-trieval.The collecting of bilingual terminology is often challenging and time-consuming because texts to be aligned are usually in different languages such as Chinese and English and there are significant differences in many cases. Thus bilingual terminology extraction and alignment becomes more important and brings more and more attention in the information processing and it plays an important role in cross-language retrieval,building bilingual dictionaries and machine translation research.The development of bilingual terminology extraction and alignment will benefit the building of translation memory in the field of machine-assisted translation and it can improve the quality of the machine translations while adding the bilingual terminology information.We propose an automatic Chinese-English terminology alignment algorithm based on the order and position feature information of words.The algorithm improves the terminology alignment of two-step strategy about extracting bilingual terms by integrating the order and position feature information of words in phrase-basedmachine translation.The experimental corpus we used is the journals in CSSCI from the year of 1 998 to 2012,mainly including the titles and abstracts in Chinese and English.In our experiment,37206 complete English titles and abstracts of many papers are launched including a total of 1.63 million words in Chinese and 1 910000 words in English.The algorithm improves accuracy rate of term alignment especially in the case of lower probability of terms translation while

  12. Preparation of ellagic acid molecularly imprinted polymeric microspheres based on distillation-precipitation polymerization for the efficient purification of a crude extract.

    Science.gov (United States)

    Zhang, Hua; Zhao, Shangge; Zhang, Lu; Han, Bo; Yao, Xincheng; Chen, Wen; Hu, Yanli

    2016-08-01

    Molecularly imprinted polymeric microspheres with a high recognition ability toward the template molecule, ellagic acid, were synthesized based on distillation-precipitation polymerization. The as-obtained polymers were characterized by scanning electron microscopy, infrared spectroscopy, and thermogravimetric analysis. Static, dynamic, and selective binding tests were adopted to study the binding properties and the molecular recognition ability of the prepared polymers for ellagic acid. The results indicated that the maximum static adsorption capacity of the prepared polymers toward ellagic acid was 37.07 mg/g and the adsorption equilibrium time was about 100 min when the concentration of ellagic acid was 40 mg/mL. Molecularly imprinted polymeric microspheres were also highly selective toward ellagic acid compared with its analogue quercetin. It was found that the content of ellagic acid in the pomegranate peel extract was enhanced from 23 to 86% after such molecularly imprinted solid-phase extraction process. This work provides an efficient way for effective separation and enrichment of ellagic acid from complex matrix, which is especially valuable in industrial production. PMID:27311588

  13. Microbial diversity in fecal samples depends on DNA extraction method

    DEFF Research Database (Denmark)

    Mirsepasi, Hengameh; Persson, Søren; Struve, Carsten;

    2014-01-01

    BACKGROUND: There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study...... was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). FINDINGS: In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France......) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals. DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained...

  14. Event extraction for DNA methylation

    OpenAIRE

    Ohta Tomoko; Pyysalo Sampo; Miwa Makoto; Tsujii Jun’ichi

    2011-01-01

    Abstract Background We consider the task of automatically extracting DNA methylation events from the biomedical domain literature. DNA methylation is a key mechanism of epigenetic control of gene expression and implicated in many cancers, but there has been little study of automatic information extraction for DNA methylation. Results We present an annotation scheme for DNA methylation following the representation of the BioNLP shared task on event extraction, select a set of 200 abstracts inc...

  15. Chelating resin immobilizing carboxymethylated polyethyleneimine for selective solid-phase extraction of trace elements: Effect of the molecular weight of polyethyleneimine and its carboxymethylation rate.

    Science.gov (United States)

    Kagaya, Shigehiro; Kajiwara, Takehiro; Gemmei-Ide, Makoto; Kamichatani, Waka; Inoue, Yoshinori

    2016-01-15

    The effect of the molecular weight of polyethyleneimine (PEI), defined as a compound having two or more ethyleneamine units, and of its carboxymethylation rate (CM/N), represented by the ratio of ion-exchange capacity to the amount of N on the resin, on the selective solid-phase extraction ability of the chelating resin immobilizing carboxymethylated (CM) PEI was investigated. The chelating resins (24 types) were prepared by immobilization of diethylenetriamine, triethylenetetramine, tetraethylenepentamine, pentaethylenehexamine, PEI300 (MW=ca. 300), and PEI600 (MW=ca. 600) on methacrylate resins, followed by carboxymethylation with various amounts of sodium monochloroacetate. When resins with approximately the same CM/N ratio (0.242-0.271) were used, the recovery of Cd, Co, Cu, Fe, Ni, Pb, Ti, Zn, and alkaline earth elements increased with increasing the molecular weight of PEIs under acidic and weakly acidic conditions; however, the extraction behavior of Mo and V was only slightly affected. This was probably due to the increase in N content of the resin, resulting in an increase in carboxylic acid groups; the difference in the molecular weight of PEIs immobilized on the resin exerts an insignificant influence on the selective extraction ability. The CM/N ratio considerably affected the extraction behavior for various elements. Under acidic and neutral conditions, the recovery of Cd, Co, Cu, Fe, Ni, Pb, Ti, and Zn increased with increasing CM/N values. However, under these conditions, the recovery of alkaline earth elements was considerably low when a resin with low CM/N ratio was used. This is presumably attributed to the different stability constants of the complexes of these elements with aminocarboxylic acids and amines, and to the electrostatic repulsion between the elements and the protonated amino groups in the CM-PEI. The recovery of Mo and V decreased or varied with increasing CM/N values, suggesting that the extraction of these elements occurred mainly

  16. Evaluation and optimization of nucleic acid extraction methods for the molecular analysis of bacterial communities associated with corrored steel

    NARCIS (Netherlands)

    F. Marty; J.-F. Ghiglione; S. Païsse; H. Gueuné; L. Quillet; M.C.M. van Loosdrecht; G. Muyzer

    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

  17. 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.

  18. 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.

  19. Molecularly imprinted polymer-sol-gel tablet toward micro-solid phase extraction: I. Determination of methadone in human plasma utilizing liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    El-Beqqali, Aziza; Abdel-Rehim, Mohamed

    2016-09-14

    In the present work molecularly imprinted sol-gel tablet (MIP-Tablet) was prepared. The MIP-sol-gel was prepared as a thin layer on polyethylene material in a tablet form. Methadone-d9 was selected as the template and 3-(propylmethacrylate)-trimethoxysilane was used as precursor. MIP-Tablet was applied for micro-solid phase extraction (μ-SPE). The MIP-Tablet was used for the determination of methadone in human plasma samples utilizing liquid chromatography-tandem mass spectrometry; and each tablet could be used twenty times. The extraction time was 10 min while desorption time was 6 min. Factors affecting the extraction efficiency such as desorption solvents, sample pH, salt addition, extraction time, desorption time and adsorption capacity were investigated. The calibration curves were obtained within the range of 5-5000 ng/mL using methadone in human plasma samples. The coefficients of determination (r(2)) values were ≥0.999 for all runs and the extraction recovery was >80%. The accuracy values for quality control samples varied from +3.6 to +9.7% and the inter-day precision (RSD %) values were ranged from 5.0 to 8.0%. The limit of detection was 1.0 ng/mL and the lower limit of quantification was 5 ng/mL utilizing methadone in human plasma samples. PMID:27566346

  20. Simple, quantitative method for low molecular weight dissolved organic matter extracted from natural waters based upon high performance counter-current chromatography.

    Science.gov (United States)

    Rojas, Alfonso; Sandron, Sara; Wilson, Richard; Davies, Noel W; Haddad, Paul R; Shellie, Robert A; Nesterenko, Pavel N; Paull, Brett

    2016-02-25

    A simple, high-performance counter-current chromatography method with sequential UV absorbance (254 nm) and evaporative light scattering detection (ELSD) was developed for the quantification of pre-extracted low molecular weight dissolved organic matter (DOM) extracted from natural waters. The method requires solid-phase extraction (SPE) extraction of only small volumes of water samples, here using poly(styrenedivinylbenzene)-based extraction cartridges (Varian PPL). The extracted and concentrated DOM was quantified using reversed-phase high-performance counter-current chromatography (HPCCC), with a water/methanol (5:5) mobile phase and hexane/ethyl acetate (3:7) stationary phase. The critical chromatographic parameters were optimised, applying a revolution speed of 1900 rpm and a flow-rate of 1 mL min(-1). Under these conditions, 50 μL of extracted DOM solution could be injected and quantified using calibration against a reference natural dissolved material (Suwannee River), based upon UV absorbance at 254 nm and ELSD detection. Both detection methods provided excellent linearity (R(2) > 0.995) for DOM across the concentration ranges of interest, with limits of detection of 4 μg ml(-1) and 7 μg ml(-1) for ELSD and UV absorbance, respectively. The method was validated for peak area precision (95% recovery). The developed method was applied to the determination of the concentration of DOM in seawater, based upon initial sample volumes as small as 20 mL. PMID:26851093

  1. Method of information extraction of marbling image characteristic and automatic classification for beef%牛肉大理石花纹图像特征信息提取及自动分级方法

    Institute of Scientific and Technical Information of China (English)

    周彤; 彭彦昆

    2013-01-01

    . Light intensity was regulated through a light controller, and the distance between the camera lens and the beef samples was adjusted though translation stages in the image acquisition device. Collected images were automatically stored in the computer for further image processing. First, some methods such as image denoising, background removal, and image enhancement were adopted to preprocess the image to obtain a region of interest (ROI). In this step, the image was cropped to separate the beef from the background. Then, an iteration method was used to segment the beef area, obtain the beef marbling area and fat area. The redundant fat area was removed to extract an effective rib-eye region. Ten characteristic parameters of beef marbling namely, the rate of marbling area in the rib-eye region, the number of large grain fat, medium grain fat, small grain fat, total grain fat, the density of large grain fat, medium grain fat, small grain fat, total grain fat and, the evenness degree of fat distribution in the rib-eye region can reflect the amount of marbling and its distribution. So they were used to establish principal component regression (PCR) model. The PCR model result yielded a correction coefficient (Rv) of 0.88 and a standard error of prediction (SEP) of 0.56. And the PCR model showed that the rate of the marbling area in the rib-eye region had the greatest effect on the grade of beef marbling. Fisher discriminant functions were constructed based on the PCR model results to classify the grade of beef marbling. Experimental results showed that the classification accuracy was 97.0%in the calibration set and 91.2%in the prediction set. On this basis, a software system was developed for the automatic grading of beef marbling. A corresponding hardware device was also developed, controlled by the software system for real time application. The speed and accuracy of the algorithm were verified with theoretical analysis and a practical test. Through tests, the average

  2. Practical automatic Arabic license plate recognition system

    Science.gov (United States)

    Mohammad, Khader; Agaian, Sos; Saleh, Hani

    2011-02-01

    Since 1970's, the need of an automatic license plate recognition system, sometimes referred as Automatic License Plate Recognition system, has been increasing. A license plate recognition system is an automatic system that is able to recognize a license plate number, extracted from image sensors. In specific, Automatic License Plate Recognition systems are being used in conjunction with various transportation systems in application areas such as law enforcement (e.g. speed limit enforcement) and commercial usages such as parking enforcement and automatic toll payment private and public entrances, border control, theft and vandalism control. Vehicle license plate recognition has been intensively studied in many countries. Due to the different types of license plates being used, the requirement of an automatic license plate recognition system is different for each country. [License plate detection using cluster run length smoothing algorithm ].Generally, an automatic license plate localization and recognition system is made up of three modules; license plate localization, character segmentation and optical character recognition modules. This paper presents an Arabic license plate recognition system that is insensitive to character size, font, shape and orientation with extremely high accuracy rate. The proposed system is based on a combination of enhancement, license plate localization, morphological processing, and feature vector extraction using the Haar transform. The performance of the system is fast due to classification of alphabet and numerals based on the license plate organization. Experimental results for license plates of two different Arab countries show an average of 99 % successful license plate localization and recognition in a total of more than 20 different images captured from a complex outdoor environment. The results run times takes less time compared to conventional and many states of art methods.

  3. 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.

  4. 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

  5. Analysis of the influence of tectonics on the evolution valley network based on the SRTM DEM and the relationship of automatically extracted lineaments and the tectonic faults, Jemma River basin, Ethiopia

    Science.gov (United States)

    Kusák, Michal

    2016-04-01

    The Ethiopian Highland is good example of high plateau landscape formed by combination of tectonic uplift and episodic volcanism (Kazmin, 1975; Pik et al., 2003; Gani et al., 2009). Deeply incised gorges indicate active fluvial erosion which leads to instabilities of over-steepened slopes. In this study we focus on Jemma River basin which is a left tributary of Abay - Blue Nile to assess the influence of neotectonics on the evolution of its river and valley network. Tectonic lineaments, shape of valley networks, direction of river courses and intensity of fluvial erosion were compared in six subregions which were delineate beforehand by means of morphometric analysis. The influence of tectonics on the valley network is low in the older deep and wide canyons and in the and on the high plateau covered with Tertiary lava flows while younger upper part of the canyons it is high. Furthermore, the coincidence of the valley network with the tectonic lineaments differs in the subregions. The fluvial erosion along the main tectonic zones (NE-SW) direction made the way for backward erosion possible to reach far distant areas in E for the fluvial erosion. This tectonic zone also separates older areas in the W from the youngest landscape evolution subregions in the E, next to the Rift Valley. We studied the functions that can automatically extract lineaments in programs ArcGIS 10.1 and PCI Geomatica. The values of input parameters and their influence of the final shape and number of lineaments. A map of automated extracted lineaments was created and compared with 1) the tectonic faults by Geology Survey of Ethiopia (1996); and 2) the lineaments based on visual interpretation of by the author. The comparation of lineaments by automated visualization in GIS and visual interpretation of lineaments by the author proves that both sets of lineaments are in the same azimuth (NE-SW) - the same direction as the orientation of the rift. But it the mapping of lineaments by automated

  6. A Statistical Approach to Automatic Speech Summarization

    Science.gov (United States)

    Hori, Chiori; Furui, Sadaoki; Malkin, Rob; Yu, Hua; Waibel, Alex

    2003-12-01

    This paper proposes a statistical approach to automatic speech summarization. In our method, a set of words maximizing a summarization score indicating the appropriateness of summarization is extracted from automatically transcribed speech and then concatenated to create a summary. The extraction process is performed using a dynamic programming (DP) technique based on a target compression ratio. In this paper, we demonstrate how an English news broadcast transcribed by a speech recognizer is automatically summarized. We adapted our method, which was originally proposed for Japanese, to English by modifying the model for estimating word concatenation probabilities based on a dependency structure in the original speech given by a stochastic dependency context free grammar (SDCFG). We also propose a method of summarizing multiple utterances using a two-level DP technique. The automatically summarized sentences are evaluated by summarization accuracy based on a comparison with a manual summary of speech that has been correctly transcribed by human subjects. Our experimental results indicate that the method we propose can effectively extract relatively important information and remove redundant and irrelevant information from English news broadcasts.

  7. A Statistical Approach to Automatic Speech Summarization

    Directory of Open Access Journals (Sweden)

    Chiori Hori

    2003-02-01

    Full Text Available This paper proposes a statistical approach to automatic speech summarization. In our method, a set of words maximizing a summarization score indicating the appropriateness of summarization is extracted from automatically transcribed speech and then concatenated to create a summary. The extraction process is performed using a dynamic programming (DP technique based on a target compression ratio. In this paper, we demonstrate how an English news broadcast transcribed by a speech recognizer is automatically summarized. We adapted our method, which was originally proposed for Japanese, to English by modifying the model for estimating word concatenation probabilities based on a dependency structure in the original speech given by a stochastic dependency context free grammar (SDCFG. We also propose a method of summarizing multiple utterances using a two-level DP technique. The automatically summarized sentences are evaluated by summarization accuracy based on a comparison with a manual summary of speech that has been correctly transcribed by human subjects. Our experimental results indicate that the method we propose can effectively extract relatively important information and remove redundant and irrelevant information from English news broadcasts.

  8. Molecularly imprinted solid phase extraction using stable isotope labeled compounds as template and liquid chromatography-mass spectrometry for trace analysis of bisphenol A in water sample

    International Nuclear Information System (INIS)

    We have developed a molecularly imprinted polymer (MIP) using a stable isotope labeled compound as the template molecule and called it the ''isotope molecularly imprinted polymer'' (IMIP). In this study, bisphenol A (BPA) was used as the model compound. None imprinted polymer (NIP), MIP, dummy molecularly imprinted polymer (DMIP) and IMIP were prepared by the suspension polymerization method using without template, BPA, 4-tert-butylphenol (BP) and bisphenol A-d16 (BPA-d16), respectively. The polymers were subjected to molecularly imprinted solid phase extraction (MI-SPE), and the extracted samples were subjected to liquid chromatography-mass spectrometry (LC-MS). Although the leakage of BPA-d16 from the IMIP was observed and that of BPA was not observed. The selectivity factors of MIP and IMIP for BPA were 4.45 and 4.43, respectively. Therefore, IMIP had the same molecular recognition ability as MIP. When MI-SPE with IMIP was used and followed by LC-MS in the analysis of river water sample, the detection limit of BPA was 1 ppt with high sensitivity. Moreover, the average recovery was higher than 99.8% (R.S.D.: 3.7%) by using bisphenol A-13C12 (BPA-13C12) as the surrogate standard. In addition, the IMIP were employed in MI-SPE of BPA in river water sample by LC-MS. The concentration of BPA in the river water sample was determined to be 32 pg ml-1. We confirmed that it was possible to measure trace amounts of a target analyte by MI-SPE using IMIP

  9. Molecularly imprinted solid-phase extraction for the determination of ten macrolide drugs residues in animal muscles by liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Song, Xuqin; Zhou, Tong; Liu, Qingying; Zhang, Meiyu; Meng, Chenying; Li, Jiufeng; He, Limin

    2016-10-01

    A simple and sensitive method based on molecularly imprinted solid-phase extraction coupled with liquid chromatography-tandem mass spectrometry was developed for the determination of the residues of ten macrolide drugs in swine, cattle and chicken muscles samples. The molecularly imprinted polymers (MIPs) were synthesized using tylosin as a template and methacrylic acid as a functional monomer. Samples were extracted with sodium borate buffer solution and ethyl acetate, and purified by the MIP cartridge. The results showed that the cartridge exhibited good recognition performance for macrolides, and better purification effect than the traditional solid-phase extraction cartridges. Recoveries of analytes at three spiking levels 1, 5 and 20μgkg(-1) ranged from 60.7% to 100.3% with the relative standard deviations less than 14%. The limits of detection of the method were between 0.1 and 0.4μgkg(-1). The method is useful for the routine monitoring of the residues of macrolide drugs in animal muscles. PMID:27132837

  10. Dispersive solid-phase extraction based on magnetic dummy molecularly imprinted microspheres for selective screening of phthalates in plastic bottled beverages.

    Science.gov (United States)

    Qiao, Jindong; Wang, Mingyu; Yan, Hongyuan; Yang, Gengliang

    2014-04-01

    A new magnetic dummy molecularly imprinted dispersive solid-phase extraction (MAG-MIM-dSPE) coupled with gas chromatography-FID was developed for selective determination of phthalates in plastic bottled beverages. The new magnetic dummy molecularly imprinted microspheres (MAG-MIM) using diisononyl phthalate as a template mimic were synthesized by coprecipitation coupled with aqueous suspension polymerization and were successfully applied as the adsorbents for MAG-MIM-dSPE to extract and isolate five phthalates from plastic bottled beverages. Validation experiments showed that the MAG-MIM-dSPE method had good linearity at 0.0040-0.40 μg/mL (0.9991-0.9998), good precision (3.1-6.9%), and high recovery (89.5-101.3%), and limits of detection were obtained in a range of 0.53-1.2 μg/L. The presented MAG-MIM-dSPE method combines the quick separation of magnetic particles, special selectivity of MIM, and high extraction efficiency of dSPE, which could potentially be applied to selective screening of phthalates in beverage products.

  11. Molecularly Imprinted Dispersive Solid-Phase Extraction for the Determination of Triazine Herbicides in Grape Seeds by High-Performance Liquid Chromatography.

    Science.gov (United States)

    Li, Xinpei; Wang, Yuanpeng; Sun, Qun; Xu, Bo; Yang, Zhaoqing; Wang, Xinghua

    2016-05-01

    Molecular imprinting technique, regarded as one of the current state-of-the-art researches, was incorporated with the simple dispersive solid-phase extraction (MI-DSPE) in this work for the extraction of triazine herbicides in grape seeds. The atrazine molecularly imprinted polymers (MIPs) were successfully prepared and characterized by scanning electron microscopy and Fourier transform infrared spectroscopy. The imprinting particles were used as the adsorbent in DSPE. Thus, a simple, rapid and selective method based on MIPs coupled with DSPE was established for the simultaneous cleaning-up and quantitative extraction of four triazine herbicides in grape seeds. The experiment parameters, including type of washing solvents, washing time and type of eluting solvents, were investigated and optimized. The performance of the present method was validated by high-performance liquid chromatography. Good linear responses were obtained in concentration range of 0.010-5.0 µg g(-1)with correlation coefficients (r(2)) higher than 0.9993. The recoveries at two spiked levels (1.0 and 2.0 µg g(-1)) were between 81.2 and 113.0% with relative deviations ranging from 1.2 to 10.7%. The limits of detection were ranged between 0.006 and 0.013 µg g(-1), which were lower than the values required by European regulations. PMID:27013667

  12. Synthesis of lab-in-a-pipette-tip extraction using hydrophilic nano-sized dummy molecularly imprinted polymer for purification and analysis of prednisolone.

    Science.gov (United States)

    Arabi, Maryam; Ghaedi, Mehrorang; Ostovan, Abbas; Wang, Shaobin

    2016-10-15

    A novel pipette-tip based on nano-sized dummy molecularly imprinted polymer (PT-DMIP) assisted by ultrasonication for the effective enrichment and analysis of prednisolone from urine samples was developed. The PT-DMIP cartridge was prepared by packing the dummy molecularly imprinted polymer at the tip of the micropipette. The polymerization used betamethasone (BM) as the dummy template, 3-aminopropyltrimethoxysilane (APTMS) as the functionalized monomer, tetraethyl orthosilicate (TEOS) as the cross-linker and aluminum ion (Al(3+)) as a dopant to produce Lewis acid sites in the silica matrix for metal coordinative interactions with the analyte. Compared to conventional solid phase extraction (SPE), the PT-DMIP is cost-effective, fast, and easy to handle, while the system is very approachable and reduces the consumption of toxic organic solvent. HPLC-UV analysis revealed successful applicability of the sorbent for highly efficient extraction of perdnisolone from urine matrices. The extraction recovery was investigated and optimum conditions were obtained using central composite design. Good linearity for prednisolone in the range of 0.22-220μgL(-1) with regression coefficients of 0.99 reveals high applicability of the method for trace analysis. Under the optimized conditions, the recoveries are 89.0-96.1 with relative standard deviations (RSD) of less than 9.0%. PMID:27442150

  13. Molecularly imprinted solid-phase extraction combined with electrochemical oxidation fluorimetry for the determination of methotrexate in human serum and urine

    Science.gov (United States)

    Chen, Suming; Zhang, Zhujun

    2008-06-01

    The method of synthesis and evaluation of molecularly imprinted polymers was reported. As a selective solid-phase extraction sorbent, the polymers were coupled with electrochemical fluorimetry detection for the efficient determination of methotrexate in serum and urine. Methotrexate was preconcentrated in the molecularly imprinted solid-phase extraction microcolumn packed with molecularly imprinted polymers, and then eluted. The eluate was detected by fluorescence spectrophotometer after electrochemical oxidation. The conditions of preconcentration, elution, electrochemical oxidation and determination were carefully studied. Under the selected experimental conditions, the calibration graph of the fluorescence intensity versus methotrexate concentration was linear from 4 × 10 -9 g mL -1 to 5 × 10 -7 g mL -1, and the detection limit was 8.2 × 10 -10 g mL -1 (3 σ). The relative standard deviation was 3.92% ( n = 7) for 1 × 10 -7 g mL -1 methotrexate. The experiments showed that the selectivity and sensitivity of fluorimetry could be greatly improved by the proposed method. This method has been successfully applied to the determination of methotrexate. At the same time, the binding characteristics of the polymers to the methotrexate were evaluated by batch and dynamic methods.

  14. Improving molecular detection of fungal DNA in formalin-fixed paraffin-embedded tissues: comparison of five tissue DNA extraction methods using panfungal PCR.

    Science.gov (United States)

    Muñoz-Cadavid, C; Rudd, S; Zaki, S R; Patel, M; Moser, S A; Brandt, M E; Gómez, B L

    2010-06-01

    DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissues is difficult and requires special protocols in order to extract small amounts of DNA suitable for amplification. Most described methods report an amplification success rate between 60 and 80%; therefore, there is a need to improve molecular detection and identification of fungi in FFPE tissue. Eighty-one archived FFPE tissues with a positive Gomori methenamine silver (GMS) stain were evaluated using five different commercial DNA extraction kits with some modifications. Three different panfungal PCR assays were used to detect fungal DNA, and two housekeeping genes were used to assess the presence of amplifiable DNA and to detect PCR inhibitors. The sensitivities of the five extraction protocols were compared, and the quality of DNA detection (calculated for each kit as the number of housekeeping gene PCR-positive samples divided by the total number of samples) was 60 to 91% among the five protocols. The efficiencies of the three different panfungals used (calculated as the number of panfungal-PCR-positive samples divided by the number of housekeeping gene PCR-positive samples) were 58 to 93%. The panfungal PCR using internal transcribed spacer 3 (ITS3) and ITS4 primers yielded a product in most FFPE tissues. Two of the five DNA extraction kits (from TaKaRa and Qiagen) showed similar and promising results. However, one method (TaKaRa) could extract fungal DNA from 69 of the 74 FFPE tissues from which a housekeeping gene could be amplified and was also cost-effective, with a nonlaborious protocol. Factors such as sensitivity, cost, and labor will help guide the selection of the most appropriate method for the needs of each laboratory.

  15. Testing a Low Molecular Mass Fraction of a Mushroom (Lentinus edodes Extract Formulated as an Oral Rinse in a Cohort of Volunteers

    Directory of Open Access Journals (Sweden)

    Caterina Signoretto

    2011-01-01

    Full Text Available 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 found to exert these activities in in vitro experiments against potential oral pathogens. We therefore conducted a clinical trial in which we tested an LMM fraction of shiitake mushroom extract formulated in a mouthrinse in 30 young volunteers, comparing the results with those obtained in two identical cohorts, one of which received water (placebo and the other Listerine. Plaque index, gingival index and bacterial counts in plaque samples were determined in all volunteers over the 11 days of the clinical trial. Statistically significant differences (P<0.05 were obtained for the plaque index on day 12 in subjects treated with mushroom versus placebo, while for the gingival index significant differences were found for both mushroom versus placebo and mushroom versus Listerine. Decreases in total bacterial counts and in counts of specific oral pathogens were observed for both mushroom extract and Listerine in comparison with placebo. The data suggest that a mushroom extract may prove beneficial in controlling dental caries and/or gingivitis/periodontitis.

  16. Identification and characterization of low molecular weight polyphenols in berry leaf extracts by HPLC-DAD and LC-ESI/MS.

    Science.gov (United States)

    Oszmiański, Jan; Wojdyło, Aneta; Gorzelany, Józef; Kapusta, Ireneusz

    2011-12-28

    This paper reports the results of qualitative and quantitative analyses of low molecular weight phenolics from five berry leaf extract using HPLC-DAD and LC-ESI/MS. The identification of the black currant, raspberry, bilberry, honeysuckle, and strawberry leaf phytochemicals was based on the comparison of UV-vis absorption maxima (λ(max)) and mass spectral analysis. The peak identification in samples was also based on comparisons of the retention times (t(R)) of the isolated phytochemical standards. Knowledge of the precise phenolic profile of berry leaves may offer a scientific basis to put the underutilized berry leaves to good use as very cheap raw materials for polyphenol extract production. These studies indicated that these leaves can be used as a good and cheap source of bioactive constituents. These results suggest that berry leaves are a potential source of phenolics and have potential pro-healthy properties to contribute to human health.

  17. Molecular preservation by extraction and fixation, mPREF: a method for small molecule biomarker analysis and histology on exactly the same tissue

    Directory of Open Access Journals (Sweden)

    Shuster Jeffrey R

    2011-12-01

    Full Text Available Abstract Background Histopathology is the standard method for cancer diagnosis and grading to assess aggressiveness in clinical biopsies. Molecular biomarkers have also been described that are associated with cancer aggressiveness, however, the portion of tissue analyzed is often processed in a manner that is destructive to the tissue. We present here a new method for performing analysis of small molecule biomarkers and histology in exactly the same biopsy tissue. Methods Prostate needle biopsies were taken from surgical prostatectomy specimens and first fixed, each in a separate vial, in 2.5 ml of 80% methanol:water. The biopsies were fixed for 24 hrs at room temperature and then removed and post-processed using a non-formalin-based fixative (UMFIX, embedded, and analyzed by hematoxylin and eosin (H&E and by immunohistochemical (IHC staining. The retained alcohol pre-fixative was analyzed for small molecule biomarkers by mass spectrometry. Results H&E analysis was successful following the pre-fixation in 80% methanol. The presence or absence of tumor could be readily determined for all 96 biopsies analyzed. A subset of biopsy sections was analyzed by IHC, and cancerous and non-cancerous regions could be readily visualized by PIN4 staining. To demonstrate the suitability for analysis of small molecule biomarkers, 28 of the alcohol extracts were analyzed using a mass spectrometry-based metabolomics platform. All extracts tested yielded successful metabolite profiles. 260 named biochemical compounds were detected in the alcohol extracts. A comparison of the relative levels of compounds in cancer containing vs. non-cancer containing biopsies showed differences for 83 of the compounds. A comparison of the results with prior published reports showed good agreement between the current method and prior reported biomarker discovery methods that involve tissue destructive methods. Conclusions The Molecular Preservation by Extraction and Fixation (m

  18. Fingerprint Feature Extraction Algorithm

    Directory of Open Access Journals (Sweden)

    Mehala. G

    2014-03-01

    Full Text Available The goal of this paper is to design an efficient Fingerprint Feature Extraction (FFE algorithm to extract the fingerprint features for Automatic Fingerprint Identification Systems (AFIS. FFE algorithm, consists of two major subdivisions, Fingerprint image preprocessing, Fingerprint image postprocessing. A few of the challenges presented in an earlier are, consequently addressed, in this paper. The proposed algorithm is able to enhance the fingerprint image and also extracting true minutiae.

  19. Automatic Payroll Deposit System.

    Science.gov (United States)

    Davidson, D. B.

    1979-01-01

    The Automatic Payroll Deposit System in Yakima, Washington's Public School District No. 7, directly transmits each employee's salary amount for each pay period to a bank or other financial institution. (Author/MLF)

  20. 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.

  1. Molecularly imprinted polymer for caffeic acid by precipitation polymerization and its application to extraction of caffeic acid and chlorogenic acid from Eucommia ulmodies leaves.

    Science.gov (United States)

    Miura, Chitose; Matsunaga, Hisami; Haginaka, Jun

    2016-08-01

    Molecularly imprinted polymers (MIPs) for caffeic acid (CA) were prepared using 4-vinylpyridine and methacrylamide (MAM) as functional monomers, divinylbenzene as a crosslinker and acetonitrile-toluene (3:1, v/v) as a porogen by precipitation polymerization. The use of MAM as the co-monomer resulted in the formation of microsphere MIPs and non-imprinted polymers (NIPs) with ca. 3- and 5-μm particle diameters, respectively. Binding experiments and Scatchard analyses revealed that the binding capacity and affinity of the MIP to CA are higher than those of the NIP. The retention and molecular-recognition properties of the prepared MIPs were evaluated using water-acetonitrile and sodium phosphate buffer-acetonitrile as mobile phases in hydrophilic interaction chromatography (HILIC) and reversed-phase chromatography, respectively. In HILIC mode, the MIP showed higher molecular-recognition ability for CA than in reversed-phase mode. In addition to shape recognition, hydrophilic interactions seem to work for the recognition of CA on the MIP in HILIC mode, while hydrogen bonding and hydrophobic interactions seem to work for the recognition of CA in reversed-phase mode. The MIP had a specific molecular-recognition ability for CA in HILIC mode, while other structurally related compounds, such as chlorogenic acid (CGA), gallic acid, protocatechuic acid and vanillic acid, could not be recognized by the MIP. Furthermore, the MIP was successfully applied for extraction of CA and CGA in the leaves of Eucommia ulmodies in HILIC mode. PMID:26776340

  2. 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.

  3. Poder Antioxidante de Extractos de Romero Concentrados por Destilación Molecular Antioxidant Potential of Rosemary Extracts Concentrated by Molecular Distillation

    OpenAIRE

    M.A. Martinello; Pramparo, M.

    2005-01-01

    Se ha estudiado el poder antioxidativo de extractos de romero concentrados por destilación molecular. Las hojas de romero fueron molidas y secadas previamente a la extracción, la cual fue llevada a cabo en un equipo de lixiviación de lecho fijo utilizando alcohol isopropílico como solvente. El solvente fue separado del extracto mediante destilación bajo vacío. El rendimiento promedio de extracción fue del 15,5%. El extracto resultante, verde y altamente viscoso, fue sometido a concentración p...

  4. Application of an inexpensive and high-throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing eggs

    DEFF Research Database (Denmark)

    Montero-Pau, Javier; Gómez, Africa; Muñoz, Joaquin

    2008-01-01

    We describe the application of a simple, low-cost, and effective method of DNA extraction (hot sodium hydroxide and Tris, HotSHOT) to the diapausing propagules of continental aquatic invertebrates for its use in PCR amplification. We illustrate the use of the technique in cladocerans, rotifers...

  5. WEB CONTENT EXTRACTION USING HYBRID APPROACH

    OpenAIRE

    K. Nethra; Anitha, J; Thilagavathi, G

    2014-01-01

    The World Wide Web has rich source of voluminous and heterogeneous information which continues to expand in size and complexity. Many Web pages are unstructured and semi-structured, so it consists of noisy information like advertisement, links, headers, footers etc. This noisy information makes extraction of Web content tedious. Many techniques that were proposed for Web content extraction are based on automatic extraction and hand crafted rule generation. Automatic extraction technique is do...

  6. Effective Approaches For Extraction Of Keywords

    Directory of Open Access Journals (Sweden)

    Jasmeen Kaur

    2010-11-01

    Full Text Available Keywords are index terms that contain most important information. Automatic keyword extraction is the task to identify a small set of words , keyphrases or keywords from a document that can describe the meaning of document. Keyword extraction is considered as core technology of all automatic processing for text materials. In this paper, a Survey of Keyword Extraction techniques have been presented that can be applied to extract effective keywords that uniquely identify a document.

  7. Water-compatible dummy molecularly imprinted resin prepared in aqueous solution for green miniaturized solid-phase extraction of plant growth regulators.

    Science.gov (United States)

    Wang, Mingyu; Chang, Xiaochen; Wu, Xingyu; Yan, Hongyuan; Qiao, Fengxia

    2016-08-01

    A water-compatible dummy molecularly imprinted resin (MIR) was synthesized in water using melamine, urea, and formaldehyde as hydrophilic monomers of co-polycondensation. A triblock copolymer (PEO-PPO-PEO, P123) was used as porogen to dredge the network structure of MIR, and N-(1-naphthyl) ethylenediamine dihydrochloride, which has similar shape and size to the target analytes, was the dummy template of molecular imprinting. The obtained MIR was used as the adsorbent in a green miniaturized solid-phase extraction (MIR⬜mini-SPE) of plant growth regulators, and there was no organic solvent used in the entire MIR⬜mini-SPE procedure. The calibration linearity of MIR⬜mini-SPE⬜HPLC method was obtained in a range 5⬜250ngmL(↙1) for IAA, IPA, IBA, and NAA with correlation coefficient (r) Ⱕ0.9998. Recoveries at three spike levels are in the range of 87.6⬜100.0% for coconut juice with relative standard deviations Ⱔ8.1%. The MIR⬜mini-SPE method possesses the advantages of environmental friendliness, simple operation, and high efficiency, so it is potential to apply the green pretreatment strategy to extraction of trace analytes in aqueous samples. PMID:27378249

  8. Water-compatible dummy molecularly imprinted resin prepared in aqueous solution for green miniaturized solid-phase extraction of plant growth regulators.

    Science.gov (United States)

    Wang, Mingyu; Chang, Xiaochen; Wu, Xingyu; Yan, Hongyuan; Qiao, Fengxia

    2016-08-01

    A water-compatible dummy molecularly imprinted resin (MIR) was synthesized in water using melamine, urea, and formaldehyde as hydrophilic monomers of co-polycondensation. A triblock copolymer (PEO-PPO-PEO, P123) was used as porogen to dredge the network structure of MIR, and N-(1-naphthyl) ethylenediamine dihydrochloride, which has similar shape and size to the target analytes, was the dummy template of molecular imprinting. The obtained MIR was used as the adsorbent in a green miniaturized solid-phase extraction (MIR⬜mini-SPE) of plant growth regulators, and there was no organic solvent used in the entire MIR⬜mini-SPE procedure. The calibration linearity of MIR⬜mini-SPE⬜HPLC method was obtained in a range 5⬜250ngmL(↙1) for IAA, IPA, IBA, and NAA with correlation coefficient (r) Ⱕ0.9998. Recoveries at three spike levels are in the range of 87.6⬜100.0% for coconut juice with relative standard deviations Ⱔ8.1%. The MIR⬜mini-SPE method possesses the advantages of environmental friendliness, simple operation, and high efficiency, so it is potential to apply the green pretreatment strategy to extraction of trace analytes in aqueous samples.

  9. A novel surface molecularly imprinted polymer as the solid-phase extraction adsorbent for the selective determination of ampicillin sodium in milk and blood samples$

    Institute of Scientific and Technical Information of China (English)

    Ningli Wu; Qiang Fu; Zhimin Luo; Yanhui Ge; Pengqi Guo; Kangli Du; Weili Tang; Wei Du; Aiguo Zeng; Chun Chang

    2016-01-01

    Surface molecularly imprinted polymers (SMIPs) for selective adsorption of ampicillin sodium were synthesized using surface molecular imprinting technique with silica gel as a support. The physical and morphological characteristics of the polymers were investigated by scanning electron microscope (SEM), Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), elemental analysis and nitrogen adsorption–desorption test. The obtained results showed that the SMIPs displayed great adsorption capacity (13.5μg/mg), high recognition ability (the imprinted factor is 3.2) and good binding kinetics for ampicillin sodium. Finally, as solid phase extraction adsorbents, the SMIPs coupled with HPLC method were validated and applied for the enrichment, purification and determination of ampicillin sodium in real milk and blood samples. The averages of spiked accuracy ranged from 92.1%to 107.6%. The relative standard deviations of intra-and inter-day precisions were less than 4.6%. This study provides a new and promising method for enriching, extracting and determining ampicillin sodium in complex biological samples.

  10. Glyoxal-Urea-Formaldehyde Molecularly Imprinted Resin as Pipette Tip Solid-Phase Extraction Adsorbent for Selective Screening of Organochlorine Pesticides in Spinach.

    Science.gov (United States)

    Yang, Chen; Lv, Tianwei; Yan, Hongyuan; Wu, Gaochan; Li, Haonan

    2015-11-01

    A new kind of glyoxal-urea-formaldehyde molecularly imprinted resin (GUF-MIR) was synthesized by a glyoxal-urea-formaldehyde (GUF) gel imprinting method with 4,4'-dichlorobenzhydrol as a dummy template. The obtained GUF-MIR was characterized by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT-IR) and applied as a selective adsorbent of miniaturized pipet tip solid-phase extraction (PT-SPE) for the separation and extraction of three organochlorine pesticides (dicofol (DCF), dichlorodiphenyl dichloroethane (DDD), and tetradifon) in spinach samples. The proposed pretreatment procedures of spinach samples involved only 5.0 mg of GUF-MIR, 0.7 mL of MeOH-H2O (1:1, v/v) (washing solvent), and 0.6 mL of cyclohexane-ethyl acetate (9:1, v/v) (elution solvent). In comparison with other adsorbents (such as silica gel, C18, NH2-silica gel, and neutral alumina (Al2O3-N)), GUF-MIR showed higher adsorption and purification capacity for DCF, DDD, and tetradifon in aqueous solution. The average recoveries at three spiked levels ranged from 89.1% to 101.9% with relative standard deviations (RSDs) ≤ 7.1% (n = 3). The presented GUF-MIR-PT-SPE method combines the advantages of molecularly imprinted polymers (MIPs), GUF, and PT-SPE and can be used in polar solutions with high affinity and selectivity to the analytes in complex samples.

  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. To Remove or Not to Remove? The Challenge of Extracting the Template to Make the Cavities Available in Molecularly Imprinted Polymers (MIPs

    Directory of Open Access Journals (Sweden)

    Angel Concheiro

    2011-07-01

    Full Text Available Template removal is a critical step in the preparation of most molecularly imprinted polymers (MIPs. The polymer network itself and the affinity of the imprinted cavities for the template make its removal hard. If there are remaining template molecules in the MIPs, less cavities will be available for rebinding, which decreases efficiency. Furthermore, if template bleeding occurs during analytical applications, errors will arise. Despite the relevance to the MIPs performance, template removal has received scarce attention and is currently the least cost-effective step of the MIP development. Attempts to reach complete template removal may involve the use of too drastic conditions in conventional extraction techniques, resulting in the damage or the collapse of the imprinted cavities. Advances in the extraction techniques in the last decade may provide optimized tools. The aim of this review is to analyze the available data on the efficiency of diverse extraction techniques for template removal, paying attention not only to the removal yield but also to MIPs performance. Such an analysis is expected to be useful for opening a way to rational approaches for template removal (minimizing the costs of solvents and time instead of the current trial-and-error methods.

  13. On-line restricted access molecularly imprinted solid phase extraction of ivermectin in meat samples followed by HPLC-UV analysis.

    Science.gov (United States)

    de Lima, Marcela Marília; Vieira, André Coutinho; Martins, Isarita; Boralli, Vanessa Bergamin; Borges, Keyller Bastos; Figueiredo, Eduardo Costa

    2016-04-15

    A new restricted access molecularly imprinted polymer coated with bovine serum albumin (RAMIP-BSA) was synthesized, characterized and used for direct analysis of ivermectin from bovine meat samples, in a two-dimensional liquid chromatography system with UV detection. Ivermectin, 4-vynilpiridine and ethylene glycol dimethacrylate were employed as template, functional monomer and cross-linker, respectively. A BSA layer was cross-linked around the polymer, resulting in a biocompatible chemical barrier able to eliminate about 100% of protein from the samples. Ivermectin was extracted from the minced meat samples through a solvent extraction using methanol:water (70:30, v:v), and the extracts were directly injected into the two-dimensional liquid chromatography system, without any other treatment. Samples, fortified with ivermectin from 50 to 500 μg kg(-1), were used to build the analytical calibration curve (r=0.996). The limit of quantification was 50 μg kg(-1). Precision and accuracy presented variation coefficients, as well as relative errors lower than 17.0% and within -18.5% and 22.0%, respectively.

  14. Simultaneous extraction from clinical biopsies of high-molecular-weight DNA and RNA: comparative characterization by biotinylated and 32P-labeled probes on Southern and Northern blots

    International Nuclear Information System (INIS)

    A method for efficient simultaneous extraction of high-molecular-weight DNA and RNA from solid mammalian tissues including clinical biopsies is described. It is based on the disruption and subsequent melting of deep frozen tissue in the presence of frozen phenol and nucleic acid extraction buffer; this allows for simultaneous disruption of tissue and inactivation of nucleases. The yield is about 0.7-5.8 mg of DNA and 0.5-8.1 mg of total RNA/g of tissue depending upon the tissue type; this is higher than the yield of other methods tested. Analysis of total RNA by denaturing gel electrophoresis, and of DNA and poly(A)+ RNA by Southern and Northern blot hybridization using 32P and biotinylated probes, indicated that c-Ha-ras gene and its transcripts were undegraded. Biotinylated and 32P probes had approximately the same sensitivity in detecting nucleic acids on Southern and Northern blots. This extraction procedure is simple and, when used with biotinylated probes, is rapid, inexpensive, and nonhazardous. The methodology can be modified for use with other clinical samples and cells grown in culture

  15. 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.

  16. Using Protege for Automatic Ontology Instantiation

    OpenAIRE

    Alani, Harith; Kim, Sanghee; Millard, David E.; Weal, Mark J.; Hall, Wendy; Lewis, Paul H.; Shadbolt, Nigel

    2004-01-01

    This paper gives an overview on the use of Protégé in the Artequakt system, which integrated Protégé with a set of natural language tools to automatically extract knowledge about artists from web documents and instantiate a given ontology. Protégé was also linked to structured templates that generate documents from the knowledge fragments it maintains.

  17. Molecularly imprinted polymer for chlorogenic acid by modified precipitation polymerization and its application to extraction of chlorogenic acid from Eucommia ulmodies leaves.

    Science.gov (United States)

    Miura, Chitose; Li, Hui; Matsunaga, Hisami; Haginaka, Jun

    2015-10-10

    Molecularly imprinted polymers (MIPs) for chlorogenic acid (CGA) were prepared by modified precipitation polymerization using methacrylic acid as a functional monomer, divinylbenzene as a crosslinker and methanol or dimethylsulfoxide as a co-solvent. The prepared MIPs were microspheres with a narrow particle size distribution. Binding experiments and Scatchard analyses revealed that two classes of binding sites, high and low affinity sites, were formed on the MIP. The retention and molecular-recognition properties of the prepared MIP were evaluated using a mixture of water and acetonitrile as a mobile phase in hydrophilic interaction chromatography. With an increase of acetonitrile content, the retention factor of CGA was increased on the MIP. In addition to shape recognition, hydrophilic interactions seem to work for the recognition of CGA on the MIP. The MIP had a specific molecular-recognition ability for CGA, while other related compounds, such as caffeic acid, gallic acid, protocatechuic acid and vanillic acid, could not be recognized by the MIP. Furthermore, the MIP for CGA was successfully applied for extraction of CGA in the leaves of Eucommia ulmodies. PMID:26037163

  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. Prevention Effects and Possible Molecular Mechanism of Mulberry Leaf Extract and its Formulation on Rats with Insulin-Insensitivity.

    Science.gov (United States)

    Liu, Yan; Li, Xuemei; Xie, Chen; Luo, Xiuzhen; Bao, Yonggang; Wu, Bin; Hu, Yuchi; Zhong, Zhong; Liu, Chang; Li, MinJie

    2016-01-01

    For centuries, mulberry leaf has been used in traditional Chinese medicine for the treatment of diabetes. This study aims to test the prevention effects of a proprietary mulberry leaf extract (MLE) and a formula consisting of MLE, fenugreek seed extract, and cinnamon cassia extract (MLEF) on insulin resistance development in animals. MLE was refined to contain 5% 1-deoxynojirimycin by weight. MLEF was formulated by mixing MLE with cinnamon cassia extract and fenugreek seed extract at a 6:5:3 ratio (by weight). First, the acute toxicity effects of MLE on ICR mice were examined at 5 g/kg BW dose. Second, two groups of normal rats were administrated with water or 150 mg/kg BW MLE per day for 29 days to evaluate MLE's effect on normal animals. Third, to examine the effects of MLE and MLEF on model animals, sixty SD rats were divided into five groups, namely, (1) normal, (2) model, (3) high-dose MLE (75 mg/kg BW) treatment; (4) low-dose MLE (15 mg/kg BW) treatment; and (5) MLEF (35 mg/kg BW) treatment. On the second week, rats in groups (2)-(5) were switched to high-energy diet for three weeks. Afterward, the rats were injected (ip) with a single dose of 105 mg/kg BW alloxan. After four more days, fasting blood glucose, post-prandial blood glucose, serum insulin, cholesterol, and triglyceride levels were measured. Last, liver lysates from animals were screened with 650 antibodies for changes in the expression or phosphorylation levels of signaling proteins. The results were further validated by Western blot analysis. We found that the maximum tolerance dose of MLE was greater than 5 g/kg in mice. The MLE at a 150 mg/kg BW dose showed no effect on fast blood glucose levels in normal rats. The MLE at a 75 mg/kg BW dose and MLEF at a 35 mg/kg BW dose, significantly (p < 0.05) reduced fast blood glucose levels in rats with impaired glucose and lipid metabolism. In total, 34 proteins with significant changes in expression and phosphorylation levels were identified. The

  20. Optical sensing of phenylalanine in urine via extraction with magnetic molecularly imprinted poly(ethylene-co-vinyl alcohol) nanoparticles

    Science.gov (United States)

    Hsu, Chung-Yi; Lee, Mei-Hwa; Thomas, James L.; Shih, Ching-Ping; Hung, Tzu-Lin; Whang, Thou-Jen; Lin, Hung-Yin

    2015-07-01

    Incorporation of superparamagnetic nanoparticles into molecularly imprinted polymers (MIPs) is useful for both bioseparations and for concentration and sensing of biomedically relevant target molecules in physiological fluids, through the application of a magnetic field. In this study, we combined the separation and concentration of a target (phenylalanine) in urine, using magnetic molecularly imprinted polymeric composite nanoparticles, with optical sensing, to improve assay sensitivity. This target is important as a catecholamine precursor, and as an important amino acid constituent of proteins. Poly(ethylene-co-vinyl alcohol)s were imprinted with target molecules, and showed a high imprinting effectiveness (target binding compared with binding to non-imprinted polymer particles.) Fluorescence spectrophotometry was used to measure binding of the target, and also binding of possible interfering compounds. These measurements suggest that functional groups on phenylalanine dominate the selectivity of the synthesized MIPs. Finally, the composite nanoparticles were used to separate and sense the target molecule in urine by Raman scattering microscopy.

  1. Magnetic molecularly imprinted polymer for the selective extraction of sildenafil, vardenafil and their analogs from herbal medicines.

    Science.gov (United States)

    Chen, Fang-Fang; Xie, Xiao-Yu; Shi, Yan-Ping

    2013-10-15

    The successfully developed magnetic molecularly imprinted polymers (MMIPs) toward six synthetic phosphodiesterase type-5 (PDE-5) inhibitors were described. Sildenafil was used as template for the preparation of MMIPs using superparamagnetic core-shell nanoparticle as supporter. The obtained MMIPs were characterized using transmission electron microscope, Fourier transform infrared, X-ray diffraction, and vibrating sample magnetometer. High performance liquid chromatography (HPLC) with diode array detector (DAD) was used for the analysis of target analytes. The application of MMIPs as selective sorbent in the cleanup of herbal medicine samples prior to HPLC offered simple sample preparation. The adsorption capacity and selectivity of prepared MMIPs and magnetic non-molecularly imprinted polymers were investigated. The binding isotherms were obtained for sildenafil and fitted by Freundlich isotherm model. Structurally similar compound of sildenafil and a reference compound protocatechuic acid were used for investing the selective recognition of MMIPs. PMID:24054622

  2. Optical sensing of phenylalanine in urine via extraction with magnetic molecularly imprinted poly(ethylene-co-vinyl alcohol) nanoparticles.

    Science.gov (United States)

    Hsu, Chung-Yi; Lee, Mei-Hwa; Thomas, James L; Shih, Ching-Ping; Hung, Tzu-Lin; Whang, Thou-Jen; Lin, Hung-Yin

    2015-07-31

    Incorporation of superparamagnetic nanoparticles into molecularly imprinted polymers (MIPs) is useful for both bioseparations and for concentration and sensing of biomedically relevant target molecules in physiological fluids, through the application of a magnetic field. In this study, we combined the separation and concentration of a target (phenylalanine) in urine, using magnetic molecularly imprinted polymeric composite nanoparticles, with optical sensing, to improve assay sensitivity. This target is important as a catecholamine precursor, and as an important amino acid constituent of proteins. Poly(ethylene-co-vinyl alcohol)s were imprinted with target molecules, and showed a high imprinting effectiveness (target binding compared with binding to non-imprinted polymer particles.) Fluorescence spectrophotometry was used to measure binding of the target, and also binding of possible interfering compounds. These measurements suggest that functional groups on phenylalanine dominate the selectivity of the synthesized MIPs. Finally, the composite nanoparticles were used to separate and sense the target molecule in urine by Raman scattering microscopy.

  3. Preparation of molecularly imprinted solid-phase microextraction fiber for the selective removal and extraction of the antiviral drug abacavir in environmental and biological matrices.

    Science.gov (United States)

    Terzopoulou, Zoi; Papageorgiou, Myrsini; Kyzas, George Z; Bikiaris, Dimitrios N; Lambropoulou, Dimitra A

    2016-03-24

    In the present study, a molecularly imprinted solid-phase microextraction fiber (MIP-SPMEf) 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 (Qmax) was determined by Langmuir- Freundlich model and was 149 mg/g for MIP-SPMEf. 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. PMID:26944990

  4. Cyto•IQ: an adaptive cytometer for extracting the noisy dynamics of molecular interactions in live cells

    Science.gov (United States)

    Ball, David A.; Moody, Stephen E.; Peccoud, Jean

    2010-02-01

    We have developed a fundamentally new type of cytometer to track the statistics of dynamic molecular interactions in hundreds of individual live cells within a single experiment. This entirely new high-throughput experimental system, which we have named Cyto•IQ, reports statistical, rather than image-based data for a large cellular population. Like a flow cytometer, Cyto•IQ rapidly measures several fluorescent probes in a large population of cells to yield a reduced statistical model that is matched to the experimental goals set by the user. However, Cyto•IQ moves beyond flow cytometry by tracking multiple probes in individual cells over time. Using adaptive learning algorithms, we process data in real time to maximize the convergence of the statistical model parameter estimators. Software controlling Cyto•IQ integrates existing open source applications to interface hardware components, process images, and adapt the data acquisition strategy based on previously acquired data. These innovations allow the study of larger populations of cells, and molecular interactions with more complex dynamics, than is possible with traditional microscope-based approaches. Cyto•IQ supports research to characterize the noisy dynamics of molecular interactions controlling biological processes.

  5. 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

  6. Automatic utilities auditing

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Colin Boughton [Energy Metering Technology (United Kingdom)

    2000-08-01

    At present, energy audits represent only snapshot situations of the flow of energy. The normal pattern of energy audits as seen through the eyes of an experienced energy auditor is described. A brief history of energy auditing is given. It is claimed that the future of energy auditing lies in automatic meter reading with expert data analysis providing continuous automatic auditing thereby reducing the skill element. Ultimately, it will be feasible to carry out auditing at intervals of say 30 minutes rather than five years.

  7. 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...... camera. We approach this problem by modelling it as a dynamic multi-objective optimisation problem and show how this metaphor allows a much richer expressiveness than a classical single objective approach. Finally, we showcase the application of a multi-objective evolutionary algorithm to generate a shot...

  8. Determination of boron in waters and in water extracts from wastes by molecular and atomic absorption spectrometry following preliminary boron separation by extraction of its complex with 2-ethylhexane-1,3-diol

    International Nuclear Information System (INIS)

    Two methods for boron determination were developed and tested. The analysis is based on boron separation and preconcentration by extraction from an acid aqueous solution into a chloroform solution of 2-ethylhexane-1,3-diol followed by reextraction into aqueous sodium hydroxide, and subsequent molecular absorption spectroscopic determination with curcumine at 543 nm or atomic absorption spectroscopic determination at 249.8 nm in a nitrous oxide-acetylene flame. The limits of determination (3s criterion) for the two methods are 0.002 and 0.1 mg/l, respectively. The methods were compared with the conventional procedure based on the use of azomethine-H. While the sensitivities of the methods are comparable (the limit of determination for the azomethine-H method is 0.02 mg/l), the proposed methods exhibit a better reliability and are widely applicable to the determination of total boron in all types of water and water extracts. (author) 3 tabs., 37 refs

  9. Automatic detection of moving objects in video surveillance

    OpenAIRE

    Guezouli, Larbi; Belhani, Hanane

    2016-01-01

    This work is in the field of video surveillance including motion detection. The video surveillance is one of essential techniques for automatic video analysis to extract crucial information or relevant scenes in video surveillance systems. The aim of our work is to propose solutions for the automatic detection of moving objects in real time with a surveillance camera. The detected objects are objects that have some geometric shape (circle, ellipse, square, and rectangle).

  10. Supported liquid membrane-protected molecularly imprinted beads for the solid phase micro-extraction of triazines from environmental waters.

    Science.gov (United States)

    Turiel, E; Díaz-Álvarez, M; Martín-Esteban, A

    2016-02-01

    In this work, a novel methodology based on the combination of MIP technology with micro solid-phase extraction in a hollow fibre device for the trace enrichment and cleanup of triazines in environmental waters is described. All parameters affecting both migration of triazines from samples to the lumen of the fibre and rebinding into MIP sites have been carefully optimized. Final conditions included, addition of 20% NaCl to the sample to produce salting-out effect, extraction of analytes during 45min with orbital stirring at 750rpm, and then washing the fibre with toluene during 5min to allow selective recognition of triazines before elution in HPLC inserts containing 450μL of a methanol/acetic acid mixture (95/5, v/v). Under optimum conditions, quantitative recoveries for simazine, cyanazine, atrazine, propazine and terbutylazine, were achieved both in surface, ground and tap water samples, with relative standard deviations lower than 10.6%, and limits of detection in the low ngL(-1) concentration level. PMID:26777780

  11. 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 abstract...

  12. Direct detection of circulating free DNA extracted from serum samples of breast cancer using locked nucleic acid molecular beacon.

    Science.gov (United States)

    Gui, Zhen; Wang, Quanbo; Li, Jinchang; Zhu, Mingchen; Yu, Lili; Xun, Tang; Yan, Feng; Ju, Huangxian

    2016-07-01

    As an emerging noninvasive blood biomarker, circulating free DNA (cfDNA) can be utilized to assess diagnosis, progression and evaluate prognosis of cancer. However, cfDNAs are not "naked", they can be part of complexes, or are bound to the surface of the cells via proteins, which make the detection more challenging. Here, a simple method for the detection of Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) DNA exacted from serum of breast cancer (BC) has been developed using a novel locked nucleic acid molecular beacon (LNA-MB). In order to enhance the stability and detection efficiency of the probe in biofluids, we design a shared-stem molecular beacon containing a 27-mer loop and a 4-mer stem with DNA/LNA alternating bases. The fluorescence is released in the presence of target. The detection procedure is simple and can be completed within 1h. This method shows a sensitive response to UHRF1 DNA with a dynamic range of 3 orders of magnitude. The limit of detection is 11nM (S/N=3) with excellent selectivity. It can discriminate UHRF1 DNA from three-base mismatched DNA with a high specificity. More importantly, this method can distinguish the expression of serum UHRF1 DNA among 5 breast cancer patients and 5 healthy controls. The mentioned superiority may suggest that this assay can be served as a promising noninvasive detection tool for early BC diagnosis and monitoring.

  13. Direct detection of circulating free DNA extracted from serum samples of breast cancer using locked nucleic acid molecular beacon.

    Science.gov (United States)

    Gui, Zhen; Wang, Quanbo; Li, Jinchang; Zhu, Mingchen; Yu, Lili; Xun, Tang; Yan, Feng; Ju, Huangxian

    2016-07-01

    As an emerging noninvasive blood biomarker, circulating free DNA (cfDNA) can be utilized to assess diagnosis, progression and evaluate prognosis of cancer. However, cfDNAs are not "naked", they can be part of complexes, or are bound to the surface of the cells via proteins, which make the detection more challenging. Here, a simple method for the detection of Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) DNA exacted from serum of breast cancer (BC) has been developed using a novel locked nucleic acid molecular beacon (LNA-MB). In order to enhance the stability and detection efficiency of the probe in biofluids, we design a shared-stem molecular beacon containing a 27-mer loop and a 4-mer stem with DNA/LNA alternating bases. The fluorescence is released in the presence of target. The detection procedure is simple and can be completed within 1h. This method shows a sensitive response to UHRF1 DNA with a dynamic range of 3 orders of magnitude. The limit of detection is 11nM (S/N=3) with excellent selectivity. It can discriminate UHRF1 DNA from three-base mismatched DNA with a high specificity. More importantly, this method can distinguish the expression of serum UHRF1 DNA among 5 breast cancer patients and 5 healthy controls. The mentioned superiority may suggest that this assay can be served as a promising noninvasive detection tool for early BC diagnosis and monitoring. PMID:27154709

  14. The protective effects of Schisandra chinensis fruit extract and its lignans against cardiovascular disease: a review of the molecular mechanisms.

    Science.gov (United States)

    Chun, Jung Nyeo; Cho, Minsoo; So, Insuk; Jeon, Ju-Hong

    2014-09-01

    Schisandra chinensis fruit extract (SCE) has traditionally been used as an oriental medicine for the treatment of various human diseases, including cardiovascular disease. Advances in scientific knowledge and analytical technologies provide opportunities for translational research involving S. chinensis; such research may contribute to future drug discovery. To date, emerging experimental evidence supports the therapeutic effects of the SCE or its bioactive lignan ingredients in cardiovascular disease, unraveling the mechanistic basis for their pharmacological actions. In the present review, we highlight SCE and its lignans as promising resources for the development of safe, effective, and multi-targeted agents against cardiovascular disease. Moreover, we offer novel insight into future challenges and perspective on S. chinensis research to future clinical investigations and healthcare strategies.

  15. A newly developed molecularly imprinted polymer on the surface of TiO2 for selective extraction of triazine herbicides residues in maize, water, and soil.

    Science.gov (United States)

    Geng, Hao Ran; Miao, Shan Shan; Jin, She Feng; Yang, Hong

    2015-11-01

    A new surface molecularly imprinted polymer (MIP) based on nano-TiO2 was developed using propazine (Pro) as a template molecule, ethyleneglycol dimethacrylate (EGDMA) as a crosslinker, methacrylic acid (MAA) as a functional monomer, and 2,2'-azobis (isobutyronitrile) (AIBN) as an initiator. Structures of the newly synthesized surface MIPs were characterized by Fourier transmission infrared spectrometry (FT-IR), scanning electron microscope (SEM), transmission electron microscope (TEM), and X-ray diffraction (XRD). The MIP had a good adsorption capacity and high recognition selectivity to propazine. Meanwhile, it exhibited a cross-selectivity for simazine (Sim) and atrazine (Atr). The MIPs were used as a solid phase extraction (SPE) material. Concomitant extraction, purification, and determination of three pesticides (Pro, Sim, and Atr) residues in water, soil, and maize plant and grain samples were performed by MIP-SPE coupled with high performance liquid chromatography (HPLC). The highly selective separation and enrichment of Pro, Atr, and Sim from the complex environmental media can be achieved. Thus, the newly developed technique provides an analytical platform to quantify the trace amount of Pro, Sim, and Atr residues in multi environmental media and food source. PMID:26410737

  16. Efficient determination of protocatechuic acid in fruit juices by selective and rapid magnetic molecular imprinted solid phase extraction coupled with HPLC.

    Science.gov (United States)

    Xie, Lianwu; Guo, Junfang; Zhang, Yuping; Shi, Shuyun

    2014-08-13

    Magnetic molecular imprinted polymers (MMIPs) have been prepared as solid phase material to selectively extract protocatechuic acid (PCA) from fruit juices with high capacity and fast binding kinetics. The resulting MMIPs were characterized by TEM, FT-IR, TGA, and VSM. The adsorption process between PCA and MMIPs followed Langumuir adsorption isotherm with maximum adsorption capacity at 7.5 mg/g and pseudo-second-order reaction kinetics with fast binding kinetics (equilibrium time at 40 min). In addition, the prepared MMIPs showed rapid magnetic separation (10 s) and reusability (retained 94.9% after six cycles). Subsequently, MMIPs were successfully applied for selective enrichment and determination of PCA from fruit juices (0.45 μg/mL in grape juice but not detected in apple juice, pineapple juice, orange juice, and peach juice) with satisfactory recoveries (92-107%). The results indicated that synthesized MMIPs can be used for efficient and selective extraction of PCA from complex matrices. PMID:25075753

  17. Molecularly imprinted polymer microspheres prepared by Pickering emulsion polymerization for selective solid-phase extraction of eight bisphenols from human urine samples.

    Science.gov (United States)

    Yang, Jiajia; Li, Yun; Wang, Jincheng; Sun, Xiaoli; Cao, Rong; Sun, Hao; Huang, Chaonan; Chen, Jiping

    2015-05-01

    The bisphenol A (BPA) imprinted polymer microspheres were prepared by simple Pickering emulsion polymerization. Compared to traditional bulk polymerization, both high yields of polymer and good control of particle sizes were achieved. The characterization results of scanning electron microscopy and nitrogen adsorption-desorption measurements showed that the obtained molecularly imprinted polymer microsphere (MIPMS) particles possessed regular spherical shape, narrow diameter distribution (30-60 μm), a specific surface area (S(BET)) of 281.26 m(2) g(-1) and a total pore volume (V(t)) of 0.459 cm(3) g(-1). Good specific adsorption capacity for BPA was obtained in the sorption experiment and good class selectivity for BPA and its seven structural analogs (bisphenol F, bisphenol B, bisphenol E, bisphenol AF, bisphenol S, bisphenol AP and bisphenol Z) was demonstrated by the chromatographic evaluation experiment. The MIPMS as solid-phase extraction (SPE) packing material was then evaluated for extraction and clean-up of these bisphenols (BPs) from human urine samples. An accurate and sensitive analytical method based on the MIPMS-SPE coupled with HPLC-DAD has been successfully established for simultaneous determination of eight BPs from human urine samples with detection limits of 1.2-2.2 ng mL(-1). The recoveries of BPs for urine samples at two spiking levels (100 and 500 ng mL(-1) for each BP) were in the range of 81.3-106.7% with RSD values below 8.3%.

  18. Magnetic molecularly imprinted polymer nanoparticles for the solid-phase extraction of paracetamole from plasma samples, followed its determination by HPLC

    International Nuclear Information System (INIS)

    We are presenting magnetic molecularly imprinted polymer nanoparticles (m-MIPs) for solid-phase extraction and sample clean-up of paracetamole. The m-MIPs were prepared from magnetite (Fe3O4) as the magnetic component, paracetamole as the template, methacrylic acid as a functional monomer, and 2-(methacrylamido) ethyl methacrylate as a cross-linker. The m-MIPs were then characterized by transmission electron microscopy, FT-IR spectroscopy, X-ray diffraction and vibrating sample magnetometry. The m-MIPs were applied to the extraction of paracetamole from human blood plasma samples. Following its elution from the column loaded with the m-MIPs with an acetonitrile-buffer (9:1) mixture, it was submitted to HPLC analysis. Paracetamole can be quantified by this method in the 1 μg L−1 to 300 μg L−1 concentration range. The limit of detection and limit of quantification in plasma samples are 0.17 and 0.4 μg L−1. The preconcentration factor of the m-MIPs is 40. The HPLC method shows good precision (4.5 % at 50 μg L−1 levels) and recoveries (between 83 and 91 %) from spiked plasma samples. (author)

  19. Fingerprint Feature Extraction Algorithm

    OpenAIRE

    Mehala. G

    2014-01-01

    The goal of this paper is to design an efficient Fingerprint Feature Extraction (FFE) algorithm to extract the fingerprint features for Automatic Fingerprint Identification Systems (AFIS). FFE algorithm, consists of two major subdivisions, Fingerprint image preprocessing, Fingerprint image postprocessing. A few of the challenges presented in an earlier are, consequently addressed, in this paper. The proposed algorithm is able to enhance the fingerprint image and also extractin...

  20. Preparation of magnetic dummy molecularly imprinted polymers for selective extraction and analysis of salicylic acid in Actinidia chinensis.

    Science.gov (United States)

    You, Qing-Ping; Peng, Mi-Jun; Zhang, Yu-Ping; Guo, Jun-Fang; Shi, Shu-Yun

    2014-01-01

    Compounds with strong intramolecular hydrogen bonds (e.g., salicylic acid) have weak intermolecular hydrogen bonding interactions between them and functional monomers in the imprinting process. Consequently, the corresponding molecularly imprinted polymers (MIPs) have no specific adsorption ability. Here, the first magnetic dummy MIPs (MDMIPs) based on benzonic acid as dummy template are successfully developed and evaluated with respect to the applications in selective enrichment and analysis of salicylic acid from complex mixtures. Various parameters affecting absorption/desorption were evaluated for achieving optimal recovery and reducing nonspecific interactions. The prepared MDMIPs showed high adsorption capacity, good selectivity, rapid kinetic binding (40 min) and magnetic separation (5 s), high reproducibility (RSDsalicylic acid was quantified (0.2 μg/g of fresh mass) in Actinidia chinensis by high-performance liquid chromatography.

  1. Automatic bootstrapping and tracking of object contours.

    Science.gov (United States)

    Chiverton, John; Xie, Xianghua; Mirmehdi, Majid

    2012-03-01

    A new fully automatic object tracking and segmentation framework is proposed. The framework consists of a motion-based bootstrapping algorithm concurrent to a shape-based active contour. The shape-based active contour uses finite shape memory that is automatically and continuously built from both the bootstrap process and the active-contour object tracker. A scheme is proposed to ensure that the finite shape memory is continuously updated but forgets unnecessary information. Two new ways of automatically extracting shape information from image data given a region of interest are also proposed. Results demonstrate that the bootstrapping stage provides important motion and shape information to the object tracker. This information is found to be essential for good (fully automatic) initialization of the active contour. Further results also demonstrate convergence properties of the content of the finite shape memory and similar object tracking performance in comparison with an object tracker with unlimited shape memory. Tests with an active contour using a fixed-shape prior also demonstrate superior performance for the proposed bootstrapped finite-shape-memory framework and similar performance when compared with a recently proposed active contour that uses an alternative online learning model. PMID:21908256

  2. Review on the Study of Supercritical CO2 Extraction and Molecular Distillation Technology%超临界CO2萃取与分子蒸馏技术的研究综述

    Institute of Scientific and Technical Information of China (English)

    张运晖; 赵瑛; 罗俊杰

    2013-01-01

    This paper expounds the principle and main application field of supercritical CO2 extraction and molecular distillation technology, analysis of the advantages of Supercritical CO2 extraction technology and molecular distillation technology combination.%  阐述了超临界CO2萃取技术和分子蒸馏技术的工作原理及主要应用领域,分析了超临界CO2萃取技术与分子蒸馏技术联用的优势。

  3. 影像与LiDAR数据信息融合复杂场景下的道路自动提取%Automatic Road Extraction in Complex Scenes Based on Information Fusion from LiDAR Data and Remote Sensing Imagery

    Institute of Scientific and Technical Information of China (English)

    李怡静; 胡翔云; 张剑清; 江万寿; 张永军

    2012-01-01

    Automatic road extraction from remote sensing images in urban area has been a very challenging task due to the complexity of the scene, especially in the occluded or shadowed areas. An integrated method to fuse LiDAR data and high resolution imagery for automatic extraction of road centrelines is proposed. Firstly, theLiDAR point cloud is filtered to get the ground points whose intensity data is used to detect initial road centrelines and key points of the roads. A road model is then built on the intensity and dispersion of the ground points as well as spectral information obtained from the high resolution image. Based on the model, the dynamic programming algorithm is applied to find the optimal road centrelines linking the key points which are selected by evaluation. The experimental results indicate its effectiveness in automatic road extraction in urban and complex scenes.%城区的道路自动提取受场景复杂度的影响一直是极具挑战的任务,尤其是阴影和遮挡较严重地区的道路提取难度较大。结合LiDAR数据和高分辨率遥感影像,提出一种自动道路提取方法。该方法首先对滤波后的点云强度信息获取初始道路中线及道路关键点;将地面点云强度、离散度及高分辨率遥感影像光谱数据多重信息融合建立道路模型,并以优化后的道路关键点作为种子点利用动态规划计算模型最优解,进一步提取道路网。试验表明,该方法在城市复杂场景下的自动提取主要道路是有效的。

  4. Conformational Ensemble of hIAPP Dimer: Insight into the Molecular Mechanism by which a Green Tea Extract inhibits hIAPP Aggregation.

    Science.gov (United States)

    Mo, Yuxiang; Lei, Jiangtao; Sun, Yunxiang; Zhang, Qingwen; Wei, Guanghong

    2016-01-01

    Small oligomers formed early along human islet amyloid polypeptide (hIAPP) aggregation is responsible for the cell death in Type II diabetes. The epigallocatechin gallate (EGCG), a green tea extract, was found to inhibit hIAPP fibrillation. However, the inhibition mechanism and the conformational distribution of the smallest hIAPP oligomer - dimer are mostly unknown. Herein, we performed extensive replica exchange molecular dynamic simulations on hIAPP dimer with and without EGCG molecules. Extended hIAPP dimer conformations, with a collision cross section value similar to that observed by ion mobility-mass spectrometry, were observed in our simulations. Notably, these dimers adopt a three-stranded antiparallel β-sheet and contain the previously reported β-hairpin amyloidogenic precursor. We find that EGCG binding strongly blocks both the inter-peptide hydrophobic and aromatic-stacking interactions responsible for inter-peptide β-sheet formation and intra-peptide interaction crucial for β-hairpin formation, thus abolishes the three-stranded β-sheet structures and leads to the formation of coil-rich conformations. Hydrophobic, aromatic-stacking, cation-π and hydrogen-bonding interactions jointly contribute to the EGCG-induced conformational shift. This study provides, on atomic level, the conformational ensemble of hIAPP dimer and the molecular mechanism by which EGCG inhibits hIAPP aggregation. PMID:27620620

  5. 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)

    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, Ka, and the apparent maximum number of binding sites, Qmax, were estimated to be 1.25 x 105 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.

  6. Molecularly imprinted layer-coated silica nanoparticles for selective solid-phase extraction of bisphenol A from chemical cleansing and cosmetics samples

    Energy Technology Data Exchange (ETDEWEB)

    Zhu Rong; Zhao Wenhui; Zhai Meijuan; Wei Fangdi; Cai Zheng; Sheng Na [School of Pharmacy, Nanjing Medical University, Hanzhong Road 140, Nanjing, Jiangsu 210029 (China); Hu Qin, E-mail: huqin@njmu.edu.cn [School of Pharmacy, Nanjing Medical University, Hanzhong Road 140, Nanjing, Jiangsu 210029 (China)

    2010-01-25

    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{sub a}, and the apparent maximum number of binding sites, Q{sub max}, were estimated to be 1.25 x 10{sup 5} mL {mu}mol{sup -1} and 16.4 {mu}mol g{sup -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.

  7. 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.

  8. Bone Samples Extracted from Embalmed Subjects Are Not Appropriate for the Assessment of Bone Quality at the Molecular Level Using Raman Spectroscopy.

    Science.gov (United States)

    Pascart, Tristan; Cortet, Bernard; Olejnik, Cecile; Paccou, Julien; Migaud, Henri; Cotten, Anne; Delannoy, Yann; During, Alexandrine; Hardouin, Pierre; Penel, Guillaume; Falgayrac, Guillaume

    2016-03-01

    Bone samples extracted from embalmed cadavers are commonly used as controls in the study of bone. The effects of embalmment on the molecular composition of bone are unknown. The objective of this study was to determine the effect of embalmment on the molecular composition and structure of bone, as evaluated by Raman spectroscopy. Bone samples of femoral heads from five embalmed donors and five fresh-frozen donors were compared using Raman microspectroscopy with DuoScan technology. Physicochemical parameters simultaneously describing the organic and mineral phases of bone were compared using the Mann-Whitney U test. Partial least squares discriminant analysis (PLS-DA) was used to determine specific Raman spectral features of each group. Study of the mineral phase showed a 15% reduction of the mineral-to-matrix ratio (p < 0.001), an 8% decrease of type B carbonate substitution (p < 0.001), and a 2% increase in crystallinity (p < 0.001) in the embalmed donors group compared to those of the fresh donors group. Regarding the organic phase of bone, the hydroxyproline-to-proline ratio was increased by 18% in the embalmed group (p < 0.001), with no variation in both the relative proteoglycan content (GAG/CH3) (p = 0.08) and collagen maturity (p = 0.57). PLS-DA showed that the embalmed group was characterized mainly by peaks assigned to hydroxyproline, lipids, and collagen. Embalmment induces significant modifications of the molecular composition of bone. Bone samples from embalmed subjects should be avoided as controls for Raman spectroscopy studies. Preservation procedures performed prior to bone sampling should be reported in studies using human cadaver samples. PMID:26824493

  9. Novel sponge-like molecularly imprinted mesoporous silica material for selective isolation of bisphenol A and its analogues from sediment extracts

    International Nuclear Information System (INIS)

    Highlights: • Novel sponge-like molecularly imprinted mesoporous silica was synthesized. • Extraordinarily large specific surface area and highly interconnected 3-D porous network. • High specific adsorption capacity and fast adsorption kinetics for BPA. • Good class-selectivity and clean-up effect for bisphenols in sediment under SPE mode. • Good recoveries and sensitivity for bisphenols using the MISMS–SPE coupled with HPLC–DAD method. - Abstract: Bisphenol A (BPA) imprinted sponge mesoporous silica was synthesized using a combination of semi-covalent molecular imprinting and simple self-assembly process. The molecularly imprinted sponge mesoporous silica (MISMS) material obtained was characterized by FT-IR, scanning electron microscopy, transmission electron microscopy, and nitrogen adsorption–desorption measurements. The results show that the MISMS possessed a large specific surface area (850.55 m2 g−1) and a highly interconnected 3-D porous network. As a result, the MISMS demonstrated a superior specific adsorption capacity of 169.22 μmol g−1 and fast adsorption kinetics (reaching equilibrium within 3 min) for BPA. Good class selectivity for BPA and its analogues (bisphenol F, bisphenol B, bisphenol E and bisphenol AF) was also demonstrated by the sorption experiment. The MISMS as solid-phase extraction (SPE) material was then evaluated for isolation and clean-up of these bisphenols (BPs) from sediment samples. An accurate and sensitive analytical method based on the MISMS–SPE coupled with HPLC–DAD has been successfully established for simultaneous determination of five BPs in river sediments with detection limits of 0.43–0.71 ng g−1 dry weight (dw). The recoveries of BPs for lyophilizated sediment samples at two spiking levels (50 and 500 ng g−1 dw for each BP) were in the range of 75.5–105.5% with RSD values below 7.5%

  10. Novel sponge-like molecularly imprinted mesoporous silica material for selective isolation of bisphenol A and its analogues from sediment extracts

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jiajia [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, Yun; Wang, Jincheng [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); Sun, Xiaoli [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Shah, Syed Mazhar [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); Cao, Rong [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Chen, Jiping, E-mail: chenjp@dicp.ac.cn [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China)

    2015-01-01

    Highlights: • Novel sponge-like molecularly imprinted mesoporous silica was synthesized. • Extraordinarily large specific surface area and highly interconnected 3-D porous network. • High specific adsorption capacity and fast adsorption kinetics for BPA. • Good class-selectivity and clean-up effect for bisphenols in sediment under SPE mode. • Good recoveries and sensitivity for bisphenols using the MISMS–SPE coupled with HPLC–DAD method. - Abstract: Bisphenol A (BPA) imprinted sponge mesoporous silica was synthesized using a combination of semi-covalent molecular imprinting and simple self-assembly process. The molecularly imprinted sponge mesoporous silica (MISMS) material obtained was characterized by FT-IR, scanning electron microscopy, transmission electron microscopy, and nitrogen adsorption–desorption measurements. The results show that the MISMS possessed a large specific surface area (850.55 m{sup 2} g{sup −1}) and a highly interconnected 3-D porous network. As a result, the MISMS demonstrated a superior specific adsorption capacity of 169.22 μmol g{sup −1} and fast adsorption kinetics (reaching equilibrium within 3 min) for BPA. Good class selectivity for BPA and its analogues (bisphenol F, bisphenol B, bisphenol E and bisphenol AF) was also demonstrated by the sorption experiment. The MISMS as solid-phase extraction (SPE) material was then evaluated for isolation and clean-up of these bisphenols (BPs) from sediment samples. An accurate and sensitive analytical method based on the MISMS–SPE coupled with HPLC–DAD has been successfully established for simultaneous determination of five BPs in river sediments with detection limits of 0.43–0.71 ng g{sup −1} dry weight (dw). The recoveries of BPs for lyophilizated sediment samples at two spiking levels (50 and 500 ng g{sup −1} dw for each BP) were in the range of 75.5–105.5% with RSD values below 7.5%.

  11. Automatic Artist Recognition of Songs for Advanced Retrieval

    Institute of Scientific and Technical Information of China (English)

    ZHU Song-hao; LIU Yun-cai

    2008-01-01

    Automatic recognition of artists is very important in acoustic music indexing, browsing, and contentbased acoustic music retrieving, but synchronously it is still a challenging errand to extract the most representative and salient attributes to depict diversiform artists. In this paper, we developed a novel system to complete the reorganization of artist automatically. The proposed system can efficiently identify the artist's voice of a raw song by analyzing substantive features extracted from both pure music and singing song mixed with accompanying music. The experiments on different genres of songs illustrate that the proposed system is possible.

  12. Bioanalytics of mycotoxins and development of dedicated analyte-selective molecularly imprinted materials for solid-phase extraction

    International Nuclear Information System (INIS)

    Mycotoxins are secondary metabolites produced by several fungal species, growing on agricultural products during cultivation, harvest, transport or storage. Ochratoxin A (OTA) is a mycotoxin of great natural abundance and can be found in various plant products. Due to its frequent occurrence and toxic properties many countries have set up tolerance levels for OTA. Thus, the need for sensitive analytical and in particular selective sample preparation methods for analyte enrichment and removal of interfering matrix compounds is obvious. Molecular imprinting generates polymeric matrices that can selectively recognize and bind target molecules. It was previously demonstrated that molecularly imprinted polymers (MIPs) can be employed in sample preparation. MIPs capable of recognizing OTA have been prepared using an analyte mimic approach. Crucial to the success was the introduction of a novel class of quinuclidine-derived functional monomers which utilize ionic binding increments and hydrophobic interactions for selective recognition of the target analyte and its mimics. Since optimization of SPE procedures demonstrated the convenient use of several solvent systems, the developed MIPs represents an enrichment for the field of mycotoxin analysis. Zeranol has been widely adopted as a growth stimulant for cattle and other animals due to its anabolic and estrogenic properties. Application of zeranol has been banned in the European Union since 1985. Researchers, however, found that the illegal administration of this anabolic agent may not be the only source of zeranol residues in biologically relevant matrices. Previously, it was demonstrated that zeranol was also formed in vivo from the mycotoxins zearalenone (ZON) and α-zearalenol that are carried over from mycotoxin contaminated feed into the animal body. A fast, robust and sensitive LC-MS method for the determination for these compounds in urine and tissue samples has been developed. Crucial for the achievement of low

  13. 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.

  14. Automatic Program Reports

    OpenAIRE

    Lígia Maria da Silva Ribeiro; Gabriel de Sousa Torcato David

    2007-01-01

    To profit from the data collected by the SIGARRA academic IS, a systematic setof graphs and statistics has been added to it and are available on-line. Thisanalytic information can be automatically included in a flexible yearly report foreach program as well as in a synthesis report for the whole school. Somedifficulties in the interpretation of some graphs led to the definition of new keyindicators and the development of a data warehouse across the university whereeffective data consolidation...

  15. 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....

  16. Automatic Differentiation Variational Inference

    OpenAIRE

    Kucukelbir, Alp; Tran, Dustin; Ranganath, Rajesh; Gelman, Andrew; Blei, David M.

    2016-01-01

    Probabilistic modeling is iterative. A scientist posits a simple model, fits it to her data, refines it according to her analysis, and repeats. However, fitting complex models to large data is a bottleneck in this process. Deriving algorithms for new models can be both mathematically and computationally challenging, which makes it difficult to efficiently cycle through the steps. To this end, we develop automatic differentiation variational inference (ADVI). Using our method, the scientist on...

  17. Synthesis and characterization of core–shell magnetic molecularly imprinted polymer nanoparticles for selective extraction of tizanidine in human plasma

    Indian Academy of Sciences (India)

    GOLALEH SHEYKHAGHAEI; MOAYAD HOSSAINI SADR; SALAH KHANAHMADZADEH

    2016-06-01

    In this study, simple, effective and general processes were used for the synthesis of a new nanomolecularly imprinted polymers (MIPs) layer on magnetic Fe3O4 nanoparticles (NPs) with uniform core–shell structure by combining surface imprinting and nanotechniques. The first step for the synthesis of magnetic NPs was co-precipitation of Fe$^{2+}$ and Fe$^{3+}$ in an ammonia solution. Then, an SiO$_2$ shell was coated on the magnetic core with the Stöber method. Subsequently, the C$=$C groups were grafted onto the silica-modified Fe$_3$O$_4$ surface by 3-(trimethoxysilyl) propyl methacrylate. Finally, MIPs films were formed on the surface of Fe$_3$O$_4$@SiO$_2$ by the copolymerization of C$=$C end groups with methacrylic acid (functional monomer), ethylene glycol dimethacrylate (crosslinker),2,2-azobisisobutyronitrile (initiator) and tizanidine (template molecule). The products were characterized using techniques that included Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), UV spectrophotometry, transmission electron microscopy (TEM) and vibrating sample magnetometer (VSM). Measurement of tizanidine through use of the core–shell magnetic molecularly imprinted polymers nanoparticles (MMIPs-NPs) in human plasma samples compared to the paracetamol showed that the synthesized nanosized MMIP for tizanidine has acted selectively.

  18. Automatic Facial Expression Analysis A Survey

    Directory of Open Access Journals (Sweden)

    C.P. Sumathi

    2013-01-01

    Full Text Available The Automatic Facial Expression Recognition has been one of the latest research topic since1990’s.There have been recent advances in detecting face, facial expression recognition andclassification. There are multiple methods devised for facial feature extraction which helps in identifyingface and facial expressions. This paper surveys some of the published work since 2003 till date. Variousmethods are analysed to identify the Facial expression. The Paper also discusses about the facialparameterization using Facial Action Coding System(FACS action units and the methods whichrecognizes the action units parameters using facial expression data that are extracted. Various kinds offacial expressions are present in human face which can be identified based on their geometric features,appearance features and hybrid features . The two basic concepts of extracting features are based onfacial deformation and facial motion. This article also identifies the techniques based on thecharacteristics of expressions and classifies the suitable methods that can be implemented.

  19. Water-compatible graphene oxide/molecularly imprinted polymer coated stir bar sorptive extraction of propranolol from urine samples followed by high performance liquid chromatography-ultraviolet detection.

    Science.gov (United States)

    Fan, Wenying; He, Man; You, Linna; Zhu, Xuewei; Chen, Beibei; Hu, Bin

    2016-04-22

    Due to the high selectivity and stability, molecularly imprinted polymers (MIPs) have been successfully applied in stir bar sorptive extraction (SBSE) as a special coating to improve the selective extraction capability for target analytes. However, traditional MIPs usually suffer from incompatibility in aqueous media and low adsorption capacity, which limit the application of MIP coated stir bar in aqueous samples. To solve these problems, a water-compatible graphene oxides (GO)/MIP composite coated stir bar was prepared in this work by in situ polymerization. The prepared water-compatible GO/MIP coated stir bar presented good mechanical strength and chemical stability, and its recognition ability in aqueous samples was improved due to the polymerization of MIP in water environment, the adsorption capacity for target analytes was also increased by the addition of GO in MIP pre-polymer solution. Based on it, a method of water-compatible GO/MIP coated stir bar sorptive extraction combined with high performance liquid chromatography-ultraviolet detector (HPLV-UV) was proposed for the analysis of propranolol (PRO) in aqueous solution. The influencing factors of SBSE, such as sample pH, salt effect, stirring rate, extraction time, desorption solvent and desorption time, were optimized, and the analytical performance of the developed SBSE-HPLC-UV method was evaluated under the optimized conditions. The limit of detection (LOD) of the proposed method for PRO was about 0.37 μg L(-1), and the enrichment factor (EF) was 59.7-fold (theoretical EF was 100-fold). The reproducibility was also investigated at concentrations of 5 μg L(-1) and the relative standard deviation (RSD) was found to be 7.3% (n=7). The proposed method of GO/MIP coating-SBSE-HPLC-UV was successfully applied for the assay of the interested PRO drug in urine samples, and further extended to the investigation of the excretion of the drugs by monitoring the variation of the concentration of PRO in urine

  20. 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

    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......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...

  1. Molecular mechanisms of apoptosis induced by Scorpio water extract in human hepatoma HepG2 cells

    Institute of Scientific and Technical Information of China (English)

    Kang-Beom Kwon; Eun-Kyung Kim; Jung-Gook Lim; Eun-Sil Jeong; Byung-Cheul Shin; Young-Se Jeon; Kang-San Kim; Eun-A Seo; Do-Gon Ryu

    2005-01-01

    AIM: To clarify the mechanism underlying the anti-mutagenic and anti-cancer activities of Scorpio water extract (SWE).METHODS: Human hepatoma HepG2 cells were incubated with various concentrations of SWE. After 24-h incubation,cytotoxicity and apoptosis evaluations were determined by MTT and DNA fragmentation assay, respectively. After treatment with SWE, mitochondrial membrane potential(MMP) was determined by measuring the retention of the dye 3,3'-dihexyloxacarbocyanine (DiOC6(3)) and the protein expression including cytochrome C and poly-(ADPribose) polymerase (PARP)were measured by Western blotting. Caspase-3 and -9 enzyme activities were measured using specific fluorescence dyes such as Ac-DEVD-AFC and Ac-LEHD-AFC.RESULTS: We found that treatment with SWE induced apoptosis as confirmed by discontinuous DNA fragmentation in cultured human hepatoma HepG2 cells. Our investigation also showed that SWE-induced apoptosis of HepG2 cells were associated with intracellular events including disruption of MMP, increased translocation of cytochrome C from mitochondria to cytosol, activation of caspase-3,and PARP. Pre-treatment of N-acetyl-Asp-Glu-Val-Asp-CHO(Ac-DEVD-CHO), a caspase-3 specific inhibitor, or cydosporin A (CsA), an inhibitor of MMP disruption, completely abolished SWE-induced DNA fragmentation.CONCLUSION: These results suggest that SWE possibly causes mitochondrial damage, leading to cytochrome C release into cytosol and activation of caspases resulting in PARP cleavage and execution of apoptotic cell death in HepG2 cells. These results further suggest that Scorpio may be a valuable agent of therapeutic intervention of human hepatomas.

  2. 一种用于Web信息抽取的页面信息本体自动学习方法%An Automatic Ontology Learning Approach Based on Web Information Items for Web Information Extraction

    Institute of Scientific and Technical Information of China (English)

    柳佳刚; 龙军; 李泽军

    2011-01-01

    钟对基于Web页面信息本体的信息抽取中,需人工根据待抽信息项的概念和对应的实例值来建立本体的缺点,设计一个页面信息本体的自动学习方法.论文利用前期在基于DOM的页面相似路径归纳学习算法和基于PAT-tree的自动关键词识别算法上的研究成果,使用改进的TF·IDF统计方法和复合事件的关联规则算法完成概念和概念间关系的学习,建立页面信息本体,减少建立本体的人工工作量.%According to the weakness of building ontology needs manually designated concepts and instances from the basic information of web, an automatic ontology learning approach based on web information items is designed. Utilizing preresearch that an arithmetic of an inductive learning based on DOM for the similar path of information items and an approach for identifying automatic keyword based on PAT-tree, the learning for the concepts and the relation between concepts is implemented by using an approved TFIDF statistic method and an algorithm of composite event association rule, the information item ontology is built, the manual workload for building ontology is reduce

  3. Automatic modulation recognition of communication signals

    CERN Document Server

    Azzouz, Elsayed Elsayed

    1996-01-01

    Automatic modulation recognition is a rapidly evolving area of signal analysis. In recent years, interest from the academic and military research institutes has focused around the research and development of modulation recognition algorithms. Any communication intelligence (COMINT) system comprises three main blocks: receiver front-end, modulation recogniser and output stage. Considerable work has been done in the area of receiver front-ends. The work at the output stage is concerned with information extraction, recording and exploitation and begins with signal demodulation, that requires accurate knowledge about the signal modulation type. There are, however, two main reasons for knowing the current modulation type of a signal; to preserve the signal information content and to decide upon the suitable counter action, such as jamming. Automatic Modulation Recognition of Communications Signals describes in depth this modulation recognition process. Drawing on several years of research, the authors provide a cr...

  4. Automatic breast density classification using neural network

    Science.gov (United States)

    Arefan, D.; Talebpour, A.; Ahmadinejhad, N.; Kamali Asl, A.

    2015-12-01

    According to studies, the risk of breast cancer directly associated with breast density. Many researches are done on automatic diagnosis of breast density using mammography. In the current study, artifacts of mammograms are removed by using image processing techniques and by using the method presented in this study, including the diagnosis of points of the pectoral muscle edges and estimating them using regression techniques, pectoral muscle is detected with high accuracy in mammography and breast tissue is fully automatically extracted. In order to classify mammography images into three categories: Fatty, Glandular, Dense, a feature based on difference of gray-levels of hard tissue and soft tissue in mammograms has been used addition to the statistical features and a neural network classifier with a hidden layer. Image database used in this research is the mini-MIAS database and the maximum accuracy of system in classifying images has been reported 97.66% with 8 hidden layers in neural network.

  5. Automatic breast density classification using neural network

    International Nuclear Information System (INIS)

    According to studies, the risk of breast cancer directly associated with breast density. Many researches are done on automatic diagnosis of breast density using mammography. In the current study, artifacts of mammograms are removed by using image processing techniques and by using the method presented in this study, including the diagnosis of points of the pectoral muscle edges and estimating them using regression techniques, pectoral muscle is detected with high accuracy in mammography and breast tissue is fully automatically extracted. In order to classify mammography images into three categories: Fatty, Glandular, Dense, a feature based on difference of gray-levels of hard tissue and soft tissue in mammograms has been used addition to the statistical features and a neural network classifier with a hidden layer. Image database used in this research is the mini-MIAS database and the maximum accuracy of system in classifying images has been reported 97.66% with 8 hidden layers in neural network

  6. Autotract: automatic cleaning and tracking of fibers

    Science.gov (United States)

    Prieto, Juan C.; Yang, Jean Y.; Budin, François; Styner, Martin

    2016-03-01

    We propose a new tool named Autotract to automate fiber tracking in diffusion tensor imaging (DTI). Autotract uses prior knowledge from a source DTI and a set of corresponding fiber bundles to extract new fibers for a target DTI. Autotract starts by aligning both DTIs and uses the source fibers as seed points to initialize a tractography algorithm. We enforce similarity between the propagated source fibers and automatically traced fibers by computing metrics such as fiber length and fiber distance between the bundles. By analyzing these metrics, individual fiber tracts can be pruned. As a result, we show that both bundles have similar characteristics. Additionally, we compare the automatically traced fibers against bundles previously generated and validated in the target DTI by an expert. This work is motivated by medical applications in which known bundles of fiber tracts in the human brain need to be analyzed for multiple datasets.

  7. 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

  8. Collision-induced dissociation pathways of yeast sphingolipids and their molecular profiling in total lipid extracts: a study by quadrupole TOF and linear ion trap-orbitrap mass spectrometry

    DEFF Research Database (Denmark)

    Ejsing, Christer S.; Moehring, Thomas; Bahr, Ute;

    2006-01-01

    and the long chain base moieties in individual molecular species. By selecting m/z of class-specific fragment ions for multiple precursor ion scanning, we profiled yeast sphingolipids in total lipid extracts on a QqTOF mass spectrometer. Thus, a combination of QqTOF and LTQ Orbitrap mass spectrometry lends...

  9. 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}.

  10. Molecularly imprinted polymer solid-phase extraction coupled to square wave voltammetry at carbon fibre microelectrodes for the determination of fenbendazole in beef liver.

    Science.gov (United States)

    Guzmán-Vázquez de Prada, A; Loaiza, Oscar A; Serra, B; Morales, D; Martínez-Ruiz, P; Reviejo, A J; Pingarrón, J M

    2007-05-01

    A molecularly imprinted polymer was developed and used for solid-phase extraction (MISPE) of the antihelmintic fenbendazole in beef liver samples. Detection of the analyte was accomplished using square wave voltammetry (SWV) at a cylindrical carbon fibre microelectrode (CFME). A mixture of MeOH/HAc (9:1) was employed both as eluent in the MISPE system and as working medium for electrochemical detection of fenbendazole. The limit of detection was 1.9x10(-7) mol L-1 (57 microg L-1), which was appropriate for the determination of fenbendazole at the maximum residue level permitted by the European Commission (500 microg kg-1 in liver). Given that the SW voltammetric analysis could not be directly performed in the sample extract as a consequence of interference from some sample components, a sample clean-up with a MIP for selectively retaining fenbendazole was performed. The MIP was synthesized using a 1:8:22 template/methacrylic acid/ethylene glycol dimethacrylate ratio. A Britton-Robinson Buffer of pH 9.0 was selected for retaining fenbendazole in the MIP cartridges, and an eluent volume of 5.0 mL at a flow rate of 2.0 mL min-1 was chosen in the elution step. Cross-reactivity with the MIP was observed for other benzimidazoles. The synthesized MIP exhibited a good selectivity for benzimidazoles with respect to other veterinary drugs. The applicability of the MISPE-SWV method was tested with beef liver samples, spiked with fenbendazole at 5,000 and 500 microg kg-1. Results obtained for ten different liver samples yielded mean recoveries of (95+/-12)% and (96+/-11)% for the upper and lower concentration level, respectively.

  11. 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.

  12. Adherence Reduction of Campylobacter jejuni and Campylobacter coli Strains to HEp-2 Cells by Mannan Oligosaccharides and a High-Molecular-Weight Component of Cranberry Extract.

    Science.gov (United States)

    Ramirez-Hernandez, Alejandra; Rupnow, John; Hutkins, Robert W

    2015-08-01

    Campylobacter infections are a leading cause of human bacterial gastroenteritis in the United States and are a major cause of diarrheal disease throughout the world. Colonization and subsequent infection and invasion of Campylobacter require that the bacteria adhere to the surface of host cells. Agents that inhibit adherence could be used prophylactically to reduce Campylobacter carriage and infection. Mannan oligosaccharides (MOS) have been used as a feed supplement in livestock animals to improve performance and to replace growth-promoting antibiotics. However, MOS and other nondigestible oligosaccharides may also prevent pathogen colonization by inhibiting adherence in the gastrointestinal tract. In addition, plant extracts, including those derived from cranberries, have been shown to have antiadherence activity against pathogens. The goal of this study was to assess the ability of MOS and cranberry fractions to serve as antiadherence agents against strains of Campylobacter jejuni and Campylobacter coli. Adherence experiments were performed using HEp-2 cells. Significant reductions in adherence of C. jejuni 29438, C. jejuni 700819, C. jejuni 3329, and C. coli 43485 were observed in the presence of MOS (up to 40 mg/ml) and with a high-molecular-weight fraction of cranberry extract (up to 3 mg/ml). However, none of the tested materials reduced adherence of C. coli BAA-1061. No additive effect in adherence inhibition was observed for an MOS-cranberry blend. These results suggest that both components, MOS and cranberry, could be used to reduce Campylobacter colonization and carriage in livestock animals and potentially limit human exposure to this pathogen. PMID:26219363

  13. Quantitation and determination of molecular weight distribution of residual water soluble extractable polyamines in DMP 504, a poly-alkylamine bile acid sequestrant, by aqueous high performance size exclusion chromatography.

    Science.gov (United States)

    Juliano, K; Champion, W L; Schreiber, M A; Blackwell, J A

    1997-11-01

    A high performance size exclusion chromatography (HPSEC) method with refractive index detection for quantitation and molecular weight determination of extractable water soluble polyamines (SPA) in a novel proprietary polymeric pharmaceutical compound (DMP 504) is described. The extracted polyamines are synthetic impurities as well as potential degradation products of the polymer. Data for calibration, precision, solution stability, and limits of detection and quantitation are presented to validate the suitability of this method for its intended purpose. Response linearity for the poly(2-vinylpyridine) standard is demonstrated between 10 and 1000 micrograms ml-1, equivalent to 0.005% and 0.5% (w/w) in DMP 504. Molecular weight distributions of SPA extracted from DMP 504 are presented. No increase in SPA is detected in DMP 504 over 6 months storage at room temperature.

  14. KEYWORD EXTRACTION FOR PUNJABI LAGUAGE

    Directory of Open Access Journals (Sweden)

    KAMALDEEP KAUR

    2011-06-01

    Full Text Available This paper introduces keyword extraction for Punjabi language. Keywords are the index terms that contain the most important information about the contents of the document. Automatic keyword extraction is the task to identify a small set of words, keyphrases or keywords from a document that can describe the meaning ofdocument. Not much work has been done in keyword extraction for Indian languages in general and Punjabi in particular. Adequate annotated corpora are not yet available in Punjabi. The paper represents the Automatic keyword extraction system for Punjabi language to find words from a document which convey the completemeaning of the text. First we survey about the various approaches available for keyword extraction, then represent our hybrid approach for Punjabi. A number of features are used to extract keywords effectively. The experimental results are shown.

  15. Automatic Configuration in NTP

    Institute of Scientific and Technical Information of China (English)

    Jiang Zongli(蒋宗礼); Xu Binbin

    2003-01-01

    NTP is nowadays the most widely used distributed network time protocol, which aims at synchronizing the clocks of computers in a network and keeping the accuracy and validation of the time information which is transmitted in the network. Without automatic configuration mechanism, the stability and flexibility of the synchronization network built upon NTP protocol are not satisfying. P2P's resource discovery mechanism is used to look for time sources in a synchronization network, and according to the network environment and node's quality, the synchronization network is constructed dynamically.

  16. 自动电位滴定测定马蹄提取物中多酚类化合物%Determination of Polyphenols in Chinese Water Chestnut Extraction by Automatic Potentiometric Titration

    Institute of Scientific and Technical Information of China (English)

    汤亚芳; 黄广凤

    2016-01-01

    建立电位滴定法测定马蹄中多酚类化合物含量的定量分析方法。以高锰酸钾为氧化剂,在强酸性介质中,以没食子酸为参照,用二阶微分法确定待测样品试液的滴定终点电位,对马蹄提取物中的多酚类化合物进行自动滴定,并与可见分光光度法进行对比。方法的RSD为1.29%(n=5),平均回收率为99.34%。结果表明,本方法体系可以完成对多酚类物质的快速测定。%The automatically potentiometric titration was used to determine polyphenols in Chinese Water chestnut. The sample was tested used potassium permanganate as an oxidant in strong acid medium , gallic acid as reference, and the result was compared with the visible spectrophotometry. The RSD of method was 1.29%(n=5), and the average recovery was 99.34%. The results showed that the methodology can be completed on the rapid determination of polyphenols.

  17. Janus: Automatic Ontology Builder from XSD Files

    CERN Document Server

    Bedini, Ivan; Gardarin, Georges

    2010-01-01

    The construction of a reference ontology for a large domain still remains an hard human task. The process is sometimes assisted by software tools that facilitate the information extraction from a textual corpus. Despite of the great use of XML Schema files on the internet and especially in the B2B domain, tools that offer a complete semantic analysis of XML schemas are really rare. In this paper we introduce Janus, a tool for automatically building a reference knowledge base starting from XML Schema files. Janus also provides different useful views to simplify B2B application integration.

  18. Automatic pattern recognition

    OpenAIRE

    Petheram, R.J.

    1989-01-01

    In this thesis the author presents a new method for the location, extraction and normalisation of discrete objects found in digital images. The extraction is by means of sub-pixcel contour following around the object. The normalisation obtains and removes the information concerning size, orientation and location of the object within an image. Analyses of the results are carried out to determine the confidence in recognition of patterns, and methods of cross correlation of object descriptions ...

  19. Simulation of emission molecular spectra by a semi-automatic programme package: the case of C2 and CN diatomic molecules emitting during laser ablation of a graphite target in nitrogen environment.

    Science.gov (United States)

    Acquaviva, S

    2004-07-01

    Some emission spectra of diatomic molecules were calculated by a semi-automatic programme package in order to infer the rotational and vibrational temperatures in Boltzmann distribution by comparing them with the corresponding experimental ones. The calculation procedure was applied in the case of CN radical and C2 molecule whose optical emission spectra were recorded during pulsed excimer laser ablation of a graphite target in low-pressure nitrogen environment. Computed similar or dissimilar values of rotational and vibrational temperatures let to verify the existence or not of local thermodynamic equilibrium and to hypothesise the temporal range necessary to establish it in such experiments.

  20. Automatic personnel contamination monitor

    International Nuclear Information System (INIS)

    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)

  1. 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.

  2. 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.

  3. Fernblock (Polypodium leucotomos Extract): Molecular Mechanisms and Pleiotropic Effects in Light-Related Skin Conditions, Photoaging and Skin Cancers, a Review

    Science.gov (United States)

    Parrado, Concepcion; Mascaraque, Marta; Gilaberte, Yolanda; Juarranz, Angeles; Gonzalez, Salvador

    2016-01-01

    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. PMID:27367679

  4. Chip-based molecularly imprinted monolithic capillary array columns coated GO/SiO2 for selective extraction and sensitive determination of rhodamine B in chili powder.

    Science.gov (United States)

    Zhai, Haiyun; Huang, Lu; Chen, Zuanguang; Su, Zihao; Yuan, Kaisong; Liang, Guohuan; Pan, Yufang

    2017-01-01

    A novel solid-phase extraction chip embedded with array columns of molecularly imprinted polymer-coated silanized graphene oxide (GO/SiO2-MISPE) was established to detect trace rhodamine B (RB) in chili powder. GO/SiO2-MISPE monolithic columns for RB detection were prepared by optimizing the supporting substrate, template, and polymerizing monomer under mild water bath conditions. Adsorption capacity and specificity, which are critical properties for the application of the GO/SiO2-MISPE monolithic column, were investigated. GO/SiO2-MIP was examined by scanning electron microscopy (SEM) and Fourier transform-infrared spectroscopy. The recovery and the intraday and interday relative standard deviations for RB ranged from 83.7% to 88.4% and 2.5% to 4.0% and the enrichment factors were higher than 110-fold. The chip-based array columns effectively eliminated impurities in chili powder, indicating that the chip-based GO/SiO2-MISPE method was reliable for RB detection in food samples using high-performance liquid chromatography. Accordingly, this method has direct applications for monitoring potentially harmful dyes in processed food. PMID:27507523

  5. Automatic analysis of trabecular bone structure from knee MRI

    DEFF Research Database (Denmark)

    Marques, Joselene; Granlund, Rabia; Lillholm, Martin;

    2012-01-01

    We investigated the feasibility of quantifying osteoarthritis (OA) by analysis of the trabecular bone structure in low-field knee MRI. Generic texture features were extracted from the images and subsequently selected by sequential floating forward selection (SFFS), following a fully automatic, un...

  6. 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

    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....

  7. SAUNA—a system for automatic sampling, processing, and analysis of radioactive xenon

    Science.gov (United States)

    Ringbom, A.; Larson, T.; Axelsson, A.; Elmgren, K.; Johansson, C.

    2003-08-01

    A system for automatic sampling, processing, and analysis of atmospheric radioxenon has been developed. From an air sample of about 7 m3 collected during 12 h, 0.5 cm3 of xenon is extracted, and the atmospheric activities from the four xenon isotopes 133Xe, 135Xe, 131mXe, and 133mXe are determined with a beta-gamma coincidence technique. The collection is performed using activated charcoal and molecular sieves at ambient temperature. The sample preparation and quantification are performed using preparative gas chromatography. The system was tested under routine conditions for a 5-month period, with average minimum detectable concentrations below 1 mBq/ m3 for all four isotopes.

  8. 帕金森病患者红外线数字化步态测量数据的半自动提取方法的建立%Semi-automatic Extraction Method to Establish for the PD Gait Data of Infrared Digital Measurement

    Institute of Scientific and Technical Information of China (English)

    于昌琳; 沈林勇; 胡小吾; 钱晋武; 吴曦

    2014-01-01

    Many neurological diseases and bone-damaged diseases can cause movement disorder leading to abnormal gait,such as Parkinson′s disease.It will be more accurate to evaluate the rehabilitation of some disease through quantitative evaluation of gait param-eters instead of qualitative evaluation by doctor′s visual inspection.At present,the common method to make quantitative analysis of gait is to collect the three-dimensional coordinates of human body through the motion capture devices,then to extract the gait charac-teristics through the three-dimensional coordinates.During the extraction process,it is difficult to conduct completely automatic selec-tion due to the large masses of the original data,the complexity of completely manual processing,as well as the numerous cases of the demarcation points of clinical gait.In this case,with the combination of the advantages of multiple softwares,we utilize matlab to select demarcation points manually and then automatically extracted the displaying results of gait characteristics in friendly interface in order to realize the semi-automatic processing of three -dimensional coordinates,thus managing to extract the gait parameters efficiently as well as reflect the individual characteristics of clinical gait for Parkinson′s disease accurately.%很多神经性疾病和骨骼损伤性疾病都会造成运动障碍导致异常步态,帕金森症就是其中的一种,通过步态参数定量评估代替医生目测定性评估,可以更准确的对疾病进行康复评估。目前,对步态定量分析常用的方法是通过运动捕捉仪采集人体三维坐标,再通过三维坐标提取步态特征。在提取过程中,由于原始数据庞大,完全手工处理繁复,同时自动处理中临床步态分界点情况众多,完全自动选取存在困难。本研究结合多个软件的优势,利用matlab绘图手工选取分界点,再自动提取步态特征在友好界面中显示结果,实现对

  9. Utilization of LiDAR and tidal gauge data for automatic extracting high and low tide lines%联合机载LiDAR数据和潮汐数据自动提取潮位线

    Institute of Scientific and Technical Information of China (English)

    张良; 马洪超; 邬建伟

    2012-01-01

    首先,联合机载激光雷达(LiDAR)数据提取的海岸带数字表面模型(DSM)与验潮站数据提取的高、低潮面进行相交运算,生成“水陆二值图像”,然后对其以提取边缘的方式提取高、低潮线;针对LiDAR光束无法穿透水体导致低潮线附近DSM为无效值的缺陷,采取移动趋势面拟合法外推概略低潮线附近DSM,在此基础上重新提取更精确的低潮线.实验表明,该方法能在较少人工干预的情况下有效提取高、低潮线.%First, a binary image containing only land and ocean pixels is generated by intersecting the LiDAR-derived shore digital surface model (DSM) and the ocean surface derived from tidal gauge data. Then a series of image processing algorithms are applied to extract preliminary high and low tide lines. Since LiDAR pulses can not penetrate into water, some regions near the low tide line may have invalid DSM values. In order to overcome this disadvantage, a mobile trend surface fitting method is used to extrapolate the DSM near low water lines, hence more accurate low tide lines can be extracted- Experimental results show that this method can extract high and low tide lines effectively with less manual labors.

  10. Study of Feature Extraction Based on Autoregressive Modeling in ECG Automatic Diagnosis%ECG信号自动诊断中回归建模法特征提取的研究

    Institute of Scientific and Technical Information of China (English)

    葛丁飞; 侯北平; 项新建

    2007-01-01

    This article explores the ability of multivariate autoregressive model (MAR) and scalar AR model to extract the features from two-lead electrocardiogram signals in order to classify certain cardiac arrhythmias. The classification performance of four different ECG feature sets based on the model coefficients are shown. The data in the analysis including normal sinus rhythm,atria premature contraction, premature ventricular contraction, ventricular tachycardia, ventricular fibrillation and superventricular tachycardia is obtained from the MIT-BIH database. The classification is performed using a quadratic discriminant function. The results show the MAR coefficients produce the best results among the four ECG representations and the MAR modeling is a useful classification and diagnosis tool.

  11. A Method of Automatic Keyword Extraction Based on Word Span%基于词跨度的中文文本关键词自动提取方法

    Institute of Scientific and Technical Information of China (English)

    谢晋

    2012-01-01

    针对中文文本关键词提取方法中普遍存在的噪声干扰问题,本文提出一种基于词跨度的关键词自动提取方法。该方法通过在传统的关键词权重计算方法中,加入词跨因子,利用词跨度来过滤高频噪声数据,以达到降低噪声干扰的效果。整个关键词提取过程通过分词计算、停用词过滤、特征统计和权重计算,选出若干个能够表达文章主旨的关键词。复旦大学语料库的实验结果表明,该方法提高了关键词提取的精度,并且具备良好的稳定性。%Considering the noise interference problem commonly existing in keyword extraction, this paper proposes a new keyword extraction method in Chinese text by analyzing word span. The proposed scheme analyzes the relative importance of a word to a text through measuring the distance between the positions of this word appearing firstly and lastly in the given text. This distance, called word span, indicates the scope of the word appearing. Since a significant difference exists between the word spans of keyword and noise word, it is a valuable idea to adopt word span to precisely recognize and filter out the.noises. Here, word span is used to calculate the final weights of keywords extracted from text by analyzing characters including frequency, location and POS(part of speech). Some experiments were compete based on Fudan University Corpus, in which different types of texts were made to test this method. The results showed that this approach improved the quality of the keyword extraction, and had a stable performance effect on various texts.

  12. 融合纹理特征和空间关系的TM影像海岸线自动提取%Automatic Extraction of Coastline from TM Image Integrating Texture and Spatial Relationship

    Institute of Scientific and Technical Information of China (English)

    周亚男; 朱志文; 沈占锋; 程熙

    2012-01-01

    The authors present an effective approach and spatial relationship of imagery. Firstly, the image other is land), exploiting the texture and MNDWI, to extracting coastline from TM imagery, integrating texture area is classified into two main categories (one is water, the which are extracted from the input image. Secondly, the segmentation above is dealt with locally using mathematical morphology and the small heterogeneous regions in water and land are filled using the region growing method, relying on the spatial relationships and expert knowledge about the coastline. Finally, vectorizing the segmented image generates the final coastline, and the coastline is assessed by the proposed evaluation system, which is found on the matching of two lines. The experimental results demonstrate that the proposed method is able to accurately extract coastlines from TM image of Liaodong Peninsula. Moreover, texture and spatial relationships are useful information for coastline extraction.%针对以往研究中简单运用影像单一特征(光谱特征或者空间关系)提取海岸线的不足,在提取过程中逐步融人区域纹理特征、空间关系和经验知识,提出一种融合纹理特征和空间关系的海岸线自动提取方法:首先利用影像的水体指数和纹理特征,对影像水、陆区域进行二值分割;然后结合空间关系和经验知识,对分割结果进行优化和后处理,并生成矢量海岸线;最后,利用基于线匹配的岸线精度评价准则,分析岸线提取结果。将该方法运用到辽东半岛复杂背景条件下TM影像的海岸线提取实验中,取得了良好的实验效果,证明纹理和空间关系在海岸线提取中具有重要作用。

  13. Determination of Artificial Sweetener 4-Ethoxyphenylurea in Succade by Automatic Solid-phase Extraction and High Performance Chromatography with Fluorescence Method%全自动固相萃取-高效液相色谱荧光法测定蜜饯中人工合成甜味剂对乙氧基苯脲含量

    Institute of Scientific and Technical Information of China (English)

    陈章捷; 陈金凤; 张艳燕; 钟坚海; 魏晶晶

    2014-01-01

    提出了高效液相色谱法测定蜜饯中人工合成甜味剂对乙氧基苯脲含量的方法。样品采用醋酸-醋酸铵缓冲液超声提取,全自动固相萃取仪净化,SB-C18反相色谱柱分离,荧光检测器检测。对乙氧基苯脲在0~10 mg/L范围内的线性相关系数为0.9987,方法定量限(S/N=10)小于0.1 mg/kg。以三种空白蜜饯为基体,在3个添加水平进行加标回收试验,平均回收率在81.7%~92.4%之间,相对标准偏差(n=6)在2.4%~6.8%之间。%High performance liquid chromatography is applied for the determination of artificial sweete-ner 4-Ethoxyphenylurea in succade.The sample is ultrasonic extracted with acetic acid/ammonium acetate buffer solution and purified by automatic solid-phase extraction.The extract is separated by SB-C1 8 column and detected by fluorescence detector.The value of correlation coefficient in the range of 0 to 10 mg/L is 0.9987.The limit of quantity (S/N=10)is less than 0.1 mg/kg.Using blank sample of succade as matrixes,the recovery is tested at 3 different concentration levels and the values of recovery are in the range of 81.7% to 92.4% with RSDs (n=6)in the range of 2.4% to 6.8%.

  14. Towards a Pattern-based Automatic Generation of Logical Specifications for Software Models

    OpenAIRE

    Klimek, Radoslaw

    2014-01-01

    The work relates to the automatic generation of logical specifications, considered as sets of temporal logic formulas, extracted directly from developed software models. The extraction process is based on the assumption that the whole developed model is structured using only predefined workflow patterns. A method of automatic transformation of workflow patterns to logical specifications is proposed. Applying the presented concepts enables bridging the gap between the benefits of deductive rea...

  15. Automatic road network extraction in high resolution SAR images based on MRF%基于MRF的高分辨率SAR图像道路网自动提取

    Institute of Scientific and Technical Information of China (English)

    程江华; 高贵; 库锡树; 孙即祥

    2012-01-01

    It is extremely difficult to extract road networks from high resolution synthetic aperture radar (SAR) images due to the presence of various disturbances.Markov random field (MRF) model can make full use of the imagery contextual characters and priori knowledge,which have been widely used to extract road networks.However,there exist some problems such as slow solution and many parameters setting of these type methods.In order to reduce the computation of subsequent iterative solution of MRF,pre-linking is firstly introduced to remove numerous false line elements based on the spatial relationship among them.Then the improved road networks Markov function model is established to label road networks.SAR images with 1 meter resolution are tested in the experiment.The results show the effectivity of the method mentioned above in high resolution SAR imagery road network extraction.%各种干扰的存在使得高分辨率合成孔径雷达(synthetic aperture radar,SAR)图像道路网的提取变得异常困难.马尔可夫随机场(Markov random field,MRF)模型能够充分利用道路图像的上下文特征以及先验知识,在道路网提取中得到广泛应用,但存在求解过程偏慢及参数设置偏多问题.首先根据道路空间几何特征关系对提取出的线基元进行预连接,以此减少虚假连接给MRF迭代求解带来的运算量;然后建立MRF道路网改进模型对道路网进行快速标记.使用1m机载高分辨率SAR图像进行实验,结果验证了该方法的有效性.

  16. Molecularly imprinted polymer microspheres prepared by Pickering emulsion polymerization for selective solid-phase extraction of eight bisphenols from human urine samples

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jiajia [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, Yun; Wang, Jincheng [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); Sun, Xiaoli; Cao, Rong [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Sun, Hao [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); Department of Chemistry, Liaoning University, Shenyang 110000 (China); Huang, Chaonan [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Chen, Jiping, E-mail: chenjp@dicp.ac.cn [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China)

    2015-05-04

    Highlights: • BPA imprinted polymer microspheres were prepared by Pickering emulsion polymerization. • Regular spherical shape and narrow diameter distribution. • Good specific adsorption capacity for BPA. • Good class-selectivity and clean-up efficiency for bisphenols in human urine under SPE mode. • Good recoveries and sensitivity for bisphenols using the MIPMS-SPE coupled with HPLC-DAD method. - Abstract: The bisphenol A (BPA) imprinted polymer microspheres were prepared by simple Pickering emulsion polymerization. Compared to traditional bulk polymerization, both high yields of polymer and good control of particle sizes were achieved. The characterization results of scanning electron microscopy and nitrogen adsorption–desorption measurements showed that the obtained molecularly imprinted polymer microsphere (MIPMS) particles possessed regular spherical shape, narrow diameter distribution (30–60 μm), a specific surface area (S{sub BET}) of 281.26 m{sup 2} g{sup −1} and a total pore volume (V{sub t}) of 0.459 cm{sup 3} g{sup −1}. Good specific adsorption capacity for BPA was obtained in the sorption experiment and good class selectivity for BPA and its seven structural analogs (bisphenol F, bisphenol B, bisphenol E, bisphenol AF, bisphenol S, bisphenol AP and bisphenol Z) was demonstrated by the chromatographic evaluation experiment. The MIPMS as solid-phase extraction (SPE) packing material was then evaluated for extraction and clean-up of these bisphenols (BPs) from human urine samples. An accurate and sensitive analytical method based on the MIPMS-SPE coupled with HPLC-DAD has been successfully established for simultaneous determination of eight BPs from human urine samples with detection limits of 1.2–2.2 ng mL{sup −1}. The recoveries of BPs for urine samples at two spiking levels (100 and 500 ng mL{sup −1} for each BP) were in the range of 81.3–106.7% with RSD values below 8.3%.

  17. Alkali cation extraction by calix[4]crown-6 to room-temperature ionic liquids. The effect of solvent anion and humidity investigated by molecular dynamics simulations.

    Science.gov (United States)

    Sieffert, N; Wipff, G

    2006-01-26

    We report a molecular dynamics study on the solvation of M+ (Na+ to Cs+) alkali cations and of their LM+ complexes with a calix[4]arene host (L = 1,3-dimethoxy-calix[4]arene-crown-6 in the 1,3-alternate conformation) in the [BMI][PF6] and [BMI][Tf2N] room-temperature ionic liquids "ILs" based on the BMI+ (1-butyl-3-methylimidazolium) cation. The comparison of the two liquids and the dry versus humid form of the former one (with a 1:1 ratio of H2O and BMI+PF6- species) reveals the importance of humidity: in [BMI][PF6]-dry as in the [BMI][Tf2N] liquid, the first solvation shell of the "naked" M+ ions is composed of solvent anions only (four PF6- anions, and from four to five Tf2N- anions, respectively, quasi-neutralized by a surrounding cage of BMI+ cations), while in the [BMI][PF6]-humid IL, it comprises from one to three solvent anions and about four H2O molecules. In the LM+ complexes, the cation is shielded from solvent, but still somewhat interacts with a solvent anion in the dry ILs and with water in the humid IL. We also report tests on M+ interactions with solvent anions PF6- and Tf2N- in the gas phase, showing that the AMBER results are in satisfactory agreement with QM results obtained at different levels of theory. The question of ion recognition by L is then examined by free energy perturbation studies in the three liquids, predicting a high Cs+/Na+ selectivity upon liquid extraction from an aqueous phase, in agreement with experimental results on a parent calixarene host. A similar Cs+/Na+ selectivity is predicted upon complexation in a homogeneous IL phase, mainly due to the desolvation energy of the free cations. Thus, despite their polar character, ionic liquids qualitatively behave as classical weakly polar organic liquids (e.g., choroform) as far as liquid-liquid extraction is concerned but more like polar liquids (water, alcohols) as far as complexation in a single phase is concerned.

  18. Preparation of photonic-magnetic responsive molecularly imprinted microspheres and their application to fast and selective extraction of 17β-estradiol.

    Science.gov (United States)

    Peng, Hailong; Luo, Mei; Xiong, Hua; Yu, Ningxiang; Ning, Fangjian; Fan, Jieping; Zeng, Zheling; Li, Jinhua; Chen, Lingxin

    2016-04-15

    Photonic-magnetic responsive molecularly imprinted microspheres (PM-MIMs) were prepared by seed polymerization, through suitable functionalization of magnetic nanoparticles for further coating with photoresponsive functional monomer and imprinted layers, and then were successfully applied to the fast and selective extraction of 17β-estradiol (17β-E2) from real samples. The PM-MIMs possessed a sandwich micro-spherical structure containing Fe3O4 core, SiO2 middle layer, and MIPs shell with thickness of 25 nm. The PM-MIMs displayed excellent photoresponsive properties and could be rapidly separated from solutions under an external magnet. The PM-MIMs had specific affinity towards 17β-E2 with high adsorption capacity (Qmax=0.84 mg g(-1)) and fast binding kinetics (Kd=26.08 mg L(-1)). The PM-MIMs proved to be an ideal photoswitch with the ability of reversible uptake and release of 17β-E2 upon alternate 365 and 440 nm irradiation: 45.0% of 17β-E2 released from the PM-MIMs upon 365 nm irradiation, and 94.0% of the released 17β-E2 was rebound to the PM-MIMs at 440 nm. Accordingly, the PM-MIMs were applied for fast separation and extraction of 17β-E2 followed by HPLC-UV determination, presenting the low limit of detection (LOD, S/N=3) and quantification (LOQ, S/N=10) of 0.18 and 0.62 μmol L(-1), respectively. The high recoveries for spiked milk powder and drinking water samples were in the range of 97.5-113.0% with relative standard deviations less than 4.4%. This study reasonably combined photonic response, magnetic separation and surface imprinting, which endowed the PM-MIMs with significant advantages of high adsorption capacity and fast binding kinetics, convenient separation and recycled use, and simple rapid eco-benign adsorption/elution processes for template molecules. Thus, the PM-MIMs based method may be a simple, rapid, convenient, cost-effective and environmentally-friendly way for simultaneous separation, enrichment and detection of trace 17β-E2 in

  19. A Method of Automatic Extraction of Image Control Points for UAV Image Based on POS Data%一种基于POS数据的无人机影像自动展绘控制点方法

    Institute of Scientific and Technical Information of China (English)

    鲁恒; 李永树; 江禹

    2011-01-01

    The Unmanned Aerial Vehicle (UAV) images have the characteristics of high overlapping degree and heavy image processing workload. In order to improve the efficiency of UAV photogrammetry and take the advantages of fast mapping by the UAV technology, a method of extraction of image control points by correcting POS data was put forward. According to the principle of correct UAV POS data, POS data correction model was established and POS data error correction parameter were acquired by layout a small amount of the control points in regional network, and the corrected POS data were used in extraction of UAV images control points. The study results show that the method for UAV image rapid processing has good practical value.%针对无人机影像重叠度高,影像处理工作量大的特点,为了提高无人机摄影测量的工作效率,充分发挥无人机技术快速成图的优点,提出了一种利用改正后POS数据自动展绘控制点的方法.该方法根据无人机POS数据纠正原理,通过在区域网内布设少量控制点,建立POS数据改正模型,从而获取POS数据误差改正参数对原始POS数据进行改正,利用改正后POS数据在无人机影像上自动展绘控制点.研究结果表明,该方法对于无人机影像快速处理具有较好的实用价值.

  20. Super pixel density based clustering automatic image classification method

    Science.gov (United States)

    Xu, Mingxing; Zhang, Chuan; Zhang, Tianxu

    2015-12-01

    The image classification is an important means of image segmentation and data mining, how to achieve rapid automated image classification has been the focus of research. In this paper, based on the super pixel density of cluster centers algorithm for automatic image classification and identify outlier. The use of the image pixel location coordinates and gray value computing density and distance, to achieve automatic image classification and outlier extraction. Due to the increased pixel dramatically increase the computational complexity, consider the method of ultra-pixel image preprocessing, divided into a small number of super-pixel sub-blocks after the density and distance calculations, while the design of a normalized density and distance discrimination law, to achieve automatic classification and clustering center selection, whereby the image automatically classify and identify outlier. After a lot of experiments, our method does not require human intervention, can automatically categorize images computing speed than the density clustering algorithm, the image can be effectively automated classification and outlier extraction.