Use of advanced techniques for the extraction of phenolic compounds from Tunisian olive leaves: phenolic composition and cytotoxicity against human breast cancer cells.

PubMed

Taamalli, Amani; Arráez-Román, David; Barrajón-Catalán, Enrique; Ruiz-Torres, Verónica; Pérez-Sánchez, Almudena; Herrero, Miguel; Ibañez, Elena; Micol, Vicente; Zarrouk, Mokhtar; Segura-Carretero, Antonio; Fernández-Gutiérrez, Alberto

2012-06-01

A comparison among different advanced extraction techniques such as microwave-assisted extraction (MAE), supercritical fluid extraction (SFE) and pressurized liquid extraction (PLE), together with traditional solid-liquid extraction, was performed to test their efficiency towards the extraction of phenolic compounds from leaves of six Tunisian olive varieties. Extractions were carried out at the best selected conditions for each technique; the obtained extracts were chemically characterized using high-performance liquid chromatography (HPLC) coupled to electrospray time-of-flight mass spectrometry (ESI-TOF-MS) and electrospray ion trap tandem mass spectrometry (ESI-IT-MS(2)). As expected, higher extraction yields were obtained for PLE while phenolic profiles were mainly influenced by the solvent used as optimum in the different extraction methods. A larger number of phenolic compounds, mostly of a polar character, were found in the extracts obtained by using MAE. Best extraction yields do not correlate with highest cytotoxic activity against breast cancer cells, indicating that cytotoxicity is highly dependent on the presence of certain compounds in the extracts, although not exclusively on a single compound. Therefore, a multifactorial behavior is proposed for the anticancer activity of olive leaf compounds. Copyright © 2012 Elsevier Ltd. All rights reserved.

Aged garlic has more potent antiglycation and antioxidant properties compared to fresh garlic extract in vitro

PubMed Central

Elosta, Abdulhakim; Slevin, Mark; Rahman, Khalid; Ahmed, Nessar

2017-01-01

Protein glycation involves formation of early (Amadori) and late advanced glycation endproducts (AGEs) together with free radicals via autoxidation of glucose and Amadori products. Glycation and increased free radical activity underlie the pathogenesis of diabetic complications. This study investigated whether aged garlic has more potent antiglycation and antioxidant properties compared to fresh garlic extract in vitro in a cell-free system. Proteins were glycated by incubation with sugars (glucose, methylglyoxal or ribose) ±5–15 mg/mL of aged and fresh garlic extracts. Advanced glycation endproducts were measured using SDS-PAGE gels and by ELISA whereas Amadori products were assessed by the fructosamine method. Colorimetric methods were used to assess antioxidant activity, free radical scavenging capacity, protein-bound carbonyl groups, thiol groups and metal chelation activities in addition to phenolic, total flavonoid and flavonol content of aged and fresh garlic extracts. Aged garlic inhibited AGEs by 56.4% compared to 33.5% for an equivalent concentration of fresh garlic extract. Similarly, aged garlic had a higher total phenolic content (129 ± 1.8 mg/g) compared to fresh garlic extract (56 ± 1.2 mg/g). Aged garlic has more potent antiglycation and antioxidant properties compared to fresh garlic extract and is more suitable for use in future in vivo studies. PMID:28051097

Forest Roadidentification and Extractionof Through Advanced Log Matching Techniques

NASA Astrophysics Data System (ADS)

Zhang, W.; Hu, B.; Quist, L.

2017-10-01

A novel algorithm for forest road identification and extraction was developed. The algorithm utilized Laplacian of Gaussian (LoG) filter and slope calculation on high resolution multispectral imagery and LiDAR data respectively to extract both primary road and secondary road segments in the forest area. The proposed method used road shape feature to extract the road segments, which have been further processed as objects with orientation preserved. The road network was generated after post processing with tensor voting. The proposed method was tested on Hearst forest, located in central Ontario, Canada. Based on visual examination against manually digitized roads, the majority of roads from the test area have been identified and extracted from the process.

Evolution of Quantitative Measures in NMR: Quantum Mechanical qHNMR Advances Chemical Standardization of a Red Clover (Trifolium pratense) Extract

PubMed Central

2017-01-01

Chemical standardization, along with morphological and DNA analysis ensures the authenticity and advances the integrity evaluation of botanical preparations. Achievement of a more comprehensive, metabolomic standardization requires simultaneous quantitation of multiple marker compounds. Employing quantitative 1H NMR (qHNMR), this study determined the total isoflavone content (TIfCo; 34.5–36.5% w/w) via multimarker standardization and assessed the stability of a 10-year-old isoflavone-enriched red clover extract (RCE). Eleven markers (nine isoflavones, two flavonols) were targeted simultaneously, and outcomes were compared with LC-based standardization. Two advanced quantitative measures in qHNMR were applied to derive quantities from complex and/or overlapping resonances: a quantum mechanical (QM) method (QM-qHNMR) that employs 1H iterative full spin analysis, and a non-QM method that uses linear peak fitting algorithms (PF-qHNMR). A 10 min UHPLC-UV method provided auxiliary orthogonal quantitation. This is the first systematic evaluation of QM and non-QM deconvolution as qHNMR quantitation measures. It demonstrates that QM-qHNMR can account successfully for the complexity of 1H NMR spectra of individual analytes and how QM-qHNMR can be built for mixtures such as botanical extracts. The contents of the main bioactive markers were in good agreement with earlier HPLC-UV results, demonstrating the chemical stability of the RCE. QM-qHNMR advances chemical standardization by its inherent QM accuracy and the use of universal calibrants, avoiding the impractical need for identical reference materials. PMID:28067513

Analysis of live cell images: Methods, tools and opportunities.

PubMed

Nketia, Thomas A; Sailem, Heba; Rohde, Gustavo; Machiraju, Raghu; Rittscher, Jens

2017-02-15

Advances in optical microscopy, biosensors and cell culturing technologies have transformed live cell imaging. Thanks to these advances live cell imaging plays an increasingly important role in basic biology research as well as at all stages of drug development. Image analysis methods are needed to extract quantitative information from these vast and complex data sets. The aim of this review is to provide an overview of available image analysis methods for live cell imaging, in particular required preprocessing image segmentation, cell tracking and data visualisation methods. The potential opportunities recent advances in machine learning, especially deep learning, and computer vision provide are being discussed. This review includes overview of the different available software packages and toolkits. Copyright © 2017. Published by Elsevier Inc.

Analysis of edible oil processing options for the BIO-Plex advanced life support system

NASA Technical Reports Server (NTRS)

Greenwalt, C. J.; Hunter, J.

2000-01-01

Edible oil is a critical component of the proposed plant-based Advanced Life Support (ALS) diet. Soybean, peanut, and single-cell oil are the oil source options to date. In terrestrial manufacture, oil is ordinarily extracted with hexane, an organic solvent. However, exposed solvents are not permitted in the spacecraft environment or in enclosed human tests by National Aeronautics and Space Administration due to their potential danger and handling difficulty. As a result, alternative oil-processing methods will need to be utilized. Preparation and recovery options include traditional dehulling, crushing, conditioning, and flaking, extrusion, pressing, water extraction, and supercritical extraction. These processing options were evaluated on criteria appropriate to the Advanced Life Support System and BIO-Plex application including: product quality, product stability, waste production, risk, energy needs, labor requirements, utilization of nonrenewable resources, usefulness of by-products, and versatility and mass of equipment to determine the most appropriate ALS edible oil-processing operation.

Advances in organic-inorganic hybrid sorbents for the extraction of organic and inorganic pollutants in different types of food and environmental samples.

PubMed

Ng, Nyuk-Ting; Kamaruddin, Amirah Farhan; Wan Ibrahim, Wan Aini; Sanagi, Mohd Marsin; Abdul Keyon, Aemi S

2018-01-01

The efficiency of the extraction and removal of pollutants from food and the environment has been an important issue in analytical science. By incorporating inorganic species into an organic matrix, a new material known as an organic-inorganic hybrid material is formed. As it possesses high selectivity, permeability, and mechanical and chemical stabilities, organic-inorganic hybrid materials constitute an emerging research field and have become popular to serve as sorbents in various separaton science methods. Here, we review recent significant advances in analytical solid-phase extraction employing organic-inorganic composite/nanocomposite sorbents for the extraction of organic and inorganic pollutants from various types of food and environmental matrices. The physicochemical characteristics, extraction properties, and analytical performances of sorbents are discussed; including morphology and surface characteristics, types of functional groups, interaction mechanism, selectivity and sensitivity, accuracy, and regeneration abilities. Organic-inorganic hybrid sorbents combined with extraction techniques are highly promising for sample preparation of various food and environmental matrixes with analytes at trace levels. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of Intracellular Metabolites from Microorganisms: Quenching and Extraction Protocols

PubMed Central

Villas-Boas, Silas G.; Aggio, Raphael

2017-01-01

Sample preparation is one of the most important steps in metabolome analysis. The challenges of determining microbial metabolome have been well discussed within the research community and many improvements have already been achieved in last decade. The analysis of intracellular metabolites is particularly challenging. Environmental perturbations may considerably affect microbial metabolism, which results in intracellular metabolites being rapidly degraded or metabolized by enzymatic reactions. Therefore, quenching or the complete stop of cell metabolism is a pre-requisite for accurate intracellular metabolite analysis. After quenching, metabolites need to be extracted from the intracellular compartment. The choice of the most suitable metabolite extraction method/s is another crucial step. The literature indicates that specific classes of metabolites are better extracted by different extraction protocols. In this review, we discuss the technical aspects and advancements of quenching and extraction of intracellular metabolite analysis from microbial cells. PMID:29065530

Development of an Ammonium Sulfate DNA Extraction Method for Obtaining Amplifiable DNA in a Small Number of Cells and Its Application to Clinical Specimens

PubMed Central

Oh, Seo Young; Kim, Wook Youn; Hwang, Tae Sook; Han, Hye Seung; Lim, So Dug; Kim, Wan Seop

2013-01-01

DNA extraction from microdissected cells has become essential for handling clinical specimens with advances in molecular pathology. Conventional methods have limitations for extracting amplifiable DNA from specimens containing a small number of cells. We developed an ammonium sulfate DNA extraction method (A) and compared it with two other methods (B and C). DNA quality and quantity, β-globin amplification, and detectability of two cancer associated gene mutations were evaluated. Method A showed the best DNA yield, particularly when the cell number was very low. Amplification of the β-globin gene using DNA from the SNU 790 cell line and papillary thyroid carcinoma (PTC) cells extracted with Method A demonstrated the strongest band. BRAF V600E mutation analysis using ethanol-fixed PTC cells from a patient demonstrated both a “T” peak increase and an adjacent “A” peak decrease when 25 and 50 cells were extracted, whereas mutant peaks were too low to be analyzed using the other two methods. EGFR mutation analysis using formalin-fixed paraffin-embedded lung cancer tissues demonstrated a mutant peak with Method A, whereas the mutant peak was undetectable with Methods B or C. Method A yielded the best DNA quantity and quality with outstanding efficiency, particularly when paucicellular specimens were used. PMID:23691506

Extraction of valuable compounds from mangosteen pericarps by hydrothermal assisted sonication

NASA Astrophysics Data System (ADS)

Machmudah, Siti; Lestari, Sarah Duta; Shiddiqi, Qifni Yasa'Ash; Widiyastuti, Winardi, Sugeng; Wahyudiono, Kanda, Hideki; Goto, Motonobu

2015-12-01

Valuable compounds, such as xanthone and phenolic compounds, from mangosteen pericarps was extracted by hydrothermal treatment at temperatures of 120-160 °C and pressures of 5 MPa using batch and semi-batch extractor. This method is a simple and environmentally friendly extraction method requiring no chemicals other than water. Under these conditions, there is possibility for the formation of phenolic compounds from mangosteen pericarps from decomposition of bounds between lignin, cellulose, and hemicellulose via autohydrolysis. In order to increase the amount of extracted valuable compounds, sonication pre-treament was performed prior to the hydrothermal extraction process. 30 min of sonication pre-treatment could increase significantly the amount of xanthone and phenolic compounds mangosteen pericarps extraction. In batch-system, the xanthone recovery approach to 100 % at 160 °C with 30 min sonication pre-treatment for 150 min extraction time. Under semi-batch process, the total phenolic compounds in the extract was 217 mg/g sample at 160 °C with 30 min sonication pre-treatment for 150 min total extraction time. The results revealed that hydrothermal extraction assisted sonication pre-treatment is applicable method for the isolation of polyphenolic compounds from other types of biomass and may lead to an advanced plant biomass components extraction technology.

An in-advance stable isotope labeling strategy for relative analysis of multiple acidic plant hormones in sub-milligram Arabidopsis thaliana seedling and a single seed.

PubMed

Sun, Xiaohong; Ouyang, Yue; Chu, Jinfang; Yan, Jing; Yu, Yan; Li, Xiaoqiang; Yang, Jun; Yan, Cunyu

2014-04-18

A sensitive and reliable in-advance stable isotope labeling strategy was developed for simultaneous relative quantification of 8 acidic plant hormones in sub-milligram amount of plant materials. Bromocholine bromide (BETA) and its deuterated counterpart D9-BETA were used to in-advance derivatize control and sample extracts individually, which were then combined and subjected to solid-phase extraction (SPE) purification followed by UPLC-MS/MS analysis. Relative quantification of target compounds was obtained by calculation of the peak area ratios of BETA/D9-BETA labeled plant hormones. The in-advance stable isotope labeling strategy realized internal standard-based relative quantification of multiple kinds of plant hormones independent of availability of internal standard of every analyte with enhanced sensitivity of 1-3 orders of magnitude. Meanwhile, the in-advance labeling contributes to higher sample throughput and more reliability. The method was successfully applied to determine 8 plant hormones in 0.8mg DW (dry weight) of seedlings and 4 plant hormones from single seed of Arabidopsis thaliana. The results show the potential of the method in relative quantification of multiple plant hormones in tiny plant tissues or organs, which will advance the knowledge of the crosstalk mechanism of plant hormones. Copyright © 2014 Elsevier B.V. All rights reserved.

Review on the Extraction Methods of Crude oil from all Generation Biofuels in last few Decades

NASA Astrophysics Data System (ADS)

Bhargavi, G.; Nageswara Rao, P.; Renganathan, S.

2018-03-01

The ever growing demand for the energy fuels, economy of oil, depletion of energy resources and environmental protection are the inevitable challenges required to be solved meticulously in future decades in order to sustain the life of humans and other creatures. Switching to alternate fuels that are renewable, biodegradable, economically and environmentally friendly can quench the minimum thirst of fuel demands, in addition to mitigation of climate changes. At this moment, production of biofuels has got prominence. The term biofuels broadly refer to the fuels derived from living matter either animals or plants. Among the competent biofuels, biodiesel is one of the promising alternates for diesel engines. Biodiesel is renewable, environmentally friendly, safe to use with wide applications and biodegradable. Due to which, it has become a major focus of intensive global research and development of alternate energy. The present review has been focused specifically on biodiesel. Concerning to the biodiesel production, the major steps includes lipid extraction followed by esterification/transesterification. For the extraction of lipids, several extraction techniques have been put forward irrespective of the generations and feed stocks used. This review provides theoretical background on the two major extraction methods, mechanical and chemical extraction methods. The practical issues of each extraction method such as efficiency of extraction, extraction time, oil sources and its pros and cons are discussed. It is conceived that congregating information on oil extraction methods may helpful in further research advancements to ease biofuel production.

Inter-comparison of Methods for Extracting Subsurface Layers from SHARAD Radargrams over Martian polar regions

NASA Astrophysics Data System (ADS)

Xiong, S.; Muller, J.-P.; Carretero, R. C.

2017-09-01

Subsurface layers are preserved in the polar regions on Mars, representing a record of past climate changes on Mars. Orbital radar instruments, such as the Mars Advanced Radar for Subsurface and Ionosphere Sounding (MARSIS) onboard ESA Mars Express (MEX) and the SHAllow RADar (SHARAD) onboard the Mars Reconnaissance Orbiter (MRO), transmit radar signals to Mars and receive a set of return signals from these subsurface regions. Layering is a prominent subsurface feature, which has been revealed by both MARSIS and SHARAD radargrams over both polar regions on Mars. Automatic extraction of these subsurface layering is becoming increasingly important as there is now over ten years' of data archived. In this study, we investigate two different methods for extracting these subsurface layers from SHARAD data and compare the results against delineated layers derived manually to validate which methods is better for extracting these layers automatically.

Accurate Modeling Method for Cu Interconnect

NASA Astrophysics Data System (ADS)

Yamada, Kenta; Kitahara, Hiroshi; Asai, Yoshihiko; Sakamoto, Hideo; Okada, Norio; Yasuda, Makoto; Oda, Noriaki; Sakurai, Michio; Hiroi, Masayuki; Takewaki, Toshiyuki; Ohnishi, Sadayuki; Iguchi, Manabu; Minda, Hiroyasu; Suzuki, Mieko

This paper proposes an accurate modeling method of the copper interconnect cross-section in which the width and thickness dependence on layout patterns and density caused by processes (CMP, etching, sputtering, lithography, and so on) are fully, incorporated and universally expressed. In addition, we have developed specific test patterns for the model parameters extraction, and an efficient extraction flow. We have extracted the model parameters for 0.15μm CMOS using this method and confirmed that 10%τpd error normally observed with conventional LPE (Layout Parameters Extraction) was completely dissolved. Moreover, it is verified that the model can be applied to more advanced technologies (90nm, 65nm and 55nm CMOS). Since the interconnect delay variations due to the processes constitute a significant part of what have conventionally been treated as random variations, use of the proposed model could enable one to greatly narrow the guardbands required to guarantee a desired yield, thereby facilitating design closure.

Microwave-Assisted Hydro-Distillation of Essential Oil from Rosemary: Comparison with Traditional Distillation

PubMed Central

Moradi, Sara; Fazlali, Alireza; Hamedi, Hamid

Background: Hydro-distillation (HD) method is a traditional technique which is used in most industrial companies. Microwave-assisted Hydro-distillation (MAHD) is an advanced HD technique utilizing a microwave oven in the extraction process. Methods: In this research, MAHD of essential oils from the aerial parts (leaves) of rosemary (Rosmarinus officinalis L.) was studied and the results were compared with those of the conventional HD in terms of extraction time, extraction efficiency, chemical composition, quality of the essential oils and cost of the operation. Results: Microwave hydro-distillation was superior in terms of saving energy and extraction time (30 min, compared to 90 min in HD). Chromatography was used for quantity analysis of the essential oils composition. Quality of essential oil improved in MAHD method due to an increase of 17% in oxygenated compounds. Conclusion: Consequently, microwave hydro-distillation can be used as a substitute of traditional hydro-distillation. PMID:29296263

The Agent of extracting Internet Information with Lead Order

NASA Astrophysics Data System (ADS)

Mo, Zan; Huang, Chuliang; Liu, Aijun

In order to carry out e-commerce better, advanced technologies to access business information are in need urgently. An agent is described to deal with the problems of extracting internet information that caused by the non-standard and skimble-scamble structure of Chinese websites. The agent designed includes three modules which respond to the process of extracting information separately. A method of HTTP tree and a kind of Lead algorithm is proposed to generate a lead order, with which the required web can be retrieved easily. How to transform the extracted information structuralized with natural language is also discussed.

External Magnetic Field Reduction Techniques for the Advanced Stirling Radioisotope Generator

NASA Technical Reports Server (NTRS)

Niedra, Janis M.; Geng, Steven M.

2013-01-01

Linear alternators coupled to high efficiency Stirling engines are strong candidates for thermal-to-electric power conversion in space. However, the magnetic field emissions, both AC and DC, of these permanent magnet excited alternators can interfere with sensitive instrumentation onboard a spacecraft. Effective methods to mitigate the AC and DC electromagnetic interference (EMI) from solenoidal type linear alternators (like that used in the Advanced Stirling Convertor) have been developed for potential use in the Advanced Stirling Radioisotope Generator. The methods developed avoid the complexity and extra mass inherent in data extraction from multiple sensors or the use of shielding. This paper discusses these methods, and also provides experimental data obtained during breadboard testing of both AC and DC external magnetic field devices.

A thesis on the Development of an Automated SWIFT Edge Detection Algorithm

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

Trujillo, Christopher J.

Throughout the world, scientists and engineers such as those at Los Alamos National Laboratory, perform research and testing unique only to applications aimed towards advancing technology, and understanding the nature of materials. With this testing, comes a need for advanced methods of data acquisition and most importantly, a means of analyzing and extracting the necessary information from such acquired data. In this thesis, I aim to produce an automated method implementing advanced image processing techniques and tools to analyze SWIFT image datasets for Detonator Technology at Los Alamos National Laboratory. Such an effective method for edge detection and point extractionmore » can prove to be advantageous in analyzing such unique datasets and provide for consistency in producing results.« less

Application of FT-IR Classification Method in Silica-Plant Extracts Composites Quality Testing

NASA Astrophysics Data System (ADS)

Bicu, A.; Drumea, V.; Mihaiescu, D. E.; Purcareanu, B.; Florea, M. A.; Trică, B.; Vasilievici, G.; Draga, S.; Buse, E.; Olariu, L.

2018-06-01

Our present work is concerned with the validation and quality testing efforts of mesoporous silica - plant extracts composites, in order to sustain the standardization process of plant-based pharmaceutical products. The synthesis of the silica support were performed by using a TEOS based synthetic route and CTAB as a template, at room temperature and normal pressure. The silica support was analyzed by advanced characterization methods (SEM, TEM, BET, DLS and FT-IR), and loaded with Calendula officinalis and Salvia officinalis standardized extracts. Further desorption studies were performed in order to prove the sustained release properties of the final materials. Intermediate and final product identification was performed by a FT-IR classification method, using the MID-range of the IR spectra, and statistical representative samples from repetitive synthetic stages. The obtained results recommend this analytical method as a fast and cost effective alternative to the classic identification methods.

Use of partial dissolution techniques in geochemical exploration

USGS Publications Warehouse

Chao, T.T.

1984-01-01

Application of partial dissolution techniques to geochemical exploration has advanced from an early empirical approach to an approach based on sound geochemical principles. This advance assures a prominent future position for the use of these techniques in geochemical exploration for concealed mineral deposits. Partial dissolution techniques are classified as single dissolution or sequential multiple dissolution depending on the number of steps taken in the procedure, or as "nonselective" extraction and as "selective" extraction in terms of the relative specificity of the extraction. The choice of dissolution techniques for use in geochemical exploration is dictated by the geology of the area, the type and degree of weathering, and the expected chemical forms of the ore and of the pathfinding elements. Case histories have illustrated many instances where partial dissolution techniques exhibit advantages over conventional methods of chemical analysis used in geochemical exploration. ?? 1984.

Research of infrared laser based pavement imaging and crack detection

NASA Astrophysics Data System (ADS)

Hong, Hanyu; Wang, Shu; Zhang, Xiuhua; Jing, Genqiang

2013-08-01

Road crack detection is seriously affected by many factors in actual applications, such as some shadows, road signs, oil stains, high frequency noise and so on. Due to these factors, the current crack detection methods can not distinguish the cracks in complex scenes. In order to solve this problem, a novel method based on infrared laser pavement imaging is proposed. Firstly, single sensor laser pavement imaging system is adopted to obtain pavement images, high power laser line projector is well used to resist various shadows. Secondly, the crack extraction algorithm which has merged multiple features intelligently is proposed to extract crack information. In this step, the non-negative feature and contrast feature are used to extract the basic crack information, and circular projection based on linearity feature is applied to enhance the crack area and eliminate noise. A series of experiments have been performed to test the proposed method, which shows that the proposed automatic extraction method is effective and advanced.

Low Cost Design of an Advanced Encryption Standard (AES) Processor Using a New Common-Subexpression-Elimination Algorithm

NASA Astrophysics Data System (ADS)

Chen, Ming-Chih; Hsiao, Shen-Fu

In this paper, we propose an area-efficient design of Advanced Encryption Standard (AES) processor by applying a new common-expression-elimination (CSE) method to the sub-functions of various transformations required in AES. The proposed method reduces the area cost of realizing the sub-functions by extracting the common factors in the bit-level XOR/AND-based sum-of-product expressions of these sub-functions using a new CSE algorithm. Cell-based implementation results show that the AES processor with our proposed CSE method has significant area improvement compared with previous designs.

Research on feature extraction techniques of Hainan Li brocade pattern

NASA Astrophysics Data System (ADS)

Zhou, Yuping; Chen, Fuqiang; Zhou, Yuhua

2016-03-01

Hainan Li brocade skills has been listed as world non-material cultural heritage preservation, therefore, the research on Hainan Li brocade patterns plays an important role in Li brocade culture inheritance. The meaning of Li brocade patterns was analyzed and the shape feature extraction techniques to original Li brocade patterns were advanced in this paper, based on the contour tracking algorithm. First, edge detection was made on the design patterns, and then the morphological closing operation was used to smooth the image, and finally contour tracking was used to extract the outer contours of Li brocade patterns. The extracted contour features were processed by means of morphology, and digital characteristics of contours are obtained by invariant moments. At last, different patterns of Li brocade design are briefly analyzed according to the digital characteristics. The results showed that the pattern extraction method to Li brocade pattern shapes is feasible and effective according to above method.

Common Bile Duct Stones Detected After Cholecystectomy:Advancement into the Duodenum via the Percutaneous Route

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

Ozcan, Nevzat, E-mail: nevzatcan@yahoo.com; Erdogan, Nuri; Baskol, Mevlut

2003-04-15

Purpose: To report our experience in the use of percutaneous extraction of common bile duct stones detected in the post-cholecystectomy period. Methods: Forty-two patients in whom endoscopic cannulation and/or sphincterotomy had failed or could not be done due to several reasons underwent balloon dilatation of the ampulla of Vater and subsequent advancement of the stones via the percutaneous transhepatic route or T-tube tract. Results: The procedure was successful in 42 cases. In three patients, stones were crushed in the common bile duct and pushed as fragments into the duodenum. In all cases transient adverse effects were observed. There were nomore » major complications. All cases were checked with ultrasonography for 6 months after the procedure. Conclusion: Percutaneous extraction of common bile duct stones is an effective method of treatment with a high success rate,low complication rate and shorter hospital stay. It may serve as an alternative method in cases where endoscopic removal of stones fails.« less

Antimicrobial potential of selected brown seaweeds from Vedalai coastal waters, Gulf of Mannar

PubMed Central

Manivannan, K; Karthikai devi, G; Anantharaman, P; Balasubramanian, T

2011-01-01

Objective To evaluate the antimicrobial activity of Turbinaria conoides (T. conoides), Padina gymnospora (P. gymnospora) and Sargassum tenerrimum against human bacterial and fungal pathogens. Methods The antimicrobial activities of the extracts against various organisms were tested by using disc diffusion method. Results The methanol extract showed the better result than the other extracts. Whereas, the strong antibacterial inhibition was noted in methanol extracts of P. gymnospora against Bacillus subtilus (26.33±1.86) and the mild inhibition of ethanol extracts from T. conoides against Klebsiella pneumoniae (2.33±0.51). Acetone extraction of P. gymnospora had strong antifungal inhibition against Cryptococcus neoformans (23.00±1.78), and acetone extract of T. conoides had mild inhibition against Aspergillus niger (3.00±0.89). Conclusions The seven different solvent extracts of seaweeds used in the present study have shown significant bacterial action. Further, a detailed study on the principle compound in the seaweeds which is responsible for antimicrobial activity is still needed and it can be achieved by using advanced separation techniques. PMID:23569739

ITER structural design criteria and their extension to advanced reactor blankets*1

NASA Astrophysics Data System (ADS)

Majumdar, S.; Kalinin, G.

2000-12-01

Applications of the recent ITER structural design criteria (ISDC) are illustrated by two components. First, the low-temperature-design rules are applied to copper alloys that are particularly prone to irradiation embrittlement at relatively low fluences at certain temperatures. Allowable stresses are derived and the impact of the embrittlement on allowable surface heat flux of a simple first-wall/limiter design is demonstrated. Next, the high-temperature-design rules of ISDC are applied to evaporation of lithium and vapor extraction (EVOLVE), a blanket design concept currently being investigated under the US Advanced Power Extraction (APEX) program. A single tungsten first-wall tube is considered for thermal and stress analyses by finite-element method.

Comparison of Enzymatic and Ultrasonic Extraction of Albumin from Defatted Pumpkin (Cucurbita pepo)
Seed Powder

PubMed Central

Tu, Gia Loi; Bui, Thi Hoang Nga; Tran, Thi Thu Tra; Ton, Nu Minh Nguyet

2015-01-01

Summary In this study, ultrasound- and enzyme-assisted extractions of albumin (water-soluble protein group) from defatted pumpkin (Cucurbita pepo) seed powder were compared. Both advanced extraction techniques strongly increased the albumin yield in comparison with conventional extraction. The extraction rate was two times faster in the ultrasonic extraction than in the enzymatic extraction. However, the maximum albumin yield was 16% higher when using enzymatic extraction. Functional properties of the pumpkin seed albumin concentrates obtained using the enzymatic, ultrasonic and conventional methods were then evaluated. Use of hydrolase for degradation of cell wall of the plant material did not change the functional properties of the albumin concentrate in comparison with the conventional extraction. The ultrasonic extraction enhanced water-holding, oil-holding and emulsifying capacities of the pumpkin seed albumin concentrate, but slightly reduced the foaming capacity, and emulsion and foam stability. PMID:27904383

Comparison of Enzymatic and Ultrasonic Extraction of Albumin from Defatted Pumpkin (Cucurbita pepo)
Seed Powder.

PubMed

Tu, Gia Loi; Bui, Thi Hoang Nga; Tran, Thi Thu Tra; Ton, Nu Minh Nguyet; Man Le, Van Viet

2015-12-01

In this study, ultrasound- and enzyme-assisted extractions of albumin (water-soluble protein group) from defatted pumpkin ( Cucurbita pepo ) seed powder were compared. Both advanced extraction techniques strongly increased the albumin yield in comparison with conventional extraction. The extraction rate was two times faster in the ultrasonic extraction than in the enzymatic extraction. However, the maximum albumin yield was 16% higher when using enzymatic extraction. Functional properties of the pumpkin seed albumin concentrates obtained using the enzymatic, ultrasonic and conventional methods were then evaluated. Use of hydrolase for degradation of cell wall of the plant material did not change the functional properties of the albumin concentrate in comparison with the conventional extraction. The ultrasonic extraction enhanced water-holding, oil-holding and emulsifying capacities of the pumpkin seed albumin concentrate, but slightly reduced the foaming capacity, and emulsion and foam stability.

Advance in ERG Analysis: From Peak Time and Amplitude to Frequency, Power, and Energy

PubMed Central

Lina, Jean-Marc; Lachapelle, Pierre

2014-01-01

Purpose. To compare time domain (TD: peak time and amplitude) analysis of the human photopic electroretinogram (ERG) with measures obtained in the frequency domain (Fourier analysis: FA) and in the time-frequency domain (continuous (CWT) and discrete (DWT) wavelet transforms). Methods. Normal ERGs (n = 40) were analyzed using traditional peak time and amplitude measurements of the a- and b-waves in the TD and descriptors extracted from FA, CWT, and DWT. Selected descriptors were also compared in their ability to monitor the long-term consequences of disease process. Results. Each method extracted relevant information but had distinct limitations (i.e., temporal and frequency resolutions). The DWT offered the best compromise by allowing us to extract more relevant descriptors of the ERG signal at the cost of lesser temporal and frequency resolutions. Follow-ups of disease progression were more prolonged with the DWT (max 29 years compared to 13 with TD). Conclusions. Standardized time domain analysis of retinal function should be complemented with advanced DWT descriptors of the ERG. This method should allow more sensitive/specific quantifications of ERG responses, facilitate follow-up of disease progression, and identify diagnostically significant changes of ERG waveforms that are not resolved when the analysis is only limited to time domain measurements. PMID:25061605

Evaluation of Planetary Boundary Layer Scheme Sensitivities for the Purpose of Parameter Estimation

EPA Science Inventory

Meteorological model errors caused by imperfect parameterizations generally cannot be overcome simply by optimizing initial and boundary conditions. However, advanced data assimilation methods are capable of extracting significant information about parameterization behavior from ...

Applications of supercritical fluid extraction (SFE) of palm oil and oil from natural sources.

PubMed

Akanda, Mohammed Jahurul Haque; Sarker, Mohammed Zaidul Islam; Ferdosh, Sahena; Manap, Mohd Yazid Abdul; Ab Rahman, Nik Norulaini Nik; Ab Kadir, Mohd Omar

2012-02-10

Supercritical fluid extraction (SFE), which has received much interest in its use and further development for industrial applications, is a method that offers some advantages over conventional methods, especially for the palm oil industry. SC-CO₂ refers to supercritical fluid extraction (SFE) that uses carbon dioxide (CO₂) as a solvent which is a nontoxic, inexpensive, nonflammable, and nonpolluting supercritical fluid solvent for the extraction of natural products. Almost 100% oil can be extracted and it is regarded as safe, with organic solvent-free extracts having superior organoleptic profiles. The palm oil industry is one of the major industries in Malaysia that provides a major contribution to the national income. Malaysia is the second largest palm oil and palm kernel oil producer in the World. This paper reviews advances in applications of supercritical carbon dioxide (SC-CO₂) extraction of oils from natural sources, in particular palm oil, minor constituents in palm oil, producing fractionated, refined, bleached, and deodorized palm oil, palm kernel oil and purified fatty acid fractions commendable for downstream uses as in toiletries and confectionaries.

Recent advances in the development of extraction chromatographic materials for the isolation of radionuclides from biological and environmental samples.

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

Dietz, M. L.

1998-11-30

The determination of low levels of radionuclides in environmental and biological samples is often hampered by the complex and variable nature of the samples. One approach to circumventing this problem is to incorporate into the analytical scheme a separation and preconcentration step by which the species of interest can be isolated from the major constituents of the sample. Extraction chromatography (EXC), a form of liquid chromatography in which the stationary phase comprises an extractant or a solution of an extractant in an appropriate diluent coated onto an inert support, provides a simple and efficient means of performing a wide varietymore » of metal ion separations. Recent advances in extractant design, in particular the development of extractants capable of metal ion recognition or of strong complex formation even in acidic media, have substantially improved the utility of the method. For the preconcentration of actinides, for example, an EXC resin consisting of a liquid diphosphonic acid supported on a polymeric substrate has been shown to exhibit extraordinarily strong retention of these elements from acidic chloride media. This resin, together with other related materials, can provide the basis of a number of efficient and flexible schemes for the separation and preconcentration of radionuclides form a variety of samples for subsequent determination.« less

Microwave-Assisted Hydro-Distillation of Essential Oil from Rosemary: Comparison with Traditional Distillation.

PubMed

Moradi, Sara; Fazlali, Alireza; Hamedi, Hamid

2018-01-01

Hydro-distillation (HD) method is a traditional technique which is used in most industrial companies. Microwave-assisted Hydro-distillation (MAHD) is an advanced HD technique utilizing a microwave oven in the extraction process. In this research, MAHD of essential oils from the aerial parts (leaves) of rosemary ( Rosmarinus officinalis L. ) was studied and the results were compared with those of the conventional HD in terms of extraction time, extraction efficiency, chemical composition, quality of the essential oils and cost of the operation. Microwave hydro-distillation was superior in terms of saving energy and extraction time (30 min , compared to 90 min in HD). Chromatography was used for quantity analysis of the essential oils composition. Quality of essential oil improved in MAHD method due to an increase of 17% in oxygenated compounds. Consequently, microwave hydro-distillation can be used as a substitute of traditional hydro-distillation.

Advances in Statistical Methods for Substance Abuse Prevention Research

PubMed Central

MacKinnon, David P.; Lockwood, Chondra M.

2010-01-01

The paper describes advances in statistical methods for prevention research with a particular focus on substance abuse prevention. Standard analysis methods are extended to the typical research designs and characteristics of the data collected in prevention research. Prevention research often includes longitudinal measurement, clustering of data in units such as schools or clinics, missing data, and categorical as well as continuous outcome variables. Statistical methods to handle these features of prevention data are outlined. Developments in mediation, moderation, and implementation analysis allow for the extraction of more detailed information from a prevention study. Advancements in the interpretation of prevention research results include more widespread calculation of effect size and statistical power, the use of confidence intervals as well as hypothesis testing, detailed causal analysis of research findings, and meta-analysis. The increased availability of statistical software has contributed greatly to the use of new methods in prevention research. It is likely that the Internet will continue to stimulate the development and application of new methods. PMID:12940467

[Recent advances of synthetic biology for production of functional ingredients in Chinese materia medica].

PubMed

Su, Xin-Yao; Xue, Jian-Ping; Wang, Cai-Xia

2016-11-01

The functional ingredients in Chinese materia medica are the main active substance for traditional Chinese medicine and most of them are secondary metabolites derivatives. Until now,the main method to obtain those functional ingredients is through direct extraction from the Chinese materia medica. However, the income is very low because of the high extraction costs and the decreased medicinal plants. Synthetic biology technology, as a new and microbial approach, can be able to carry out large-scale production of functional ingredients and greatly ease the shortage of traditional Chinese medicine ingredients. This review mainly focused on the recent advances in synthetic biology for the functional ingredients production. Copyright© by the Chinese Pharmaceutical Association.

Phytochemical Constituents and Antimicrobial Activity of the Ethanol and Chloroform Crude Leaf Extracts of Spathiphyllum cannifolium (Dryand. ex Sims) Schott.

PubMed

Dhayalan, Arunachalam; Gracilla, Daniel E; Dela Peña, Renato A; Malison, Marilyn T; Pangilinan, Christian R

2018-01-01

The study investigated the medicinal properties of Spathiphyllum cannifolium (Dryand. ex Sims) Schott as a possible source of antimicrobial compounds. The phytochemical constituents were screened using qualitative methods and the antibacterial and antifungal activities were determined using agar well diffusion method. One-way analysis of variance and Fisher's least significant difference test were used. The phytochemical screening showed the presence of sterols, flavonoids, alkaloids, saponins, glycosides, and tannins in both ethanol and chloroform leaf extracts, but triterpenes were detected only in the ethanol leaf extract. The antimicrobial assay revealed that the chloroform leaf extract inhibited Candida albicans, Escherichia coli, Staphylococcus aureus, Bacillus subtilis, and Pseudomonas aeruginosa , whereas the ethanol leaf extract inhibited E. coli , S. aureus , and B. subtilis only. The ethanol and chloroform leaf extracts exhibited the highest zone of inhibition against B. subtilis . The antifungal assay showed that both the leaf extracts have no bioactivity against Aspergillus niger and C. albicans . Results suggest that chloroform is the better solvent for the extraction of antimicrobial compounds against the test organisms used in this study. Findings of this research will add new knowledge in advancing drug discovery and development in the Philippines.

User-oriented summary extraction for soccer video based on multimodal analysis

NASA Astrophysics Data System (ADS)

Liu, Huayong; Jiang, Shanshan; He, Tingting

2011-11-01

An advanced user-oriented summary extraction method for soccer video is proposed in this work. Firstly, an algorithm of user-oriented summary extraction for soccer video is introduced. A novel approach that integrates multimodal analysis, such as extraction and analysis of the stadium features, moving object features, audio features and text features is introduced. By these features the semantic of the soccer video and the highlight mode are obtained. Then we can find the highlight position and put them together by highlight degrees to obtain the video summary. The experimental results for sports video of world cup soccer games indicate that multimodal analysis is effective for soccer video browsing and retrieval.

A novel key-frame extraction approach for both video summary and video index.

PubMed

Lei, Shaoshuai; Xie, Gang; Yan, Gaowei

2014-01-01

Existing key-frame extraction methods are basically video summary oriented; yet the index task of key-frames is ignored. This paper presents a novel key-frame extraction approach which can be available for both video summary and video index. First a dynamic distance separability algorithm is advanced to divide a shot into subshots based on semantic structure, and then appropriate key-frames are extracted in each subshot by SVD decomposition. Finally, three evaluation indicators are proposed to evaluate the performance of the new approach. Experimental results show that the proposed approach achieves good semantic structure for semantics-based video index and meanwhile produces video summary consistent with human perception.

A review study on the effect of Iranian herbal medicines against in vitro replication of herpes simplex virus

PubMed Central

Moradi, Mohammad-Taghi; Rafieian-Kopaei, Mahmoud; Karimi, Ali

2016-01-01

Objective: There are a number of published data indicating in vitro anti-HSV activity of some of Iranian herbal extracts with no systematic review to discuss these results. Therefore, this article was aimed to review and discuss the methods carried out and the phytochemistry and bioactivity of the extracts used and also conclusions provided in these publications. Materials and Methods: Published articles both in English (from Medline, Science Direct, EMBASE, Scopus, Pro Quest, Google scholar, Cochrane Library) and in Persian (from SID, Iran Medex and Magiran) databases, from 1966 to October 2014 were incorporated in this review. The in vitro studies that lacked CC50, IC50, were excluded. Results: Only 42 published reports were found to examine Iranian herbs against HSV replication in vitro. Seventeen out of 42 studies in which 23 kinds of medicinal plants were subjected to crude extraction were included. The review of data showed that some of the herbal extracts including Hyssopus officinalis methanolic extract, Melissa officinalis aqueous extract, Quercus persica L. hydroalcoholic extract and Securigeras ecuridaca methanolic extract with selective index (SI) of 234, 877, >778 and 250, respectively were highly effective against HSV in vitro. Conclusion: More comprehensive studies using more advanced methods are needed to be done to achieve promising anti-HSV agents from the bioactive compounds isolated from these herbs. PMID:27761420

Response monitoring using quantitative ultrasound methods and supervised dictionary learning in locally advanced breast cancer

NASA Astrophysics Data System (ADS)

Gangeh, Mehrdad J.; Fung, Brandon; Tadayyon, Hadi; Tran, William T.; Czarnota, Gregory J.

2016-03-01

A non-invasive computer-aided-theragnosis (CAT) system was developed for the early assessment of responses to neoadjuvant chemotherapy in patients with locally advanced breast cancer. The CAT system was based on quantitative ultrasound spectroscopy methods comprising several modules including feature extraction, a metric to measure the dissimilarity between "pre-" and "mid-treatment" scans, and a supervised learning algorithm for the classification of patients to responders/non-responders. One major requirement for the successful design of a high-performance CAT system is to accurately measure the changes in parametric maps before treatment onset and during the course of treatment. To this end, a unified framework based on Hilbert-Schmidt independence criterion (HSIC) was used for the design of feature extraction from parametric maps and the dissimilarity measure between the "pre-" and "mid-treatment" scans. For the feature extraction, HSIC was used to design a supervised dictionary learning (SDL) method by maximizing the dependency between the scans taken from "pre-" and "mid-treatment" with "dummy labels" given to the scans. For the dissimilarity measure, an HSIC-based metric was employed to effectively measure the changes in parametric maps as an indication of treatment effectiveness. The HSIC-based feature extraction and dissimilarity measure used a kernel function to nonlinearly transform input vectors into a higher dimensional feature space and computed the population means in the new space, where enhanced group separability was ideally obtained. The results of the classification using the developed CAT system indicated an improvement of performance compared to a CAT system with basic features using histogram of intensity.

Endoscopic versus Percutaneous Biliary Drainage in Palliation of Advanced Malignant Hilar Obstruction: A Meta-Analysis and Systematic Review

PubMed Central

Dharmapuri, Sirish; Duvvuri, Abhiram; Dharmapuri, Sowmya; Boddireddy, Raghuveer; Moole, Vishnu; Yedama, Prathyusha; Bondalapati, Naveen; Uppu, Achuta

2016-01-01

Background. Palliation in advanced unresectable hilar malignancies can be achieved by endoscopic (EBD) or percutaneous transhepatic biliary drainage (PTBD). It is unclear if one approach is superior to the other in this group of patients. Aims. Compare clinical outcomes of EBD versus PTBD. Methods. (i) Study Selection Criterion. Studies using PTBD and EBD for palliation of advanced unresectable hilar malignancies. (ii) Data Collection and Extraction. Articles were searched in Medline, PubMed, and Ovid journals. (iii) Statistical Method. Fixed and random effects models were used to calculate the pooled proportions. Results. Initial search identified 786 reference articles, in which 62 articles were selected and reviewed. Data was extracted from nine studies (N = 546) that met the inclusion criterion. The pooled odds ratio for successful biliary drainage in PTBD versus EBD was 2.53 (95% CI = 1.57 to 4.08). Odds ratio for overall adverse effects in PTBD versus EBD groups was 0.81 (95% CI = 0.52 to 1.26). Odds ratio for 30-day mortality rate in PTBD group versus EBD group was 0.84 (95% CI = 0.37 to 1.91). Conclusions. In patients with advanced unresectable hilar malignancies, palliation with PTBD seems to be superior to EBD. PTBD is comparable to EBD in regard to overall adverse effects and 30-day mortality. PMID:27648439

Extraction of Extended Small-Scale Objects in Digital Images

NASA Astrophysics Data System (ADS)

Volkov, V. Y.

2015-05-01

Detection and localization problem of extended small-scale objects with different shapes appears in radio observation systems which use SAR, infra-red, lidar and television camera. Intensive non-stationary background is the main difficulty for processing. Other challenge is low quality of images, blobs, blurred boundaries; in addition SAR images suffer from a serious intrinsic speckle noise. Statistics of background is not normal, it has evident skewness and heavy tails in probability density, so it is hard to identify it. The problem of extraction small-scale objects is solved here on the basis of directional filtering, adaptive thresholding and morthological analysis. New kind of masks is used which are open-ended at one side so it is possible to extract ends of line segments with unknown length. An advanced method of dynamical adaptive threshold setting is investigated which is based on isolated fragments extraction after thresholding. Hierarchy of isolated fragments on binary image is proposed for the analysis of segmentation results. It includes small-scale objects with different shape, size and orientation. The method uses extraction of isolated fragments in binary image and counting points in these fragments. Number of points in extracted fragments is normalized to the total number of points for given threshold and is used as effectiveness of extraction for these fragments. New method for adaptive threshold setting and control maximises effectiveness of extraction. It has optimality properties for objects extraction in normal noise field and shows effective results for real SAR images.

Protein extraction from methanol fixed paraffin embedded tissue blocks: A new possibility using cell blocks

PubMed Central

Kokkat, Theresa J.; McGarvey, Diane; Patel, Miral S.; Tieniber, Andrew D.; LiVolsi, Virginia A.; Baloch, Zubair W.

2013-01-01

Background: Methanol fixed and paraffin embedded (MFPE) cellblocks are an essential cytology preparation. However, MFPE cellblocks often contain limited material and their relatively small size has caused them to be overlooked in biomarker discovery. Advances in the field of molecular biotechnology have made it possible to extract proteins from formalin fixed and paraffin embedded (FFPE) tissue blocks. In contrast, there are no established methods for extracting proteins from MFPE cellblocks. We investigated commonly available CHAPS (3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate) buffer, as well as two commercially available Qiagen® kits and compared their effectiveness on MFPE tissue for protein yields. Materials and Methods: MFPE blocks were made by Cellient™ automated system using human tissue specimens from normal and malignant specimens collected in ThinPrep™ Vials. Protein was extracted from Cellient-methanol fixed and paraffin embedded blocks with CHAPS buffer method as well as FFPE and Mammalian Qiagen® kits. Results: Comparison of protein yields demonstrated the effectiveness of various protein extraction methods on MFPE cellblocks. Conclusion: In the current era of minimally invasive techniques to obtain minimal amount of tissue for diagnostic and prognostic purposes, the use of commercial and lab made buffer on low weight MFPE scrapings obtained by Cellient® processor opens new possibilities for protein biomarker research. PMID:24403950

A simple and accurate HPLC method for fecal bile acid profile in healthy and cirrhotic subjects: validation by GC-MS and LC-MS[S

PubMed Central

Kakiyama, Genta; Muto, Akina; Takei, Hajime; Nittono, Hiroshi; Murai, Tsuyoshi; Kurosawa, Takao; Hofmann, Alan F.; Pandak, William M.; Bajaj, Jasmohan S.

2014-01-01

We have developed a simple and accurate HPLC method for measurement of fecal bile acids using phenacyl derivatives of unconjugated bile acids, and applied it to the measurement of fecal bile acids in cirrhotic patients. The HPLC method has the following steps: 1) lyophilization of the stool sample; 2) reconstitution in buffer and enzymatic deconjugation using cholylglycine hydrolase/sulfatase; 3) incubation with 0.1 N NaOH in 50% isopropanol at 60°C to hydrolyze esterified bile acids; 4) extraction of bile acids from particulate material using 0.1 N NaOH; 5) isolation of deconjugated bile acids by solid phase extraction; 6) formation of phenacyl esters by derivatization using phenacyl bromide; and 7) HPLC separation measuring eluted peaks at 254 nm. The method was validated by showing that results obtained by HPLC agreed with those obtained by LC-MS/MS and GC-MS. We then applied the method to measuring total fecal bile acid (concentration) and bile acid profile in samples from 38 patients with cirrhosis (17 early, 21 advanced) and 10 healthy subjects. Bile acid concentrations were significantly lower in patients with advanced cirrhosis, suggesting impaired bile acid synthesis. PMID:24627129

Digital Phase-Locked Loop With Phase And Frequency Feedback

NASA Technical Reports Server (NTRS)

Thomas, J. Brooks

1991-01-01

Advanced design for digital phase-lock loop (DPLL) allows loop gains higher than those used in other designs. Divided into two major components: counterrotation processor and tracking processor. Notable features include use of both phase and rate-of-change-of-phase feedback instead of frequency feedback alone, normalized sine phase extractor, improved method for extracting measured phase, and improved method for "compressing" output rate.

Can matrix solid phase dispersion (MSPD) be more simplified? Application of solventless MSPD sample preparation method for GC-MS and GC-FID analysis of plant essential oil components.

PubMed

Wianowska, Dorota; Dawidowicz, Andrzej L

2016-05-01

This paper proposes and shows the analytical capabilities of a new variant of matrix solid phase dispersion (MSPD) with the solventless blending step in the chromatographic analysis of plant volatiles. The obtained results prove that the use of a solvent is redundant as the sorption ability of the octadecyl brush is sufficient for quantitative retention of volatiles from 9 plants differing in their essential oil composition. The extraction efficiency of the proposed simplified MSPD method is equivalent to the efficiency of the commonly applied variant of MSPD with the organic dispersing liquid and pressurized liquid extraction, which is a much more complex, technically advanced and highly efficient technique of plant extraction. The equivalency of these methods is confirmed by the variance analysis. The proposed solventless MSPD method is precise, accurate, and reproducible. The recovery of essential oil components estimated by the MSPD method exceeds 98%, which is satisfactory for analytical purposes. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparative evaluation of total RNA extraction methods in Theobroma cacao using shoot apical meristems.

PubMed

Silva, D V; Branco, S M J; Holanda, I S A; Royaert, S; Motamayor, J C; Marelli, J P; Corrêa, R X

2016-03-04

Theobroma cacao is a species of great economic importance with its beans used for chocolate production. The tree has been a target of various molecular studies. It contains many polyphenols, which complicate the extraction of nucleic acids with the extraction protocols requiring a large amount of plant material. These issues, therefore, necessitate the optimization of the protocols. The aim of the present study was to evaluate different methods for extraction of total RNA from shoot apical meristems of T. cacao 'CCN 51' and to assess the influence of storage conditions for the meristems on the extraction. The study also aimed to identify the most efficient protocol for RNA extraction using a small amount of plant material. Four different protocols were evaluated for RNA extraction using one shoot apical meristem per sample. Among these protocols, one that was more efficient was then tested to extract RNA using four different numbers of shoot apical meristems, subjected to three different storage conditions. The best protocol was tested for cDNA amplification using reverse transcription-polymerase chain reaction; the cDNA quality was determined to be satisfactory for molecular analyses. The study revealed that with the best RNA extraction protocol, one shoot apical meristem was sufficient for extraction of high-quality total RNA. The results obtained might enable advances in genetic analyses and molecular studies using reduced amount of plant material.

Full-Scale Turbofan Engine Noise-Source Separation Using a Four-Signal Method

NASA Technical Reports Server (NTRS)

Hultgren, Lennart S.; Arechiga, Rene O.

2016-01-01

Contributions from the combustor to the overall propulsion noise of civilian transport aircraft are starting to become important due to turbofan design trends and expected advances in mitigation of other noise sources. During on-ground, static-engine acoustic tests, combustor noise is generally sub-dominant to other engine noise sources because of the absence of in-flight effects. Consequently, noise-source separation techniques are needed to extract combustor-noise information from the total noise signature in order to further progress. A novel four-signal source-separation method is applied to data from a static, full-scale engine test and compared to previous methods. The new method is, in a sense, a combination of two- and three-signal techniques and represents an attempt to alleviate some of the weaknesses of each of those approaches. This work is supported by the NASA Advanced Air Vehicles Program, Advanced Air Transport Technology Project, Aircraft Noise Reduction Subproject and the NASA Glenn Faculty Fellowship Program.

Electromembrane extraction combined with gas chromatography for quantification of tricyclic antidepressants in human body fluids.

PubMed

Davarani, Saied Saeed Hosseiny; Najarian, Amin Morteza; Nojavan, Saeed; Tabatabaei, Mohammad-Ali

2012-05-06

Recent advances in electromembrane extraction (EME) methodology calls for effective and accessible detection methods. Using imipramine and clomipramine as model therapeutics, this proof-of-principle work combines EME with gas chromatography analysis employing a flame ionization detector (FID). The drugs were extracted from acidic aqueous sample solutions, through a supported liquid membrane (SLM) consisting of 2-nitrophenyl octyl ether (NPOE) impregnated on the walls of the hollow fiber. EME parameters, such as SLM composition, type of ion carrier, pH and the composition of donor and acceptor solutions, agitation speed, extraction voltage, and extraction time were studied in detail. Under optimized conditions, the therapeutics were effectively extracted from different matrices with recoveries ranging from 90 to 95%. The samples were preconcentrated 270-280 times prior to GC analysis. Reliable linearity was also achieved for calibration curves with a regression coefficient of at least 0.995. Detection limits and intra-day precision (n=3) were less than 0.7 ng mL(-1) and 8.5%, respectively. Finally, method was applied to determination and quantification of drugs in human plasma and urine samples and satisfactory results were achieved. Copyright © 2012 Elsevier B.V. All rights reserved.

Cancer diagnosis marker extraction for soft tissue sarcomas based on gene expression profiling data by using projective adaptive resonance theory (PART) filtering method

PubMed Central

Takahashi, Hiro; Nemoto, Takeshi; Yoshida, Teruhiko; Honda, Hiroyuki; Hasegawa, Tadashi

2006-01-01

Background Recent advances in genome technologies have provided an excellent opportunity to determine the complete biological characteristics of neoplastic tissues, resulting in improved diagnosis and selection of treatment. To accomplish this objective, it is important to establish a sophisticated algorithm that can deal with large quantities of data such as gene expression profiles obtained by DNA microarray analysis. Results Previously, we developed the projective adaptive resonance theory (PART) filtering method as a gene filtering method. This is one of the clustering methods that can select specific genes for each subtype. In this study, we applied the PART filtering method to analyze microarray data that were obtained from soft tissue sarcoma (STS) patients for the extraction of subtype-specific genes. The performance of the filtering method was evaluated by comparison with other widely used methods, such as signal-to-noise, significance analysis of microarrays, and nearest shrunken centroids. In addition, various combinations of filtering and modeling methods were used to extract essential subtype-specific genes. The combination of the PART filtering method and boosting – the PART-BFCS method – showed the highest accuracy. Seven genes among the 15 genes that are frequently selected by this method – MIF, CYFIP2, HSPCB, TIMP3, LDHA, ABR, and RGS3 – are known prognostic marker genes for other tumors. These genes are candidate marker genes for the diagnosis of STS. Correlation analysis was performed to extract marker genes that were not selected by PART-BFCS. Sixteen genes among those extracted are also known prognostic marker genes for other tumors, and they could be candidate marker genes for the diagnosis of STS. Conclusion The procedure that consisted of two steps, such as the PART-BFCS and the correlation analysis, was proposed. The results suggest that novel diagnostic and therapeutic targets for STS can be extracted by a procedure that includes the PART filtering method. PMID:16948864

Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery.

PubMed

Gonzalez, Graciela H; Tahsin, Tasnia; Goodale, Britton C; Greene, Anna C; Greene, Casey S

2016-01-01

Precision medicine will revolutionize the way we treat and prevent disease. A major barrier to the implementation of precision medicine that clinicians and translational scientists face is understanding the underlying mechanisms of disease. We are starting to address this challenge through automatic approaches for information extraction, representation and analysis. Recent advances in text and data mining have been applied to a broad spectrum of key biomedical questions in genomics, pharmacogenomics and other fields. We present an overview of the fundamental methods for text and data mining, as well as recent advances and emerging applications toward precision medicine. © The Author 2015. Published by Oxford University Press.

Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery

PubMed Central

Gonzalez, Graciela H.; Tahsin, Tasnia; Goodale, Britton C.; Greene, Anna C.

2016-01-01

Precision medicine will revolutionize the way we treat and prevent disease. A major barrier to the implementation of precision medicine that clinicians and translational scientists face is understanding the underlying mechanisms of disease. We are starting to address this challenge through automatic approaches for information extraction, representation and analysis. Recent advances in text and data mining have been applied to a broad spectrum of key biomedical questions in genomics, pharmacogenomics and other fields. We present an overview of the fundamental methods for text and data mining, as well as recent advances and emerging applications toward precision medicine. PMID:26420781

Contactless physiological signals extraction based on skin color magnification

NASA Astrophysics Data System (ADS)

Suh, Kun Ha; Lee, Eui Chul

2017-11-01

Although the human visual system is not sufficiently sensitive to perceive blood circulation, blood flow caused by cardiac activity makes slight changes on human skin surfaces. With advances in imaging technology, it has become possible to capture these changes through digital cameras. However, it is difficult to obtain clear physiological signals from such changes due to its fineness and noise factors, such as motion artifacts and camera sensing disturbances. We propose a method for extracting physiological signals with improved quality from skin colored-videos recorded with a remote RGB camera. The results showed that our skin color magnification method reveals the hidden physiological components remarkably in the time-series signal. A Korea Food and Drug Administration-approved heart rate monitor was used for verifying the resulting signal synchronized with the actual cardiac pulse, and comparisons of signal peaks showed correlation coefficients of almost 1.0. In particular, our method can be an effective preprocessing before applying additional postfiltering techniques to improve accuracy in image-based physiological signal extractions.

Metabolite profiling on apple volatile content based on solid phase microextraction and gas-chromatography time of flight mass spectrometry.

PubMed

Aprea, Eugenio; Gika, Helen; Carlin, Silvia; Theodoridis, Georgios; Vrhovsek, Urska; Mattivi, Fulvio

2011-07-15

A headspace SPME GC-TOF-MS method was developed for the acquisition of metabolite profiles of apple volatiles. As a first step, an experimental design was applied to find out the most appropriate conditions for the extraction of apple volatile compounds by SPME. The selected SPME method was applied in profiling of four different apple varieties by GC-EI-TOF-MS. Full scan GC-MS data were processed by MarkerLynx software for peak picking, normalisation, alignment and feature extraction. Advanced chemometric/statistical techniques (PCA and PLS-DA) were used to explore data and extract useful information. Characteristic markers of each variety were successively identified using the NIST library thus providing useful information for variety classification. The developed HS-SPME sampling method is fully automated and proved useful in obtaining the fingerprint of the volatile content of the fruit. The described analytical protocol can aid in further studies of the apple metabolome. Copyright © 2011 Elsevier B.V. All rights reserved.

Extraction of drainage networks from large terrain datasets using high throughput computing

NASA Astrophysics Data System (ADS)

Gong, Jianya; Xie, Jibo

2009-02-01

Advanced digital photogrammetry and remote sensing technology produces large terrain datasets (LTD). How to process and use these LTD has become a big challenge for GIS users. Extracting drainage networks, which are basic for hydrological applications, from LTD is one of the typical applications of digital terrain analysis (DTA) in geographical information applications. Existing serial drainage algorithms cannot deal with large data volumes in a timely fashion, and few GIS platforms can process LTD beyond the GB size. High throughput computing (HTC), a distributed parallel computing mode, is proposed to improve the efficiency of drainage networks extraction from LTD. Drainage network extraction using HTC involves two key issues: (1) how to decompose the large DEM datasets into independent computing units and (2) how to merge the separate outputs into a final result. A new decomposition method is presented in which the large datasets are partitioned into independent computing units using natural watershed boundaries instead of using regular 1-dimensional (strip-wise) and 2-dimensional (block-wise) decomposition. Because the distribution of drainage networks is strongly related to watershed boundaries, the new decomposition method is more effective and natural. The method to extract natural watershed boundaries was improved by using multi-scale DEMs instead of single-scale DEMs. A HTC environment is employed to test the proposed methods with real datasets.

Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics.

PubMed

Stark, Lucy; Giersch, Tina; Wünschiers, Röbbe

2014-10-01

Understanding the microbial population in anaerobic digestion is an essential task to increase efficient substrate use and process stability. The metabolic state, represented e.g. by the transcriptome, of a fermenting system can help to find markers for monitoring industrial biogas production to prevent failures or to model the whole process. Advances in next-generation sequencing make transcriptomes accessible for large-scale analyses. In order to analyze the metatranscriptome of a mixed-species sample, isolation of high-quality RNA is the first step. However, different extraction methods may yield different efficiencies in different species. Especially in mixed-species environmental samples, unbiased isolation of transcripts is important for meaningful conclusions. We applied five different RNA-extraction protocols to nine taxonomic diverse bacterial species. Chosen methods are based on various lysis and extraction principles. We found that the extraction efficiency of different methods depends strongly on the target organism. RNA isolation of gram-positive bacteria was characterized by low yield whilst from gram-negative species higher concentrations can be obtained. Transferring our results to mixed-species investigations, such as metatranscriptomics with biofilms or biogas plants, leads to the conclusion that particular microorganisms might be over- or underrepresented depending on the method applied. Special care must be taken when using such metatranscriptomics data for, e.g. process modeling. Copyright © 2013 Elsevier Ltd. All rights reserved.

Longwall top coal caving (LTCC) mining technologies with roof softening by hydraulic fracturing method

NASA Astrophysics Data System (ADS)

Klishin, V.; Nikitenko, S.; Opruk, G.

2018-05-01

The paper discusses advanced top coal caving technologies for thick coal seams and addresses some issues of incomplete coal extraction, which can result in the environmental damage, landscape change, air and water pollution and endogenous fires. The authors put forward a fundamentally new, having no equivalent and ecology-friendly method to difficult-to-cave roof coal – directional hydraulic fracturing and nonexplosive disintegration.

Emerging Trends in Microwave Processing of Spices and Herbs.

PubMed

Rahath Kubra, Ismail; Kumar, Devender; Jagan Mohan Rao, Lingamallu

2016-10-02

Today, spices are integral part of our food as they provide sensory attributes such as aroma, color, flavour and taste to food. Further their antimicrobial, antioxidant, pharmaceutical and nutritional properties are also well known. Since spices are seasonal so their availability can be extended year round by adopting different preservation techniques. Drying and extraction are most important methods for preservation and value addition to spices. There are different techniques for drying of spices with their own advantages and limitations. A novel, non-conventional technique for drying of spices is use of microwave radiation. This technique proved to be very rapid, and also provide a good quality product. Similarly, there are a number of non-conventional extraction methods in use that are all, in principle, solid-liquid extractions but which introduce some form of additional energy to the process in order to facilitate the transfer of analytes from sample to solvent. This paper reviews latest advances in the use of microwave energy for drying of spices and herbs. Also, the review describes the potential application of microwave energy for extraction of essential oil/bioactive components from spices and herbs and the advantages of microwave-assisted process over the other extraction processes generally employed for extraction. It also showcases some recent research results on microwave drying/extraction from spices and herbs.

Nucleic acid extraction techniques and application to the microchip.

PubMed

Price, Carol W; Leslie, Daniel C; Landers, James P

2009-09-07

As recently as the early 1990s, DNA purification was time-consuming, requiring the use of toxic, hazardous reagents. The advent of solid phase extraction techniques and the availability of commercial kits for quick and reliable DNA extraction has relegated those early techniques largely to the history books. High quality DNA can now be extracted from whole blood, serum, saliva, urine, stool, cerebral spinal fluid, tissues, and cells in less time without sacrificing recovery. Having achieved such a radical change in the methodology of DNA extraction, focus has shifted to adapting these methods to a miniaturized system, or "lab-on-a-chip" (A. Manz, N. Graber and H. M. Widmer, Sens. Actuators, B, 1990, 1, 244-248). Manz et al.'s concept of a "miniaturized total chemical analysis system" (microTAS) involved a silicon chip that incorporated sample pretreatment, separation and detection. This review will focus on the first of these steps, sample pretreatment in the form of DNA purification. The intention of this review is to provide an overview of the fundamentals of nucleic acid purification and solid phase extraction (SPE) and to discuss specific microchip DNA extraction successes and challenges. In order to fully appreciate the advances in DNA purification, a brief review of the history of DNA extraction is provided so that the reader has an understanding of the impact that the development of SPE techniques have had. This review will highlight the different methods of nucleic acid extraction (Table 1), including relevant citations, but without an exhaustive summary of the literature. A recent review by Wen et al. (J. Wen, L. A. Legendre, J. M. Bienvenue and J. P. Landers, Anal. Chem., 2008, 80, 6472-6479) covers solid phase extraction methods with a greater focus on their incorporation into integrated microfluidic systems.

Solid-Phase Extraction (SPE): Principles and Applications in Food Samples.

PubMed

Ötles, Semih; Kartal, Canan

2016-01-01

Solid-Phase Extraction (SPE) is a sample preparation method that is practised on numerous application fields due to its many advantages compared to other traditional methods. SPE was invented as an alternative to liquid/liquid extraction and eliminated multiple disadvantages, such as usage of large amount of solvent, extended operation time/procedure steps, potential sources of error, and high cost. Moreover, SPE can be plied to the samples combined with other analytical methods and sample preparation techniques optionally. SPE technique is a useful tool for many purposes through its versatility. Isolation, concentration, purification and clean-up are the main approaches in the practices of this method. Food structures represent a complicated matrix and can be formed into different physical stages, such as solid, viscous or liquid. Therefore, sample preparation step particularly has an important role for the determination of specific compounds in foods. SPE offers many opportunities not only for analysis of a large diversity of food samples but also for optimization and advances. This review aims to provide a comprehensive overview on basic principles of SPE and its applications for many analytes in food matrix.

Scan Line Based Road Marking Extraction from Mobile LiDAR Point Clouds.

PubMed

Yan, Li; Liu, Hua; Tan, Junxiang; Li, Zan; Xie, Hong; Chen, Changjun

2016-06-17

Mobile Mapping Technology (MMT) is one of the most important 3D spatial data acquisition technologies. The state-of-the-art mobile mapping systems, equipped with laser scanners and named Mobile LiDAR Scanning (MLS) systems, have been widely used in a variety of areas, especially in road mapping and road inventory. With the commercialization of Advanced Driving Assistance Systems (ADASs) and self-driving technology, there will be a great demand for lane-level detailed 3D maps, and MLS is the most promising technology to generate such lane-level detailed 3D maps. Road markings and road edges are necessary information in creating such lane-level detailed 3D maps. This paper proposes a scan line based method to extract road markings from mobile LiDAR point clouds in three steps: (1) preprocessing; (2) road points extraction; (3) road markings extraction and refinement. In preprocessing step, the isolated LiDAR points in the air are removed from the LiDAR point clouds and the point clouds are organized into scan lines. In the road points extraction step, seed road points are first extracted by Height Difference (HD) between trajectory data and road surface, then full road points are extracted from the point clouds by moving least squares line fitting. In the road markings extraction and refinement step, the intensity values of road points in a scan line are first smoothed by a dynamic window median filter to suppress intensity noises, then road markings are extracted by Edge Detection and Edge Constraint (EDEC) method, and the Fake Road Marking Points (FRMPs) are eliminated from the detected road markings by segment and dimensionality feature-based refinement. The performance of the proposed method is evaluated by three data samples and the experiment results indicate that road points are well extracted from MLS data and road markings are well extracted from road points by the applied method. A quantitative study shows that the proposed method achieves an average completeness, correctness, and F-measure of 0.96, 0.93, and 0.94, respectively. The time complexity analysis shows that the scan line based road markings extraction method proposed in this paper provides a promising alternative for offline road markings extraction from MLS data.

Scan Line Based Road Marking Extraction from Mobile LiDAR Point Clouds†

PubMed Central

Yan, Li; Liu, Hua; Tan, Junxiang; Li, Zan; Xie, Hong; Chen, Changjun

2016-01-01

Mobile Mapping Technology (MMT) is one of the most important 3D spatial data acquisition technologies. The state-of-the-art mobile mapping systems, equipped with laser scanners and named Mobile LiDAR Scanning (MLS) systems, have been widely used in a variety of areas, especially in road mapping and road inventory. With the commercialization of Advanced Driving Assistance Systems (ADASs) and self-driving technology, there will be a great demand for lane-level detailed 3D maps, and MLS is the most promising technology to generate such lane-level detailed 3D maps. Road markings and road edges are necessary information in creating such lane-level detailed 3D maps. This paper proposes a scan line based method to extract road markings from mobile LiDAR point clouds in three steps: (1) preprocessing; (2) road points extraction; (3) road markings extraction and refinement. In preprocessing step, the isolated LiDAR points in the air are removed from the LiDAR point clouds and the point clouds are organized into scan lines. In the road points extraction step, seed road points are first extracted by Height Difference (HD) between trajectory data and road surface, then full road points are extracted from the point clouds by moving least squares line fitting. In the road markings extraction and refinement step, the intensity values of road points in a scan line are first smoothed by a dynamic window median filter to suppress intensity noises, then road markings are extracted by Edge Detection and Edge Constraint (EDEC) method, and the Fake Road Marking Points (FRMPs) are eliminated from the detected road markings by segment and dimensionality feature-based refinement. The performance of the proposed method is evaluated by three data samples and the experiment results indicate that road points are well extracted from MLS data and road markings are well extracted from road points by the applied method. A quantitative study shows that the proposed method achieves an average completeness, correctness, and F-measure of 0.96, 0.93, and 0.94, respectively. The time complexity analysis shows that the scan line based road markings extraction method proposed in this paper provides a promising alternative for offline road markings extraction from MLS data. PMID:27322279

Skills Required for Nursing Career Advancement: A Qualitative Study

PubMed Central

Sheikhi, Mohammad Reza; Fallahi-Khoshnab, Masoud; Mohammadi, Farahnaz; Oskouie, Fatemeh

2016-01-01

Background Nurses require certain skills for progression in their field. Identifying these skills can provide the context for nursing career advancement. Objectives This study aimed to identify the skills needed for nurses’ career advancement. Materials and Methods A qualitative approach using content analysis was adopted to study a purposive sample of eighteen nurses working in teaching hospitals affiliated with the Qazvin, Shahid Beheshti, and Iran Universities of Medical Sciences. The data were collected through semi-structured interviews, and analyzed using conventional content analysis. Results The three themes extracted from the data included interpersonal capabilities, competency for career success, and personal capacities. The results showed that acquiring a variety of skills is essential for career advancement. Conclusions The findings showed that personal, interpersonal, and functional skills can facilitate nurses’ career advancement. The effects of these skills on career advancement depend on a variety of conditions that require further studies. PMID:27556054

Optofluidic time-stretch microscopy: recent advances

NASA Astrophysics Data System (ADS)

Lei, Cheng; Nitta, Nao; Ozeki, Yasuyuki; Goda, Keisuke

2018-06-01

Flow cytometry is an indispensable method for valuable applications in numerous fields such as immunology, pathology, pharmacology, molecular biology, and marine biology. Optofluidic time-stretch microscopy is superior to conventional flow cytometry methods for its capability to acquire high-quality images of single cells at a high-throughput exceeding 10,000 cells per second. This makes it possible to extract copious information from cellular images for accurate cell detection and analysis with the assistance of machine learning. Optofluidic time-stretch microscopy has proven its effectivity in various applications, including microalga-based biofuel production, evaluation of thrombotic disorders, as well as drug screening and discovery. In this review, we discuss the principles and recent advances of optofluidic time-stretch microscopy.

[Community-acquired pneumonia--from medical technologist].

PubMed

Yamanaka, Kiyoharu

2002-07-01

The main causative microorganisms of Community-acquired pneumonia are Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus. Especially the causative microorganisms affecting whole body basic disease, persons of advanced age, and alcoholic patients are Moraxella catarrhalis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Candida spp., Cryptococcus spp., Aspergillus spp., Pneumocystis carinii and anaerobic bacteria. Other microorganisms involved in epidemic disease, action condition (travel around hot springs etc.) and pet breeding environments are Mycoplasma pneumoniae, Legionella pnumophila, Chlamydia spp., respiratory syncytial virus, influenza virus, and adeno virus. We suggest methods of advancing the microscopic and microbiological examination and report, and quickly obtaining clinical information and extracting the clinical specimen. We also describe the inspection method for a case "Legionella pneumonia" that was discussed during this symposium.

Optofluidic time-stretch microscopy: recent advances

NASA Astrophysics Data System (ADS)

Lei, Cheng; Nitta, Nao; Ozeki, Yasuyuki; Goda, Keisuke

2018-04-01

Flow cytometry is an indispensable method for valuable applications in numerous fields such as immunology, pathology, pharmacology, molecular biology, and marine biology. Optofluidic time-stretch microscopy is superior to conventional flow cytometry methods for its capability to acquire high-quality images of single cells at a high-throughput exceeding 10,000 cells per second. This makes it possible to extract copious information from cellular images for accurate cell detection and analysis with the assistance of machine learning. Optofluidic time-stretch microscopy has proven its effectivity in various applications, including microalga-based biofuel production, evaluation of thrombotic disorders, as well as drug screening and discovery. In this review, we discuss the principles and recent advances of optofluidic time-stretch microscopy.

Pyrolysis kinetics and combustion of thin wood using advanced cone calorimetry test method

Treesearch

Mark A. Dietenberger

2011-01-01

Mechanistic pyrolysis kinetics analysis of extractives, holocellulose, and lignin in solid wood over entire heating regime was possible using specialized cone calorimeter test and new mathematical analysis tools. Added hardware components include: modified sample holder for thin specimen with tiny thermocouples, methane ring burner with stainless steel mesh above cone...

What Does Corpus Linguistics Have to Offer to Language Assessment?

ERIC Educational Resources Information Center

Xi, Xiaoming

2017-01-01

In recent years, continuing advances in technology have increased the capacity to automate the extraction of a range of linguistic features of texts and thus have provided the impetus for the substantial growth of corpus linguistics. While corpus linguistic tools and methods have been used extensively in second language learning research, they…

Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013

PubMed Central

2015-01-01

Background Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical literature. In this paper, we present the Cancer Genetics (CG) and Pathway Curation (PC) tasks, two event extraction tasks introduced in the BioNLP Shared Task 2013. The CG task focuses on cancer, emphasizing the extraction of physiological and pathological processes at various levels of biological organization, and the PC task targets reactions relevant to the development of biomolecular pathway models, defining its extraction targets on the basis of established pathway representations and ontologies. Results Six groups participated in the CG task and two groups in the PC task, together applying a wide range of extraction approaches including both established state-of-the-art systems and newly introduced extraction methods. The best-performing systems achieved F-scores of 55% on the CG task and 53% on the PC task, demonstrating a level of performance comparable to the best results achieved in similar previously proposed tasks. Conclusions The results indicate that existing event extraction technology can generalize to meet the novel challenges represented by the CG and PC task settings, suggesting that extraction methods are capable of supporting the construction of knowledge bases on the molecular mechanisms of cancer and the curation of biomolecular pathway models. The CG and PC tasks continue as open challenges for all interested parties, with data, tools and resources available from the shared task homepage. PMID:26202570

Aged garlic extract and S-allyl cysteine prevent formation of advanced glycation endproducts.

PubMed

Ahmad, Muhammad Saeed; Pischetsrieder, Monika; Ahmed, Nessar

2007-04-30

Hyperglycaemia causes increased protein glycation and the formation of advanced glycation endproducts which underlie the complications of diabetes and ageing. Glycation is accompanied by metal-catalysed oxidation of glucose and Amadori products to form free radicals capable of protein fragmentation. Aged garlic extract is a potent antioxidant with established lipid-lowering effects attributed largely to a key ingredient called S-allyl cysteine. This study investigated the ability of aged garlic extract and S-allyl cysteine to inhibit advanced glycation in vitro. Bovine serum albumin (BSA) was glycated in the presence of Cu(2+) ions and different concentrations of aged garlic extract and protein fragmentation was examined by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Lysozyme was glycated by glucose or methylglyoxal in the presence of different concentrations of aged garlic extract or S-allyl cysteine with subsequent analysis of glycation-derived crosslinking using SDS-PAGE. Amadori-rich protein was prepared by dialysing lysozyme that had been glycated by ribose for 24 h. This ribated lysozyme was reincubated and the effects of aged garlic extract, S-allyl cysteine and pyridoxamine on glycation-induced crosslinking was monitored. Aged garlic extract inhibited metal-catalysed protein fragmentation. Both aged garlic extract and S-allyl cysteine inhibited formation of glucose and methylglyoxal derived advanced glycation endproducts and showed potent Amadorin activity when compared to pyridoxamine. S-allyl cysteine inhibited formation of carboxymethyllysine (CML), a non-crosslinked advanced glycation endproduct derived from oxidative processes. Further studies are required to assess whether aged garlic extract and S-allyl cysteine can protect against the harmful effects of glycation and free radicals in diabetes and ageing.

Incipient fault feature extraction of rolling bearings based on the MVMD and Teager energy operator.

PubMed

Ma, Jun; Wu, Jiande; Wang, Xiaodong

2018-06-04

Aiming at the problems that the incipient fault of rolling bearings is difficult to recognize and the number of intrinsic mode functions (IMFs) decomposed by variational mode decomposition (VMD) must be set in advance and can not be adaptively selected, taking full advantages of the adaptive segmentation of scale spectrum and Teager energy operator (TEO) demodulation, a new method for early fault feature extraction of rolling bearings based on the modified VMD and Teager energy operator (MVMD-TEO) is proposed. Firstly, the vibration signal of rolling bearings is analyzed by adaptive scale space spectrum segmentation to obtain the spectrum segmentation support boundary, and then the number K of IMFs decomposed by VMD is adaptively determined. Secondly, the original vibration signal is adaptively decomposed into K IMFs, and the effective IMF components are extracted based on the correlation coefficient criterion. Finally, the Teager energy spectrum of the reconstructed signal of the effective IMF components is calculated by the TEO, and then the early fault features of rolling bearings are extracted to realize the fault identification and location. Comparative experiments of the proposed method and the existing fault feature extraction method based on Local Mean Decomposition and Teager energy operator (LMD-TEO) have been implemented using experimental data-sets and a measured data-set. The results of comparative experiments in three application cases show that the presented method can achieve a fairly or slightly better performance than LMD-TEO method, and the validity and feasibility of the proposed method are proved. Copyright © 2018. Published by Elsevier Ltd.

Anti-Advanced Glycation End-product and Free Radical Scavenging Activity of Plants from the Yucatecan Flora

PubMed Central

Dzib-Guerra, Wendy del C.; Escalante-Erosa, Fabiola; García-Sosa, Karlina; Derbré, Séverine; Blanchard, Patricia; Richomme, Pascal; Peña-Rodríguez, Luis M.

2016-01-01

Background: Formation and accumulation of advanced glycation end-products (AGE) is recognized as a major pathogenic process in diabetic complications, atherosclerosis and cardiovascular diseases. In addition, reactive oxygen species and free radicals have also been reported to participate in AGE formation and in cell damage. Natural products with antioxidant and antiAGE activity have great therapeutic potential in the treatment of diabetes, hypertension and related complications. Objective: to test ethanolic extracts and aqueous-traditional preparations of plants used to treat diabetes, hypertension and obesity in Yucatecan traditional medicine for their anti-AGE and free radical scavenging activities. Materials and Methods: ethanolic extracts of leaves, stems and roots of nine medicinal plants, together with their traditional preparations, were prepared and tested for their anti-AGE and antioxidant activities using the inhibition of advanced glycation end products and DPPH radical scavenging assays, respectively. Results: the root extract of C. fistula (IC50= 0.1 mg/mL) and the leaf extract of P. auritum (IC50= 0.35 mg/mL) presented significant activity against vesperlysine and pentosidine-like AGE. Although none of the aqueous traditional preparations showed significant activity in the anti-AGE assay, both the traditional preparations and the ethanolic extracts of E. tinifolia, M. zapota, O. campechianum and P. auritum showed significant activity in the DPPH reduction assay. Conclusions: the results suggest that the metabolites responsible for the detected radical-scavenging activity are different to those involved in inhibiting AGE formation; however, the extracts with antioxidant activity may contain other metabolites which are able to prevent AGE formation through a different mechanism. SUMMARY Ethanolic extracts from nine plants used to treat diabetes, hypertension and obesity in Yucatecan traditional medicine were tested for their anti-AGE and free radical scavenging activities.Significant activity against vesperlysine and pentosidine-like AGE was detected in the root extract of Cassia fistula and the leaf extract of Piper auritum.Traditional preparations and the ethanolic extracts of Ehretia tinifolia, Manilkara zapota, Ocimum campechianum and Piper auritum showed significant activity in the DPPH reduction assay.Results suggest that the metabolites responsible for the detected radical-scavenging activity are different to those involved in inhibiting AGE formation. Abbreviations Used: AGE: Advanced glycation end-product; DPPH: 2,2-Diphenyl-1-picrylhydrazyl; DM: Diabetes mellitus; ROS: Reactive oxygen species; BSA: Bovine serum albumin; EtOH: Ethanol; EtOAc: Ethyl acetate; ANOVA: Analysis of variance; BA: Brosimum alicastrum; BS: Bunchosia swartziana; CF: Cassia fistula; CN: Cocos nucifera; ET: Ehretia tinifolia; MZ: Manilkara zapota; OC: Ocimum campechianum; PA: Piper auritum; RM: Rhizophora mangle; L: Leaves; S: Stems; R: Roots; T: traditional preparation; I: Inflorescences; W: Water PMID:27695268

Advancements in noncontact, multiparameter physiological measurements using a webcam.

PubMed

Poh, Ming-Zher; McDuff, Daniel J; Picard, Rosalind W

2011-01-01

We present a simple, low-cost method for measuring multiple physiological parameters using a basic webcam. By applying independent component analysis on the color channels in video recordings, we extracted the blood volume pulse from the facial regions. Heart rate (HR), respiratory rate, and HR variability (HRV, an index for cardiac autonomic activity) were subsequently quantified and compared to corresponding measurements using Food and Drug Administration-approved sensors. High degrees of agreement were achieved between the measurements across all physiological parameters. This technology has significant potential for advancing personal health care and telemedicine.

Preferred color correction for digital LCD TVs

NASA Astrophysics Data System (ADS)

Kim, Kyoung Tae; Kim, Choon-Woo; Ahn, Ji-Young; Kang, Dong-Woo; Shin, Hyun-Ho

2009-01-01

Instead of colorimetirc color reproduction, preferred color correction is applied for digital TVs to improve subjective image quality. First step of the preferred color correction is to survey the preferred color coordinates of memory colors. This can be achieved by the off-line human visual tests. Next step is to extract pixels of memory colors representing skin, grass and sky. For the detected pixels, colors are shifted towards the desired coordinates identified in advance. This correction process may result in undesirable contours on the boundaries between the corrected and un-corrected areas. For digital TV applications, the process of extraction and correction should be applied in every frame of the moving images. This paper presents a preferred color correction method in LCH color space. Values of chroma and hue are corrected independently. Undesirable contours on the boundaries of correction are minimized. The proposed method change the coordinates of memory color pixels towards the target color coordinates. Amount of correction is determined based on the averaged coordinate of the extracted pixels. The proposed method maintains the relative color difference within memory color areas. Performance of the proposed method is evaluated using the paired comparison. Results of experiments indicate that the proposed method can reproduce perceptually pleasing images to viewers.

Recent advances in continuum plasticity: phenomenological modeling and experimentation using X-ray diffraction

NASA Astrophysics Data System (ADS)

Edmiston, John Kearney

This work explores the field of continuum plasticity from two fronts. On the theory side, we establish a complete specification of a phenomenological theory of plasticity for single crystals. The model serves as an alternative to the popular crystal plasticity formulation. Such a model has been previously proposed in the literature; the new contribution made here is the constitutive framework and resulting simulations. We calibrate the model to available data and use a simple numerical method to explore resulting predictions in plane strain boundary value problems. Results show promise for further investigation of the plasticity model. Conveniently, this theory comes with a corresponding experimental tool in X-ray diffraction. Recent advances in hardware technology at synchrotron sources have led to an increased use of the technique for studies of plasticity in the bulk of materials. The method has been successful in qualitative observations of material behavior, but its use in quantitative studies seeking to extract material properties is open for investigation. Therefore in the second component of the thesis several contributions are made to synchrotron X-ray diffraction experiments, in terms of method development as well as the quantitative reporting of constitutive parameters. In the area of method development, analytical tools are developed to determine the available precision of this type of experiment—a crucial aspect to determine if the method is to be used for quantitative studies. We also extract kinematic information relating to intragranular inhomogeneity which is not accessible with traditional methods of data analysis. In the area of constitutive parameter identification, we use the method to extract parameters corresponding to the proposed formulation of plasticity for a titanium alloy (HCP) which is continuously sampled by X-ray diffraction during uniaxial extension. These results and the lessons learned from the efforts constitute early reporting of the quantitative profitability of undertaking such a line of experimentation for the study of plastic deformation processes.

Recent advances in analytical methods for the determination of 4-alkylphenols and bisphenol A in solid environmental matrices: A critical review.

PubMed

Salgueiro-González, N; Castiglioni, S; Zuccato, E; Turnes-Carou, I; López-Mahía, P; Muniategui-Lorenzo, S

2018-09-18

The problem of endocrine disrupting compounds (EDCs) in the environment has become a worldwide concern in recent decades. Besides their toxicological effects at low concentrations and their widespread use in industrial and household applications, these pollutants pose a risk for non-target organisms and also for public safety. Analytical methods to determine these compounds at trace levels in different matrices are urgently needed. This review critically discusses trends in analytical methods for well-known EDCs like alkylphenols and bisphenol A in solid environmental matrices, including sediment and aquatic biological samples (from 2006 to 2018). Information about extraction, clean-up and determination is covered in detail, including analytical quality parameters (QA/QC). Conventional and novel analytical techniques are compared, with their advantages and drawbacks. Ultrasound assisted extraction followed by solid phase extraction clean-up is the most widely used procedure for sediment and aquatic biological samples, although softer extraction conditions have been employed for the latter. The use of liquid chromatography followed by tandem mass spectrometry has greatly increased in the last five years. The majority of these methods have been employed for the analysis of river sediments and bivalve molluscs because of their usefulness in aquatic ecosystem (bio)monitoring programs. Green, simple, fast analytical methods are now needed to determine these compounds in complex matrices. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparing deep learning and concept extraction based methods for patient phenotyping from clinical narratives.

PubMed

Gehrmann, Sebastian; Dernoncourt, Franck; Li, Yeran; Carlson, Eric T; Wu, Joy T; Welt, Jonathan; Foote, John; Moseley, Edward T; Grant, David W; Tyler, Patrick D; Celi, Leo A

2018-01-01

In secondary analysis of electronic health records, a crucial task consists in correctly identifying the patient cohort under investigation. In many cases, the most valuable and relevant information for an accurate classification of medical conditions exist only in clinical narratives. Therefore, it is necessary to use natural language processing (NLP) techniques to extract and evaluate these narratives. The most commonly used approach to this problem relies on extracting a number of clinician-defined medical concepts from text and using machine learning techniques to identify whether a particular patient has a certain condition. However, recent advances in deep learning and NLP enable models to learn a rich representation of (medical) language. Convolutional neural networks (CNN) for text classification can augment the existing techniques by leveraging the representation of language to learn which phrases in a text are relevant for a given medical condition. In this work, we compare concept extraction based methods with CNNs and other commonly used models in NLP in ten phenotyping tasks using 1,610 discharge summaries from the MIMIC-III database. We show that CNNs outperform concept extraction based methods in almost all of the tasks, with an improvement in F1-score of up to 26 and up to 7 percentage points in area under the ROC curve (AUC). We additionally assess the interpretability of both approaches by presenting and evaluating methods that calculate and extract the most salient phrases for a prediction. The results indicate that CNNs are a valid alternative to existing approaches in patient phenotyping and cohort identification, and should be further investigated. Moreover, the deep learning approach presented in this paper can be used to assist clinicians during chart review or support the extraction of billing codes from text by identifying and highlighting relevant phrases for various medical conditions.

Road Network Extraction from Dsm by Mathematical Morphology and Reasoning

NASA Astrophysics Data System (ADS)

Li, Yan; Wu, Jianliang; Zhu, Lin; Tachibana, Kikuo

2016-06-01

The objective of this research is the automatic extraction of the road network in a scene of the urban area from a high resolution digital surface model (DSM). Automatic road extraction and modeling from remote sensed data has been studied for more than one decade. The methods vary greatly due to the differences of data types, regions, resolutions et al. An advanced automatic road network extraction scheme is proposed to address the issues of tedium steps on segmentation, recognition and grouping. It is on the basis of a geometric road model which describes a multiple-level structure. The 0-dimension element is intersection. The 1-dimension elements are central line and side. The 2-dimension element is plane, which is generated from the 1-dimension elements. The key feature of the presented approach is the cross validation for the three road elements which goes through the entire procedure of their extraction. The advantage of our model and method is that linear elements of the road can be derived directly, without any complex, non-robust connection hypothesis. An example of Japanese scene is presented to display the procedure and the performance of the approach.

Molecularly Imprinted Polymers for Ochratoxin A Extraction and Analysis

PubMed Central

Yu, Jorn C. C.; Lai, Edward P. C.

2010-01-01

Molecularly imprinted polymers (MIPs) are considered as polymeric materials that mimic the functionality of antibodies. MIPs have been utilized for a wide variety of applications in chromatography, solid phase extraction, immunoassays, and sensor recognition. In this article, recent advances of MIPs for the extraction and analysis of ochratoxins are discussed. Selection of functional monomers to bind ochratoxin A (OTA) with high affinities, optimization of extraction procedures, and limitations of MIPs are compared from different reports. The most relevant examples in the literature are described to clearly show how useful these materials are. Strategies on MIP preparation and schemes of analytical methods are also reviewed in order to suggest the next step that would make better use of MIPs in the field of ochratoxin research. The review ends by outlining the remaining issues and impediments. PMID:22069649

Key Relation Extraction from Biomedical Publications.

PubMed

Huang, Lan; Wang, Ye; Gong, Leiguang; Kulikowski, Casimir; Bai, Tian

2017-01-01

Within the large body of biomedical knowledge, recent findings and discoveries are most often presented as research articles. Their number has been increasing sharply since the turn of the century, presenting ever-growing challenges for search and discovery of knowledge and information related to specific topics of interest, even with the help of advanced online search tools. This is especially true when the goal of a search is to find or discover key relations between important concepts or topic words. We have developed an innovative method for extracting key relations between concepts from abstracts of articles. The method focuses on relations between keywords or topic words in the articles. Early experiments with the method on PubMed publications have shown promising results in searching and discovering keywords and their relationships that are strongly related to the main topic of an article.

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

PubMed Central

Eriksson, Per; Mourkas, Evangelos; González-Acuna, Daniel; Olsen, Björn; Ellström, Patrik

2017-01-01

ABSTRACT Introduction: Advances in the development of nucleic acid-based methods have dramatically facilitated studies of host–microbial interactions. Fecal DNA analysis can provide information about the host’s microbiota and gastrointestinal pathogen burden. Numerous studies have been conducted in mammals, yet birds are less well studied. Avian fecal DNA extraction has proved challenging, partly due to the mixture of fecal and urinary excretions and the deficiency of optimized protocols. This study presents an evaluation of the performance in avian fecal DNA extraction of six commercial kits from different bird species, focusing on penguins. Material and methods: Six DNA extraction kits were first tested according to the manufacturers’ instructions using mallard feces. The kit giving the highest DNA yield was selected for further optimization and evaluation using Antarctic bird feces. Results: Penguin feces constitute a challenging sample type: most of the DNA extraction kits failed to yield acceptable amounts of DNA. The QIAamp cador Pathogen kit (Qiagen) performed the best in the initial investigation. Further optimization of the protocol resulted in good yields of high-quality DNA from seven bird species of different avian orders. Conclusion: This study presents an optimized approach to DNA extraction from challenging avian fecal samples. PMID:29152162

Quantitative imaging biomarkers: the application of advanced image processing and analysis to clinical and preclinical decision making.

PubMed

Prescott, Jeffrey William

2013-02-01

The importance of medical imaging for clinical decision making has been steadily increasing over the last four decades. Recently, there has also been an emphasis on medical imaging for preclinical decision making, i.e., for use in pharamaceutical and medical device development. There is also a drive towards quantification of imaging findings by using quantitative imaging biomarkers, which can improve sensitivity, specificity, accuracy and reproducibility of imaged characteristics used for diagnostic and therapeutic decisions. An important component of the discovery, characterization, validation and application of quantitative imaging biomarkers is the extraction of information and meaning from images through image processing and subsequent analysis. However, many advanced image processing and analysis methods are not applied directly to questions of clinical interest, i.e., for diagnostic and therapeutic decision making, which is a consideration that should be closely linked to the development of such algorithms. This article is meant to address these concerns. First, quantitative imaging biomarkers are introduced by providing definitions and concepts. Then, potential applications of advanced image processing and analysis to areas of quantitative imaging biomarker research are described; specifically, research into osteoarthritis (OA), Alzheimer's disease (AD) and cancer is presented. Then, challenges in quantitative imaging biomarker research are discussed. Finally, a conceptual framework for integrating clinical and preclinical considerations into the development of quantitative imaging biomarkers and their computer-assisted methods of extraction is presented.

Mendel Meets CSI: Forensic Genotyping as a Method to Teach Genetics & DNA Science

ERIC Educational Resources Information Center

Kurowski, Scotia; Reiss, Rebecca

2007-01-01

This article describes a forensic DNA science laboratory exercise for advanced high school and introductory college level biology courses. Students use a commercial genotyping kit and genetic analyzer or gene sequencer to analyze DNA recovered from a fictitious crime scene. DNA profiling and STR genotyping are outlined. DNA extraction, PCR, and…

Pyrolysis kinetics and combustion of thin wood by an advanced cone caorimetry test method

Treesearch

Mark Dietenberger

2012-01-01

Pyrolysis kinetics analysis of extractives, holocellulose, and lignin in the solid redwood over the entire heating regime was possible by specialized cone calorimeter test and new mathematical analysis tools. Added hardware components include: modified sample holder for the thin specimen with tiny thermocouples, the methane ring burner with stainless-steel mesh above...

Mind Reading and Writing: The Future of Neurotechnology.

PubMed

Roelfsema, Pieter R; Denys, Damiaan; Klink, P Christiaan

2018-05-02

Recent advances in neuroscience and technology have made it possible to record from large assemblies of neurons and to decode their activity to extract information. At the same time, available methods to stimulate the brain and influence ongoing processing are also rapidly expanding. These developments pave the way for advanced neurotechnological applications that directly read from, and write to, the human brain. While such technologies are still primarily used in restricted therapeutic contexts, this may change in the future once their performance has improved and they become more widely applicable. Here, we provide an overview of methods to interface with the brain, speculate about potential applications, and discuss important issues associated with a neurotechnologically assisted future. Copyright © 2018 Elsevier Ltd. All rights reserved.

Accurate Identification of Cancerlectins through Hybrid Machine Learning Technology.

PubMed

Zhang, Jieru; Ju, Ying; Lu, Huijuan; Xuan, Ping; Zou, Quan

2016-01-01

Cancerlectins are cancer-related proteins that function as lectins. They have been identified through computational identification techniques, but these techniques have sometimes failed to identify proteins because of sequence diversity among the cancerlectins. Advanced machine learning identification methods, such as support vector machine and basic sequence features (n-gram), have also been used to identify cancerlectins. In this study, various protein fingerprint features and advanced classifiers, including ensemble learning techniques, were utilized to identify this group of proteins. We improved the prediction accuracy of the original feature extraction methods and classification algorithms by more than 10% on average. Our work provides a basis for the computational identification of cancerlectins and reveals the power of hybrid machine learning techniques in computational proteomics.

Toward Usable Interactive Analytics: Coupling Cognition and Computation

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

Endert, Alexander; North, Chris; Chang, Remco

Interactive analytics provide users a myriad of computational means to aid in extracting meaningful information from large and complex datasets. Much prior work focuses either on advancing the capabilities of machine-centric approaches by the data mining and machine learning communities, or human-driven methods by the visualization and CHI communities. However, these methods do not yet support a true human-machine symbiotic relationship where users and machines work together collaboratively and adapt to each other to advance an interactive analytic process. In this paper we discuss some of the inherent issues, outlining what we believe are the steps toward usable interactive analyticsmore » that will ultimately increase the effectiveness for both humans and computers to produce insights.« less

Sediment certified reference materials for the determination of polychlorinated biphenyls and organochlorine pesticides from the National Metrology Institute of Japan (NMIJ).

PubMed

Numata, Masahiko; Yarita, Takashi; Aoyagi, Yoshie; Tsuda, Yoko; Yamazaki, Misako; Takatsu, Akiko; Ishikawa, Keiichiro; Chiba, Koichi; Okamaoto, Kensaku

2007-04-01

Two marine sediment certified reference materials, NMIJ CRM 7304-a and 7305-a, have been issued by the National Metrology Institute of Japan in the National Institute of Advanced Industrial Science and Technology (NMIJ/AIST) for the determination of polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs). The raw materials of the CRMs were collected from a bay near industrial activity in Japan. Characterization of these CRMs was conducted by NMIJ, where the sediments were analyzed using multiple analytical methods such as pressurized liquid extraction (PLE), microwave-assisted extraction (MAE), saponification, Soxhlet extraction, supercritical fluid extraction (SFE), and ultrasonic extraction; the target compounds were determined by one of the primary methods of measurements, isotope dilution-mass spectrometry (ID-MS). Certified values have been provided for 14 PCB congeners (PCB numbers 3, 15, 28, 31, 70, 101, 105, 138, 153, 170, 180, 194, 206, 209) and 4 OCPs (gamma-HCH, 4,4'-DDT, 4,4'-DDE, 4,4'-DDD) in both CRMs. NMIJ CRM 7304-a has concentrations of the contaminants that are a factor of 2-15 greater than in CRM 7305-a. Both CRMs have information values for PCB homolog concentrations determined by collaborative analysis using a Japanese official method for determination of PCBs. The total PCB concentrations in the CRMs are approximately 920 and 86 microg kg(-1) dry mass respectively.

Sigma Team for Advanced Actinide Recycle FY2015 Accomplishments and Directions

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

Moyer, Bruce A.

The Sigma Team for Minor Actinide Recycle (STAAR) has made notable progress in FY 2015 toward the overarching goal to develop more efficient separation methods for actinides in support of the United States Department of Energy (USDOE) objective of sustainable fuel cycles. Research in STAAR has been emphasizing the separation of americium and other minor actinides (MAs) to enable closed nuclear fuel recycle options, mainly within the paradigm of aqueous reprocessing of used oxide nuclear fuel dissolved in nitric acid. Its major scientific challenge concerns achieving selectivity for trivalent actinides vs lanthanides. Not only is this challenge yielding to researchmore » advances, but technology concepts such as ALSEP (Actinide Lanthanide Separation) are maturing toward demonstration readiness. Efforts are organized in five task areas: 1) combining bifunctional neutral extractants with an acidic extractant to form a single process solvent, developing a process flowsheet, and demonstrating it at bench scale; 2) oxidation of Am(III) to Am(VI) and subsequent separation with other multivalent actinides; 3) developing an effective soft-donor solvent system for An(III) selective extraction using mixed N,O-donor or all-N donor extractants such as triazinyl pyridine compounds; 4) testing of inorganic and hybrid-type ion exchange materials for MA separations; and 5) computer-aided molecular design to identify altogether new extractants and complexants and theory-based experimental data interpretation. Within these tasks, two strategies are employed, one involving oxidation of americium to its pentavalent or hexavalent state and one that seeks to selectively complex trivalent americium either in the aqueous phase or the solvent phase. Solvent extraction represents the primary separation method employed, though ion exchange and crystallization play an important role. Highlights of accomplishments include: Confirmation of the first-ever electrolytic oxidation of Am(III) in a noncomplexing aqueous solution and submission of this scientific breakthrough as a paper in Science; The first-ever co-crystallization of Am(VI) with UO 2(NO 3) 2 ∙ 6H 2O, opening the door to a new approach for separating hexavalent actinides as a group; Results showing that three potentially problematic metals will not present risk in ALSEP; Improvement in ALSEP contactor stripping kinetics to acceptable performance; A comparison of centrifugal contactors vs mixer-settlers showing the former performs better in ALSEP stripping; Synthesis of new mixed N,O-donor extractants with enhanced solubility and strength for selective trivalent actinide extraction; Development of computational methods showing promise in prediction of the selectivity of new extractants for trivalent actinides vs lanthanides; An order-of-magnitude improvement in aqueous Am/Eu complexation selectivity of an alternative macrocyclic stripping agent for ALSEP, potentially enabling an option for an Am product stream free from both Ln and Cm. An alternative aqueous combination of dipicolinate complexant and malonate buffer that may present options for ALSEP and TALSPEAK (Trivalent Actinide-Lanthanide Separations by Phosphorus-reagent Extraction from Aqueous Komplexes) type separations. The ALSEP concept is advancing toward a benchtop flowsheet demonstration planned for FY 2016, and a bench-scale test bed at Idaho National Laboratory (INL) will be employed to demonstrate at least one tandem Am oxidation and separation concept. This report outlines the goals of the STAAR, significance of achieving these goals, STAAR organization around the above aims and questions, recent highlights, and future directions. The report also includes a listing of publications, reports, patents, and dissertations.« less

On-line coupling of supercritical fluid extraction and chromatographic techniques.

PubMed

Sánchez-Camargo, Andrea Del Pilar; Parada-Alfonso, Fabián; Ibáñez, Elena; Cifuentes, Alejandro

2017-01-01

This review summarizes and discusses recent advances and applications of on-line supercritical fluid extraction coupled to liquid chromatography, gas chromatography, and supercritical fluid chromatographic techniques. Supercritical fluids, due to their exceptional physical properties, provide unique opportunities not only during the extraction step but also in the separation process. Although supercritical fluid extraction is especially suitable for recovery of non-polar organic compounds, this technique can also be successfully applied to the extraction of polar analytes by the aid of modifiers. Supercritical fluid extraction process can be performed following "off-line" or "on-line" approaches and their main features are contrasted herein. Besides, the parameters affecting the supercritical fluid extraction process are explained and a "decision tree" is for the first time presented in this review work as a guide tool for method development. The general principles (instrumental and methodological) of the different on-line couplings of supercritical fluid extraction with chromatographic techniques are described. Advantages and shortcomings of supercritical fluid extraction as hyphenated technique are discussed. Besides, an update of the most recent applications (from 2005 up to now) of the mentioned couplings is also presented in this review. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microburger Biochemistry: Extraction and Spectral Characterization of Myoglyobin from Hamburger

NASA Astrophysics Data System (ADS)

Bylkas, Sheri A.; Andersson, Laura A.

1997-04-01

This experiment provides a demonstration of useful biochemical methods at a Basic or Advanced Level, depending upon the available spectrophotometric equipment. The protocol combines protein extraction, ox-i-dation and reduction, and simple spectroscopic analysis, as well as gel filtration chromatography and generation/analysis of spectral scans. Mammalian myoglobin (Mb) is a monomeric O2-binding protein that functions in muscle to store oxygen. The single iron protoporphyrin IX (heme) group is bound to protein by the amino acid Histidine93. The common, stable forms, Met-Mb and Oxy-Mb are studied because in a non-living system, red Oxy-Mb is converted to brown Met-Mb as bound O2 molecule is released. Mb is easily extracted from steak, to illustrate and address why fresh meat is red and aged meat is brown; the protein has unique spectral properties that are diagnostic for characterization of sample identity. After application of heme redox chemical methods, the MetMb or OxyMb samples can be studied spectroscopically. The color change between Oxy-Mb and Met-Mb is dramatic (illustrating bright red fresh meat vs. brown older meat), and method(s) used in this laboratory are simple, inexpensive, and non-harmful to the student.

Advanced ballistic range technology

NASA Technical Reports Server (NTRS)

Yates, Leslie A.

1994-01-01

The research conducted supported two facilities at NASA Ames Research Center: the Hypervelocity Free-Flight Aerodynamic Facility and the 16-Inch Shock Tunnel. During the grant period, a computerized film-reading system was developed, and five- and six-degree-of-freedom parameter-identification routines were written and successfully implemented. Studies of flow separation were conducted, and methods to extract phase shift information from finite-fringe interferograms were developed. Methods for constructing optical images from Computational Fluid Dynamics solutions were also developed, and these methods were used for one-to-one comparisons of experiment and computations.

Radiomic machine-learning classifiers for prognostic biomarkers of advanced nasopharyngeal carcinoma.

PubMed

Zhang, Bin; He, Xin; Ouyang, Fusheng; Gu, Dongsheng; Dong, Yuhao; Zhang, Lu; Mo, Xiaokai; Huang, Wenhui; Tian, Jie; Zhang, Shuixing

2017-09-10

We aimed to identify optimal machine-learning methods for radiomics-based prediction of local failure and distant failure in advanced nasopharyngeal carcinoma (NPC). We enrolled 110 patients with advanced NPC. A total of 970 radiomic features were extracted from MRI images for each patient. Six feature selection methods and nine classification methods were evaluated in terms of their performance. We applied the 10-fold cross-validation as the criterion for feature selection and classification. We repeated each combination for 50 times to obtain the mean area under the curve (AUC) and test error. We observed that the combination methods Random Forest (RF) + RF (AUC, 0.8464 ± 0.0069; test error, 0.3135 ± 0.0088) had the highest prognostic performance, followed by RF + Adaptive Boosting (AdaBoost) (AUC, 0.8204 ± 0.0095; test error, 0.3384 ± 0.0097), and Sure Independence Screening (SIS) + Linear Support Vector Machines (LSVM) (AUC, 0.7883 ± 0.0096; test error, 0.3985 ± 0.0100). Our radiomics study identified optimal machine-learning methods for the radiomics-based prediction of local failure and distant failure in advanced NPC, which could enhance the applications of radiomics in precision oncology and clinical practice. Copyright © 2017 Elsevier B.V. All rights reserved.

Conventional and Advanced Separations in Mass Spectrometry-Based Metabolomics: Methodologies and Applications

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

Heyman, Heino M.; Zhang, Xing; Tang, Keqi

2016-02-16

Metabolomics is the quantitative analysis of all metabolites in a given sample. Due to the chemical complexity of the metabolome, optimal separations are required for comprehensive identification and quantification of sample constituents. This chapter provides an overview of both conventional and advanced separations methods in practice for reducing the complexity of metabolite extracts delivered to the mass spectrometer detector, and covers gas chromatography (GC), liquid chromatography (LC), capillary electrophoresis (CE), supercritical fluid chromatography (SFC) and ion mobility spectrometry (IMS) separation techniques coupled with mass spectrometry (MS) as both uni-dimensional and as multi-dimensional approaches.

Advancing Understanding of the +4 Metal Extractant Thenoyltrifluoroacetonate (TTA-); Synthesis and Structure of MIVTTA4 (MIV = Zr, Hf, Ce, Th, U, Np, Pu) and MIII(TTA)4- (MIII = Ce, Nd, Sm, Yb).

PubMed

Cary, Samantha K; Livshits, Maksim; Cross, Justin N; Ferrier, Maryline G; Mocko, Veronika; Stein, Benjamin W; Kozimor, Stosh A; Scott, Brian L; Rack, Jeffrey J

2018-04-02

Thenoyltrifluoroacetone (HTTA)-based extractions represent popular methods for separating microscopic amounts of transuranic actinides (i.e., Np and Pu) from macroscopic actinide matrixes (e.g. bulk uranium). It is well-established that this procedure enables +4 actinides to be selectively removed from +3, + 5, and +6 f-elements. However, even highly skilled and well-trained researchers find this process complicated and (at times) unpredictable. It is difficult to improve the HTTA extraction-or find alternatives-because little is understood about why this separation works. Even the identities of the extracted species are unknown. In addressing this knowledge gap, we report here advances in fundamental understanding of the HTTA-based extraction. This effort included comparatively evaluating HTTA complexation with +4 and +3 metals (M IV = Zr, Hf, Ce, Th, U, Np, and Pu vs M III = Ce, Nd, Sm, and Yb). We observed +4 metals formed neutral complexes of the general formula M IV (TTA) 4 . Meanwhile, +3 metals formed anionic M III (TTA) 4 - species. Characterization of these M(TTA) 4 x- ( x = 0, 1) compounds by UV-vis-NIR, IR, 1 H and 19 F NMR, single-crystal X-ray diffraction, and X-ray absorption spectroscopy (both near-edge and extended fine structure) was critical for determining that Np IV (TTA) 4 and Pu IV (TTA) 4 were the primary species extracted by HTTA. Furthermore, this information lays the foundation to begin developing and understanding of why the HTTA extraction works so well. The data suggest that the solubility differences between M IV (TTA) 4 and M III (TTA) 4 - are likely a major contributor to the selectivity of HTTA extractions for +4 cations over +3 metals. Moreover, these results will enable future studies focused on explaining HTTA extractions preference for +4 cations, which increases from Np IV to Pu IV , Hf IV , and Zr IV .

Component spectra extraction from terahertz measurements of unknown mixtures.

PubMed

Li, Xian; Hou, D B; Huang, P J; Cai, J H; Zhang, G X

2015-10-20

The aim of this work is to extract component spectra from unknown mixtures in the terahertz region. To that end, a method, hard modeling factor analysis (HMFA), was applied to resolve terahertz spectral matrices collected from the unknown mixtures. This method does not require any expertise of the user and allows the consideration of nonlinear effects such as peak variations or peak shifts. It describes the spectra using a peak-based nonlinear mathematic model and builds the component spectra automatically by recombination of the resolved peaks through correlation analysis. Meanwhile, modifications on the method were made to take the features of terahertz spectra into account and to deal with the artificial baseline problem that troubles the extraction process of some terahertz spectra. In order to validate the proposed method, simulated wideband terahertz spectra of binary and ternary systems and experimental terahertz absorption spectra of amino acids mixtures were tested. In each test, not only the number of pure components could be correctly predicted but also the identified pure spectra had a good similarity with the true spectra. Moreover, the proposed method associated the molecular motions with the component extraction, making the identification process more physically meaningful and interpretable compared to other methods. The results indicate that the HMFA method with the modifications can be a practical tool for identifying component terahertz spectra in completely unknown mixtures. This work reports the solution to this kind of problem in the terahertz region for the first time, to the best of the authors' knowledge, and represents a significant advance toward exploring physical or chemical mechanisms of unknown complex systems by terahertz spectroscopy.

Improved Methods for Capture, Extraction, and Quantitative Assay of Environmental DNA from Asian Bigheaded Carp (Hypophthalmichthys spp.)

PubMed Central

Turner, Cameron R.; Miller, Derryl J.; Coyne, Kathryn J.; Corush, Joel

2014-01-01

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species. PMID:25474207

Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.).

PubMed

Turner, Cameron R; Miller, Derryl J; Coyne, Kathryn J; Corush, Joel

2014-01-01

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.

Advances in Candida detection platforms for clinical and point-of-care applications

PubMed Central

Safavieh, Mohammadali; Coarsey, Chad; Esiobu, Nwadiuto; Memic, Adnan; Vyas, Jatin Mahesh; Shafiee, Hadi; Asghar, Waseem

2016-01-01

Invasive candidiasis remains one of the most serious community and healthcare-acquired infections worldwide. Conventional Candida detection methods based on blood and plate culture are time-consuming and require at least 2–4 days to identify various Candida species. Despite considerable advances for candidiasis detection, the development of simple, compact and portable point-of-care diagnostics for rapid and precise testing that automatically performs cell lysis, nucleic acid extraction, purification and detection still remains a challenge. Here, we systematically review most prominent conventional and nonconventional techniques for the detection of various Candida species, including Candida staining, blood culture, serological testing and nucleic acid-based analysis. We also discuss the most advanced lab on a chip devices for candida detection. PMID:27093473

How Are They Now? Longer Term Effects of eCoaching through Online Bug-in-Ear Technology

ERIC Educational Resources Information Center

Rock, Marcia L.; Schumacker, Randall E.; Gregg, Madeleine; Howard, Pamela W.; Gable, Robert A.; Zigmond, Naomi

2014-01-01

In this study, using mixed methods, we investigated the longer term effects of eCoaching through advanced online bug-in-ear (BIE) technology. Quantitative data on five dependent variables were extracted from 14 participants' electronically archived video files at three points in time--Spring 1 (i.e., baseline, which was the first semester of…

Production of Oxygen from Lunar Regolith using Molten Oxide Electrolysis

NASA Technical Reports Server (NTRS)

Sibille, Laurent; Sadoway, Donald R.; Sirk, Aislinn; Tripathy, Prabhat; Melendez, Orlando; Standish, Evan; Dominquez, Jesus A.; Stefanescu, Doru M.; Curreri, Peter A.; Poizeau, Sophie

2009-01-01

This slide presentation reviews the possible use of molten oxide electrolysis to extract oxygen from the Lunar Regolith. The presentation asserts that molten regolith electrolysis has advanced to be a useful method for production of oxygen and metals in situ on the Moon. The work has demonstrated an 8 hour batch of electrolysis at 5 amps using Iridium inert anodes.

Filling the gap between biology and computer science

PubMed Central

Aguilar-Ruiz, Jesús S; Moore, Jason H; Ritchie, Marylyn D

2008-01-01

This editorial introduces BioData Mining, a new journal which publishes research articles related to advances in computational methods and techniques for the extraction of useful knowledge from heterogeneous biological data. We outline the aims and scope of the journal, introduce the publishing model and describe the open peer review policy, which fosters interaction within the research community. PMID:18822148

Differential Nuclear and Mitochondrial DNA Preservation in Post-Mortem Teeth with Implications for Forensic and Ancient DNA Studies

PubMed Central

Higgins, Denice; Rohrlach, Adam B.; Kaidonis, John; Townsend, Grant; Austin, Jeremy J.

2015-01-01

Major advances in genetic analysis of skeletal remains have been made over the last decade, primarily due to improvements in post-DNA-extraction techniques. Despite this, a key challenge for DNA analysis of skeletal remains is the limited yield of DNA recovered from these poorly preserved samples. Enhanced DNA recovery by improved sampling and extraction techniques would allow further advancements. However, little is known about the post-mortem kinetics of DNA degradation and whether the rate of degradation varies between nuclear and mitochondrial DNA or across different skeletal tissues. This knowledge, along with information regarding ante-mortem DNA distribution within skeletal elements, would inform sampling protocols facilitating development of improved extraction processes. Here we present a combined genetic and histological examination of DNA content and rates of DNA degradation in the different tooth tissues of 150 human molars over short-medium post-mortem intervals. DNA was extracted from coronal dentine, root dentine, cementum and pulp of 114 teeth via a silica column method and the remaining 36 teeth were examined histologically. Real time quantification assays based on two nuclear DNA fragments (67 bp and 156 bp) and one mitochondrial DNA fragment (77 bp) showed nuclear and mitochondrial DNA degraded exponentially, but at different rates, depending on post-mortem interval and soil temperature. In contrast to previous studies, we identified differential survival of nuclear and mtDNA in different tooth tissues. Futhermore histological examination showed pulp and dentine were rapidly affected by loss of structural integrity, and pulp was completely destroyed in a relatively short time period. Conversely, cementum showed little structural change over the same time period. Finally, we confirm that targeted sampling of cementum from teeth buried for up to 16 months can provide a reliable source of nuclear DNA for STR-based genotyping using standard extraction methods, without the need for specialised equipment or large-volume demineralisation steps. PMID:25992635

An analysis of methods used to synthesize evidence and grade recommendations in food-based dietary guidelines

PubMed Central

Blake, Phillipa; Durão, Solange; Naude, Celeste E; Bero, Lisa

2018-01-01

Abstract Evidence-informed guideline development methods underpinned by systematic reviews ensure that guidelines are transparently developed, free from overt bias, and based on the best available evidence. Only recently has the nutrition field begun using these methods to develop public health nutrition guidelines. Given the importance of following an evidence-informed approach and recent advances in related methods, this study sought to describe the methods used to synthesize evidence, rate evidence quality, grade recommendations, and manage conflicts of interest (COIs) in national food-based dietary guidelines (FBDGs). The Food and Agriculture Organization’s FBDGs database was searched to identify the latest versions of FBDGs published from 2010 onward. Relevant data from 32 FBDGs were extracted, and the findings are presented narratively. This study shows that despite advances in evidence-informed methods for developing dietary guidelines, there are variations and deficiencies in methods used to review evidence, rate evidence quality, and grade recommendations. Dietary guidelines should follow systematic and transparent methods and be informed by the best available evidence, while considering important contextual factors and managing conflicts of interest. PMID:29425371

Morphological Feature Extraction for Automatic Registration of Multispectral Images

NASA Technical Reports Server (NTRS)

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.

FY10 Report on Multi-scale Simulation of Solvent Extraction Processes: Molecular-scale and Continuum-scale Studies

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

Wardle, Kent E.; Frey, Kurt; Pereira, Candido

2014-02-02

This task is aimed at predictive modeling of solvent extraction processes in typical extraction equipment through multiple simulation methods at various scales of resolution. We have conducted detailed continuum fluid dynamics simulation on the process unit level as well as simulations of the molecular-level physical interactions which govern extraction chemistry. Through combination of information gained through simulations at each of these two tiers along with advanced techniques such as the Lattice Boltzmann Method (LBM) which can bridge these two scales, we can develop the tools to work towards predictive simulation for solvent extraction on the equipment scale (Figure 1). Themore » goal of such a tool-along with enabling optimized design and operation of extraction units-would be to allow prediction of stage extraction effrciency under specified conditions. Simulation efforts on each of the two scales will be described below. As the initial application of FELBM in the work performed during FYl0 has been on annular mixing it will be discussed in context of the continuum-scale. In the future, however, it is anticipated that the real value of FELBM will be in its use as a tool for sub-grid model development through highly refined DNS-like multiphase simulations facilitating exploration and development of droplet models including breakup and coalescence which will be needed for the large-scale simulations where droplet level physics cannot be resolved. In this area, it can have a significant advantage over traditional CFD methods as its high computational efficiency allows exploration of significantly greater physical detail especially as computational resources increase in the future.« less

TU-D-207B-03: Early Assessment of Response to Chemoradiotherapy Based On Textural Analysis of Pre and Mid-Treatment FDG-PET Image in Locally Advanced Head and Neck Cancer

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

Cui, Y; Pollom, E; Loo, B

Purpose: To evaluate whether tumor textural features extracted from both pre- and mid-treatment FDG-PET images predict early response to chemoradiotherapy in locally advanced head and neck cancer, and investigate whether they provide complementary value to conventional volume-based measurements. Methods: Ninety-four patients with locally advanced head and neck cancers were retrospectively studied. All patients received definitive chemoradiotherapy and underwent FDG-PET planning scans both before and during treatment. Within the primary tumor we extracted 6 textural features based on gray-level co-occurrence matrices (GLCM): entropy, dissimilarity, contrast, correlation, energy, and homogeneity. These image features were evaluated for their predictive power of treatment responsemore » to chemoradiotherapy in terms of local recurrence free survival (LRFS) and progression free survival (PFS). Logrank test were used to assess the statistical significance of the stratification between low- and high-risk groups. P-values were adjusted for multiple comparisons by the false discovery rate (FDR) method. Results: All six textural features extracted from pre-treatment PET images significantly differentiated low- and high-risk patient groups for LRFS (P=0.011–0.038) and PFS (P=0.029–0.034). On the other hand, none of the textural features on mid-treatment PET images was statistically significant in stratifying LRFS (P=0.212–0.445) or PFS (P=0.168–0.299). An imaging signature that combines textural feature (GLCM homogeneity) and metabolic tumor volume showed an improved performance for predicting LRFS (hazard ratio: 22.8, P<0.0001) and PFS (hazard ratio: 13.9, P=0.0005) in leave-one-out cross validation. Intra-tumor heterogeneity measured by textural features was significantly lower in mid-treatment PET images than in pre-treatment PET images (T-test: P<1.4e-6). Conclusion: Tumor textural features on pretreatment FDG-PET images are predictive for response to chemoradiotherapy in locally advanced head and neck cancer. The complementary information offered by textural features improves patient stratification and may potentially aid in personalized risk-adaptive therapy.« less

ctDNA Determination of EGFR Mutation Status in European and Japanese Patients with Advanced NSCLC: The ASSESS Study.

PubMed

Reck, Martin; Hagiwara, Koichi; Han, Baohui; Tjulandin, Sergei; Grohé, Christian; Yokoi, Takashi; Morabito, Alessandro; Novello, Silvia; Arriola, Edurne; Molinier, Olivier; McCormack, Rose; Ratcliffe, Marianne; Normanno, Nicola

2016-10-01

To offer patients with EGFR mutation-positive advanced NSCLC appropriate EGFR tyrosine kinase inhibitor treatment, mutation testing of tumor samples is required. However, tissue/cytologic samples are not always available or evaluable. The large, noninterventional diagnostic ASSESS study (NCT01785888) evaluated the utility of circulating free tumor-derived DNA (ctDNA) from plasma for EGFR mutation testing. ASSESS was conducted in 56 centers (in Europe and Japan). Eligible patients (with newly diagnosed locally advanced/metastatic treatment-naive advanced NSCLC) provided diagnostic tissue/cytologic and plasma samples. DNA extracted from tissue/cytologic samples was subjected to EGFR mutation testing using local practices; designated laboratories performed DNA extraction/mutation testing of blood samples. The primary end point was level of concordance of EGFR mutation status between matched tissue/cytologic and plasma samples. Of 1311 patients enrolled, 1288 were eligible. Concordance of mutation status in 1162 matched samples was 89% (sensitivity 46%, specificity 97%, positive predictive value 78%, and negative predictive value 90%). A group of 25 patients with apparent false-positive plasma results was overrepresented for cytologic samples, use of less sensitive tissue testing methodologies, and smoking habits associated with high EGFR mutation frequency, indicative of false-negative tumor results. In cases in which plasma and tumor samples were tested with identical highly sensitive methods, positive predictive value/sensitivity were generally improved. These real-world data suggest that ctDNA is a feasible sample for EGFR mutation analysis. It is important to conduct mutation testing of both tumor and plasma samples in specialized laboratories, using robust/sensitive methods to ensure that patients receive appropriate treatments that target the molecular features of their disease. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Collection and Extraction of Occupational Air Samples for Analysis of Fungal DNA.

PubMed

Lemons, Angela R; Lindsley, William G; Green, Brett J

2018-05-02

Traditional methods of identifying fungal exposures in occupational environments, such as culture and microscopy-based approaches, have several limitations that have resulted in the exclusion of many species. Advances in the field over the last two decades have led occupational health researchers to turn to molecular-based approaches for identifying fungal hazards. These methods have resulted in the detection of many species within indoor and occupational environments that have not been detected using traditional methods. This protocol details an approach for determining fungal diversity within air samples through genomic DNA extraction, amplification, sequencing, and taxonomic identification of fungal internal transcribed spacer (ITS) regions. ITS sequencing results in the detection of many fungal species that are either not detected or difficult to identify to species level using culture or microscopy. While these methods do not provide quantitative measures of fungal burden, they offer a new approach to hazard identification and can be used to determine overall species richness and diversity within an occupational environment.

Micromagnetic measurement for characterization of ferromagnetic materials' microstructural properties

NASA Astrophysics Data System (ADS)

Zhang, Shuo; Shi, Xiaodong; Udpa, Lalita; Deng, Yiming

2018-05-01

Magnetic Barkhausen noise (MBN) is measured in low carbon steels and the relationship between carbon content and parameter extracted from MBN signal has been investigated. The parameter is extracted experimentally by fitting the original profiles with two Gaussian curves. The gap between two peaks (ΔG) of fitted Gaussian curves shows a better linear relationship with carbon contents of samples in the experiment. The result has been validated with simulation by Monte Carlo method. To ensure the sensitivity of measurement, advanced multi-objective optimization algorithm Non-dominant sorting genetic algorithm III (NSGA III) has been used to fulfill the optimization of the magnetic core of sensor.

Advanced analytical techniques for the extraction and characterization of plant-derived essential oils by gas chromatography with mass spectrometry.

PubMed

Waseem, Rabia; Low, Kah Hin

2015-02-01

In recent years, essential oils have received a growing interest because of the positive health effects of their novel characteristics such as antibacterial, antifungal, and antioxidant activities. For the extraction of plant-derived essential oils, there is the need of advanced analytical techniques and innovative methodologies. An exhaustive study of hydrodistillation, supercritical fluid extraction, ultrasound- and microwave-assisted extraction, solid-phase microextraction, pressurized liquid extraction, pressurized hot water extraction, liquid-liquid extraction, liquid-phase microextraction, matrix solid-phase dispersion, and gas chromatography (one- and two-dimensional) hyphenated with mass spectrometry for the extraction through various plant species and analysis of essential oils has been provided in this review. Essential oils are composed of mainly terpenes and terpenoids with low-molecular-weight aromatic and aliphatic constituents that are particularly important for public health. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Generalized Feature Extraction for Wrist Pulse Analysis: From 1-D Time Series to 2-D Matrix.

PubMed

Dimin Wang; Zhang, David; Guangming Lu

2017-07-01

Traditional Chinese pulse diagnosis, known as an empirical science, depends on the subjective experience. Inconsistent diagnostic results may be obtained among different practitioners. A scientific way of studying the pulse should be to analyze the objectified wrist pulse waveforms. In recent years, many pulse acquisition platforms have been developed with the advances in sensor and computer technology. And the pulse diagnosis using pattern recognition theories is also increasingly attracting attentions. Though many literatures on pulse feature extraction have been published, they just handle the pulse signals as simple 1-D time series and ignore the information within the class. This paper presents a generalized method of pulse feature extraction, extending the feature dimension from 1-D time series to 2-D matrix. The conventional wrist pulse features correspond to a particular case of the generalized models. The proposed method is validated through pattern classification on actual pulse records. Both quantitative and qualitative results relative to the 1-D pulse features are given through diabetes diagnosis. The experimental results show that the generalized 2-D matrix feature is effective in extracting both the periodic and nonperiodic information. And it is practical for wrist pulse analysis.

Characterization of Anthocyanins in Perilla frutescens var. acuta Extract by Advanced UPLC-ESI-IT-TOF-MSn Method and Their Anticancer Bioactivity.

PubMed

He, Yan-Kang; Yao, You-Yuan; Chang, Ya-Ning

2015-05-19

The anthocyanin extract from a domestic Perilla cultivar (Perilla frutescens var. acuta) were isolated and characterized with high mass accuracy and multi-dimensional fragmentation by means of ultra-performance liquid chromatography (UPLC) and electrospray ionization-ion trap-time of flight mass spectrometry analysis (ESI-IT-TOF-MSn). The new developed and applied LC-MS method focused on in-depth screening of anthocyanin compounds with similar structures which also provided a new approach of anthocyanin characterization without the use of external standards. Selective detection of interested anthocyanins was achieved utilizing extracted ion chromatogram (EIC) analysis, while MSn spectra were recorded to allow identification of the anthocyanin based on characteristic fragmentation patterns. Seven anthocyanins including one feruloyl (Cyanidin 3-O-feruloylglucoside-5-O-glucoside), two caffeoyl (Cyanidin 3-O-caffeoylglucoside-5-O-glucoside, Cyanidin 3-O-caffeoylglucoside-5-O-malonylglucoside) and four coumaroyl substituted anthocyanins (Cis-shisonin, Malonyl-cis-shisonin, Shisonin, and Malonyl-shisonin) were identified. Annexin-V FITC/PI flow cytometric assay was performed to analyze the influence of anthocyanin extract of P. frutescens var. acuta on cell apoptosis. The results suggested that Perilla anthocyanins can induce Hela cell apoptosis by a dose dependent manner.

Advanced Optimal Extraction for the Spitzer/IRS

NASA Astrophysics Data System (ADS)

Lebouteiller, V.; Bernard-Salas, J.; Sloan, G. C.; Barry, D. J.

2010-02-01

We present new advances in the spectral extraction of pointlike sources adapted to the Infrared Spectrograph (IRS) on board the Spitzer Space Telescope. For the first time, we created a supersampled point-spread function of the low-resolution modules. We describe how to use the point-spread function to perform optimal extraction of a single source and of multiple sources within the slit. We also examine the case of the optimal extraction of one or several sources with a complex background. The new algorithms are gathered in a plug-in called AdOpt which is part of the SMART data analysis software.

In vitro antimicrobial activity of Combretum molle (Combretaceae) against Staphylococcus aureus and Streptococcus agalactiae isolated from crossbred dairy cows with clinical mastitis.

PubMed

Regassa, Fekadu; Araya, Mengistu

2012-08-01

Following the rapidly expanding dairy enterprise, mastitis has remained the most economically damaging disease. The objective of this study was mainly to investigate the in vitro antibacterial activities of ethanol extracts of Combretum molle (R.Br.Ex.G.Don) Engl & Diels (Combretaceae) against antibiotic-resistant and susceptible Staphylococcus aureus and Streptococcus agalactiae isolated from clinical cases of bovine mastitis using agar disc diffusion method. The leaf and bark extracts showed antibacterial activity against S. aureus at concentrations of 3 mg/ml while the stem and seed extract did not show any bioactivity. Although both leaf and bark extracts were handled in the same manner, the antibacterial activity of the bark extract against the bacterial strains had declined gradually to a lower level as time advanced after extraction. The leaf extract had sustained bioactivity for longer duration. The susceptibility of the bacteria to the leaf extract is not obviously different between S. aureus and S. agalactiae. Also, there was no difference in susceptibility to the leaf extract between the antibiotic-resistant and antibiotic-sensitive bacteria. Further phytochemical and in vivo efficacy and safety studies are required to evaluate the therapeutic value of the plant against bovine mastitis.

Advancing the role of the pharmacy technician: A systematic review.

PubMed

Mattingly, Ashlee N; Mattingly, T Joseph

To summarize the findings of a literature search on advancing the role of pharmacy technicians, including the types of training identified and the potential costs and benefits to both the technician and the pharmacy. A literature search of Scopus, Embase, and Medline was conducted on January 11, 2017. Original research, research reports, case studies, or association reports were included for review. Articles were considered to be relevant based on identification of an advanced pharmacy technician role or addressing additional training/education for technician functions. A standard data extraction form was used to collect study authors, article title, year published, journal title, study design, brief description of methods, primary outcome measures, advanced technician roles identified, additional education or training addressed, and additional costs and benefits identified in each article. A total of 33 articles were included for full review and data extraction. Study design varied, with 17 (52%) quantitative, 1 (3%) qualitative, 5 (15%) mixed-method, and 10 (30%) case study designs. Seventeen (52%) of the studies included were published after 2006. The mechanism of training was primarily through supervised on-the-job training, allowing technicians to assume administrative-based positions that facilitated a pharmacist-led clinical service, with either the pharmacist or the pharmacy receiving the greatest benefits. Although the literature supports technicians performing advanced roles in the pharmacy, resulting in either improved patient outcomes or opportunities for pharmacists to engage in additional clinical services, the benefits to the technician were primarily indirect, such as an increase in job satisfaction or a more desirable work schedule. If a technician is to take on additional roles that require completion of a formalized training or educational program, benefits that are more tangible may help to inspire technicians to pursue these roles. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Challenges and Opportunities for Extracting Cardiovascular Risk Biomarkers from Imaging Data

NASA Astrophysics Data System (ADS)

Kakadiaris, I. A.; Mendizabal-Ruiz, E. G.; Kurkure, U.; Naghavi, M.

Complications attributed to cardiovascular diseases (CDV) are the leading cause of death worldwide. In the United States, sudden heart attack remains the number one cause of death and accounts for the majority of the 280 billion burden of cardiovascular diseases. In spite of the advancements in cardiovascular imaging techniques, the rate of deaths due to unpredicted heart attack remains high. Thus, novel computational tools are of critical need, in order to mine quantitative parameters from the imaging data for early detection of persons with a high likelihood of developing a heart attack in the near future (vulnerable patients). In this paper, we present our progress in the research of computational methods for the extraction of cardiovascular risk biomarkers from cardiovascular imaging data. In particular, we focus on the methods developed for the analysis of intravascular ultrasound (IVUS) data.

Determination of methylmercury in marine biota samples with advanced mercury analyzer: method validation.

PubMed

Azemard, Sabine; Vassileva, Emilia

2015-06-01

In this paper, we present a simple, fast and cost-effective method for determination of methyl mercury (MeHg) in marine samples. All important parameters influencing the sample preparation process were investigated and optimized. Full validation of the method was performed in accordance to the ISO-17025 (ISO/IEC, 2005) and Eurachem guidelines. Blanks, selectivity, working range (0.09-3.0ng), recovery (92-108%), intermediate precision (1.7-4.5%), traceability, limit of detection (0.009ng), limit of quantification (0.045ng) and expanded uncertainty (15%, k=2) were assessed. Estimation of the uncertainty contribution of each parameter and the demonstration of traceability of measurement results was provided as well. Furthermore, the selectivity of the method was studied by analyzing the same sample extracts by advanced mercury analyzer (AMA) and gas chromatography-atomic fluorescence spectrometry (GC-AFS). Additional validation of the proposed procedure was effectuated by participation in the IAEA-461 worldwide inter-laboratory comparison exercises. Copyright © 2014 Elsevier Ltd. All rights reserved.

Section Curve Reconstruction and Mean-Camber Curve Extraction of a Point-Sampled Blade Surface

PubMed Central

Li, Wen-long; Xie, He; Li, Qi-dong; Zhou, Li-ping; Yin, Zhou-ping

2014-01-01

The blade is one of the most critical parts of an aviation engine, and a small change in the blade geometry may significantly affect the dynamics performance of the aviation engine. Rapid advancements in 3D scanning techniques have enabled the inspection of the blade shape using a dense and accurate point cloud. This paper proposes a new method to achieving two common tasks in blade inspection: section curve reconstruction and mean-camber curve extraction with the representation of a point cloud. The mathematical morphology is expanded and applied to restrain the effect of the measuring defects and generate an ordered sequence of 2D measured points in the section plane. Then, the energy and distance are minimized to iteratively smoothen the measured points, approximate the section curve and extract the mean-camber curve. In addition, a turbine blade is machined and scanned to observe the curvature variation, energy variation and approximation error, which demonstrates the availability of the proposed method. The proposed method is simple to implement and can be applied in aviation casting-blade finish inspection, large forging-blade allowance inspection and visual-guided robot grinding localization. PMID:25551467

Section curve reconstruction and mean-camber curve extraction of a point-sampled blade surface.

PubMed

Li, Wen-long; Xie, He; Li, Qi-dong; Zhou, Li-ping; Yin, Zhou-ping

2014-01-01

The blade is one of the most critical parts of an aviation engine, and a small change in the blade geometry may significantly affect the dynamics performance of the aviation engine. Rapid advancements in 3D scanning techniques have enabled the inspection of the blade shape using a dense and accurate point cloud. This paper proposes a new method to achieving two common tasks in blade inspection: section curve reconstruction and mean-camber curve extraction with the representation of a point cloud. The mathematical morphology is expanded and applied to restrain the effect of the measuring defects and generate an ordered sequence of 2D measured points in the section plane. Then, the energy and distance are minimized to iteratively smoothen the measured points, approximate the section curve and extract the mean-camber curve. In addition, a turbine blade is machined and scanned to observe the curvature variation, energy variation and approximation error, which demonstrates the availability of the proposed method. The proposed method is simple to implement and can be applied in aviation casting-blade finish inspection, large forging-blade allowance inspection and visual-guided robot grinding localization.

Advanced eddy current test signal analysis for steam generator tube defect classification and characterization

NASA Astrophysics Data System (ADS)

McClanahan, James Patrick

Eddy Current Testing (ECT) is a Non-Destructive Examination (NDE) technique that is widely used in power generating plants (both nuclear and fossil) to test the integrity of heat exchanger (HX) and steam generator (SG) tubing. Specifically for this research, laboratory-generated, flawed tubing data were examined. The purpose of this dissertation is to develop and implement an automated method for the classification and an advanced characterization of defects in HX and SG tubing. These two improvements enhanced the robustness of characterization as compared to traditional bobbin-coil ECT data analysis methods. A more robust classification and characterization of the tube flaw in-situ (while the SG is on-line but not when the plant is operating), should provide valuable information to the power industry. The following are the conclusions reached from this research. A feature extraction program acquiring relevant information from both the mixed, absolute and differential data was successfully implemented. The CWT was utilized to extract more information from the mixed, complex differential data. Image Processing techniques used to extract the information contained in the generated CWT, classified the data with a high success rate. The data were accurately classified, utilizing the compressed feature vector and using a Bayes classification system. An estimation of the upper bound for the probability of error, using the Bhattacharyya distance, was successfully applied to the Bayesian classification. The classified data were separated according to flaw-type (classification) to enhance characterization. The characterization routine used dedicated, flaw-type specific ANNs that made the characterization of the tube flaw more robust. The inclusion of outliers may help complete the feature space so that classification accuracy is increased. Given that the eddy current test signals appear very similar, there may not be sufficient information to make an extremely accurate (>95%) classification or an advanced characterization using this system. It is necessary to have a larger database fore more accurate system learning.

Prognostic value of metabolic metrics extracted from baseline PET images in NSCLC

PubMed Central

Carvalho, Sara; Leijenaar, Ralph T.H.; Velazquez, Emmanuel Rios; Oberije, Cary; Parmar, Chintan; van Elmpt, Wouter; Reymen, Bart; Troost, Esther G.C.; Oellers, Michel; Dekker, Andre; Gillies, Robert; Aerts, Hugo J.W.L.; Lambin, Philippe

2015-01-01

Background Maximum, mean and peak SUV of primary tumor at baseline FDG-PET scans, have often been found predictive for overall survival in non-small cell lung cancer (NSCLC) patients. In this study we further investigated the prognostic power of advanced metabolic metrics derived from Intensity-Volume Histograms (IVH) extracted from PET imaging. Methods A cohort of 220 NSCLC patients (mean age, 66.6 years; 149 men, 71 women), stages I-IIIB, treated with radiotherapy with curative intent were included (NCT00522639). Each patient underwent standardized pre-treatment CT-PET imaging. Primary GTV was delineated by an experienced radiation oncologist on CT-PET images. Common PET descriptors such as maximum, mean and peak SUV, and metabolic tumor volume (MTV) were quantified. Advanced descriptors of metabolic activity were quantified by IVH. These comprised 5 groups of features: Absolute and Relative Volume above Relative Intensity threshold (AVRI and RVRI), Absolute and Relative Volume above Absolute Intensity threshold (AVAI and RVAI), and Absolute Intensity above Relative Volume threshold (AIRV). MTV was derived from the IVH curves for volumes with SUV above 2.5, 3 and 4, and of 40% and 50% maximum SUV. Univariable analysis using Cox Proportional Hazard Regression was performed for overall survival assessment. Results Relative volume above higher SUV (80 %) was an independent predictor of OS (p = 0.05). None of the possible surrogates for MTV based on volumes above SUV of 3, 40% and 50% of maximum SUV showed significant associations with OS (p (AVAI3) = 0.10, p (AVAI4) = 0.22, p (AVRI40%) = 0.15, p (AVRI50%) = 0.17). Maximum and peak SUV (r = 0.99) revealed no prognostic value for OS (p (maximum SUV) = 0.20, p (peak SUV) = 0.22). Conclusions New methods using more advanced imaging features extracted from PET were analyzed. Best prognostic value for OS of NSCLC patients was found for relative portions of the tumor above higher uptakes (80% SUV). PMID:24047338

Wakefield Computations for the CLIC PETS using the Parallel Finite Element Time-Domain Code T3P

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

Candel, A; Kabel, A.; Lee, L.

In recent years, SLAC's Advanced Computations Department (ACD) has developed the high-performance parallel 3D electromagnetic time-domain code, T3P, for simulations of wakefields and transients in complex accelerator structures. T3P is based on advanced higher-order Finite Element methods on unstructured grids with quadratic surface approximation. Optimized for large-scale parallel processing on leadership supercomputing facilities, T3P allows simulations of realistic 3D structures with unprecedented accuracy, aiding the design of the next generation of accelerator facilities. Applications to the Compact Linear Collider (CLIC) Power Extraction and Transfer Structure (PETS) are presented.

Pelvic artery calcification detection on CT scans using convolutional neural networks

NASA Astrophysics Data System (ADS)

Liu, Jiamin; Lu, Le; Yao, Jianhua; Bagheri, Mohammadhadi; Summers, Ronald M.

2017-03-01

Artery calcification is observed commonly in elderly patients, especially in patients with chronic kidney disease, and may affect coronary, carotid and peripheral arteries. Vascular calcification has been associated with many clinical outcomes. Manual identification of calcification in CT scans requires substantial expert interaction, which makes it time-consuming and infeasible for large-scale studies. Many works have been proposed for coronary artery calcification detection in cardiac CT scans. In these works, coronary artery extraction is commonly required for calcification detection. However, there are few works about abdominal or pelvic artery calcification detection. In this work, we present a method for automatic pelvic artery calcification detection on CT scan. This method uses the recent advanced faster region-based convolutional neural network (R-CNN) to directly identify artery calcification without a need for artery extraction since pelvic artery extraction itself is challenging. Our method first generates category-independent region proposals for each slice of the input CT scan using region proposal networks (RPN). Then, each region proposal is jointly classified and refined by softmax classifier and bounding box regressor. We applied the detection method to 500 images from 20 CT scans of patients for evaluation. The detection system achieved a 77.4% average precision and a 85% sensitivity at 1 false positive per image.

Selective and comprehensive analysis of organohalogen compounds by GC × GC-HRTofMS and MS/MS.

PubMed

Hashimoto, Shunji; Zushi, Yasuyuki; Takazawa, Yoshikatsu; Ieda, Teruyo; Fushimi, Akihiro; Tanabe, Kiyoshi; Shibata, Yasuyuki

2018-03-01

Thousands of organohalogen compounds, including hazardous chemicals such as polychlorinated biphenyls (PCBs) and other persistent organic pollutants (POPs), were selectively and simultaneously detected and identified with simple, or no, purification from environmental sample extracts by using several advanced methods. The methods used were software extraction from two-dimensional gas chromatography-high-resolution time-of-flight mass spectrometry (GC × GC-HRTofMS) data, measurement by negative chemical ionization with HRTofMS, and neutral loss scanning (NLS) with GC × GC-MS/MS. Global and selective detection of organochlorines and bromines in environmental samples such as sediments and fly ash was achieved by NLS using GC × GC-MS/MS (QQQ), with the expected losses of 35 Cl and 79 Br. We confirmed that negative chemical ionization was effective for sensitive and selective ionization of organohalogens, even using GC × GC-HRTofMS. The 2D total ion chromatograms obtained by using negative chemical ionization and selective extraction of organohalogens using original software from data measured by electron impact ionization were very similar; the software thus functioned well to extract organohalogens. Combining measurements made by using these different methods will help to detect organohalogens selectively and globally. However, to compare the data obtained by individual measurements, the retention times of the peaks on the 2D chromatograms need to match.

Low temperature synthesis of hierarchical TiO 2 nanostructures for high performance perovskite solar cells by pulsed laser deposition

DOE PAGES

Yang, Bin; Mahjouri-Samani, Masoud; Rouleau, Christopher M.; ...

2016-06-10

A promising way to advance perovskite solar cells is to improve the quality of the electron transport material e.g., titanium dioxide (TiO 2) in a direction that increases electron transport and extraction. Although dense TiO 2 films are easily grown in solution, efficient electron extraction suffers due to a lack of interfacial contact area with the perovskite. Conversely, mesoporous films do offer high surface-area-to-volume ratios, thereby promoting efficient electron extraction, but their morphology is relatively difficult to control via conventional solution synthesis methods. Here, a pulsed laser deposition method was used to assemble TiO 2 nanoparticles into TiO 2 hierarchicalmore » nanoarchitectures having the anatase crystal structure, and prototype solar cells employing these structures yielded power conversion efficiencies of ~ 14%. Our approach demonstrates a way to grow high aspect-ratio TiO 2 nanostructures for improved interfacial contact between TiO 2 and perovskite materials, leading to high electron-hole pair separation and electron extraction efficiencies for superior photovoltaic performance. In addition, compared to conventional solution-processed TiO 2 films that require 500 °C to obtain a good crystallinity, our relatively low temperature (300 °C) TiO 2 processing method may promote reduced energy-consumption during device fabrication as well as enable compatibility with various flexible polymer substrates.« less

Determination of pesticides in sewage sludge from an agro-food industry using QuEChERS extraction followed by analysis with liquid chromatography-tandem mass spectrometry.

PubMed

Ponce-Robles, Laura; Rivas, Gracia; Esteban, Belen; Oller, Isabel; Malato, Sixto; Agüera, Ana

2017-10-01

An analytical method was developed and validated for the determination of ten pesticides in sewage sludge coming from an agro-food industry. The method was based on the application of Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) extraction for solid sewage sludge and SPE extraction for sludge aqueous phase, followed by liquid chromatography (LC) coupled to hybrid quadrupole/linear ion trap mass spectrometry (QqLIT-MS). The QuEChERS method was reported 14 years ago and nowadays is mainly applied to the analysis of pesticides in food. More recent applications have been reported in other matrices as sewage sludge, but the complexity of the matrix makes necessary the optimization of the cleanup step to improve the efficiency of the analysis. With this aim, several dispersive solid-phase extraction cleanup sorbents were tested, choosing C18 + PSA as a d-SPE sorbent. The proposed method was satisfactorily validated for most compounds investigated, showing recoveries higher than 80% in most cases, with the only exception of prochloraz (71%) at low concentration level. Limits of quantification were lower than 40 ng l -1 in the aqueous phase and below 40 ng g -1 in the solid phase for the majority of the analytes. The method was applied to solid sludge and the sludge aqueous phase coming from an agro-food industry which processes fruits and vegetables. Graphical abstract Application of LC/MS/MS advanced analytical techniques for determination of pesticides contained in sewage sludge.

Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane

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

Nickels, Jonathan D.; Chatterjee, Sneha; Mostofian, Barmak

Lipid extracts are an excellent choice of model biomembrane; however at present, there are no commercially available lipid extracts or computational models that mimic microbial membranes containing the branched-chain fatty acids found in many pathogenic and industrially relevant bacteria. Here, we advance the extract of Bacillus subtilis as a standard model for these diverse systems, providing a detailed experimental description and equilibrated atomistic bilayer model included as Supporting Information to this Letter and at (http://cmb.ornl.gov/members/cheng). The development and validation of this model represents an advance that enables more realistic simulations and experiments on bacterial membranes and reconstituted bacterial membrane proteins.

A conifer-friendly high-throughput α-cellulose extraction method for δ13C and δ18O stable isotope ratio analysis

NASA Astrophysics Data System (ADS)

Lin, W.; Noormets, A.; domec, J.; King, J. S.; Sun, G.; McNulty, S.

2012-12-01

Wood stable isotope ratios (δ13C and δ18O) offer insight to water source and plant water use efficiency (WUE), which in turn provide a glimpse to potential plant responses to changing climate, particularly rainfall patterns. The synthetic pathways of cell wall deposition in wood rings differ in their discrimination ratios between the light and heavy isotopes, and α-cellulose is broadly seen as the best indicator of plant water status due to its local and temporal fixation and to its high abundance within the wood. To use the effects of recent severe droughts on the WUE of loblolly pine (Pinus taeda) throughout Southeastern USA as a harbinger of future changes, an effort has been undertaken to sample the entire range of the species and to sample the isotopic composition in a consistent manner. To be able to accommodate the large number of samples required by this analysis, we have developed a new high-throughput method for α-cellulose extraction, which is the rate-limiting step in such an endeavor. Although an entire family of methods has been developed and perform well, their throughput in a typical research lab setting is limited to 16-75 samples per week with intensive labor input. The resin exclusion step in conifersis is particularly time-consuming. We have combined the recent advances of α-cellulose extraction in plant ecology and wood science, including a high-throughput extraction device developed in the Potsdam Dendro Lab and a simple chemical-based resin exclusion method. By transferring the entire extraction process to a multiport-based system allows throughputs of up to several hundred samples in two weeks, while minimizing labor requirements to 2-3 days per batch of samples.

Direct Printing of Stretchable Elastomers for Highly Sensitive Capillary Pressure Sensors.

PubMed

Liu, Wenguang; Yan, Chaoyi

2018-03-28

We demonstrate the successful fabrication of highly sensitive capillary pressure sensors using an innovative 3D printing method. Unlike conventional capacitive pressure sensors where the capacitance changes were due to the pressure-induced interspace variations between the parallel plate electrodes, in our capillary sensors the capacitance was determined by the extrusion and extraction of liquid medium and consequent changes of dielectric constants. Significant pressure sensitivity advances up to 547.9 KPa -1 were achieved. Moreover, we suggest that our innovative capillary pressure sensors can adopt a wide range of liquid mediums, such as ethanol, deionized water, and their mixtures. The devices also showed stable performances upon repeated pressing cycles. The direct and versatile printing method combined with the significant performance advances are expected to find important applications in future stretchable and wearable electronics.

Automatic Extraction of Road Markings from Mobile Laser Scanning Data

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Extraction of advanced geospatial intelligence (AGI) from commercial synthetic aperture radar imagery

NASA Astrophysics Data System (ADS)

Kanberoglu, Berkay; Frakes, David

2017-04-01

The extraction of objects from advanced geospatial intelligence (AGI) products based on synthetic aperture radar (SAR) imagery is complicated by a number of factors. For example, accurate detection of temporal changes represented in two-color multiview (2CMV) AGI products can be challenging because of speckle noise susceptibility and false positives that result from small orientation differences between objects imaged at different times. These cases of apparent motion can result in 2CMV detection, but they obviously differ greatly in terms of significance. In investigating the state-of-the-art in SAR image processing, we have found that differentiating between these two general cases is a problem that has not been well addressed. We propose a framework of methods to address these problems. For the detection of the temporal changes while reducing the number of false positives, we propose using adaptive object intensity and area thresholding in conjunction with relaxed brightness optical flow algorithms that track the motion of objects across time in small regions of interest. The proposed framework for distinguishing between actual motion and misregistration can lead to more accurate and meaningful change detection and improve object extraction from a SAR AGI product. Results demonstrate the ability of our techniques to reduce false positives up to 60%.

Determination of well flat band condition in thin film FDSOI transistors using C-V measurement for accurate parameter extraction

NASA Astrophysics Data System (ADS)

Mohamad, B.; Leroux, C.; Reimbold, G.; Ghibaudo, G.

2018-01-01

For advanced gate stacks, effective work function (WFeff) and equivalent oxide thickness (EOT) are fundamental parameters for technology optimization. On FDSOI transistors, and contrary to the bulk technologies, while EOT can still be extracted at strong inversion from the typical gate-to-channel capacitance (Cgc), it is no longer the case for WFeff due to the disappearance of an observable flat band condition on capacitance characteristics. In this work, a new experimental method, the Cbg(VBG) characteristic, is proposed in order to extract the well flat band condition (VFB, W). This characteristic enables an accurate and direct evaluation of WFeff. Moreover, using the previous extraction of the gate oxide (tfox), and buried oxide (tbox) from typical capacitance characteristics (Cgc and Cbc), it allows the extraction of the channel thickness (tch). Furthermore, the measurement of the well flat band condition on Cbg(VBG) characteristics for two different Si and SiGe channel also proves the existence of a dipole at the SiGe/SiO2 interface.

Wells for In Situ Extraction of Volatiles from Regolith (WIEVR)

NASA Technical Reports Server (NTRS)

Walton, Otis R.

2013-01-01

A document discusses WIEVRs, a means to extract water ice more efficiently than previous approaches. This water may exist in subsurface deposits on the Moon, in many NEOs (Near- Earth Objects), and on Mars. The WIEVR approach utilizes heat from the Sun to vaporize subsurface ice; the water (or other volatile) vapor is transported to a surface collection vessel where it is condensed (and collected). The method does not involve mining and extracting regolith before removing the frozen volatiles, so it uses less energy and is less costly than approaches that require mining of regolith. The only drilling required for establishing the WIEVR collection/recovery system is a well-bore drill hole. In its simplest form, the WIEVRs will function without pumps, compressors, or other gas-moving equipment, relying instead on diffusive transport and thermally induced convection of the vaporized volatiles for transport to the collection location(s). These volatile extraction wells could represent a significant advance in extraction efficiency for recovery of frozen volatiles in subsurface deposits on the Moon, Mars, or other extraterrestrial bodies.

A modified extraction and clean-up procedure for the detection and determination of parathion-methyl and chlorpyrifos residues in tea.

PubMed

Shanker, A; Sood, C; Kumar, V; Ravindranath, S D

2001-05-01

Recent advances in methodology and instrumentation have made possible the detection and determination of pesticides at microgram kg-1 (ppb) levels. The sensitivity of a method of analysis depends greatly on the efficient extraction of the pesticide and the subsequent clean-up of the extract. The extract from green tea leaves is a mixture of aroma components, polyphenols and caffeine. The preparation of made tea from green tea leaves adds to this complexity by concentrating these coextractives. Conventional clean-up techniques provide poor recoveries for parathion-methyl and chlorpyrifos from both green tea leaves and made tea. This arises from interference by caffeine during gas chromatography, as it has a similar retention time to the two pesticides and peaks overlap. A modification to the protocol based on a solvent partitioning process using dichloromethane and subsequent washing of the extracts with warm water removed the caffeine, and pigments were removed by column chromatography. Recoveries ranging from 80 to 90% were then obtained for both pesticides.

Automated solid-phase extraction and liquid chromatography for assay of cyclosporine in whole blood.

PubMed

Kabra, P M; Wall, J H; Dimson, P

1987-12-01

In this rapid, precise, accurate, cost-effective, automated liquid-chromatographic procedure for determining cyclosporine in whole blood, the cyclosporine is extracted from 0.5 mL of whole blood together with 300 micrograms of cyclosporin D per liter, added as internal standard, by using an Advanced Automated Sample Processing unit. The on-line solid-phase extraction is performed on an octasilane sorbent cartridge, which is interfaced with a RP-8 guard column and an octyl analytical column, packed with 5-microns packing material. Both columns are eluted with a mobile phase containing acetonitrile/methanol/water (53/20/27 by vol) at a flow rate of 1.5 mL/min and column temperature of 70 degrees C. Absolute recovery of cyclosporine exceeded 85% and the standard curve was linear to 5000 micrograms/L. Within-run and day-to-day CVs were less than 8%. Correlation between automated and manual Bond-Elut extraction methods was excellent (r = 0.987). None of 18 drugs and four steroids tested interfered.

Recent Advances in On-Line Methods Based on Extraction for Speciation Analysis of Chromium in Environmental Matrices.

PubMed

Trzonkowska, Laura; Leśniewska, Barbara; Godlewska-Żyłkiewicz, Beata

2016-07-03

The biological activity of Cr(III) and Cr(VI) species, their chemical behavior, and toxic effects are dissimilar. The speciation analysis of Cr(III) and Cr(VI) in environmental matrices is then of great importance and much research has been devoted to this area. This review presents recent developments in on-line speciation analysis of chromium in such samples. Flow systems have proved to be excellent tools for automation of sample pretreatment, separation/preconcentration of chromium species, and their detection by various instrumental techniques. Analytical strategies used in chromium speciation analysis discussed in this review are divided into categories based on selective extraction/separation of chromium species on solid sorbents and liquid-liquid extraction of chromium species. The most popular strategy is that based on solid-phase extraction. Therefore, this review shows the potential of novel materials designed and used for selective binding of chromium species. The progress in miniaturization of measurement systems is also presented.

Selective extraction and enrichment of multiphosphorylated peptides using polyarginine-coated diamond nanoparticles.

PubMed

Chang, Chia-Kai; Wu, Chih-Che; Wang, Yi-Sheng; Chang, Huan-Cheng

2008-05-15

Despite recent advances in phosphopeptide research, detection and characterization of multiply phosphorylated peptides have been a challenge. This work presents a new strategy that not only can effectively extract phosphorylated peptides from complex samples but also can selectively enrich multiphosphorylated peptides for direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis. Polyarginine-coated diamond nanoparticles are the solid-phase extraction supports used for this purpose. The supports show an exceptionally high affinity for multiphosphorylated peptides due to multiple arginine-phosphate interactions. The efficacy of this method was demonstrated by analyzing a small volume (50 microL) of tryptic digests of proteins such as beta-casein, alpha-casein, and nonfat milk at a concentration as low as 1 x 10 (-9) M. The concentration is markedly lower than that can be achieved by using other currently available technologies. We quantified the enhanced selectivity and detection sensitivity of the method using mixtures composed of mono- and tetraphosphorylated peptide standards. This new affinity-based protocol is expected to find useful applications in characterizing multiple phosphorylation sites on proteins of interest in complex and dilute analytes.

Cortical Signal Analysis and Advances in Functional Near-Infrared Spectroscopy Signal: A Review.

PubMed

Kamran, Muhammad A; Mannan, Malik M Naeem; Jeong, Myung Yung

2016-01-01

Functional near-infrared spectroscopy (fNIRS) is a non-invasive neuroimaging modality that measures the concentration changes of oxy-hemoglobin (HbO) and de-oxy hemoglobin (HbR) at the same time. It is an emerging cortical imaging modality with a good temporal resolution that is acceptable for brain-computer interface applications. Researchers have developed several methods in last two decades to extract the neuronal activation related waveform from the observed fNIRS time series. But still there is no standard method for analysis of fNIRS data. This article presents a brief review of existing methodologies to model and analyze the activation signal. The purpose of this review article is to give a general overview of variety of existing methodologies to extract useful information from measured fNIRS data including pre-processing steps, effects of differential path length factor (DPF), variations and attributes of hemodynamic response function (HRF), extraction of evoked response, removal of physiological noises, instrumentation, and environmental noises and resting/activation state functional connectivity. Finally, the challenges in the analysis of fNIRS signal are summarized.

Cortical Signal Analysis and Advances in Functional Near-Infrared Spectroscopy Signal: A Review

PubMed Central

Kamran, Muhammad A.; Mannan, Malik M. Naeem; Jeong, Myung Yung

2016-01-01

Functional near-infrared spectroscopy (fNIRS) is a non-invasive neuroimaging modality that measures the concentration changes of oxy-hemoglobin (HbO) and de-oxy hemoglobin (HbR) at the same time. It is an emerging cortical imaging modality with a good temporal resolution that is acceptable for brain-computer interface applications. Researchers have developed several methods in last two decades to extract the neuronal activation related waveform from the observed fNIRS time series. But still there is no standard method for analysis of fNIRS data. This article presents a brief review of existing methodologies to model and analyze the activation signal. The purpose of this review article is to give a general overview of variety of existing methodologies to extract useful information from measured fNIRS data including pre-processing steps, effects of differential path length factor (DPF), variations and attributes of hemodynamic response function (HRF), extraction of evoked response, removal of physiological noises, instrumentation, and environmental noises and resting/activation state functional connectivity. Finally, the challenges in the analysis of fNIRS signal are summarized. PMID:27375458

Efficient Method for Scalable Registration of Remote Sensing Images

NASA Astrophysics Data System (ADS)

Prouty, R.; LeMoigne, J.; Halem, M.

2017-12-01

The goal of this project is to build a prototype of a resource-efficient pipeline that will provide registration within subpixel accuracy of multitemporal Earth science data. Accurate registration of Earth-science data is imperative to proper data integration and seamless mosaicing of data from multiple times, sensors, and/or observation geometries. Modern registration methods make use of many arithmetic operations and sometimes require complete knowledge of the image domain. As such, while sensors become more advanced and are able to provide higher-resolution data, the memory resources required to properly register these data become prohibitive. The proposed pipeline employs a region of interest extraction algorithm in order to extract image subsets with high local feature density. These image subsets are then used to generate local solutions to the global registration problem. The local solutions are then 'globalized' to determine the deformation model that best solves the registration problem. The region of interest extraction and globalization routines are tested for robustness among the variety of scene-types and spectral locations provided by Earth-observing instruments such as Landsat, MODIS, or ASTER.

Traditional and Modern Cell Culture in Virus Diagnosis.

PubMed

Hematian, Ali; Sadeghifard, Nourkhoda; Mohebi, Reza; Taherikalani, Morovat; Nasrolahi, Abbas; Amraei, Mansour; Ghafourian, Sobhan

2016-04-01

Cell cultures are developed from tissue samples and then disaggregated by mechanical, chemical, and enzymatic methods to extract cells suitable for isolation of viruses. With the recent advances in technology, cell culture is considered a gold standard for virus isolation. This paper reviews the evolution of cell culture methods and demonstrates why cell culture is a preferred method for identification of viruses. In addition, the advantages and disadvantages of both traditional and modern cell culture methods for diagnosis of each type of virus are discussed. Detection of viruses by the novel cell culture methods is considered more accurate and sensitive. However, there is a need to include some more accurate methods such as molecular methods in cell culture for precise identification of viruses.

Sol-gel-graphene-based fabric-phase sorptive extraction for cow and human breast milk sample cleanup for screening bisphenol A and residual dental restorative material before analysis by HPLC with diode array detection.

PubMed

Samanidou, Victoria; Filippou, Olga; Marinou, Eirini; Kabir, Abuzar; Furton, Kenneth G

2017-06-01

Fabric-phase sorptive extraction has already been recognized as a simple and green alternative to the conventional sorbent-based sorptive microextraction techniques, using hybrid organic-inorganic sorbent coatings chemically bonded to a flexible fabric surface. Herein, we have investigated the synergistic combination of the advanced material properties offered by sol-gel graphene sorbent and the simplicity of Fabric phase sorptive extraction approach in selectively extracting bisphenol A and residual monomers including bisphenol A glycerolatedimethacrylate, urethane dimethacrylate, and triethylene glycol dimethacrylate derived dental restorative materials from cow and human breast milk samples. Different coatings were evaluated. Final method development employed sol-gel graphene coated media. The main experimental parameters influencing extraction of the compounds, such as sorbent chemistry used, sample loading conditions, elution solvent, sorption stirring time, elution time, impact of protein precipitation, amount of sample, and matrix effect, were investigated and optimized. Absolute recovery values from standard solutions were 50% for bisphenol A, 78% for T triethylene glycol dimethacrylate, 110% for urethane dimethacrylate, and 103% for bisphenol A glycerolatedimethacrylate, while respective absolute recovery values from milk were 30, 52, 104, and 42%. Method validation was performed according to European Decision 657/2002/EC in terms of selectivity, sensitivity, linearity, accuracy, and precision. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Downstream processing of stevioside and its potential applications.

PubMed

Puri, Munish; Sharma, Deepika; Tiwari, Ashok K

2011-01-01

Stevioside is a natural sweetener extracted from leaves of Stevia rebaudiana Bertoni, which is commercially produced by conventional (chemical/physical) processes. This article gives an overview of the stevioside structure, various analysis technique, new technologies required and the advances achieved in recent years. An enzymatic process is established, by which the maximum efficacy and benefit of the process can be achieved. The efficiency of the enzymatic process is quite comparable to that of other physical and chemical methods. Finally, we believe that in the future, the enzyme-based extraction will ensure more cost-effective availability of stevioside, thus assisting in the development of more food-based applications. Copyright © 2011 Elsevier Inc. All rights reserved.

Safety evaluation methodology for advanced coal extraction systems

NASA Technical Reports Server (NTRS)

Zimmerman, W. F.

1981-01-01

Qualitative and quantitative evaluation methods for coal extraction systems were developed. The analysis examines the soundness of the design, whether or not the major hazards have been eliminated or reduced, and how the reduction would be accomplished. The quantitative methodology establishes the approximate impact of hazards on injury levels. The results are weighted by peculiar geological elements, specialized safety training, peculiar mine environmental aspects, and reductions in labor force. The outcome is compared with injury level requirements based on similar, safer industries to get a measure of the new system's success in reducing injuries. This approach provides a more detailed and comprehensive analysis of hazards and their effects than existing safety analyses.

Gene regulatory network identification from the yeast cell cycle based on a neuro-fuzzy system.

PubMed

Wang, B H; Lim, J W; Lim, J S

2016-08-30

Many studies exist for reconstructing gene regulatory networks (GRNs). In this paper, we propose a method based on an advanced neuro-fuzzy system, for gene regulatory network reconstruction from microarray time-series data. This approach uses a neural network with a weighted fuzzy function to model the relationships between genes. Fuzzy rules, which determine the regulators of genes, are very simplified through this method. Additionally, a regulator selection procedure is proposed, which extracts the exact dynamic relationship between genes, using the information obtained from the weighted fuzzy function. Time-series related features are extracted from the original data to employ the characteristics of temporal data that are useful for accurate GRN reconstruction. The microarray dataset of the yeast cell cycle was used for our study. We measured the mean squared prediction error for the efficiency of the proposed approach and evaluated the accuracy in terms of precision, sensitivity, and F-score. The proposed method outperformed the other existing approaches.

Recent Advances in the Separation of Rare Earth Elements Using Mesoporous Hybrid Materials.

PubMed

Hu, Yimu; Florek, Justyna; Larivière, Dominic; Fontaine, Frédéric-Georges; Kleitz, Freddy

2018-05-27

Over the past decades, the need for rare earth elements (REEs) has increased substantially, mostly because these elements are used as valuable additives in advanced technologies. However, the difference in ionic radius between neighboring REEs is small, which renders an efficient sized-based separation extremely challenging. Among different types of extraction methods, solid-phase extraction (SPE) is a promising candidate, featuring high enrichment factor, rapid adsorption kinetics, reduced solvent consumption and minimized waste generation. The great challenge remains yet to develop highly efficient and selective adsorbents for this process. In this regard, ordered mesoporous materials (OMMs) possess high specific surface area, tunable pore size, large pore volume, as well as stable and interconnected frameworks with active pore surfaces for functionalization. Such features meet the requirements for enhanced adsorbents, not only providing huge reactional interface and large surface capable of accommodating guest species, but also enabling the possibility of ion-specific binding for enrichment and separation purposes. This short personal account summarizes some of the recent advances in the use of porous hybrid materials as selective sorbents for REE separation and purification, with particular attention devoted to ordered mesoporous silica and carbon-based sorbents. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Influence of moderate to severe chronic periodontitis on dental pulp

PubMed Central

Fatemi, K; Disfani, R; Zare, R; Moeintaghavi, A; Ali, Saadat A.; Boostani, H. R

2012-01-01

Background: The relationship between periodontal disease and dental pulp changes is controversial and has been debated for many years. This human study was performed to evaluate the possible effects of moderate to advanced periodontal disease on the different aspect of dental pulp structure. Materials and Methods: Twenty hopeless permanent teeth were extracted from systemically healthy adults because of moderate to advanced chronic periodontitis, with a bone loss of >6 mm and a mobility of grade 2 or 3. Upon extraction, the apical 2 to 3 mm of the roots were immediately sectioned. Four to five sections were mounted on each slide, and every third slide was stained with hematoxylin and eosin. The specimens were histologically processed and examined by an oral pathologist. Results: Non-inflamed pulp, with partial or complete necrosis in some sections and several non-necrotic sections, was found in only 6.3% of teeth. Most teeth (58.3%) displayed edematous pulps. Slightly fibrotic pulps were seen in 52.1% of sections. Odontoblastic integrity was seen in 31.3% of teeth. Most teeth (77.1%) displayed no pulp stones. In 43.8% of teeth, the pulp vessels displayed dilatation. Conclusions: Moderate to advanced periodontal disease can affect the dental pulp. Careful consideration of diagnostic and treatment planing in patients with endodontic-periodontal involvement is therefore recommended. PMID:23493524

Latent component-based gear tooth fault detection filter using advanced parametric modeling

NASA Astrophysics Data System (ADS)

Ettefagh, M. M.; Sadeghi, M. H.; Rezaee, M.; Chitsaz, S.

2009-10-01

In this paper, a new parametric model-based filter is proposed for gear tooth fault detection. The designing of the filter consists of identifying the most proper latent component (LC) of the undamaged gearbox signal by analyzing the instant modules (IMs) and instant frequencies (IFs) and then using the component with lowest IM as the proposed filter output for detecting fault of the gearbox. The filter parameters are estimated by using the LC theory in which an advanced parametric modeling method has been implemented. The proposed method is applied on the signals, extracted from simulated gearbox for detection of the simulated gear faults. In addition, the method is used for quality inspection of the produced Nissan-Junior vehicle gearbox by gear profile error detection in an industrial test bed. For evaluation purpose, the proposed method is compared with the previous parametric TAR/AR-based filters in which the parametric model residual is considered as the filter output and also Yule-Walker and Kalman filter are implemented for estimating the parameters. The results confirm the high performance of the new proposed fault detection method.

Quantification of a bacterial secondary metabolite by SERS combined with SLM extraction for bioprocess monitoring.

PubMed

Morelli, Lidia; Andreasen, Sune Zoëga; Jendresen, Christian Bille; Nielsen, Alex Toftgaard; Emnéus, Jenny; Zór, Kinga; Boisen, Anja

2017-11-20

During the last few decades, great advances have been reached in high-throughput design and building of genetically engineered microbial strains, leading to a need for fast and reliable screening methods. We developed and optimized a microfluidic supported liquid membrane (SLM) extraction device and combined it with surface enhanced Raman scattering (SERS) sensing for the screening of a biological process, namely for the quantification of a bacterial secondary metabolite, p-coumaric acid (pHCA), produced by Escherichia coli. The microfluidic device proved to be robust and reusable, enabling efficient removal of interfering compounds from the real samples, reaching more than 13-fold up-concentration of the donor at 10 μL min -1 flow rate. With this method, we quantified pHCA directly from the bacterial supernatant, distinguishing between various culture conditions based on the pHCA production yield. The obtained data showed good correlation with HPLC analysis.

Pharmacological Properties of Biocompounds from Spores of the Lingzhi or Reishi Medicinal Mushroom Ganoderma lucidum (Agaricomycetes): A Review.

PubMed

Soccol, Carlos Ricardo; Bissoqui, Lucas Yamasaki; Rodrigues, Cristine; Rubel, Rosalia; Sella, Sandra R B R; Leifa, Fan; de Souza Vandenberghe, Luciana Porto; Soccol, Vanete Thomaz

2016-01-01

Ganoderma lucidum is a well-known representative of mushrooms that have been used in traditional Chinese medicine for centuries. New discoveries related to this medicinal mushroom and its biological properties are frequently reported. However, only recently have scientists started to pay special attention to G. lucidum spores. This is in part because of the recent development of methods for breaking the spore wall and extracting biocompounds from the spore. Although some research groups are working with G. lucidum spores, data in the literature are still limited, and the methods used have not been systematized. This review therefore describes the main advances in techniques for breaking the spore wall and extracting biocompounds from the spore. In addition, the major active components identified and their biological properties, such as neurological activity and antiaging and cell-protective effects, are investigated because these are of importance for potential drug development.

Plant cell tissue culture: A potential source of chemicals

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

Scott, C.D.; Dougall, D.K.

1987-08-01

Higher plants produce many industrially important products. Among these are drugs and medicinal chemicals, essential oils and flavors, vegetable oils and fats, fine and specialty chemicals, and even some commodity chemicals. Although, currently, whole-plant extraction is the primary means of harvesting these materials, the advent of plant cell tissue culture could be a much more effective method of producing many types of phytochemicals. The use of immobilized plant cells in an advanced bioreactor configuration with excretion of the product into the reactor medium may represent the most straightforward way of commercializing such techniques for lower-value chemicals. Important research and developmentmore » opportunities in this area include screening for plant cultures for nonmedical, lower-value chemicals; understanding and controlling plant cell physiology and biochemistry; optimizing effective immobilization methods; developing more efficient bioreactor concepts; and perfecting product extraction and purification techniques. 62 refs., 2 figs.« less

Understanding disciplinary vocabularies using a full-text enabled domain-independent term extraction approach.

PubMed

Yan, Erjia; Williams, Jake; Chen, Zheng

2017-01-01

Publication metadata help deliver rich analyses of scholarly communication. However, research concepts and ideas are more effectively expressed through unstructured fields such as full texts. Thus, the goals of this paper are to employ a full-text enabled method to extract terms relevant to disciplinary vocabularies, and through them, to understand the relationships between disciplines. This paper uses an efficient, domain-independent term extraction method to extract disciplinary vocabularies from a large multidisciplinary corpus of PLoS ONE publications. It finds a power-law pattern in the frequency distributions of terms present in each discipline, indicating a semantic richness potentially sufficient for further study and advanced analysis. The salient relationships amongst these vocabularies become apparent in application of a principal component analysis. For example, Mathematics and Computer and Information Sciences were found to have similar vocabulary use patterns along with Engineering and Physics; while Chemistry and the Social Sciences were found to exhibit contrasting vocabulary use patterns along with the Earth Sciences and Chemistry. These results have implications to studies of scholarly communication as scholars attempt to identify the epistemological cultures of disciplines, and as a full text-based methodology could lead to machine learning applications in the automated classification of scholarly work according to disciplinary vocabularies.

Nucleic acid purification from plants, animals and microbes in under 30 seconds

PubMed Central

Zou, Yiping; Wang, Yuling; Wee, Eugene; Turni, Conny; Blackall, Patrick J.; Trau, Matt; Botella, Jose Ramon

2017-01-01

Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries. PMID:29161268

Understanding disciplinary vocabularies using a full-text enabled domain-independent term extraction approach

PubMed Central

Williams, Jake; Chen, Zheng

2017-01-01

Publication metadata help deliver rich analyses of scholarly communication. However, research concepts and ideas are more effectively expressed through unstructured fields such as full texts. Thus, the goals of this paper are to employ a full-text enabled method to extract terms relevant to disciplinary vocabularies, and through them, to understand the relationships between disciplines. This paper uses an efficient, domain-independent term extraction method to extract disciplinary vocabularies from a large multidisciplinary corpus of PLoS ONE publications. It finds a power-law pattern in the frequency distributions of terms present in each discipline, indicating a semantic richness potentially sufficient for further study and advanced analysis. The salient relationships amongst these vocabularies become apparent in application of a principal component analysis. For example, Mathematics and Computer and Information Sciences were found to have similar vocabulary use patterns along with Engineering and Physics; while Chemistry and the Social Sciences were found to exhibit contrasting vocabulary use patterns along with the Earth Sciences and Chemistry. These results have implications to studies of scholarly communication as scholars attempt to identify the epistemological cultures of disciplines, and as a full text-based methodology could lead to machine learning applications in the automated classification of scholarly work according to disciplinary vocabularies. PMID:29186141

Detecting epileptic seizure with different feature extracting strategies using robust machine learning classification techniques by applying advance parameter optimization approach.

PubMed

Hussain, Lal

2018-06-01

Epilepsy is a neurological disorder produced due to abnormal excitability of neurons in the brain. The research reveals that brain activity is monitored through electroencephalogram (EEG) of patients suffered from seizure to detect the epileptic seizure. The performance of EEG detection based epilepsy require feature extracting strategies. In this research, we have extracted varying features extracting strategies based on time and frequency domain characteristics, nonlinear, wavelet based entropy and few statistical features. A deeper study was undertaken using novel machine learning classifiers by considering multiple factors. The support vector machine kernels are evaluated based on multiclass kernel and box constraint level. Likewise, for K-nearest neighbors (KNN), we computed the different distance metrics, Neighbor weights and Neighbors. Similarly, the decision trees we tuned the paramours based on maximum splits and split criteria and ensemble classifiers are evaluated based on different ensemble methods and learning rate. For training/testing tenfold Cross validation was employed and performance was evaluated in form of TPR, NPR, PPV, accuracy and AUC. In this research, a deeper analysis approach was performed using diverse features extracting strategies using robust machine learning classifiers with more advanced optimal options. Support Vector Machine linear kernel and KNN with City block distance metric give the overall highest accuracy of 99.5% which was higher than using the default parameters for these classifiers. Moreover, highest separation (AUC = 0.9991, 0.9990) were obtained at different kernel scales using SVM. Additionally, the K-nearest neighbors with inverse squared distance weight give higher performance at different Neighbors. Moreover, to distinguish the postictal heart rate oscillations from epileptic ictal subjects, and highest performance of 100% was obtained using different machine learning classifiers.

Numerical algebraic geometry: a new perspective on gauge and string theories

NASA Astrophysics Data System (ADS)

Mehta, Dhagash; He, Yang-Hui; Hauensteine, Jonathan D.

2012-07-01

There is a rich interplay between algebraic geometry and string and gauge theories which has been recently aided immensely by advances in computational algebra. However, symbolic (Gröbner) methods are severely limited by algorithmic issues such as exponential space complexity and being highly sequential. In this paper, we introduce a novel paradigm of numerical algebraic geometry which in a plethora of situations overcomes these shortcomings. The so-called `embarrassing parallelizability' allows us to solve many problems and extract physical information which elude symbolic methods. We describe the method and then use it to solve various problems arising from physics which could not be otherwise solved.

Document cards: a top trumps visualization for documents.

PubMed

Strobelt, Hendrik; Oelke, Daniela; Rohrdantz, Christian; Stoffel, Andreas; Keim, Daniel A; Deussen, Oliver

2009-01-01

Finding suitable, less space consuming views for a document's main content is crucial to provide convenient access to large document collections on display devices of different size. We present a novel compact visualization which represents the document's key semantic as a mixture of images and important key terms, similar to cards in a top trumps game. The key terms are extracted using an advanced text mining approach based on a fully automatic document structure extraction. The images and their captions are extracted using a graphical heuristic and the captions are used for a semi-semantic image weighting. Furthermore, we use the image color histogram for classification and show at least one representative from each non-empty image class. The approach is demonstrated for the IEEE InfoVis publications of a complete year. The method can easily be applied to other publication collections and sets of documents which contain images.

Proteomic platform for the identification of proteins in olive (Olea europaea) pulp.

PubMed

Capriotti, Anna Laura; Cavaliere, Chiara; Foglia, Patrizia; Piovesana, Susy; Samperi, Roberto; Stampachiacchiere, Serena; Laganà, Aldo

2013-10-24

The nutritional and cancer-protective properties of the oil extracted mechanically from the ripe fruits of Olea europaea trees are attracting constantly more attention worldwide. The preparation of high-quality protein samples from plant tissues for proteomic analysis poses many challenging problems. In this study we employed a proteomic platform based on two different extraction methods, SDS and CHAPS based protocols, followed by two precipitation protocols, TCA/acetone and MeOH precipitation, in order to increase the final number of identified proteins. The use of advanced MS techniques in combination with the Swissprot and NCBI Viridiplantae databases and TAIR10 Arabidopsis database allowed us to identify 1265 proteins, of which 22 belong to O. europaea. The application of this proteomic platform for protein extraction and identification will be useful also for other proteomic studies on recalcitrant plant/fruit tissues. Copyright © 2013. Published by Elsevier B.V.

A seismic fault recognition method based on ant colony optimization

NASA Astrophysics Data System (ADS)

Chen, Lei; Xiao, Chuangbai; Li, Xueliang; Wang, Zhenli; Huo, Shoudong

2018-05-01

Fault recognition is an important section in seismic interpretation and there are many methods for this technology, but no one can recognize fault exactly enough. For this problem, we proposed a new fault recognition method based on ant colony optimization which can locate fault precisely and extract fault from the seismic section. Firstly, seismic horizons are extracted by the connected component labeling algorithm; secondly, the fault location are decided according to the horizontal endpoints of each horizon; thirdly, the whole seismic section is divided into several rectangular blocks and the top and bottom endpoints of each rectangular block are considered as the nest and food respectively for the ant colony optimization algorithm. Besides that, the positive section is taken as an actual three dimensional terrain by using the seismic amplitude as a height. After that, the optimal route from nest to food calculated by the ant colony in each block is judged as a fault. Finally, extensive comparative tests were performed on the real seismic data. Availability and advancement of the proposed method were validated by the experimental results.

[Advance in interferogram data processing technique].

PubMed

Jing, Juan-Juan; Xiangli, Bin; Lü, Qun-Bo; Huang, Min; Zhou, Jin-Song

2011-04-01

Fourier transform spectrometry is a type of novel information obtaining technology, which integrated the functions of imaging and spectra, but the data that the instrument acquired is the interference data of the target, which is an intermediate data and couldn't be used directly, so data processing must be adopted for the successful application of the interferometric data In the present paper, data processing techniques are divided into two classes: general-purpose and special-type. First, the advance in universal interferometric data processing technique is introduced, then the special-type interferometric data extracting method and data processing technique is illustrated according to the classification of Fourier transform spectroscopy. Finally, the trends of interferogram data processing technique are discussed.

Climbing with adhesion: from bioinspiration to biounderstanding

PubMed Central

Cutkosky, Mark R.

2015-01-01

Bioinspiration is an increasingly popular design paradigm, especially as robots venture out of the laboratory and into the world. Animals are adept at coping with the variability that the world imposes. With advances in scientific tools for understanding biological structures in detail, we are increasingly able to identify design features that account for animals' robust performance. In parallel, advances in fabrication methods and materials are allowing us to engineer artificial structures with similar properties. The resulting robots become useful platforms for testing hypotheses about which principles are most important. Taking gecko-inspired climbing as an example, we show that the process of extracting principles from animals and adapting them to robots provides insights for both robotics and biology. PMID:26464786

A method for simultaneous linear optics and coupling correction for storage rings with turn-by-turn beam position monitor data

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

Yang, Xi; Huang, Xiaobiao

2016-05-13

Here, we propose a method to simultaneously correct linear optics errors and linear coupling for storage rings using turn-by-turn (TbT) beam position monitor (BPM) data. The independent component analysis (ICA) method is used to isolate the betatron normal modes from the measured TbT BPM data. The betatron amplitudes and phase advances of the projections of the normal modes on the horizontal and vertical planes are then extracted, which, combined with dispersion measurement, are used to fit the lattice model. The fitting results are used for lattice correction. Finally, the method has been successfully demonstrated on the NSLS-II storage ring.

A method for simultaneous linear optics and coupling correction for storage rings with turn-by-turn beam position monitor data

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

Yang, Xi; Huang, Xiaobiao

2016-08-01

We propose a method to simultaneously correct linear optics errors and linear coupling for storage rings using turn-by-turn (TbT) beam position monitor (BPM) data. The independent component analysis (ICA) method is used to isolate the betatron normal modes from the measured TbT BPM data. The betatron amplitudes and phase advances of the projections of the normal modes on the horizontal and vertical planes are then extracted, which, combined with dispersion measurement, are used to fit the lattice model. Furthermore, the fitting results are used for lattice correction. Our method has been successfully demonstrated on the NSLS-II storage ring.

A method for simultaneous linear optics and coupling correction for storage rings with turn-by-turn beam position monitor data

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

Yang, Xi; Huang, Xiaobiao

2016-08-01

We propose a method to simultaneously correct linear optics errors and linear coupling for storage rings using turn-by-turn (TbT) beam position monitor (BPM) data. The independent component analysis (ICA) method is used to isolate the betatron normal modes from the measured TbT BPM data. The betatron amplitudes and phase advances of the projections of the normal modes on the horizontal and vertical planes are then extracted, which, combined with dispersion measurement, are used to fit the lattice model. The fitting results are used for lattice correction. The method has been successfully demonstrated on the NSLS-II storage ring.

Detection of interaction articles and experimental methods in biomedical literature.

PubMed

Schneider, Gerold; Clematide, Simon; Rinaldi, Fabio

2011-10-03

This article describes the approaches taken by the OntoGene group at the University of Zurich in dealing with two tasks of the BioCreative III competition: classification of articles which contain curatable protein-protein interactions (PPI-ACT) and extraction of experimental methods (PPI-IMT). Two main achievements are described in this paper: (a) a system for document classification which crucially relies on the results of an advanced pipeline of natural language processing tools; (b) a system which is capable of detecting all experimental methods mentioned in scientific literature, and listing them with a competitive ranking (AUC iP/R > 0.5). The results of the BioCreative III shared evaluation clearly demonstrate that significant progress has been achieved in the domain of biomedical text mining in the past few years. Our own contribution, together with the results of other participants, provides evidence that natural language processing techniques have become by now an integral part of advanced text mining approaches.

SSAGES: Software Suite for Advanced General Ensemble Simulations

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

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniquesmore » as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.« less

SSAGES: Software Suite for Advanced General Ensemble Simulations.

PubMed

Sidky, Hythem; Colón, Yamil J; Helfferich, Julian; Sikora, Benjamin J; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S; Reid, Daniel R; Sevgen, Emre; Thapar, Vikram; Webb, Michael A; Whitmer, Jonathan K; de Pablo, Juan J

2018-01-28

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques-including adaptive biasing force, string methods, and forward flux sampling-that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

SSAGES: Software Suite for Advanced General Ensemble Simulations

NASA Astrophysics Data System (ADS)

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian; Sikora, Benjamin J.; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z.; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J.; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S.; Reid, Daniel R.; Sevgen, Emre; Thapar, Vikram; Webb, Michael A.; Whitmer, Jonathan K.; de Pablo, Juan J.

2018-01-01

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

Evaluation of three automated nucleic acid extraction systems for identification of respiratory viruses in clinical specimens by multiplex real-time PCR.

PubMed

Kim, Yoonjung; Han, Mi-Soon; Kim, Juwon; Kwon, Aerin; Lee, Kyung-A

2014-01-01

A total of 84 nasopharyngeal swab specimens were collected from 84 patients. Viral nucleic acid was extracted by three automated extraction systems: QIAcube (Qiagen, Germany), EZ1 Advanced XL (Qiagen), and MICROLAB Nimbus IVD (Hamilton, USA). Fourteen RNA viruses and two DNA viruses were detected using the Anyplex II RV16 Detection kit (Seegene, Republic of Korea). The EZ1 Advanced XL system demonstrated the best analytical sensitivity for all the three viral strains. The nucleic acids extracted by EZ1 Advanced XL showed higher positive rates for virus detection than the others. Meanwhile, the MICROLAB Nimbus IVD system was comprised of fully automated steps from nucleic extraction to PCR setup function that could reduce human errors. For the nucleic acids recovered from nasopharyngeal swab specimens, the QIAcube system showed the fewest false negative results and the best concordance rate, and it may be more suitable for detecting various viruses including RNA and DNA virus strains. Each system showed different sensitivity and specificity for detection of certain viral pathogens and demonstrated different characteristics such as turnaround time and sample capacity. Therefore, these factors should be considered when new nucleic acid extraction systems are introduced to the laboratory.

Drawing for Traffic Marking Using Bidirectional Gradient-Based Detection with MMS LIDAR Intensity

NASA Astrophysics Data System (ADS)

Takahashi, G.; Takeda, H.; Nakamura, K.

2016-06-01

Recently, the development of autonomous cars is accelerating on the integration of highly advanced artificial intelligence, which increases demand for a digital map with high accuracy. In particular, traffic markings are required to be precisely digitized since automatic driving utilizes them for position detection. To draw traffic markings, we benefit from Mobile Mapping Systems (MMS) equipped with high-density Laser imaging Detection and Ranging (LiDAR) scanners, which produces large amount of data efficiently with XYZ coordination along with reflectance intensity. Digitizing this data, on the other hand, conventionally has been dependent on human operation, which thus suffers from human errors, subjectivity errors, and low reproductivity. We have tackled this problem by means of automatic extraction of traffic marking, which partially accomplished to draw several traffic markings (G. Takahashi et al., 2014). The key idea of the method was extracting lines using the Hough transform strategically focused on changes in local reflection intensity along scan lines. However, it failed to extract traffic markings properly in a densely marked area, especially when local changing points are close each other. In this paper, we propose a bidirectional gradient-based detection method where local changing points are labelled with plus or minus group. Given that each label corresponds to the boundary between traffic markings and background, we can identify traffic markings explicitly, meaning traffic lines are differentiated correctly by the proposed method. As such, our automated method, a highly accurate and non-human-operator-dependent method using bidirectional gradient-based algorithm, can successfully extract traffic lines composed of complex shapes such as a cross walk, resulting in minimizing cost and obtaining highly accurate results.

Temporal data representation, normalization, extraction, and reasoning: A review from clinical domain

PubMed Central

Madkour, Mohcine; Benhaddou, Driss; Tao, Cui

2016-01-01

Background and Objective We live our lives by the calendar and the clock, but time is also an abstraction, even an illusion. The sense of time can be both domain-specific and complex, and is often left implicit, requiring significant domain knowledge to accurately recognize and harness. In the clinical domain, the momentum gained from recent advances in infrastructure and governance practices has enabled the collection of tremendous amount of data at each moment in time. Electronic Health Records (EHRs) have paved the way to making these data available for practitioners and researchers. However, temporal data representation, normalization, extraction and reasoning are very important in order to mine such massive data and therefore for constructing the clinical timeline. The objective of this work is to provide an overview of the problem of constructing a timeline at the clinical point of care and to summarize the state-of-the-art in processing temporal information of clinical narratives. Methods This review surveys the methods used in three important area: modeling and representing of time, Medical NLP methods for extracting time, and methods of time reasoning and processing. The review emphasis on the current existing gap between present methods and the semantic web technologies and catch up with the possible combinations. Results the main findings of this review is revealing the importance of time processing not only in constructing timelines and clinical decision support systems but also as a vital component of EHR data models and operations. Conclusions Extracting temporal information in clinical narratives is a challenging task. The inclusion of ontologies and semantic web will lead to better assessment of the annotation task and, together with medical NLP techniques, will help resolving granularity and co-reference resolution problems. PMID:27040831

Optimizing RNA Extraction of Renal Papilla Biopsy Tissue in Kidney Stone Formers: A New Methodology for Genomic Study.

PubMed

Taguchi, Kazumi; Usawachintachit, Manint; Hamamoto, Shuzo; Unno, Rei; Tzou, David T; Sherer, Benjamin A; Wang, Yongmei; Okada, Atsushi; Stoller, Marshall L; Yasui, Takahiro; Chi, Thomas

2017-09-01

Endoscopic tools have provided versatile examination and treatment for kidney stone procedures. Despite endourologists researching urinary stone disease using endoscopes to collect tissue, this tissue collection method is limited. Endoscopically removed tissues are small in size, restricting the types of genome-based examination possible. We investigated a new method of renal papilla biopsy and RNA extraction to establish a genomic research methodology for kidney stone disease. We conducted a prospective multi-institutional study and collected renal papilla specimens from consecutive percutaneous nephrolithotomy and ureteroscopy (URS) cases performed for removal of upper urinary tract stones. Renal papilla tissue was extracted using ureteroscopic biopsy forceps after stone removal. RNA was extracted using two different extraction kits, and their quantity and quality were examined. Additionally, the impact of biopsy on surgical complications was compared between cases performed with and without biopsy by matched case-control analysis adjusted for age, gender, body mass index, bilaterality, and stone burden. A total of 90 biopsies from 49 patients were performed, and the median duration between specimen collection and RNA extraction was 61 days. Both univariate and multivariate analyses showed BIGopsy ® forceps usage significantly increased the total yield (p = 0.004) and quality (p = 0.001 for A260/280, p = 0.004 for A260/A230) of extracted RNA. Extraction using the RNeasy Micro Kit ® also improved A260/A230, whereas reduced RNA integrity number of extracted RNA by univariate and multivariate analyses (p = 0.002 and p < 0.001, respectively). Moreover, matched case-control study demonstrated that endoscopic renal papilla biopsy caused no significant surgical complications, including bleeding, decreased stone clearance and hematocrit, and renal dysfunction. Biopsies during URS imparted an average of 20 minutes of procedure time over nonbiopsy cases. We demonstrate a safe methodology for optimal RNA extraction of renal papilla tissue. This technique will accelerate advanced genomic studies for kidney stone formers by facilitating larger tissue yields.

Analysis of dynamic brain oscillations: methodological advances.

PubMed

Le Van Quyen, Michel; Bragin, Anatol

2007-07-01

In recent years, new recording technologies have advanced such that, at high temporal and spatial resolutions, oscillations of neuronal networks can be identified from simultaneous, multisite recordings. However, because of the deluge of multichannel data generated by these experiments, achieving the full potential of parallel neuronal recordings also depends on the development of new mathematical methods that can extract meaningful information relating to time, frequency and space. Here, we aim to bridge this gap by focusing on up-to-date recording techniques for measurement of network oscillations and new analysis tools for their quantitative assessment. In particular, we emphasize how these methods can be applied, what property might be inferred from neuronal signals and potentially productive future directions. This review is part of the INMED and TINS special issue, Physiogenic and pathogenic oscillations: the beauty and the beast, derived from presentations at the annual INMED and TINS symposium (http://inmednet.com).

Multidimensional Processing and Visual Rendering of Complex 3D Biomedical Images

NASA Technical Reports Server (NTRS)

Sams, Clarence F.

2016-01-01

The proposed technology uses advanced image analysis techniques to maximize the resolution and utility of medical imaging methods being used during spaceflight. We utilize COTS technology for medical imaging, but our applications require higher resolution assessment of the medical images than is routinely applied with nominal system software. By leveraging advanced data reduction and multidimensional imaging techniques utilized in analysis of Planetary Sciences and Cell Biology imaging, it is possible to significantly increase the information extracted from the onboard biomedical imaging systems. Year 1 focused on application of these techniques to the ocular images collected on ground test subjects and ISS crewmembers. Focus was on the choroidal vasculature and the structure of the optic disc. Methods allowed for increased resolution and quantitation of structural changes enabling detailed assessment of progression over time. These techniques enhance the monitoring and evaluation of crew vision issues during space flight.

Bidirectional reflectance distribution function based surface modeling of non-Lambertian using intensity data of light detection and ranging.

PubMed

Li, Xiaolu; Liang, Yu; Xu, Lijun

2014-09-01

To provide a credible model for light detection and ranging (LiDAR) target classification, the focus of this study is on the relationship between intensity data of LiDAR and the bidirectional reflectance distribution function (BRDF). An integration method based on the built-in-lab coaxial laser detection system was advanced. A kind of intermediary BRDF model advanced by Schlick was introduced into the integration method, considering diffuse and specular backscattering characteristics of the surface. A group of measurement campaigns were carried out to investigate the influence of the incident angle and detection range on the measured intensity data. Two extracted parameters r and S(λ) are influenced by different surface features, which illustrate the surface features of the distribution and magnitude of reflected energy, respectively. The combination of two parameters can be used to describe the surface characteristics for target classification in a more plausible way.

Advances in Neutron Spectroscopy with Deuterated Organic Scintillators

NASA Astrophysics Data System (ADS)

Febbraro, Michael; Pain, Steve; Becchetti, Frederick

2015-10-01

Deuterated organic scintillators have shown promise as neutron detectors for nuclear science as well as applications in nuclear non-proliferation and safeguards. In particular, they can extract neutron spectra without the use of neutron time-of-flight measurement (n-ToF) utilizing spectrum unfolding techniques. This permits the measure of cross sections of bound and unbound states with high efficiency and angular coverage. In the case of measurements with radioactive ion beams where low beam intensities limit long path n-ToF, short path n-ToF can be used to discriminate neutrons of interest from room return and background neutrons. This presentation will provide recent advances with these types of detectors. Digital pulse-shape discrimination using fast waveform digitizers, spectrum unfolding methods for extraction of neutron spectra, and a new safer deuterated-xylene formulation EJ-301D will be discussed. In addition, experimental results from measurements of discrete and continuous neutron spectra which illustrate the advantage of these detectors for certain applications in nuclear physics research and nuclear security will be shown. This work is supported by NSF and DOE.

Novel images extraction model using improved delay vector variance feature extraction and multi-kernel neural network for EEG detection and prediction.

PubMed

Ge, Jing; Zhang, Guoping

2015-01-01

Advanced intelligent methodologies could help detect and predict diseases from the EEG signals in cases the manual analysis is inefficient available, for instance, the epileptic seizures detection and prediction. This is because the diversity and the evolution of the epileptic seizures make it very difficult in detecting and identifying the undergoing disease. Fortunately, the determinism and nonlinearity in a time series could characterize the state changes. Literature review indicates that the Delay Vector Variance (DVV) could examine the nonlinearity to gain insight into the EEG signals but very limited work has been done to address the quantitative DVV approach. Hence, the outcomes of the quantitative DVV should be evaluated to detect the epileptic seizures. To develop a new epileptic seizure detection method based on quantitative DVV. This new epileptic seizure detection method employed an improved delay vector variance (IDVV) to extract the nonlinearity value as a distinct feature. Then a multi-kernel functions strategy was proposed in the extreme learning machine (ELM) network to provide precise disease detection and prediction. The nonlinearity is more sensitive than the energy and entropy. 87.5% overall accuracy of recognition and 75.0% overall accuracy of forecasting were achieved. The proposed IDVV and multi-kernel ELM based method was feasible and effective for epileptic EEG detection. Hence, the newly proposed method has importance for practical applications.

Innovations in the Analysis of Chandra-ACIS Observations

NASA Astrophysics Data System (ADS)

Broos, Patrick S.; Townsley, Leisa K.; Feigelson, Eric D.; Getman, Konstantin V.; Bauer, Franz E.; Garmire, Gordon P.

2010-05-01

As members of the instrument team for the Advanced CCD Imaging Spectrometer (ACIS) on NASA's Chandra X-ray Observatory and as Chandra General Observers, we have developed a wide variety of data analysis methods that we believe are useful to the Chandra community, and have constructed a significant body of publicly available software (the ACIS Extract package) addressing important ACIS data and science analysis tasks. This paper seeks to describe these data analysis methods for two purposes: to document the data analysis work performed in our own science projects and to help other ACIS observers judge whether these methods may be useful in their own projects (regardless of what tools and procedures they choose to implement those methods). The ACIS data analysis recommendations we offer here address much of the workflow in a typical ACIS project, including data preparation, point source detection via both wavelet decomposition and image reconstruction, masking point sources, identification of diffuse structures, event extraction for both point and diffuse sources, merging extractions from multiple observations, nonparametric broadband photometry, analysis of low-count spectra, and automation of these tasks. Many of the innovations presented here arise from several, often interwoven, complications that are found in many Chandra projects: large numbers of point sources (hundreds to several thousand), faint point sources, misaligned multiple observations of an astronomical field, point source crowding, and scientifically relevant diffuse emission.

Advancing Understanding of the +4 Metal Extractant Thenoyltrifluoroacetonate (TTA –); Synthesis and Structure of M IVTTA 4 (M IV = Zr, Hf, Ce, Th, U, Np, Pu) and M III(TTA) 4 – (M III = Ce, Nd, Sm, Yb)

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

Cary, Samantha K.; Livshits, Maksim; Cross, Justin N.

Thenoyltrifluoroacetone (HTTA)-based extractions represent popular methods for separating microscopic amounts of transuranic actinides (i.e., Np and Pu) from macroscopic actinide matrixes (e.g. bulk uranium). It is well-established that this procedure enables +4 actinides to be selectively removed from +3, + 5, and +6 f-elements. However, even highly skilled and well-trained researchers find this process complicated and (at times) unpredictable. It is difficult to improve the HTTA extraction—or find alternatives—because little is understood about why this separation works. Even the identities of the extracted species are unknown. In addressing this knowledge gap, we report in this paper advances in fundamental understandingmore » of the HTTA-based extraction. This effort included comparatively evaluating HTTA complexation with +4 and +3 metals (M IV = Zr, Hf, Ce, Th, U, Np, and Pu vs M III = Ce, Nd, Sm, and Yb). We observed +4 metals formed neutral complexes of the general formula M IV(TTA) 4. Meanwhile, +3 metals formed anionic M III(TTA) 4 – species. Characterization of these M(TTA) 4 x– (x = 0, 1) compounds by UV–vis–NIR, IR, 1H and 19F NMR, single-crystal X-ray diffraction, and X-ray absorption spectroscopy (both near-edge and extended fine structure) was critical for determining that Np IV(TTA) 4 and Pu IV(TTA) 4 were the primary species extracted by HTTA. Furthermore, this information lays the foundation to begin developing and understanding of why the HTTA extraction works so well. The data suggest that the solubility differences between M IV(TTA) 4 and M III(TTA) 4 – are likely a major contributor to the selectivity of HTTA extractions for +4 cations over +3 metals. Finally and moreover, these results will enable future studies focused on explaining HTTA extractions preference for +4 cations, which increases from Np IV to Pu IV, Hf IV, and Zr IV.« less

Advancing Understanding of the +4 Metal Extractant Thenoyltrifluoroacetonate (TTA –); Synthesis and Structure of M IVTTA 4 (M IV = Zr, Hf, Ce, Th, U, Np, Pu) and M III(TTA) 4 – (M III = Ce, Nd, Sm, Yb)

DOE PAGES

Cary, Samantha K.; Livshits, Maksim; Cross, Justin N.; ...

2018-03-21

Thenoyltrifluoroacetone (HTTA)-based extractions represent popular methods for separating microscopic amounts of transuranic actinides (i.e., Np and Pu) from macroscopic actinide matrixes (e.g. bulk uranium). It is well-established that this procedure enables +4 actinides to be selectively removed from +3, + 5, and +6 f-elements. However, even highly skilled and well-trained researchers find this process complicated and (at times) unpredictable. It is difficult to improve the HTTA extraction—or find alternatives—because little is understood about why this separation works. Even the identities of the extracted species are unknown. In addressing this knowledge gap, we report in this paper advances in fundamental understandingmore » of the HTTA-based extraction. This effort included comparatively evaluating HTTA complexation with +4 and +3 metals (M IV = Zr, Hf, Ce, Th, U, Np, and Pu vs M III = Ce, Nd, Sm, and Yb). We observed +4 metals formed neutral complexes of the general formula M IV(TTA) 4. Meanwhile, +3 metals formed anionic M III(TTA) 4 – species. Characterization of these M(TTA) 4 x– (x = 0, 1) compounds by UV–vis–NIR, IR, 1H and 19F NMR, single-crystal X-ray diffraction, and X-ray absorption spectroscopy (both near-edge and extended fine structure) was critical for determining that Np IV(TTA) 4 and Pu IV(TTA) 4 were the primary species extracted by HTTA. Furthermore, this information lays the foundation to begin developing and understanding of why the HTTA extraction works so well. The data suggest that the solubility differences between M IV(TTA) 4 and M III(TTA) 4 – are likely a major contributor to the selectivity of HTTA extractions for +4 cations over +3 metals. Finally and moreover, these results will enable future studies focused on explaining HTTA extractions preference for +4 cations, which increases from Np IV to Pu IV, Hf IV, and Zr IV.« less

Novel Advances in Shotgun Lipidomics for Biology and Medicine

PubMed Central

Wang, Miao; Wang, Chunyan; Han, Rowland H.; Han, Xianlin

2015-01-01

The field of lipidomics, as coined in 2003, has made profound advances and been rapidly expanded. The mass spectrometry-based strategies of this analytical methodology-oriented research discipline for lipid analysis are largely fallen into three categories: direct infusion-based shotgun lipidomics, liquid chromatography-mass spectrometry-based platforms, and matrix-assisted laser desorption/ionization mass spectrometry-based approaches (particularly in imagining lipid distribution in tissues or cells). This review focuses on shotgun lipidomics. After briefly introducing its fundamentals, the major materials of this article cover its recent advances. These include the novel methods of lipid extraction, novel shotgun lipidomics strategies for identification and quantification of previously hardly accessible lipid classes and molecular species including isomers, and novel tools for processing and interpretation of lipidomics data. Representative applications of advanced shotgun lipidomics for biological and biomedical research are also presented in this review. We believe that with these novel advances in shotgun lipidomics, this approach for lipid analysis should become more comprehensive and high throughput, thereby greatly accelerating the lipidomics field to substantiate the aberrant lipid metabolism, signaling, trafficking, and homeostasis under pathological conditions and their underpinning biochemical mechanisms. PMID:26703190

Extraction of Caffeine--A Modern Experiment

ERIC Educational Resources Information Center

Cohen, Paul Shea; Smith, Eileen Patricia

1969-01-01

Describes an organic chemistry experiment suitable for high school students in second year or an advanced chemistry course. The techniques for the extraction and purification of caffeine from various household materials are described. Further experimentation with the extracted caffeine is suggested. (LC)

A novel approach of ensuring layout regularity correct by construction in advanced technologies

NASA Astrophysics Data System (ADS)

Ahmed, Shafquat Jahan; Vaderiya, Yagnesh; Gupta, Radhika; Parthasarathy, Chittoor; Marin, Jean-Claude; Robert, Frederic

2017-03-01

In advanced technology nodes, layout regularity has become a mandatory prerequisite to create robust designs less sensitive to variations in manufacturing process in order to improve yield and minimizing electrical variability. In this paper we describe a method for designing regular full custom layouts based on design and process co-optimization. The method includes various design rule checks that can be used on-the-fly during leaf-cell layout development. We extract a Layout Regularity Index (LRI) from the layouts based on the jogs, alignments and pitches used in the design for any given metal layer. Regularity Index of a layout is the direct indicator of manufacturing yield and is used to compare the relative health of different layout blocks in terms of process friendliness. The method has been deployed for 28nm and 40nm technology nodes for Memory IP and is being extended to other IPs (IO, standard-cell). We have quantified the gain of layout regularity with the deployed method on printability and electrical characteristics by process-variation (PV) band simulation analysis and have achieved up-to 5nm reduction in PV band.

Extracting biomedical events from pairs of text entities

PubMed Central

2015-01-01

Background Huge amounts of electronic biomedical documents, such as molecular biology reports or genomic papers are generated daily. Nowadays, these documents are mainly available in the form of unstructured free texts, which require heavy processing for their registration into organized databases. This organization is instrumental for information retrieval, enabling to answer the advanced queries of researchers and practitioners in biology, medicine, and related fields. Hence, the massive data flow calls for efficient automatic methods of text-mining that extract high-level information, such as biomedical events, from biomedical text. The usual computational tools of Natural Language Processing cannot be readily applied to extract these biomedical events, due to the peculiarities of the domain. Indeed, biomedical documents contain highly domain-specific jargon and syntax. These documents also describe distinctive dependencies, making text-mining in molecular biology a specific discipline. Results We address biomedical event extraction as the classification of pairs of text entities into the classes corresponding to event types. The candidate pairs of text entities are recursively provided to a multiclass classifier relying on Support Vector Machines. This recursive process extracts events involving other events as arguments. Compared to joint models based on Markov Random Fields, our model simplifies inference and hence requires shorter training and prediction times along with lower memory capacity. Compared to usual pipeline approaches, our model passes over a complex intermediate problem, while making a more extensive usage of sophisticated joint features between text entities. Our method focuses on the core event extraction of the Genia task of BioNLP challenges yielding the best result reported so far on the 2013 edition. PMID:26201478

Factors influencing contraceptive use and non-use among women of advanced reproductive age in Nigeria.

PubMed

Solanke, Bola Lukman

2017-01-07

Factors influencing contraceptive use and non-use among women of advanced reproductive age have been insufficiently researched in Nigeria. This study examines factors influencing contraceptive use and non-use among women of advanced reproductive age in Nigeria. Secondary data were pooled and extracted from 2008 and 2013 Nigeria Demographic and Health Surveys (NDHS). The weighted sample size was 14,450 women of advanced reproductive age. The dependent variable was current contraceptive use. The explanatory variables were selected socio-demographic characteristics and three control variables. Analyses were performed using Stata version 12. Multinomial logistic regression was applied in four models. Majority of the respondents are not using any method of contraceptive; the expected risk of using modern contraceptive relative to traditional method reduces by a factor of 0.676 for multiparous women (rrr = 0.676; CI: 0.464-0.985); the expected risk of using modern contraceptive relative to traditional method reduces by a factor of 0.611 for women who want more children (rrr = 0.611; CI: 0.493-0.757); the relative risk for using modern contraceptive relative to traditional method increases by a factor of 1.637 as maternal education reaches secondary education (rrr = 1.637; CI: 1.173-2.285); the relative risk for using modern contraceptive relative to traditional method increases by a factor of 1.726 for women in richest households (rrr = 1.726; CI: 1.038-2.871); and the expected risk of using modern contraceptive relative to traditional method increases by a factor of 1.250 for southern women (rrr = 1.250; CI: 1.200-1.818). Socio-demographic characteristics exert more influence on non-use than modern contraceptive use. The scope, content and coverage of existing BCC messages should be extended to cover the contraceptive needs and challenges of women of advanced reproductive age in the country.

Patterned Diblock Co-Polymer Thin Films as Templates for Advanced Anisotropic Metal Nanostructures.

PubMed

Roth, Stephan V; Santoro, Gonzalo; Risch, Johannes F H; Yu, Shun; Schwartzkopf, Matthias; Boese, Torsten; Döhrmann, Ralph; Zhang, Peng; Besner, Bastian; Bremer, Philipp; Rukser, Dieter; Rübhausen, Michael A; Terrill, Nick J; Staniec, Paul A; Yao, Yuan; Metwalli, Ezzeldin; Müller-Buschbaum, Peter

2015-06-17

We demonstrate glancing-angle deposition of gold on a nanostructured diblock copolymer, namely polystyrene-block-poly(methyl methacrylate) thin film. Exploiting the selective wetting of gold on the polystyrene block, we are able to fabricate directional hierarchical structures. We prove the asymmetric growth of the gold nanoparticles and are able to extract the different growth laws by in situ scattering methods. The optical anisotropy of these hierarchical hybrid materials is further probed by angular resolved spectroscopic methods. This approach enables us to tailor functional hierarchical layers in nanodevices, such as nanoantennae arrays, organic photovoltaics, and sensor electronics.

“It Depends”: Viewpoints of Patients, Physicians, and Nurses on Patient-Practitioner Prayer in the Setting of Advanced Cancer

PubMed Central

Balboni, Michael J.; Babar, Amenah; Dillinger, Jennifer; Phelps, Andrea C.; George, Emily; Block, Susan D.; Kachnic, Lisa; Hunt, Jessica; Peteet, John; Prigerson, Holly G.; VanderWeele, Tyler J.; Balboni, Tracy A.

2012-01-01

Context Although prayer potentially serves as an important practice in offering religious/spiritual support, its role in the clinical setting remains disputed. Few data exist to guide the role of patient-practitioner prayer in the setting of advanced illness. Objectives To inform the role of prayer in the setting of life-threatening illness, this study used mixed quantitative-qualitative methods to describe the viewpoints expressed by patients with advanced cancer, oncology nurses, and oncology physicians concerning the appropriateness of clinician prayer. Methods This is a cross-sectional, multisite, mixed-methods study of advanced cancer patients (n = 70), oncology physicians (n = 206), and oncology nurses (n = 115). Semistructured interviews were used to assess respondents’ attitudes toward the appropriate role of prayer in the context of advanced cancer. Theme extraction was performed based on interdisciplinary input using grounded theory. Results Most advanced cancer patients (71%), nurses (83%), and physicians (65%) reported that patient-initiated patient-practitioner prayer was at least occasionally appropriate. Furthermore, clinician prayer was viewed as at least occasionally appropriate by the majority of patients (64%), nurses (76%), and physicians (59%). Of those patients who could envision themselves asking their physician or nurse for prayer (61%), 86% would find this form of prayer spiritually supportive. Most patients (80%) viewed practitioner-initiated prayer as spiritually supportive. Open-ended responses regarding the appropriateness of patient-practitioner prayer in the advanced cancer setting revealed six themes shaping respondents’ viewpoints: necessary conditions for prayer, potential benefits of prayer, critical attitudes toward prayer, positive attitudes toward prayer, potential negative consequences of prayer, and prayer alternatives. Conclusion Most patients and practitioners view patient-practitioner prayer as at least occasionally appropriate in the advanced cancer setting, and most patients view prayer as spiritually supportive. However, the appropriateness of patient-practitioner prayer is case specific, requiring consideration of multiple factors. PMID:21276700

Computational and experimental analysis of the flow in an annular centrifugal contactor

NASA Astrophysics Data System (ADS)

Wardle, Kent E.

The annular centrifugal contactor has been developed for solvent extraction processes for recycling used nuclear fuel. The compact size and high efficiency of these contactors have made them the choice for advanced reprocessing schemes and a key equipment for a proposed future advanced fuel cycle facility. While a sufficient base of experience exists to facilitate successful operation of current contactor technology, a more complete understanding of the fluid flow within the contactor would enable further advancements in design and operation of future units and greater confidence for use of such contactors in a variety of other solvent extraction applications. This research effort has coupled computational fluid dynamics modeling with a variety of experimental measurements and observations to provide a valid detailed analysis of the flow within the centrifugal contactor. CFD modeling of the free surface flow in the annular mixing zone using the Volume of Fluid (VOF) volume tracking method combined with Large Eddy Simulation (LES) of turbulence was found to have very good agreement with the experimental measurements and observations. A detailed study of the flow and mixing for different housing vane geometries was performed and it was found that the four straight mixing vane geometry had greater mixing for the flow rate simulated and more predictable operation over a range of low to moderate flow rates. The separation zone was also modeled providing a useful description of the flow in this region and identifying critical design features. It is anticipated that this work will form a foundation for additional efforts at improving the design and operation of centrifugal contactors and provide a framework for progress towards simulation of solvent extraction processes.

[Advance in studies on antioxidant activity of propolis and its molecular mechanism].

PubMed

Zhang, Jiang-Lin; Wang, Kai; Hu, Fu-Liang

2013-08-01

Propolis is an adhesive substance mixed with plant resins collected by honeybees (Apis mellifera) and secretions from their mandibular gland and wax gland, with wide pharmacological activity and healthcare functions. Its antioxidant activity has long been regarded as one of the most important biological activities of propolis. This article summarizes studies on the antioxidant activity of propolis extracts from different geographic origins and with different extraction methods, as well as several important monomer active ingredients in propolis, and concludes the potential molecular mechanism of antioxidant activity of propolis and its monomer ingredients, with the aim of providing ideas for further studies on pharmacological activity of propolis, as well as reference for in-depth development of propolis products.

Carotenoids from microalgae: A review of recent developments.

PubMed

Gong, Mengyue; Bassi, Amarjeet

2016-12-01

Carotenoids have been receiving increasing attention due to their potential health benefits. Microalgae are recognized as a natural source of carotenoids and other beneficial byproducts. However, the production of micro-algal carotenoids is not yet sufficiently cost-effective to compete with traditional chemical synthetic methods and other technologies such as extraction from plant based sources. This review presents the recent biotechnological developments in microalgal carotenoid production. The current technologies involved in their bioprocessing including cultivation, harvesting, extraction, and purification are discussed with a specific focus on downstream processing. The recent advances in chemical and biochemical synthesis of carotenoids are also reviewed for a better understanding of suitable and economically feasible biotechnological strategies. Some possible future directions are also proposed. Copyright © 2016 Elsevier Inc. All rights reserved.

Closed retrograde retrieval of the distal broken segment of femoral cannulated intramedullary nail using a ball-tipped guide wire.

PubMed

Metikala, Sreenivasulu; Mohammed, Riazuddin

2011-07-01

Extracting broken segments of intramedullay nails from long bones can be an operative challenge, particularly from the distal end. We report a case series where a simple and reproducible technique of extracting broken femoral cannulated nails using a ball-tipped guide wire is described. This closed technique involves no additional equipment or instruments. Eight patients who underwent the described method were included in the study. The technique involves using a standard plain guide wire passed through the cannulated distal broken nail segment after extraction of the proximal nail fragment. The plain guide wire is then advanced distally into the knee joint carefully under fluoroscopy imaging. Over this wire, a 5-millimeter (mm) cannulated large drill bit is used to create a track up to the distal broken nail segment. Through the small knee wound, a ball-tipped guide wire is passed, smooth end first, till the ball engages the end of the nail. The guide wire is then extracted along with the broken nail through the proximal wound. The method was successfully used in all eight patients for removal of broken cannulated intramedullary nail from the femoral canal without any complications. All patients underwent exchange nailing with successful bone union in six months. None of the patients had any problems at the knee joint at the final follow-up. We report a technique for successful extraction of the distal fragment of broken femoral intramedullary nails without additional surgical approaches.

Treatment of pancreatic insufficiency using pancreatic extract in patients with advanced pancreatic cancer: a pilot study (PICNIC).

PubMed

Zdenkowski, Nicholas; Radvan, George; Pugliese, Leanna; Charlton, Julie; Oldmeadow, Christopher; Fraser, Allison; Bonaventura, Antonino

2017-06-01

Survival with advanced pancreatic cancer is less than 12 months. Pancreatic exocrine insufficiency may contribute to pancreatic cancer-related cachexia, via nutrient malabsorption. We aimed to determine the feasibility of prescribing pancreatic extract (Creon®) for patients with advanced pancreatic cancer. Patients with advanced pancreatic cancer, without frank malabsorption, were randomised in this feasibility study to pancreatic extract 50,000 units with meals and 25,000 units with snacks, or placebo. Standardised dietary advice was given. Anti-cancer and supportive care treatments were permitted. Outcomes included weight, body mass index (BMI), quality of life (QLQC30, PAN26), survival and nutritional assessment (PG-SGA). Eighteen patients were randomised before study closure due to slow recruitment. Baseline characteristics were well matched. Weight loss prior to randomisation was numerically greater in the pancreatic extract group (mean 0.7 vs 2.2 kg). Weight loss was numerically greater in the placebo group, however not significantly. No differences in BMI or nutrition score were seen. Quality of life did not differ between study groups. Median overall survival was 17 (95% CI 8.1-48.7) weeks in the control group, and 67.6 (95% CI 14.1-98.4) weeks in the pancreatic extract group (p = 0.1063). Only 17% (18/106) of potentially eligible patients were recruited, related to patient/family reluctance, rapid clinical deterioration and patients already prescribed pancreatic extract. A moderate pill burden was noted. Despite intriguing survival results, this study was not sufficiently feasible to proceed to a fully powered comparative study. A multi-centre study would be required to exclude a significant difference in outcomes.

ABSOLUTE BUNCH LENGTH MEASUREMENTS AT THE ALS BY INCOHERENTSYNCHROTRON RADIATION FLUCTUATION ANALYSIS

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

Sannibale, Fernando; Zolotorev, Max S.; Filippetto, Daniele

2007-06-22

By analysing the pulse to pulse intensity fluctuations ofthe radiation emitted by a charge particle in the incoherent part of thespectrum, it is possible to extract information about the spatialdistribution of the beam. At the Advanced Light Source (ALS) of theLawrence Berkeley National Laboratory, we have developed and tested asimple scheme based on this principle that allows for the absolutemeasurement of the bunch length. A description of the method and theexperimental results are presented.

Untangling cell tracks: Quantifying cell migration by time lapse image data analysis.

PubMed

Svensson, Carl-Magnus; Medyukhina, Anna; Belyaev, Ivan; Al-Zaben, Naim; Figge, Marc Thilo

2018-03-01

Automated microscopy has given researchers access to great amounts of live cell imaging data from in vitro and in vivo experiments. Much focus has been put on extracting cell tracks from such data using a plethora of segmentation and tracking algorithms, but further analysis is normally required to draw biologically relevant conclusions. Such relevant conclusions may be whether the migration is directed or not, whether the population has homogeneous or heterogeneous migration patterns. This review focuses on the analysis of cell migration data that are extracted from time lapse images. We discuss a range of measures and models used to analyze cell tracks independent of the biological system or the way the tracks were obtained. For single-cell migration, we focus on measures and models giving examples of biological systems where they have been applied, for example, migration of bacteria, fibroblasts, and immune cells. For collective migration, we describe the model systems wound healing, neural crest migration, and Drosophila gastrulation and discuss methods for cell migration within these systems. We also discuss the role of the extracellular matrix and subsequent differences between track analysis in vitro and in vivo. Besides methods and measures, we are putting special focus on the need for openly available data and code, as well as a lack of common vocabulary in cell track analysis. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Structural and functional comparison of mobile and recalcitrant humic fractions from agricultural soils

USDA-ARS?s Scientific Manuscript database

Mobile humic acid (MHA) and calcium humate (CaHA) are humic fractions sequentially extracted from soil samples. MHA is extracted by dilute NaOH, and CaHA is subsequently extracted by dilute NaOH from the dilute HCl-washed soil residues of the first extraction. This chapter reviews the recent advance...

Application of Colorimetric Solid Phase Extraction (C-SPE) to Monitoring Nickel(II) and Lead(II) in Spacecraft Water Supplies

NASA Technical Reports Server (NTRS)

Diaz, Neil C.; Gazda, Daniel B.; Fritz, James S.; Porter, Marc D.; Rutz, Jeff; Mudgett, Paul; Schultz, John

2004-01-01

Archived water samples collected on the International Space Station (ISS) and returned to Earth for analysis have, in a few instances, contained trace levels of heavy metals. Building on our previous advances using Colorimetric Solid Phase Extraction (C-SPE) as a biocide monitoring technique, we are devising methods for the low level monitoring of nickel(II), lead(II) and other heavy metals. C-SPE is a sorption-spectrophotometric platform based on the extraction of analytes onto a membrane impregnated with a colorimetric reagent that are then quantified on the surface of the membrane using a diffuse reflectance spectrophotometer. Along these lines, we have determined nickel(II) via complexation with dimethylglyoxime (DMG) and begun to examine the analysis of lead(II) by its reaction with 2,5- dimercapto-1,3,4-thiadiazole (DMTD) and 4-(2- pyridylazo)-resorcinol (PAR). These developments are also extending a new variant of C-SPE in which immobilized reagents are being incorporated into this methodology in order to optimize sample reaction conditions and to introduce the colorimetric reagent. This paper describes the status of our development of these two new methods.

Identification and extraction of the seaward edge of terrestrial vegetation using digital aerial photography

USGS Publications Warehouse

Harris, Melanie; Brock, John C.; Nayegandhi, A.; Duffy, M.; Wright, C.W.

2006-01-01

This report is created as part of the Aerial Data Collection and Creation of Products for Park Vital Signs Monitoring within the Northeast Region Coastal and Barrier Network project, which is a joint project between the National Park Service Inventory and Monitoring Program (NPS-IM), the National Aeronautics and Space Administration (NASA) Observational Sciences Branch, and the U.S. Geological Survey (USGS) Center for Coastal and Watershed Studies (CCWS). This report is one of a series that discusses methods for extracting topographic features from aerial survey data. It details step-by-step methods used to extract a spatially referenced digital line from aerial photography that represents the seaward edge of terrestrial vegetation along the coast of Assateague Island National Seashore (ASIS). One component of the NPS-IM/USGS/NASA project includes the collection of NASA aerial surveys over various NPS barrier islands and coastal parks throughout the National Park Service's Northeast Region. These aerial surveys consist of collecting optical remote sensing data from a variety of sensors, including the NASA Airborne Topographic Mapper (ATM), the NASA Experimental Advanced Airborne Research Lidar (EAARL), and down-looking digital mapping cameras.

A research framework for pharmacovigilance in health social media: Identification and evaluation of patient adverse drug event reports.

PubMed

Liu, Xiao; Chen, Hsinchun

2015-12-01

Social media offer insights of patients' medical problems such as drug side effects and treatment failures. Patient reports of adverse drug events from social media have great potential to improve current practice of pharmacovigilance. However, extracting patient adverse drug event reports from social media continues to be an important challenge for health informatics research. In this study, we develop a research framework with advanced natural language processing techniques for integrated and high-performance patient reported adverse drug event extraction. The framework consists of medical entity extraction for recognizing patient discussions of drug and events, adverse drug event extraction with shortest dependency path kernel based statistical learning method and semantic filtering with information from medical knowledge bases, and report source classification to tease out noise. To evaluate the proposed framework, a series of experiments were conducted on a test bed encompassing about postings from major diabetes and heart disease forums in the United States. The results reveal that each component of the framework significantly contributes to its overall effectiveness. Our framework significantly outperforms prior work. Published by Elsevier Inc.

Computational techniques for ECG analysis and interpretation in light of their contribution to medical advances

PubMed Central

Mincholé, Ana; Martínez, Juan Pablo; Laguna, Pablo; Rodriguez, Blanca

2018-01-01

Widely developed for clinical screening, electrocardiogram (ECG) recordings capture the cardiac electrical activity from the body surface. ECG analysis can therefore be a crucial first step to help diagnose, understand and predict cardiovascular disorders responsible for 30% of deaths worldwide. Computational techniques, and more specifically machine learning techniques and computational modelling are powerful tools for classification, clustering and simulation, and they have recently been applied to address the analysis of medical data, especially ECG data. This review describes the computational methods in use for ECG analysis, with a focus on machine learning and 3D computer simulations, as well as their accuracy, clinical implications and contributions to medical advances. The first section focuses on heartbeat classification and the techniques developed to extract and classify abnormal from regular beats. The second section focuses on patient diagnosis from whole recordings, applied to different diseases. The third section presents real-time diagnosis and applications to wearable devices. The fourth section highlights the recent field of personalized ECG computer simulations and their interpretation. Finally, the discussion section outlines the challenges of ECG analysis and provides a critical assessment of the methods presented. The computational methods reported in this review are a strong asset for medical discoveries and their translation to the clinical world may lead to promising advances. PMID:29321268

Use of Intermediate Endpoints in the Economic Evaluation of New Treatments for Advanced Cancer and Methods Adopted When Suitable Overall Survival Data are Not Available.

PubMed

Beauchemin, Catherine; Lapierre, Marie-Ève; Letarte, Nathalie; Yelle, Louise; Lachaine, Jean

2016-09-01

This study assessed the use of intermediate endpoints in the economic evaluation of new treatments for advanced cancer and the methodological approaches adopted when overall survival (OS) data are unavailable or of limited use. A systematic literature review was conducted to identify economic evaluations of treatments for advanced cancer published between 2003 and 2013. Cost-effectiveness and cost-utility analyses expressed in cost per life-year gained and cost per quality-adjusted life-year using an intermediate endpoint as an outcome measure were eligible. Characteristics of selected studies were extracted and comprised population, treatment of interest, comparator, line of treatment, study perspective, and time horizon. Use of intermediate endpoints and methods adopted when OS data were lacking were analyzed. In total, 7219 studies were identified and 100 fulfilled the eligibility criteria. Intermediate endpoints mostly used were progression-free survival and time to progression, accounting for 92 % of included studies. OS data were unavailable for analysis in nearly 25 % of economic evaluations. In the absence of OS data, studies most commonly assumed an equal risk of death for all treatment groups. Other methods included use of indirect comparison based on numerous assumptions, use of a proxy for OS, consultation with clinical experts, and use of published external information from different treatment settings. Intermediate endpoints are widely used in the economic evaluation of new treatments for advanced cancer in order to estimate OS. Currently, different methods are used in the absence of suitable OS data and the choice of an appropriate method depends on many factors including the data availability.

A multi-scale network method for two-phase flow in porous media

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

Khayrat, Karim, E-mail: khayratk@ifd.mavt.ethz.ch; Jenny, Patrick

Pore-network models of porous media are useful in the study of pore-scale flow in porous media. In order to extract macroscopic properties from flow simulations in pore-networks, it is crucial the networks are large enough to be considered representative elementary volumes. However, existing two-phase network flow solvers are limited to relatively small domains. For this purpose, a multi-scale pore-network (MSPN) method, which takes into account flow-rate effects and can simulate larger domains compared to existing methods, was developed. In our solution algorithm, a large pore network is partitioned into several smaller sub-networks. The algorithm to advance the fluid interfaces withinmore » each subnetwork consists of three steps. First, a global pressure problem on the network is solved approximately using the multiscale finite volume (MSFV) method. Next, the fluxes across the subnetworks are computed. Lastly, using fluxes as boundary conditions, a dynamic two-phase flow solver is used to advance the solution in time. Simulation results of drainage scenarios at different capillary numbers and unfavourable viscosity ratios are presented and used to validate the MSPN method against solutions obtained by an existing dynamic network flow solver.« less

CHOBS: Color Histogram of Block Statistics for Automatic Bleeding Detection in Wireless Capsule Endoscopy Video.

PubMed

Ghosh, Tonmoy; Fattah, Shaikh Anowarul; Wahid, Khan A

2018-01-01

Wireless capsule endoscopy (WCE) is the most advanced technology to visualize whole gastrointestinal (GI) tract in a non-invasive way. But the major disadvantage here, it takes long reviewing time, which is very laborious as continuous manual intervention is necessary. In order to reduce the burden of the clinician, in this paper, an automatic bleeding detection method for WCE video is proposed based on the color histogram of block statistics, namely CHOBS. A single pixel in WCE image may be distorted due to the capsule motion in the GI tract. Instead of considering individual pixel values, a block surrounding to that individual pixel is chosen for extracting local statistical features. By combining local block features of three different color planes of RGB color space, an index value is defined. A color histogram, which is extracted from those index values, provides distinguishable color texture feature. A feature reduction technique utilizing color histogram pattern and principal component analysis is proposed, which can drastically reduce the feature dimension. For bleeding zone detection, blocks are classified using extracted local features that do not incorporate any computational burden for feature extraction. From extensive experimentation on several WCE videos and 2300 images, which are collected from a publicly available database, a very satisfactory bleeding frame and zone detection performance is achieved in comparison to that obtained by some of the existing methods. In the case of bleeding frame detection, the accuracy, sensitivity, and specificity obtained from proposed method are 97.85%, 99.47%, and 99.15%, respectively, and in the case of bleeding zone detection, 95.75% of precision is achieved. The proposed method offers not only low feature dimension but also highly satisfactory bleeding detection performance, which even can effectively detect bleeding frame and zone in a continuous WCE video data.

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

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

Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.

2016-05-03

ABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. Themetabolite,protein, andlipidextraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of thismore » protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental,in vitro, and clinical). IMPORTANCEIn systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample.« less

N-nitrosodimethylamine (NDMA) removal by reverse osmosis and UV treatment and analysis via LC-MS/MS.

PubMed

Plumlee, Megan H; López-Mesas, Montserrat; Heidlberger, Andy; Ishida, Kenneth P; Reinhard, Martin

2008-01-01

N-nitrosodimethylamine (NDMA) is a probable human carcinogen found in ng/l concentrations in chlorinated and chloraminated water. A method was developed for the determination of ng/l levels of NDMA using liquid chromatography-tandem mass spectrometry (LC-MS/MS) preceded by sample concentration via solid-phase extraction with activated charcoal. Recoveries were greater than 90% and allowed a method reporting limit as low as 2ng/l. Using this method, the removal of NDMA was determined for the Interim Water Purification Facility (IWPF), an advanced wastewater treatment facility operated by the Orange County Water District (OCWD) in Southern California. The facility treats effluent from an activated sludge treatment plant with microfiltration (MF), reverse osmosis (RO), and an ultraviolet-hydrogen peroxide advanced oxidation process (UV-AOP). Six nitrosamines were surveyed: NDMA, N-nitrosomethylethylamine (NMEA), N-nitrosodiethylamine (NDEA), N-nitrosodi-n-propylamine (NDPA), N-nitrosopiperidine (NPip), and N-nitrosopyrrolidine (NPyr). Only NDMA was detected and at all treatment steps in the IWPF, with influent concentrations ranging from 20 to 59 ng/l. Removals for RO and UV ranged from 24% to 56% and 43% to 66%, respectively. Overall, 69+/-7% of the original NDMA concentration was removed from the product water across the advanced treatment process and, in combination with blending, the final concentration did not exceed the California drinking water notification level of 10 ng/l. NDMA removal data are consistent with findings reviewed for other advanced treatment facilities and laboratory studies.

Effective diagnosis of Alzheimer’s disease by means of large margin-based methodology

PubMed Central

2012-01-01

Background Functional brain images such as Single-Photon Emission Computed Tomography (SPECT) and Positron Emission Tomography (PET) have been widely used to guide the clinicians in the Alzheimer’s Disease (AD) diagnosis. However, the subjectivity involved in their evaluation has favoured the development of Computer Aided Diagnosis (CAD) Systems. Methods It is proposed a novel combination of feature extraction techniques to improve the diagnosis of AD. Firstly, Regions of Interest (ROIs) are selected by means of a t-test carried out on 3D Normalised Mean Square Error (NMSE) features restricted to be located within a predefined brain activation mask. In order to address the small sample-size problem, the dimension of the feature space was further reduced by: Large Margin Nearest Neighbours using a rectangular matrix (LMNN-RECT), Principal Component Analysis (PCA) or Partial Least Squares (PLS) (the two latter also analysed with a LMNN transformation). Regarding the classifiers, kernel Support Vector Machines (SVMs) and LMNN using Euclidean, Mahalanobis and Energy-based metrics were compared. Results Several experiments were conducted in order to evaluate the proposed LMNN-based feature extraction algorithms and its benefits as: i) linear transformation of the PLS or PCA reduced data, ii) feature reduction technique, and iii) classifier (with Euclidean, Mahalanobis or Energy-based methodology). The system was evaluated by means of k-fold cross-validation yielding accuracy, sensitivity and specificity values of 92.78%, 91.07% and 95.12% (for SPECT) and 90.67%, 88% and 93.33% (for PET), respectively, when a NMSE-PLS-LMNN feature extraction method was used in combination with a SVM classifier, thus outperforming recently reported baseline methods. Conclusions All the proposed methods turned out to be a valid solution for the presented problem. One of the advances is the robustness of the LMNN algorithm that not only provides higher separation rate between the classes but it also makes (in combination with NMSE and PLS) this rate variation more stable. In addition, their generalization ability is another advance since several experiments were performed on two image modalities (SPECT and PET). PMID:22849649

Determination of N epsilon-(carboxymethyl)lysine in foods and related systems.

PubMed

Ames, Jennifer M

2008-04-01

The sensitive and specific determination of advanced glycation end products (AGEs) is of considerable interest because these compounds have been associated with pro-oxidative and proinflammatory effects in vivo. AGEs form when carbonyl compounds, such as glucose and its oxidation products, glyoxal and methylglyoxal, react with the epsilon-amino group of lysine and the guanidino group of arginine to give structures including N epsilon-(carboxymethyl)lysine (CML), N epsilon-(carboxyethyl)lysine, and hydroimidazolones. CML is frequently used as a marker for AGEs in general. It exists in both the free or peptide-bound forms. Analysis of CML involves its extraction from the food (including protein hydrolysis to release any peptide-bound adduct) and determination by immunochemical or instrumental means. Various factors must be considered at each step of the analysis. Extraction, hydrolysis, and sample clean-up are all less straight forward for food samples, compared to plasma and tissue. The immunochemical and instrumental methods all have their advantages and disadvantages, and no perfect method exists. Currently, different procedures are being used in different laboratories, and there is an urgent need to compare, improve, and validate methods.

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

PubMed Central

Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.; Burnum-Johnson, Kristin E.; Kim, Young-Mo; Kyle, Jennifer E.; Matzke, Melissa M.; Shukla, Anil K.; Chu, Rosalie K.; Schepmoes, Athena A.; Jacobs, Jon M.; Baric, Ralph S.; Webb-Robertson, Bobbie-Jo; Smith, Richard D.

2016-01-01

ABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. The metabolite, protein, and lipid extraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental, in vitro, and clinical). IMPORTANCE In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample. Author Video: An author video summary of this article is available. PMID:27822525

Proanthocyanidin-rich extract from grape seeds attenuates the development of aortic atherosclerosis in cholesterol-fed rabbits.

PubMed

Yamakoshi, J; Kataoka, S; Koga, T; Ariga, T

1999-01-01

The aim of this study was to evaluate the antiatherosclerotic effect of proanthocyanidin-rich extracts from grape seeds in cholesterol-fed rabbits. Proanthocyanidin-rich extracts (0.1% and 1% in diets [w/w]) did not appreciably affect the changes in serum lipid profile of cholesterol-fed rabbits. The level of cholesteryl ester hydroperoxides (ChE-OOH) induced by 2,2'-azobis(2-amidinopropane-dihydrochloride (AAPH) were lower in the plasma of rabbits fed proanthocyanidin-rich extract plus cholesterol than in the plasma of rabbits fed cholesterol alone, but not in the low-density lipoprotein (LDL). Aortic malondialdehyde (MDA) content decreased in rabbits fed proanthocyanidin-rich extract. Feeding proanthocyanidin-rich extracts (0.1 and 1% in the diet) to rabbits significantly reduced severe atherosclerosis in the aorta. Immunohistochemical analysis revealed a decrease in the number of oxidized LDL-positive macrophage-derived foam cells in atherosclerotic lesions in the aorta of rabbits fed proanthocyanidin-rich extract. When proanthocyanidin-rich extract was administered orally to rats, proanthocyanidin was detected in the plasma by Porters method but not in the lipoproteins (LDL plus VLDL). In an in vitro experiment using human plasma, proanthocyanidin-rich extract added to the plasma inhibited the oxidation of cholesteryl linoleate in LDL, but not in the LDL isolated after the plasma and the extract were incubated in advance. These results suggested that proanthocyanidins, the major polyphenols in red wine, might trap reactive oxygen species in aqueous series such as plasma and interstitial fluid of the arterial wall, thereby inhibiting oxidation of LDL and showing an antiatherosclerotic activity.

Chemistry and Biochemistry of Dietary Polyphenols

PubMed Central

Tsao, Rong

2010-01-01

Polyphenols are the biggest group of phytochemicals, and many of them have been found in plant-based foods. Polyphenol-rich diets have been linked to many health benefits. This paper is intended to review the chemistry and biochemistry of polyphenols as related to classification, extraction, separation and analytical methods, their occurrence and biosynthesis in plants, and the biological activities and implications in human health. The discussions are focused on important and most recent advances in the above aspects, and challenges are identified for future research. PMID:22254006

Big Data Analytics for a Smart Green Infrastructure Strategy

NASA Astrophysics Data System (ADS)

Barrile, Vincenzo; Bonfa, Stefano; Bilotta, Giuliana

2017-08-01

As well known, Big Data is a term for data sets so large or complex that traditional data processing applications aren’t sufficient to process them. The term “Big Data” is referred to using predictive analytics. It is often related to user behavior analytics, or other advanced data analytics methods which from data extract value, and rarely to a particular size of data set. This is especially true for the huge amount of Earth Observation data that satellites constantly orbiting the earth daily transmit.

Absolute Bunch Length Measurements at the ALS by Incoherent Synchrotron Radiation Fluctuation Analysis

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

Filippetto, D.; /Frascati; Sannibale, F.

2008-01-24

By analyzing the pulse to pulse intensity fluctuations of the radiation emitted by a charge particle in the incoherent part of the spectrum, it is possible to extract information about the spatial distribution of the beam. At the Advanced Light Source (ALS) of the Lawrence Berkeley National Laboratory, we have developed and tested a simple scheme based on this principle that allows for the absolute measurement of the bunch length. A description of the method and the experimental results are presented.

Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P

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

Candel, A.; Kabel, A.; Lee, L.

In recent years, SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic time-domain code T3P. Higher-order Finite Element methods on conformal unstructured meshes and massively parallel processing allow unprecedented simulation accuracy for wakefield computations and simulations of transient effects in realistic accelerator structures. Applications include simulation of wakefield damping in the Compact Linear Collider (CLIC) power extraction and transfer structure (PETS).

Method of making ionic liquid mediated sol-gel sorbents

DOEpatents

Malik, Abdul; Shearrow, Anne M.

2017-01-31

Ionic liquid (IL)-mediated sol-gel hybrid organic-inorganic materials present enormous potential for effective use in analytical microextraction. One obstacle to materializing this prospect arises from high viscosity of ILs significantly slowing down sol-gel reactions. A method was developed which provides phosphonium-based, pyridinium-based, and imidazolium-based IL-mediated advanced sol-gel organic-inorganic hybrid materials for capillary microextraction. Scanning electron microscopy results demonstrate that ILs can serve as porogenic agents in sol-gel reactions. IL-mediated sol-gel coatings prepared with silanol-terminated polymers provided up to 28 times higher extractions compared to analogous sol-gel coatings prepared without any IL in the sol solution. This study shows that IL-generated porous morphology alone is not enough to provide effective extraction media: careful choice of the organic polymer and the precursor with close sol-gel reactivity must be made to ensure effective chemical bonding of the organic polymer to the created sol-gel material to be able to provide the desired sorbent characteristics.

Blurred Palmprint Recognition Based on Stable-Feature Extraction Using a Vese–Osher Decomposition Model

PubMed Central

Hong, Danfeng; Su, Jian; Hong, Qinggen; Pan, Zhenkuan; Wang, Guodong

2014-01-01

As palmprints are captured using non-contact devices, image blur is inevitably generated because of the defocused status. This degrades the recognition performance of the system. To solve this problem, we propose a stable-feature extraction method based on a Vese–Osher (VO) decomposition model to recognize blurred palmprints effectively. A Gaussian defocus degradation model is first established to simulate image blur. With different degrees of blurring, stable features are found to exist in the image which can be investigated by analyzing the blur theoretically. Then, a VO decomposition model is used to obtain structure and texture layers of the blurred palmprint images. The structure layer is stable for different degrees of blurring (this is a theoretical conclusion that needs to be further proved via experiment). Next, an algorithm based on weighted robustness histogram of oriented gradients (WRHOG) is designed to extract the stable features from the structure layer of the blurred palmprint image. Finally, a normalized correlation coefficient is introduced to measure the similarity in the palmprint features. We also designed and performed a series of experiments to show the benefits of the proposed method. The experimental results are used to demonstrate the theoretical conclusion that the structure layer is stable for different blurring scales. The WRHOG method also proves to be an advanced and robust method of distinguishing blurred palmprints. The recognition results obtained using the proposed method and data from two palmprint databases (PolyU and Blurred–PolyU) are stable and superior in comparison to previous high-performance methods (the equal error rate is only 0.132%). In addition, the authentication time is less than 1.3 s, which is fast enough to meet real-time demands. Therefore, the proposed method is a feasible way of implementing blurred palmprint recognition. PMID:24992328

Blurred palmprint recognition based on stable-feature extraction using a Vese-Osher decomposition model.

PubMed

Hong, Danfeng; Su, Jian; Hong, Qinggen; Pan, Zhenkuan; Wang, Guodong

2014-01-01

As palmprints are captured using non-contact devices, image blur is inevitably generated because of the defocused status. This degrades the recognition performance of the system. To solve this problem, we propose a stable-feature extraction method based on a Vese-Osher (VO) decomposition model to recognize blurred palmprints effectively. A Gaussian defocus degradation model is first established to simulate image blur. With different degrees of blurring, stable features are found to exist in the image which can be investigated by analyzing the blur theoretically. Then, a VO decomposition model is used to obtain structure and texture layers of the blurred palmprint images. The structure layer is stable for different degrees of blurring (this is a theoretical conclusion that needs to be further proved via experiment). Next, an algorithm based on weighted robustness histogram of oriented gradients (WRHOG) is designed to extract the stable features from the structure layer of the blurred palmprint image. Finally, a normalized correlation coefficient is introduced to measure the similarity in the palmprint features. We also designed and performed a series of experiments to show the benefits of the proposed method. The experimental results are used to demonstrate the theoretical conclusion that the structure layer is stable for different blurring scales. The WRHOG method also proves to be an advanced and robust method of distinguishing blurred palmprints. The recognition results obtained using the proposed method and data from two palmprint databases (PolyU and Blurred-PolyU) are stable and superior in comparison to previous high-performance methods (the equal error rate is only 0.132%). In addition, the authentication time is less than 1.3 s, which is fast enough to meet real-time demands. Therefore, the proposed method is a feasible way of implementing blurred palmprint recognition.

Evaluation of ADAM/1 model for advanced coal extraction concepts

NASA Technical Reports Server (NTRS)

Deshpande, G. K.; Gangal, M. D.

1982-01-01

Several existing computer programs for estimating life cycle cost of mining systems were evaluated. A commercially available program, ADAM/1 was found to be satisfactory in relation to the needs of the advanced coal extraction project. Two test cases were run to confirm the ability of the program to handle nonconventional mining equipment and procedures. The results were satisfactory. The model, therefore, is recommended to the project team for evaluation of their conceptual designs.

Integration of Plant Metabolomics Data with Metabolic Networks: Progresses and Challenges.

PubMed

Töpfer, Nadine; Seaver, Samuel M D; Aharoni, Asaph

2018-01-01

In the last decade, plant genome-scale modeling has developed rapidly and modeling efforts have advanced from representing metabolic behavior of plant heterotrophic cell suspensions to studying the complex interplay of cell types, tissues, and organs. A crucial driving force for such developments is the availability and integration of "omics" data (e.g., transcriptomics, proteomics, and metabolomics) which enable the reconstruction, extraction, and application of context-specific metabolic networks. In this chapter, we demonstrate a workflow to integrate gas chromatography coupled to mass spectrometry (GC-MS)-based metabolomics data of tomato fruit pericarp (flesh) tissue, at five developmental stages, with a genome-scale reconstruction of tomato metabolism. This method allows for the extraction of context-specific networks reflecting changing activities of metabolic pathways throughout fruit development and maturation.

A compact model and direct parameters extraction techniques For amorphous gallium-indium-zinc-oxide thin film transistors

NASA Astrophysics Data System (ADS)

Moldovan, Oana; Castro-Carranza, Alejandra; Cerdeira, Antonio; Estrada, Magali; Barquinha, Pedro; Martins, Rodrigo; Fortunato, Elvira; Miljakovic, Slobodan; Iñiguez, Benjamin

2016-12-01

An advanced compact and analytical drain current model for the amorphous gallium indium zinc oxide (GIZO) thin film transistors (TFTs) is proposed. Its output saturation behavior is improved by introducing a new asymptotic function. All model parameters were extracted using an adapted version of the Universal Method and Extraction Procedure (UMEM) applied for the first time for GIZO devices in a simple and direct form. We demonstrate the correct behavior of the model for negative VDS, a necessity for a complete compact model. In this way we prove the symmetry of source and drain electrodes and extend the range of applications to both signs of VDS. The model, in Verilog-A code, is implemented in Electronic Design Automation (EDA) tools, such as Smart Spice, and compared with measurements of TFTs. It describes accurately the experimental characteristics in the whole range of GIZO TFTs operation, making the model suitable for the design of circuits using these types of devices.

Remote measurement methods for 3-D modeling purposes using BAE Systems' Software

NASA Astrophysics Data System (ADS)

Walker, Stewart; Pietrzak, Arleta

2015-06-01

Efficient, accurate data collection from imagery is the key to an economical generation of useful geospatial products. Incremental developments of traditional geospatial data collection and the arrival of new image data sources cause new software packages to be created and existing ones to be adjusted to enable such data to be processed. In the past, BAE Systems' digital photogrammetric workstation, SOCET SET®, met fin de siècle expectations in data processing and feature extraction. Its successor, SOCET GXP®, addresses today's photogrammetric requirements and new data sources. SOCET GXP is an advanced workstation for mapping and photogrammetric tasks, with automated functionality for triangulation, Digital Elevation Model (DEM) extraction, orthorectification and mosaicking, feature extraction and creation of 3-D models with texturing. BAE Systems continues to add sensor models to accommodate new image sources, in response to customer demand. New capabilities added in the latest version of SOCET GXP facilitate modeling, visualization and analysis of 3-D features.

DEMETERRES project: development of innovative technologies for removing radionuclides from contaminated solid and liquid matrices

NASA Astrophysics Data System (ADS)

Chagvardieff, Pierre; Barré, Yves; Blin, Virginie; Faure, Sylvain; Fornier, Anne; Grange, Didier; Grandjean, Agnès; Guiderdoni, Emmanuel; Henner, Pascale; Siroux, Brice; Leybros, Antoine; Messalier, Marc; Paillard, Hervé; Prévost, Thierry; Rennesson, Malvina; Sarrobert, Catherine; Vavasseur, Alain; Véry, Anne-Aliénor

2017-09-01

As part of the « post-accidental » management, the DEMETERRES project (RSNR PIA) proposes to develop innovative and environmentally friendly methods for removal of cesium and strontium from soils and liquid matrices in order to rehabilitate them for an agricultural use while minimizing the volume of generated wastes in accordance with the nuclear waste existing processes. Complementary approaches are used: they are based on physico-chemical technologies (such as foams flotation, supercritical CO2 extraction, extractants in fluidized bed reactor …) and biological ones (bioextractants, phytoextraction) which concepts are described. These researches aim to design innovative and performing extractants in term of selectivity and to achieve the pilot reactor phase for each of them. These pilots will group in a network to provide a technological platform lasting the project, to which will be attached an available network of experts. The respective advances of these researches are presented, completed of tests initiated in Japan on contaminated soils through partnerships.

Rotor Wake Vortex Definition: Initial Evaluation of 3-C PIV Results of the Hart-II Study

NASA Technical Reports Server (NTRS)

Burley, Casey L.; Brooks, Thomas F.; vanderWall, Berend; Richard, Hughes; Raffel, Markus; Beaumier, Philippe; Delrieux, Yves; Lim, Joon W.; Yu, Yung H.; Tung, Chee

2002-01-01

An initial evaluation is made of extensive three-component (3C) particle image velocimetry (PIV) measurements within the wake across a rotor disk plane. The model is a 40 percent scale BO-105 helicopter main rotor in forward flight simulation. This study is part of the HART II test program conducted in the German-Dutch Wind Tunnel (DNW). Included are wake vortex field measurements over the advancing and retreating sides of the rotor operating at a typical descent landing condition important for impulsive blade-vortex interaction (BVI) noise. Also included are advancing side results for rotor angle variations from climb to steep descent. Using detailed PIV vector maps of the vortex fields, methods of extracting key vortex parameters are examined and a new method was developed and evaluated. An objective processing method, involving a center-of-vorticity criterion and a vorticity 'disk' integration, was used to determine vortex core size, strength, core velocity distribution characteristics, and unsteadiness. These parameters are mapped over the rotor disk and offer unique physical insight for these parameters of importance for rotor noise and vibration prediction.

Analysis of Big Data in Gait Biomechanics: Current Trends and Future Directions.

PubMed

Phinyomark, Angkoon; Petri, Giovanni; Ibáñez-Marcelo, Esther; Osis, Sean T; Ferber, Reed

2018-01-01

The increasing amount of data in biomechanics research has greatly increased the importance of developing advanced multivariate analysis and machine learning techniques, which are better able to handle "big data". Consequently, advances in data science methods will expand the knowledge for testing new hypotheses about biomechanical risk factors associated with walking and running gait-related musculoskeletal injury. This paper begins with a brief introduction to an automated three-dimensional (3D) biomechanical gait data collection system: 3D GAIT, followed by how the studies in the field of gait biomechanics fit the quantities in the 5 V's definition of big data: volume, velocity, variety, veracity, and value. Next, we provide a review of recent research and development in multivariate and machine learning methods-based gait analysis that can be applied to big data analytics. These modern biomechanical gait analysis methods include several main modules such as initial input features, dimensionality reduction (feature selection and extraction), and learning algorithms (classification and clustering). Finally, a promising big data exploration tool called "topological data analysis" and directions for future research are outlined and discussed.

Medical image computing for computer-supported diagnostics and therapy. Advances and perspectives.

PubMed

Handels, H; Ehrhardt, J

2009-01-01

Medical image computing has become one of the most challenging fields in medical informatics. In image-based diagnostics of the future software assistance will become more and more important, and image analysis systems integrating advanced image computing methods are needed to extract quantitative image parameters to characterize the state and changes of image structures of interest (e.g. tumors, organs, vessels, bones etc.) in a reproducible and objective way. Furthermore, in the field of software-assisted and navigated surgery medical image computing methods play a key role and have opened up new perspectives for patient treatment. However, further developments are needed to increase the grade of automation, accuracy, reproducibility and robustness. Moreover, the systems developed have to be integrated into the clinical workflow. For the development of advanced image computing systems methods of different scientific fields have to be adapted and used in combination. The principal methodologies in medical image computing are the following: image segmentation, image registration, image analysis for quantification and computer assisted image interpretation, modeling and simulation as well as visualization and virtual reality. Especially, model-based image computing techniques open up new perspectives for prediction of organ changes and risk analysis of patients and will gain importance in diagnostic and therapy of the future. From a methodical point of view the authors identify the following future trends and perspectives in medical image computing: development of optimized application-specific systems and integration into the clinical workflow, enhanced computational models for image analysis and virtual reality training systems, integration of different image computing methods, further integration of multimodal image data and biosignals and advanced methods for 4D medical image computing. The development of image analysis systems for diagnostic support or operation planning is a complex interdisciplinary process. Image computing methods enable new insights into the patient's image data and have the future potential to improve medical diagnostics and patient treatment.

Recent Advances in the Development and Application of Power Plate Transducers in Dense Gas Extraction and Aerosol Agglomeration Processes

NASA Astrophysics Data System (ADS)

Riera, E.; Cardoni, A.; Gallego-Juárez, J. A.; Acosta, V. M.; Blanco, A.; Rodríguez, G.; Blasco, M.; Herranz, L. E.

Power ultrasound (PU) is an emerging, innovative, energy saving and environmental friendly technology that is generating a great interest in sectors such as food and pharmaceutical industries, green chemistry, environmental pollution, and other processes, where sustainable and energy efficient methods are required to improve and/or produce specific effects. Two typical effects of PU are the enhancement of mass transfer in gases and liquids, and the induction of particle agglomeration in aerosols. These effects are activated by a variety of mechanisms associated to the nonlinear propagation of high amplitude ultrasonic waves such as diffusion, agitation, entrainment, turbulence, etc. During the last years a great effort has been jointly made by the Spanish National Research Council (CSIC) and the company Pusonics towards introducing novel processes into the market based on airborne ultrasonic plate transducers. This technology was specifically developed for the treatment of gas and multiphasic media characterized by low specific acoustic impedance and high acoustic absorption. Different strategies have been developed to mitigate the effects of the nonlinear dynamic behavior of such ultrasonic piezoelectric transducers in order to enhance and stabilize their response at operational power conditions. This work deals with the latter advances in the mitigation of nonlinear problems found in power transducers; besides it describes two applications assisted by ultrasound developed at semi-industrial and laboratory scales and consisting in extraction via dense gases and particle agglomeration. Dense Gas Extraction (DGE) assisted by PU is a new process with a potential to enhance the extraction kinetics with supercritical CO2. Acoustic agglomeration of fine aerosol particles has a great potential for the treatment of air pollution problems generated by particulate materials. Experimental and numerical results in both processes will be shown and discussed.

Community-Based Palliative Care and Advance Care Planning Documentation: Evidence from a Multispecialty Group.

PubMed

Tai-Seale, Ming; Yang, Yan; Dillon, Ellis; Tapper, Sharon; Lai, Steve; Yu, Peter; Allore, Heather; Ritchie, Christine

2018-02-01

With the growing public demand for access to critical health data across care settings, it is essential that advance care planning (ACP) information be included in the electronic health record (EHR) so that multiple clinicians can access it and understand individuals' preferences for end-of-life care. Community-based palliative care programs often incorporate ACP services. This study examined whether a community-based palliative care program is associated with digitally extractable ACP documentation in the EHR. Observational study using propensity score-weighted generalized estimation equations to examine patterns of digitally extractable ACP documentation. Palo Alto Medical Foundation (PAMF), a multispecialty ambulatory healthcare system in northern California. Individuals aged 65 and older with serious illnesses between January 1, 2013, and December 31, 2014 (N = 3,444). Community-based palliative care program in PAMF. Digitally extractable ACP in EHR. We found that only 14% (n = 483) of individuals with serious illnesses had digitally extractable ACP in electronic health records. Of the 6% of individuals receiving palliative care, 65% had ACP, versus 11% of those not receiving palliative care. Study results showed a strong positive association between palliative care and ACP. Only a small percentage of individuals with serious illnesses had ACP documentation in the EHR. Individuals with serious illnesses infrequently used palliative care delivered by board-certified palliative care specialists. Palliative care service use was associated with higher rates of ACP after controlling for organizational and individual characteristics using a propensity score weighting method. Scalable interventions targeted at non-palliative care clinicians for universal access to ACP are needed. © 2017, Copyright the Authors Journal compilation © 2017, The American Geriatrics Society.

Advances in Spectral-Spatial Classification of Hyperspectral Images

NASA Technical Reports Server (NTRS)

Fauvel, Mathieu; Tarabalka, Yuliya; Benediktsson, Jon Atli; Chanussot, Jocelyn; Tilton, James C.

2012-01-01

Recent advances in spectral-spatial classification of hyperspectral images are presented in this paper. Several techniques are investigated for combining both spatial and spectral information. Spatial information is extracted at the object (set of pixels) level rather than at the conventional pixel level. Mathematical morphology is first used to derive the morphological profile of the image, which includes characteristics about the size, orientation and contrast of the spatial structures present in the image. Then the morphological neighborhood is defined and used to derive additional features for classification. Classification is performed with support vector machines using the available spectral information and the extracted spatial information. Spatial post-processing is next investigated to build more homogeneous and spatially consistent thematic maps. To that end, three presegmentation techniques are applied to define regions that are used to regularize the preliminary pixel-wise thematic map. Finally, a multiple classifier system is defined to produce relevant markers that are exploited to segment the hyperspectral image with the minimum spanning forest algorithm. Experimental results conducted on three real hyperspectral images with different spatial and spectral resolutions and corresponding to various contexts are presented. They highlight the importance of spectral-spatial strategies for the accurate classification of hyperspectral images and validate the proposed methods.

Parallel processing of real-time dynamic systems simulation on OSCAR (Optimally SCheduled Advanced multiprocessoR)

NASA Technical Reports Server (NTRS)

Kasahara, Hironori; Honda, Hiroki; Narita, Seinosuke

1989-01-01

Parallel processing of real-time dynamic systems simulation on a multiprocessor system named OSCAR is presented. In the simulation of dynamic systems, generally, the same calculation are repeated every time step. However, we cannot apply to Do-all or the Do-across techniques for parallel processing of the simulation since there exist data dependencies from the end of an iteration to the beginning of the next iteration and furthermore data-input and data-output are required every sampling time period. Therefore, parallelism inside the calculation required for a single time step, or a large basic block which consists of arithmetic assignment statements, must be used. In the proposed method, near fine grain tasks, each of which consists of one or more floating point operations, are generated to extract the parallelism from the calculation and assigned to processors by using optimal static scheduling at compile time in order to reduce large run time overhead caused by the use of near fine grain tasks. The practicality of the scheme is demonstrated on OSCAR (Optimally SCheduled Advanced multiprocessoR) which has been developed to extract advantageous features of static scheduling algorithms to the maximum extent.

The bioactivity of plant extracts against representative bacterial pathogens of the lower respiratory tract

PubMed Central

Bocanegra-García, Virgilio; del Rayo Camacho-Corona, María; Ramírez-Cabrera, Mónica; Rivera, Gildardo; Garza-González, Elvira

2009-01-01

Background Lower respiratory tract infections are a major cause of illness and death. Such infections are common in intensive care units (ICU) and their lethality persists despite advances in diagnosis, treatment and prevention. In Mexico, some plants are used in traditional medicine to treat respiratory diseases or ailments such as cough, bronchitis, tuberculosis and other infections. Medical knowledge derived from traditional societies has motivated searches for new bioactive molecules derived from plants that show potent activity against bacterial pathogens. Therefore, the aim of this study was to evaluate the effect of hexanic, chloroformic (CLO), methanolic (MET) and aqueous extracts from various plants used in Mexican traditional medicine on various microorganisms associated with respiratory disease. Methods thirty-five extracts prepared from nine plants used in Mexican traditional medicine for the treatment of respiratory infections were evaluated against 15 control bacterial species and clinical isolates. Results Both chloroformic (CLO) and methanolic (MET) extracts of Larrea tridentata were active against Methicillin-resistant S. aureus, B. subtilis and L. monocytogenes. A MET extract of L. tridentata was also active against S. aureus, S. pneumoniae, S. maltophilia, E. faecalis and H. influenzae and the CLO extract was active against A. baumannii. An Aqueous extract of M. acumitata and a MET extract of N. officinale were active against S. pneumoniae. CLO and MET extracts of L. tridentata were active against clinical isolates of S. aureus, S. pneumoniae and E. faecalis. Conclusion Overall, our results support the potential use of L. tridentata as a source of antibacterial compounds. PMID:19486533

Analyzing the dynamics of cell cycle processes from fixed samples through ergodic principles

PubMed Central

Wheeler, Richard John

2015-01-01

Tools to analyze cyclical cellular processes, particularly the cell cycle, are of broad value for cell biology. Cell cycle synchronization and live-cell time-lapse observation are widely used to analyze these processes but are not available for many systems. Simple mathematical methods built on the ergodic principle are a well-established, widely applicable, and powerful alternative analysis approach, although they are less widely used. These methods extract data about the dynamics of a cyclical process from a single time-point “snapshot” of a population of cells progressing through the cycle asynchronously. Here, I demonstrate application of these simple mathematical methods to analysis of basic cyclical processes—cycles including a division event, cell populations undergoing unicellular aging, and cell cycles with multiple fission (schizogony)—as well as recent advances that allow detailed mapping of the cell cycle from continuously changing properties of the cell such as size and DNA content. This includes examples using existing data from mammalian, yeast, and unicellular eukaryotic parasite cell biology. Through the ongoing advances in high-throughput cell analysis by light microscopy, electron microscopy, and flow cytometry, these mathematical methods are becoming ever more important and are a powerful complementary method to traditional synchronization and time-lapse cell cycle analysis methods. PMID:26543196

Solvent Extraction of Copper: An Extractive Metallurgy Exercise for Undergraduate Teaching Laboratories

ERIC Educational Resources Information Center

Smellie, Iain A.; Forgan, Ross S.; Brodie, Claire; Gavine, Jack S.; Harris, Leanne; Houston, Daniel; Hoyland, Andrew D.; McCaughan, Rory P.; Miller, Andrew J.; Wilson, Liam; Woodhall, Fiona M.

2016-01-01

A multidisciplinary experiment for advanced undergraduate students has been developed in the context of extractive metallurgy. The experiment serves as a model of an important modern industrial process that combines aspects of organic/inorganic synthesis and analysis. Students are tasked to prepare a salicylaldoxime ligand and samples of the…

Review of Processing and Analytical Methods for Francisella ...

EPA Pesticide Factsheets

Journal Article The etiological agent of tularemia, Francisella tularensis, is a resilient organism within the environment and can be acquired many ways (infectious aerosols and dust, contaminated food and water, infected carcasses, and arthropod bites). However, isolating F. tularensis from environmental samples can be challenging due to its nutritionally fastidious and slow-growing nature. In order to determine the current state of the science regarding available processing and analytical methods for detection and recovery of F. tularensis from water and soil matrices, a review of the literature was conducted. During the review, analysis via culture, immunoassays, and genomic identification were the most commonly found methods for F. tularensis detection within environmental samples. Other methods included combined culture and genomic analysis for rapid quantification of viable microorganisms and use of one assay to identify multiple pathogens from a single sample. Gaps in the literature that were identified during this review suggest that further work to integrate culture and genomic identification would advance our ability to detect and to assess the viability of Francisella spp. The optimization of DNA extraction, whole genome amplification with inhibition-resistant polymerases, and multiagent microarray detection would also advance biothreat detection.

Advanced Receiver For Phase-Shift-Keyed Signals

NASA Technical Reports Server (NTRS)

Hinedi, Sami M.

1992-01-01

ARX II is second "breadboard" version of advanced receiver, a hybrid digital/analog receiving subsystem, extracting symbols and Doppler shifts from weak phase-shift-keyed signals. Useful in terrestrial digital communication systems.

Effect of the hexane extract of Piper auritum on insulin release from β-cell and oxidative stress in streptozotocin-induced diabetic rat

PubMed Central

Gutierrez, Rosa Martha Perez

2012-01-01

Background: The large-leafed perennial plant Piper auritum known as Hoja Santa, is used for its leaves that because of their spicy aromatic scent and flavor have an important presence in Mexican cuisine, and in many regions, this plant is known for its therapeutic properties. Materials and Methods: In the present study, we investigated the effect of hexane, chloroform and methanol extracts from Piper auritum on cell culture system and the effect in streptozotocin-induced type 1 diabetic rats treated by 28 days on the physiological, metabolic parameters and oxidative stress. Results: The hexane extract of P. auritum (HS) treatment significantly reduced the intake of both food, water and body weight loss as well as levels of blood glucose, serum cholesterol, triglycerides and increase HDL-cholesterol. After 4-week administration of HS antioxidant enzyme as SOD, CAT, GSH, GPx in pancreas were determined. These enzyme increased significantly compared with those of the diabetic rats control and normal animals. For all estimated, the results of HS treated groups leading to a restoration of the defense mechanism. The treatment also improves pancreatic TBARS–reactive substance level and serum NO and iNOS. To determine the insulin releasing activity, after extract treatment the serum and pancreatic sections were processed for examination of insulin-releasing activity using an immunocytochemistry kit. The results showed that administration of the hexane extract (200 and 400 mg/kg) exhibited a significant increase in serum and pancreas tissue insulin. Administration of streptozotocin decreased the insulin secretory activity in comparison with intact rats, but treatment with the HS extract increased significantly the activity of the beta cells in comparison with the diabetic control rats. The extract decreased serum glucose in streptozotocin-induced diabetic rats and increased insulin release from the beta cells of the pancreas. In cultured RIN-5F cells, we examined whether hexane extract of P. auritum would protect the pancreas-derived β-cells from oxidative stress. Moreover, HS could protect pancreatic β-cells from advanced glycation end products-induced oxidative stress. Conclusion: From these results, HS is suggested to show anti-diabetic effect by stimulating insulin-dependent and by protecting pancreatic β-cells from advanced glycation end products-induced oxidative stress. PMID:24082635

RASSOR - Regolith Advanced Surface Systems Operations Robot

NASA Technical Reports Server (NTRS)

Gill, Tracy R.; Mueller, Rob

2015-01-01

The Regolith Advanced Surface Systems Operations Robot (RASSOR) is a lightweight excavator for mining in reduced gravity. RASSOR addresses the need for a lightweight (<100 kg) robot that is able to overcome excavation reaction forces while operating in reduced gravity environments such as the moon or Mars. A nominal mission would send RASSOR to the moon to operate for five years delivering regolith feedstock to a separate chemical plant, which extracts oxygen from the regolith using H2 reduction methods. RASSOR would make 35 trips of 20 kg loads every 24 hours. With four RASSORs operating at one time, the mission would achieve 10 tonnes of oxygen per year (8 t for rocket propellant and 2 t for life support). Accessing craters in space environments may be extremely hard and harsh due to volatile resources - survival is challenging. New technologies and methods are required. RASSOR is a product of KSC Swamp Works which establishes rapid, innovative and cost effective exploration mission solutions by leveraging partnerships across NASA, industry and academia.

A moving baseline for evaluation of advanced coal extraction systems

NASA Technical Reports Server (NTRS)

Bickerton, C. R.; Westerfield, M. D.

1981-01-01

Results from the initial effort to establish baseline economic performance comparators for a program whose intent is to define, develop, and demonstrate advanced systems suitable for coal resource extraction beyond the year 2000 are reported. Systems used were selected from contemporary coal mining technology and from conservation conjectures of year 2000 technology. The analysis was also based on a seam thickness of 6 ft. Therefore, the results are specific to the study systems and the selected seam extended to other seam thicknesses.

NOVEL BINDERS AND METHODS FOR AGGLOMERATION OF ORE

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

S.K. Kawatra; T.C. Eisele; J.A. Gurtler

2004-04-01

Many metal extraction operations, such as leaching of copper, leaching of precious metals, and reduction of metal oxides to metal in high-temperature furnaces, require agglomeration of ore to ensure that reactive liquids or gases are evenly distributed throughout the ore being processed. Agglomeration of ore into coarse, porous masses achieves this even distribution of fluids by preventing fine particles from migrating and clogging the spaces and channels between the larger ore particles. Binders are critically necessary to produce agglomerates that will not break down during processing. However, for many important metal extraction processes there are no binders known that willmore » work satisfactorily. Primary examples of this are copper heap leaching, where there are no binders that will work in the acidic environment encountered in this process, and advanced ironmaking processes, where binders must function satisfactorily over an extraordinarily large range of temperatures (from room temperature up to over 1200 C). As a result, operators of many facilities see a large loss of process efficiency due to their inability to take advantage of agglomeration. The large quantities of ore that must be handled in metal extraction processes also means that the binder must be inexpensive and useful at low dosages to be economical. The acid-resistant binders and agglomeration procedures developed in this project will also be adapted for use in improving the energy efficiency and performance of a broad range of mineral agglomeration applications, particularly heap leaching and advanced primary ironmaking.« less

OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

PubMed Central

Hunter, Lawrence; Lu, Zhiyong; Firby, James; Baumgartner, William A; Johnson, Helen L; Ogren, Philip V; Cohen, K Bretonnel

2008-01-01

Background Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a diverse literature. Here we report on the design, implementation and several evaluations of OpenDMAP, an ontology-driven, integrated concept analysis system. It significantly advances the state of the art in information extraction by leveraging knowledge in ontological resources, integrating diverse text processing applications, and using an expanded pattern language that allows the mixing of syntactic and semantic elements and variable ordering. Results OpenDMAP information extraction systems were produced for extracting protein transport assertions (transport), protein-protein interaction assertions (interaction) and assertions that a gene is expressed in a cell type (expression). Evaluations were performed on each system, resulting in F-scores ranging from .26 – .72 (precision .39 – .85, recall .16 – .85). Additionally, each of these systems was run over all abstracts in MEDLINE, producing a total of 72,460 transport instances, 265,795 interaction instances and 176,153 expression instances. Conclusion OpenDMAP advances the performance standards for extracting protein-protein interaction predications from the full texts of biomedical research articles. Furthermore, this level of performance appears to generalize to other information extraction tasks, including extracting information about predicates of more than two arguments. The output of the information extraction system is always constructed from elements of an ontology, ensuring that the knowledge representation is grounded with respect to a carefully constructed model of reality. The results of these efforts can be used to increase the efficiency of manual curation efforts and to provide additional features in systems that integrate multiple sources for information extraction. The open source OpenDMAP code library is freely available at PMID:18237434

Rapid Screening of Natural Plant Extracts with Calcium Diacetate for Differential Effects Against Foodborne Pathogens and a Probiotic Bacterium.

PubMed

Colonna, William; Brehm-Stecher, Byron; Shetty, Kalidas; Pometto, Anthony

2017-12-01

This study focused on advancing a rapid turbidimetric bioassay to screen antimicrobials using specific cocktails of targeted foodborne bacterial pathogens. Specifically, to show the relevance of this rapid screening tool, the antimicrobial potential of generally recognized as safe calcium diacetate (DAX) and blends with cranberry (NC) and oregano (OX) natural extracts was evaluated. Furthermore, the same extracts were evaluated against beneficial lactic acid bacteria. The targeted foodborne pathogens evaluated were Escherichia coli O157:H7, Salmonella spp., Listeria monocytogenes, and Staphylococcus aureus using optimized initial cocktails (∼10 8 colony-forming unit/mL) containing strains isolated from human food outbreaks. Of all extracts evaluated, 0.51% (w/v) DAX in ethanol was the most effective against all four pathogens. However, DAX when reduced to 0.26% and with added blends from ethanol extractions consisting of DAX:OX (3:1), slightly outperformed or was equal to same levels of DAX alone. Subculture of wells in which no growth occurred after 1 week indicated that all water and ethanol extracts were bacteriostatic against the pathogens tested. All the targeted antimicrobials had no effect on the probiotic organism Lactobacillus plantarum. The use of such rapid screening methods combined with the use of multistrain cocktails of targeted foodborne pathogens from outbreaks will allow rapid large-scale screening of antimicrobials and enable further detailed studies in targeted model food systems.

SIGNALING PATHWAYS REGULATED BY BRASSICACEAE EXTRACT INHIBIT THE FORMATION OF ADVANCED GLYCATED END PRODUCTS IN RAT BRAIN

PubMed Central

Al-Malki, Abdulrahman L.; Barbour, Elie K.; EA, Huwait; Moselhy, Said S.; ALZahrani, Anas Hassan Saeed; Kumosani, Taha A.

2017-01-01

Background: The goal of this study was identification signaling molecules mediated the formation of AGEs in brain of rats injected with CdCl2 and the role of camel whey proteins and Brassicaceae extract on formation of AGEs in brain. Methods: Ninety male rats were randomly grouped into five groups; Normal control (GpI) and the other rats (groups II-V) were received a single dose of cadmium chloride i.p (5 μg/kg/b.w) for induction of neurodegeneration. Rats in groups III-V were treated daily with whey protein (1g/kg b.w) or Brassicaceae extract (1mg/kg b.w) or combined respectively for 12 weeks. Results: It was found that whey protein combined with Brassicaceae extract prevented the formation of AGEs and enhance the antioxidant activity compared with untreated group (p <0.001). Serum tumor necrosis factor (TNF-α) and interleukine (IL-6) levels were significantly decreased (p<0.01) in rats treated with whey protein and Brassicaceae extract formation compared with untreated. The combined treatment showed a better impact than individual ones (p<0.001). The level of cAMP but not cGMP were lowered in combined treatment than individual (p<0.01). Conclusion: It can be postulated that Whey protein + Brassicaceae extract formation could have potential benefits in the prevention of the onset and progression of neuropathy in patients. PMID:28573240

Recent trends in biological extraction of chitin from marine shell wastes: a review.

PubMed

Kaur, Surinder; Dhillon, Gurpreet Singh

2015-03-01

The natural biopolymer chitin and its deacetylated product chitosan are widely used in innumerable applications ranging from biomedicine, pharmaceuticals, food, agriculture and personal care products to environmental sector. The abundant and renewable marine processing wastes are commercially exploited for the extraction of chitin. However, the traditional chitin extraction processes employ harsh chemicals at elevated temperatures for a prolonged time which can harm its physico-chemical properties and are also held responsible for the deterioration of environmental health. In view of this, green extraction methods are increasingly gaining popularity due to their environmentally friendly nature. The bioextraction of chitin from crustacean shell wastes has been increasingly researched at the laboratory scale. However, the bioextraction of chitin is not currently exploited to its maximum potential on the commercial level. Bioextraction of chitin is emerging as a green, cleaner, eco-friendly and economical process. Specifically in the chitin extraction, microorganisms-mediated fermentation processes are highly desirable due to easy handling, simplicity, rapidity, controllability through optimization of process parameters, ambient temperature and negligible solvent consumption, thus reducing environmental impact and costs. Although, chitin production from crustacean shell waste through biological means is still at its early stage of development, it is undergoing rapid progress in recent years and showing a promising prospect. Driven by reduced energy, wastewater or solvent, advances in biological extraction of chitin along with valuable by-products will have high economic and environmental impact.

Considering context: reliable entity networks through contextual relationship extraction

NASA Astrophysics Data System (ADS)

David, Peter; Hawes, Timothy; Hansen, Nichole; Nolan, James J.

2016-05-01

Existing information extraction techniques can only partially address the problem of exploiting unreadable-large amounts text. When discussion of events and relationships is limited to simple, past-tense, factual descriptions of events, current NLP-based systems can identify events and relationships and extract a limited amount of additional information. But the simple subset of available information that existing tools can extract from text is only useful to a small set of users and problems. Automated systems need to find and separate information based on what is threatened or planned to occur, has occurred in the past, or could potentially occur. We address the problem of advanced event and relationship extraction with our event and relationship attribute recognition system, which labels generic, planned, recurring, and potential events. The approach is based on a combination of new machine learning methods, novel linguistic features, and crowd-sourced labeling. The attribute labeler closes the gap between structured event and relationship models and the complicated and nuanced language that people use to describe them. Our operational-quality event and relationship attribute labeler enables Warfighters and analysts to more thoroughly exploit information in unstructured text. This is made possible through 1) More precise event and relationship interpretation, 2) More detailed information about extracted events and relationships, and 3) More reliable and informative entity networks that acknowledge the different attributes of entity-entity relationships.

Application of Fourier transforms for microwave radiometric inversions

NASA Technical Reports Server (NTRS)

Holmes, J. J.; Balanis, C. A.; Truman, W. M.

1975-01-01

Existing microwave radiometer technology now provides a suitable method for remote determination of the ocean surface's absolute brightness temperature. To extract the brightness temperature of the water from the antenna temperature, an unstable Fredholm integral equation of the first kind is solved. Fourier transform techniques are used to invert the integral after it is placed into a cross correlation form. Application and verification of the methods to a two-dimensional modeling of a laboratory wave tank system are included. The instability of the ill-posed Fredholm equation is examined and a restoration procedure is included which smooths the resulting oscillations. With the recent availability and advances of fast Fourier transform (FFT) techniques, the method presented becomes very attractive in the evaluation of large quantities of data.

Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2014-2016).

PubMed

Breadmore, Michael C; Wuethrich, Alain; Li, Feng; Phung, Sui Ching; Kalsoom, Umme; Cabot, Joan M; Tehranirokh, Masoomeh; Shallan, Aliaa I; Abdul Keyon, Aemi S; See, Hong Heng; Dawod, Mohamed; Quirino, Joselito P

2017-01-01

One of the most cited limitations of capillary (and microchip) electrophoresis is the poor sensitivity. This review continues to update this series of biennial reviews, first published in Electrophoresis in 2007, on developments in the field of on-line/in-line concentration methods in capillaries and microchips, covering the period July 2014-June 2016. It includes developments in the field of stacking, covering all methods from field amplified sample stacking and large volume sample stacking, through to isotachophoresis, dynamic pH junction, and sweeping. Attention is also given to on-line or in-line extraction methods that have been used for electrophoresis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Versatile and efficient pore network extraction method using marker-based watershed segmentation

NASA Astrophysics Data System (ADS)

Gostick, Jeff T.

2017-08-01

Obtaining structural information from tomographic images of porous materials is a critical component of porous media research. Extracting pore networks is particularly valuable since it enables pore network modeling simulations which can be useful for a host of tasks from predicting transport properties to simulating performance of entire devices. This work reports an efficient algorithm for extracting networks using only standard image analysis techniques. The algorithm was applied to several standard porous materials ranging from sandstone to fibrous mats, and in all cases agreed very well with established or known values for pore and throat sizes, capillary pressure curves, and permeability. In the case of sandstone, the present algorithm was compared to the network obtained using the current state-of-the-art algorithm, and very good agreement was achieved. Most importantly, the network extracted from an image of fibrous media correctly predicted the anisotropic permeability tensor, demonstrating the critical ability to detect key structural features. The highly efficient algorithm allows extraction on fairly large images of 5003 voxels in just over 200 s. The ability for one algorithm to match materials as varied as sandstone with 20% porosity and fibrous media with 75% porosity is a significant advancement. The source code for this algorithm is provided.

Research activities on supercritical fluid science in food biotechnology.

PubMed

Khosravi-Darani, Kianoush

2010-06-01

This article serves as an overview, introducing the currently popular area of supercritical fluids and their uses in food biotechnology. Within each application, and wherever possible, the basic principles of the technique, as well as a description of the history, instrumentation, methodology, uses, problems encountered, and advantages over the traditional, non-supercritical methods are given. Most current commercial application of the supercritical extraction involve biologically-produced materials; the technique may be particularly relevant to the extraction of biological compounds in cases where there is a requirement for low-temperature processing, high mass-transfer rates, and negligible carrying over of the solvent into the final product. Special applications to food processing include the decaffeination of green coffee beans, the production of hops extracts, the recovery of aromas and flavors from herbs and spices, the extraction and fractionation of edible oils, and the removal of contaminants, among others. New advances, in which the extraction is combined with reaction or crystallization steps, may further increase the attractiveness of supercritical fluids in the bioprocess industries. To develop and establish a novel and effective alternative to heating treatment, the lethal action of high hydrostatic pressure CO(2) on microorganisms, with none or only a minimal heating process, has recently received a great deal of attention.

DeepGene: an advanced cancer type classifier based on deep learning and somatic point mutations.

PubMed

Yuan, Yuchen; Shi, Yi; Li, Changyang; Kim, Jinman; Cai, Weidong; Han, Zeguang; Feng, David Dagan

2016-12-23

With the developments of DNA sequencing technology, large amounts of sequencing data have become available in recent years and provide unprecedented opportunities for advanced association studies between somatic point mutations and cancer types/subtypes, which may contribute to more accurate somatic point mutation based cancer classification (SMCC). However in existing SMCC methods, issues like high data sparsity, small volume of sample size, and the application of simple linear classifiers, are major obstacles in improving the classification performance. To address the obstacles in existing SMCC studies, we propose DeepGene, an advanced deep neural network (DNN) based classifier, that consists of three steps: firstly, the clustered gene filtering (CGF) concentrates the gene data by mutation occurrence frequency, filtering out the majority of irrelevant genes; secondly, the indexed sparsity reduction (ISR) converts the gene data into indexes of its non-zero elements, thereby significantly suppressing the impact of data sparsity; finally, the data after CGF and ISR is fed into a DNN classifier, which extracts high-level features for accurate classification. Experimental results on our curated TCGA-DeepGene dataset, which is a reformulated subset of the TCGA dataset containing 12 selected types of cancer, show that CGF, ISR and DNN all contribute in improving the overall classification performance. We further compare DeepGene with three widely adopted classifiers and demonstrate that DeepGene has at least 24% performance improvement in terms of testing accuracy. Based on deep learning and somatic point mutation data, we devise DeepGene, an advanced cancer type classifier, which addresses the obstacles in existing SMCC studies. Experiments indicate that DeepGene outperforms three widely adopted existing classifiers, which is mainly attributed to its deep learning module that is able to extract the high level features between combinatorial somatic point mutations and cancer types.

[Advances in studies on multi-stage countercurrent extraction technology in traditional Chinese medicine].

PubMed

Xie, Zhi-Peng; Liu, Xue-Song; Chen, Yong; Cai, Ming; Qu, Hai-Bin; Cheng, Yi-Yu

2007-05-01

Multi-stage countercurrent extraction technology, integrating solvent extraction, repercolation with dynamic and countercurrent extraction, is a novel extraction technology for the traditional Chinese medicine. This solvent-saving, energy-saving and high-extraction-efficiency technology can at the most drive active compounds to diffuse from the herbal materials into the solvent stage by stage by creating concentration differences between the herbal materials and the solvents. This paper reviewed the basic principle, the influence factors and the research progress and trends of the equipments and the application of the multi-stage countercurrent extraction.

Advanced electron microscopy methods for the analysis of MgB2 superconductor

NASA Astrophysics Data System (ADS)

Birajdar, B.; Peranio, N.; Eibl, O.

2008-02-01

Advanced electron microscopy methods used for the analysis of superconducting MgB2 wires and tapes are described. The wires and tapes were prepared by the powder in tube method using different processing technologies and thoroughly characterised for their superconducting properties within the HIPERMAG project. Microstructure analysis on μm to nm length scales is necessary to understand the superconducting properties of MgB2. For the MgB2 phase analysis on μm scale an analytical SEM, and for the analysis on nm scale a energy-filtered STEM is used. Both the microscopes were equipped with EDX detector and field emission gun. Electron microscopy and spectroscopy of MgB2 is challenging because of the boron analysis, carbon and oxygen contamination, and the presence of large number of secondary phases. Advanced electron microscopy involves, combined SEM, EPMA and TEM analysis with artefact free sample preparation, elemental mapping and chemical quantification of point spectra. Details of the acquisition conditions and achieved accuracy are presented. Ex-situ wires show oxygen-free MgB2 colonies (a colony is a dense arrangement of several MgB2 grains) embedded in a porous and oxygen-rich matrix, introducing structural granularity. In comparison, in-situ wires are generally more dense, but show inhibited MgB2 phase formation with significantly higher fraction of B-rich secondary phases. SiC additives in the in-situ wires forms Mg2Si secondary phases. The advanced electron microscopy has been used to extract the microstructure parameters like colony size, B-rich secondary phase fraction, O mole fraction and MgB2 grain size, and establish a microstructure-critical current density model [1]. In summary, conventional secondary electron imaging in SEM and diffraction contrast imaging in the TEM are by far not sufficient and advanced electron microscopy methods are essential for the analysis of superconducting MgB2 wires and tapes.

Image analysis and modeling in medical image computing. Recent developments and advances.

PubMed

Handels, H; Deserno, T M; Meinzer, H-P; Tolxdorff, T

2012-01-01

Medical image computing is of growing importance in medical diagnostics and image-guided therapy. Nowadays, image analysis systems integrating advanced image computing methods are used in practice e.g. to extract quantitative image parameters or to support the surgeon during a navigated intervention. However, the grade of automation, accuracy, reproducibility and robustness of medical image computing methods has to be increased to meet the requirements in clinical routine. In the focus theme, recent developments and advances in the field of modeling and model-based image analysis are described. The introduction of models in the image analysis process enables improvements of image analysis algorithms in terms of automation, accuracy, reproducibility and robustness. Furthermore, model-based image computing techniques open up new perspectives for prediction of organ changes and risk analysis of patients. Selected contributions are assembled to present latest advances in the field. The authors were invited to present their recent work and results based on their outstanding contributions to the Conference on Medical Image Computing BVM 2011 held at the University of Lübeck, Germany. All manuscripts had to pass a comprehensive peer review. Modeling approaches and model-based image analysis methods showing new trends and perspectives in model-based medical image computing are described. Complex models are used in different medical applications and medical images like radiographic images, dual-energy CT images, MR images, diffusion tensor images as well as microscopic images are analyzed. The applications emphasize the high potential and the wide application range of these methods. The use of model-based image analysis methods can improve segmentation quality as well as the accuracy and reproducibility of quantitative image analysis. Furthermore, image-based models enable new insights and can lead to a deeper understanding of complex dynamic mechanisms in the human body. Hence, model-based image computing methods are important tools to improve medical diagnostics and patient treatment in future.

Food Fish Identification from DNA Extraction through Sequence Analysis

ERIC Educational Resources Information Center

Hallen-Adams, Heather E.

2015-01-01

This experiment exposed 3rd and 4th y undergraduates and graduate students taking a course in advanced food analysis to DNA extraction, polymerase chain reaction (PCR), and DNA sequence analysis. Students provided their own fish sample, purchased from local grocery stores, and the class as a whole extracted DNA, which was then subjected to PCR,…

Preliminary results of sugar maple carbohydrate and growth response under vacuum and gravity sap extraction

Treesearch

Mark L. Isselhardt; Timothy D. Perkins; Abby K. van den Berg; Paul G. Schaberg

2016-01-01

Recent technological advancements have increased the amount of sugar-enriched sap that can be extracted from sugar maple (Acer saccharum). This pilot study quantified overall sugar removal and the impacts of vacuum (60 cm Hg) and gravity sap extraction on residual nonstructural carbohydrate (NSC) concentrations and on stem and twig growth. Vacuum...

Review of the harvesting and extraction of advanced biofuels and bioproducts

Treesearch

Babette L. Marrone;  Ronald E.  Lacey;  Daniel B. Anderson;  James Bonner;  Jim Coons;  Taraka Dale;  Cara Meghan Downes;  Sandun Fernando;  Christopher  Fuller;  Brian Goodall;  Johnathan E. Holladay;  Kiran Kadam;  Daniel  Kalb;  Wei  Liu;  John B. Mott;  Zivko Nikolov;  Kimberly L. Ogden;  Richard T. Sayre;  Brian G. Trewyn;  José A. Olivares

2017-01-01

Energy-efficient and scalable harvesting and lipid extraction processes must be developed in order for the algal biofuels and bioproducts industry to thrive. The major challenge for harvesting is the handling of large volumes of cultivation water to concentrate low amounts of biomass. For lipid extraction, the major energy and cost drivers are associated with...

Experimental Determination of the Dynamic Hydraulic Transfer Function for the J-2X Oxidizer Turbopump. Part One; Methodology

NASA Technical Reports Server (NTRS)

Zoladz, Tom; Patel, Sandeep; Lee, Erik; Karon, Dave

2011-01-01

An advanced methodology for extracting the hydraulic dynamic pump transfer matrix (Yp) for a cavitating liquid rocket engine turbopump inducer+impeller has been developed. The transfer function is required for integrated vehicle pogo stability analysis as well as optimization of local inducer pumping stability. Laboratory pulsed subscale waterflow test of the J-2X oxygen turbo pump is introduced and our new extraction method applied to the data collected. From accurate measures of pump inlet and discharge perturbational mass flows and pressures, and one-dimensional flow models that represents complete waterflow loop physics, we are able to derive Yp and hence extract the characteristic pump parameters: compliance, pump gain, impedance, mass flow gain. Detailed modeling is necessary to accurately translate instrument plane measurements to the pump inlet and discharge and extract Yp. We present the MSFC Dynamic Lump Parameter Fluid Model Framework and describe critical dynamic component details. We report on fit minimization techniques, cost (fitness) function derivation, and resulting model fits to our experimental data are presented. Comparisons are made to alternate techniques for spatially translating measurement stations to actual pump inlet and discharge.

Antimicrobial, Cytotoxic, Phytotoxic and Antioxidant Potential of Heliotropium strigosum Willd.

PubMed

Khurm, Muhammad; Chaudhry, Bashir A; Uzair, Muhammad; Janbaz, Khalid H

2016-07-28

Background: Heliotropium strigosum Willd. (Chitiphal) is a medicinally important herb that belongs to the Boraginaceae family. Traditionally, this plant was used in the medication therapy of various ailments in different populations of the world. The aim of the study is to probe the therapeutic aspects of H. strigosum described in the traditional folklore history of medicines. Methods: In the present study, the dichloromethane crude extract of this plant was screened to explore the antimicrobial, cytotoxic, phytotoxic and antioxidant potential of H. strigosum . For antibacterial, antifungal and antioxidant activities, microplate alamar blue assay (MABA), agar tube dilution method and diphenyl picryl hydrazine (DPPH) radical-scavenging assay were used, respectively. The cytotoxic and phytotoxic potential were demonstrated by using brine shrimp lethality bioassay and Lemna minor assay. Results: The crude extract displayed positive cytotoxic activity in the brine shrimp lethality assay, with 23 of 30 shrimps dying at the concentration of 1000 µg/mL. It also showed moderate phytotoxic potential with percent inhibition of 50% at the concentration of 1000 µg/mL. The crude extract exhibited no significant antibacterial activity against Staphylococcus aureus , Shigella flexneri , Escherichia coli and Pseudomonas aeruginosa . Non-significant antifungal and radical scavenging activity was also shown by the dichloromethane crude extract. Conclusion: It is recommended that scientists focus on the identification and isolation of beneficial bioactive constituents with the help of advanced scientific methodologies that seems to be helpful in the synthesis of new therapeutic agents of desired interest.

Antimicrobial, Cytotoxic, Phytotoxic and Antioxidant Potential of Heliotropium strigosum Willd.

PubMed Central

Khurm, Muhammad; Chaudhry, Bashir A.; Uzair, Muhammad; Janbaz, Khalid H.

2016-01-01

Background: Heliotropium strigosum Willd. (Chitiphal) is a medicinally important herb that belongs to the Boraginaceae family. Traditionally, this plant was used in the medication therapy of various ailments in different populations of the world. The aim of the study is to probe the therapeutic aspects of H. strigosum described in the traditional folklore history of medicines. Methods: In the present study, the dichloromethane crude extract of this plant was screened to explore the antimicrobial, cytotoxic, phytotoxic and antioxidant potential of H. strigosum. For antibacterial, antifungal and antioxidant activities, microplate alamar blue assay (MABA), agar tube dilution method and diphenyl picryl hydrazine (DPPH) radical-scavenging assay were used, respectively. The cytotoxic and phytotoxic potential were demonstrated by using brine shrimp lethality bioassay and Lemna minor assay. Results: The crude extract displayed positive cytotoxic activity in the brine shrimp lethality assay, with 23 of 30 shrimps dying at the concentration of 1000 µg/mL. It also showed moderate phytotoxic potential with percent inhibition of 50% at the concentration of 1000 µg/mL. The crude extract exhibited no significant antibacterial activity against Staphylococcus aureus, Shigella flexneri, Escherichia coli and Pseudomonas aeruginosa. Non-significant antifungal and radical scavenging activity was also shown by the dichloromethane crude extract. Conclusion: It is recommended that scientists focus on the identification and isolation of beneficial bioactive constituents with the help of advanced scientific methodologies that seems to be helpful in the synthesis of new therapeutic agents of desired interest. PMID:28930129

Selective capture and rapid identification of Panax notoginseng metabolites in rat faeces by the integration of magnetic molecularly imprinted polymers and high-performance liquid chromatography coupled with orbitrap mass spectrometry.

PubMed

Cai, Qizhi; Yang, Zaiyue; Chen, Ning; Zhou, Xuemin; Hong, Junli

2016-07-15

In the present work, an advanced pretreatment method magnetic molecular imprinted polymers-dispersive solid phase extraction (MMIPs-DSPE) combined with the high sensitivity LTQ-Orbitrap mass spectrometry was applied to the complicated metabolites analysis of Traditional Chinese Medicines (TCMs) in complex matrices. The ginsenoside Rb1 magnetic molecular imprinted polymers (Rb1-MMIPs) were successfully synthesized for specific recognition and selective enrichment of Panax notoginseng saponin metabolites in rat faeces. The polymers were prepared by using Fe3O4@SiO2 as the supporting material, APTES as the functional monomer and TEOS as the cross-linker. The Rb1-MMIPs showed quick separation (10.8 emu/g), large adsorption capacity (636μmol/g), high selectivity and fast binding kinetics (25min). Dispersion solid-phase extraction using Rb1-MMIPs (Rb1-MMIPs-DSPE) integrated with LTQ-Orbitrap MS was applied to fish out and identify saponin metabolites from rat faeces, and totally 58 related compounds were detected within 20min, including 26 PPD-group and 32 PPT-group notoginsenoside metabolites. Parallel tests showed that Rb1-MMIPs-DSPE obtained the lowest matrix effects of 0.98-14.84% and captured the largest number of structural analogues compared with traditional pretreatment methods organic solvent extraction (OSE) and solid phase extraction (SPE). Copyright © 2016 Elsevier B.V. All rights reserved.

Recent Modifications and Validation of QuEChERS-dSPE Coupled to LC-MS and GC-MS Instruments for Determination of Pesticide/Agrochemical Residues in Fruits and Vegetables: Review.

PubMed

Lawal, Abubakar; Wong, Richard Chee Seng; Tan, Guan Huat; Abdulra'uf, Lukman Bola; Alsharif, Ali Mohamed Ali

2018-04-21

Fruits and vegetables constitute a major type of food consumed daily apart from whole grains. Unfortunately, the residual deposits of pesticides in these products are becoming a major health concern for human consumption. Consequently, the outcome of the long-term accumulation of pesticide residues has posed many health issues to both humans and animals in the environment. However, the residues have previously been determined using conventionally known techniques, which include liquid-liquid extraction, solid-phase extraction (SPE) and the recently used liquid-phase microextraction techniques. Despite the positive technological effects of these methods, their limitations include; time-consuming, operational difficulty, use of toxic organic solvents, low selective property and expensive extraction setups, with shorter lifespan of instrumental performances. Thus, the potential and maximum use of these methods for pesticides residue determination has resulted in the urgent need for better techniques that will overcome the highlighted drawbacks. Alternatively, attention has been drawn recently towards the use of quick, easy, cheap, effective, rugged and safe technique (QuEChERS) coupled with dispersive solid-phase extraction (dSPE) to overcome the setback challenges experienced by the previous technologies. Conclusively, the reviewed QuEChERS-dSPE techniques and the recent cleanup modifications justifiably prove to be reliable for routine determination and monitoring the concentration levels of pesticide residues using advanced instruments such as high-performance liquid chromatography, liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry.

Review of the harvesting and extraction program within the National Alliance for Advanced Biofuels and Bioproducts

DOE PAGES

Marrone, Babetta L.; Lacey, Ronald E.; Anderson, Daniel B.; ...

2017-08-07

Energy-efficient and scalable harvesting and lipid extraction processes must be developed in order for the algal biofuels and bioproducts industry to thrive. The major challenge for harvesting is the handling of large volumes of cultivation water to concentrate low amounts of biomass. For lipid extraction, the major energy and cost drivers are associated with disrupting the algae cell wall and drying the biomass before solvent extraction of the lipids. Here we review the research and development conducted by the Harvesting and Extraction Team during the 3-year National Alliance for Advanced Biofuels and Bioproducts (NAABB) algal consortium project. The harvesting andmore » extraction team investigated five harvesting and three wet extraction technologies at lab bench scale for effectiveness, and conducted a techoeconomic study to evaluate their costs and energy efficiency compared to available baseline technologies. Based on this study, three harvesting technologies were selected for further study at larger scale. We evaluated the selected harvesting technologies: electrocoagulation, membrane filtration, and ultrasonic harvesting, in a field study at minimum scale of 100 L/h. None of the extraction technologies were determined to be ready for scale-up; therefore, an emerging extraction technology (wet solvent extraction) was selected from industry to provide scale-up data and capabilities to produce lipid and lipid-extracted materials for the NAABB program. One specialized extraction/adsorption technology was developed that showed promise for recovering high value co-products from lipid extracts. Overall, the NAABB Harvesting and Extraction Team improved the readiness level of several innovative, energy efficient technologies to integrate with algae production processes and captured valuable lessons learned about scale-up challenges.« less

Review of the harvesting and extraction program within the National Alliance for Advanced Biofuels and Bioproducts

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

Marrone, Babetta L.; Lacey, Ronald E.; Anderson, Daniel B.

Energy-efficient and scalable harvesting and lipid extraction processes must be developed in order for the algal biofuels and bioproducts industry to thrive. The major challenge for harvesting is the handling of large volumes of cultivation water to concentrate low amounts of biomass. For lipid extraction, the major energy and cost drivers are associated with disrupting the algae cell wall and drying the biomass before solvent extraction of the lipids. Here we review the research and development conducted by the Harvesting and Extraction Team during the 3-year National Alliance for Advanced Biofuels and Bioproducts (NAABB) algal consortium project. The harvesting andmore » extraction team investigated five harvesting and three wet extraction technologies at lab bench scale for effectiveness, and conducted a techoeconomic study to evaluate their costs and energy efficiency compared to available baseline technologies. Based on this study, three harvesting technologies were selected for further study at larger scale. We evaluated the selected harvesting technologies: electrocoagulation, membrane filtration, and ultrasonic harvesting, in a field study at minimum scale of 100 L/h. None of the extraction technologies were determined to be ready for scale-up; therefore, an emerging extraction technology (wet solvent extraction) was selected from industry to provide scale-up data and capabilities to produce lipid and lipid-extracted materials for the NAABB program. One specialized extraction/adsorption technology was developed that showed promise for recovering high value co-products from lipid extracts. Overall, the NAABB Harvesting and Extraction Team improved the readiness level of several innovative, energy efficient technologies to integrate with algae production processes and captured valuable lessons learned about scale-up challenges.« less

Computer-aided pulmonary image analysis in small animal models

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

Xu, Ziyue; Mansoor, Awais; Mollura, Daniel J.

Purpose: To develop an automated pulmonary image analysis framework for infectious lung diseases in small animal models. Methods: The authors describe a novel pathological lung and airway segmentation method for small animals. The proposed framework includes identification of abnormal imaging patterns pertaining to infectious lung diseases. First, the authors’ system estimates an expected lung volume by utilizing a regression function between total lung capacity and approximated rib cage volume. A significant difference between the expected lung volume and the initial lung segmentation indicates the presence of severe pathology, and invokes a machine learning based abnormal imaging pattern detection system next.more » The final stage of the proposed framework is the automatic extraction of airway tree for which new affinity relationships within the fuzzy connectedness image segmentation framework are proposed by combining Hessian and gray-scale morphological reconstruction filters. Results: 133 CT scans were collected from four different studies encompassing a wide spectrum of pulmonary abnormalities pertaining to two commonly used small animal models (ferret and rabbit). Sensitivity and specificity were greater than 90% for pathological lung segmentation (average dice similarity coefficient > 0.9). While qualitative visual assessments of airway tree extraction were performed by the participating expert radiologists, for quantitative evaluation the authors validated the proposed airway extraction method by using publicly available EXACT’09 data set. Conclusions: The authors developed a comprehensive computer-aided pulmonary image analysis framework for preclinical research applications. The proposed framework consists of automatic pathological lung segmentation and accurate airway tree extraction. The framework has high sensitivity and specificity; therefore, it can contribute advances in preclinical research in pulmonary diseases.« less

Acoustic emission signal processing for rolling bearing running state assessment using compressive sensing

NASA Astrophysics Data System (ADS)

Liu, Chang; Wu, Xing; Mao, Jianlin; Liu, Xiaoqin

2017-07-01

In the signal processing domain, there has been growing interest in using acoustic emission (AE) signals for the fault diagnosis and condition assessment instead of vibration signals, which has been advocated as an effective technique for identifying fracture, crack or damage. The AE signal has high frequencies up to several MHz which can avoid some signals interference, such as the parts of bearing (i.e. rolling elements, ring and so on) and other rotating parts of machine. However, acoustic emission signal necessitates advanced signal sampling capabilities and requests ability to deal with large amounts of sampling data. In this paper, compressive sensing (CS) is introduced as a processing framework, and then a compressive features extraction method is proposed. We use it for extracting the compressive features from compressively-sensed data directly, and also prove the energy preservation properties. First, we study the AE signals under the CS framework. The sparsity of AE signal of the rolling bearing is checked. The observation and reconstruction of signal is also studied. Second, we present a method of extraction AE compressive feature (AECF) from compressively-sensed data directly. We demonstrate the energy preservation properties and the processing of the extracted AECF feature. We assess the running state of the bearing using the AECF trend. The AECF trend of the running state of rolling bearings is consistent with the trend of traditional features. Thus, the method is an effective way to evaluate the running trend of rolling bearings. The results of the experiments have verified that the signal processing and the condition assessment based on AECF is simpler, the amount of data required is smaller, and the amount of computation is greatly reduced.

LiveWire interactive boundary extraction algorithm based on Haar wavelet transform and control point set direction search

NASA Astrophysics Data System (ADS)

Cheng, Jun; Zhang, Jun; Tian, Jinwen

2015-12-01

Based on deep analysis of the LiveWire interactive boundary extraction algorithm, a new algorithm focusing on improving the speed of LiveWire algorithm is proposed in this paper. Firstly, the Haar wavelet transform is carried on the input image, and the boundary is extracted on the low resolution image obtained by the wavelet transform of the input image. Secondly, calculating LiveWire shortest path is based on the control point set direction search by utilizing the spatial relationship between the two control points users provide in real time. Thirdly, the search order of the adjacent points of the starting node is set in advance. An ordinary queue instead of a priority queue is taken as the storage pool of the points when optimizing their shortest path value, thus reducing the complexity of the algorithm from O[n2] to O[n]. Finally, A region iterative backward projection method based on neighborhood pixel polling has been used to convert dual-pixel boundary of the reconstructed image to single-pixel boundary after Haar wavelet inverse transform. The algorithm proposed in this paper combines the advantage of the Haar wavelet transform and the advantage of the optimal path searching method based on control point set direction search. The former has fast speed of image decomposition and reconstruction and is more consistent with the texture features of the image and the latter can reduce the time complexity of the original algorithm. So that the algorithm can improve the speed in interactive boundary extraction as well as reflect the boundary information of the image more comprehensively. All methods mentioned above have a big role in improving the execution efficiency and the robustness of the algorithm.

Multivariate EMD and full spectrum based condition monitoring for rotating machinery

NASA Astrophysics Data System (ADS)

Zhao, Xiaomin; Patel, Tejas H.; Zuo, Ming J.

2012-02-01

Early assessment of machinery health condition is of paramount importance today. A sensor network with sensors in multiple directions and locations is usually employed for monitoring the condition of rotating machinery. Extraction of health condition information from these sensors for effective fault detection and fault tracking is always challenging. Empirical mode decomposition (EMD) is an advanced signal processing technology that has been widely used for this purpose. Standard EMD has the limitation in that it works only for a single real-valued signal. When dealing with data from multiple sensors and multiple health conditions, standard EMD faces two problems. First, because of the local and self-adaptive nature of standard EMD, the decomposition of signals from different sources may not match in either number or frequency content. Second, it may not be possible to express the joint information between different sensors. The present study proposes a method of extracting fault information by employing multivariate EMD and full spectrum. Multivariate EMD can overcome the limitations of standard EMD when dealing with data from multiple sources. It is used to extract the intrinsic mode functions (IMFs) embedded in raw multivariate signals. A criterion based on mutual information is proposed for selecting a sensitive IMF. A full spectral feature is then extracted from the selected fault-sensitive IMF to capture the joint information between signals measured from two orthogonal directions. The proposed method is first explained using simple simulated data, and then is tested for the condition monitoring of rotating machinery applications. The effectiveness of the proposed method is demonstrated through monitoring damage on the vane trailing edge of an impeller and rotor-stator rub in an experimental rotor rig.

[Recent advances in sample preparation methods of plant hormones].

PubMed

Wu, Qian; Wang, Lus; Wu, Dapeng; Duan, Chunfeng; Guan, Yafeng

2014-04-01

Plant hormones are a group of naturally occurring trace substances which play a crucial role in controlling the plant development, growth and environment response. With the development of the chromatography and mass spectroscopy technique, chromatographic analytical method has become a widely used way for plant hormone analysis. Among the steps of chromatographic analysis, sample preparation is undoubtedly the most vital one. Thus, a highly selective and efficient sample preparation method is critical for accurate identification and quantification of phytohormones. For the three major kinds of plant hormones including acidic plant hormones & basic plant hormones, brassinosteroids and plant polypeptides, the sample preparation methods are reviewed in sequence especially the recently developed methods. The review includes novel methods, devices, extractive materials and derivative reagents for sample preparation of phytohormones analysis. Especially, some related works of our group are included. At last, the future developments in this field are also prospected.

Measuring uncertainty by extracting fuzzy rules using rough sets

NASA Technical Reports Server (NTRS)

Worm, Jeffrey A.

1991-01-01

Despite the advancements in the computer industry in the past 30 years, there is still one major deficiency. Computers are not designed to handle terms where uncertainty is present. To deal with uncertainty, techniques other than classical logic must be developed. The methods are examined of statistical analysis, the Dempster-Shafer theory, rough set theory, and fuzzy set theory to solve this problem. The fundamentals of these theories are combined to possibly provide the optimal solution. By incorporating principles from these theories, a decision making process may be simulated by extracting two sets of fuzzy rules: certain rules and possible rules. From these rules a corresponding measure of how much these rules is believed is constructed. From this, the idea of how much a fuzzy diagnosis is definable in terms of a set of fuzzy attributes is studied.

Thermal stability analysis and modelling of advanced perpendicular magnetic tunnel junctions

NASA Astrophysics Data System (ADS)

Van Beek, Simon; Martens, Koen; Roussel, Philippe; Wu, Yueh Chang; Kim, Woojin; Rao, Siddharth; Swerts, Johan; Crotti, Davide; Linten, Dimitri; Kar, Gouri Sankar; Groeseneken, Guido

2018-05-01

STT-MRAM is a promising non-volatile memory for high speed applications. The thermal stability factor (Δ = Eb/kT) is a measure for the information retention time, and an accurate determination of the thermal stability is crucial. Recent studies show that a significant error is made using the conventional methods for Δ extraction. We investigate the origin of the low accuracy. To reduce the error down to 5%, 1000 cycles or multiple ramp rates are necessary. Furthermore, the thermal stabilities extracted from current switching and magnetic field switching appear to be uncorrelated and this cannot be explained by a macrospin model. Measurements at different temperatures show that self-heating together with a domain wall model can explain these uncorrelated Δ. Characterizing self-heating properties is therefore crucial to correctly determine the thermal stability.

A predictive control framework for optimal energy extraction of wind farms

NASA Astrophysics Data System (ADS)

Vali, M.; van Wingerden, J. W.; Boersma, S.; Petrović, V.; Kühn, M.

2016-09-01

This paper proposes an adjoint-based model predictive control for optimal energy extraction of wind farms. It employs the axial induction factor of wind turbines to influence their aerodynamic interactions through the wake. The performance index is defined here as the total power production of the wind farm over a finite prediction horizon. A medium-fidelity wind farm model is utilized to predict the inflow propagation in advance. The adjoint method is employed to solve the formulated optimization problem in a cost effective way and the first part of the optimal solution is implemented over the control horizon. This procedure is repeated at the next controller sample time providing the feedback into the optimization. The effectiveness and some key features of the proposed approach are studied for a two turbine test case through simulations.

Solid-phase microextraction technology for in vitro and in vivo metabolite analysis

PubMed Central

Zhang, Qihui; Zhou, Liandi; Chen, Hua; Wang, Chong-Zhi; Xia, Zhining; Yuan, Chun-Su

2016-01-01

Analysis of endogenous metabolites in biological samples may lead to the identification of biomarkers in metabolomics studies. To achieve accurate sample analysis, a combined method of continuous quick sampling and extraction is required for online compound detection. Solid-phase microextraction (SPME) integrates sampling, extraction and concentration into a single solvent-free step for chemical analysis. SPME has a number of advantages, including simplicity, high sensitivity and a relatively non-invasive nature. In this article, we reviewed SPME technology in in vitro and in vivo analyses of metabolites after the ingestion of herbal medicines, foods and pharmaceutical agents. The metabolites of microorganisms in dietary supplements and in the gastrointestinal tract will also be examined. As a promising technology in biomedical and pharmaceutical research, SPME and its future applications will depend on advances in analytical technologies and material science. PMID:27695152

Thiazoline peptides and a tris-phenethyl urea from Didemnum molle with anti-HIV activity.

PubMed

Lu, Zhenyu; Harper, Mary Kay; Pond, Christopher D; Barrows, Louis R; Ireland, Chris M; Van Wagoner, Ryan M

2012-08-24

As part of our screening for anti-HIV agents from marine invertebrates, the MeOH extract of Didemnum molle was tested and showed moderate in vitro anti-HIV activity. Bioassay-guided fractionation of a large-scale extract allowed the identification of two new cyclopeptides, mollamides E and F (1 and 2), and one new tris-phenethyl urea, molleurea A (3). The absolute configurations were established using the advanced Marfey's method. The three compounds were evaluated for anti-HIV activity in both an HIV integrase inhibition assay and a cytoprotective cell-based assay. Compound 2 was active in both assays with IC(50) values of 39 and 78 μM, respectively. Compound 3 was active only in the cytoprotective cell-based assay, with an IC(50) value of 60 μM.

University of Washington's eScience Institute Promotes New Training and Career Pathways in Data Science

NASA Astrophysics Data System (ADS)

Stone, S.; Parker, M. S.; Howe, B.; Lazowska, E.

2015-12-01

Rapid advances in technology are transforming nearly every field from "data-poor" to "data-rich." The ability to extract knowledge from this abundance of data is the cornerstone of 21st century discovery. At the University of Washington eScience Institute, our mission is to engage researchers across disciplines in developing and applying advanced computational methods and tools to real world problems in data-intensive discovery. Our research team consists of individuals with diverse backgrounds in domain sciences such as astronomy, oceanography and geology, with complementary expertise in advanced statistical and computational techniques such as data management, visualization, and machine learning. Two key elements are necessary to foster careers in data science: individuals with cross-disciplinary training in both method and domain sciences, and career paths emphasizing alternative metrics for advancement. We see persistent and deep-rooted challenges for the career paths of people whose skills, activities and work patterns don't fit neatly into the traditional roles and success metrics of academia. To address these challenges the eScience Institute has developed training programs and established new career opportunities for data-intensive research in academia. Our graduate students and post-docs have mentors in both a methodology and an application field. They also participate in coursework and tutorials to advance technical skill and foster community. Professional Data Scientist positions were created to support research independence while encouraging the development and adoption of domain-specific tools and techniques. The eScience Institute also supports the appointment of faculty who are innovators in developing and applying data science methodologies to advance their field of discovery. Our ultimate goal is to create a supportive environment for data science in academia and to establish global recognition for data-intensive discovery across all fields.

Beyond HRV: attractor reconstruction using the entire cardiovascular waveform data for novel feature extraction.

PubMed

Aston, Philip J; Christie, Mark I; Huang, Ying H; Nandi, Manasi

2018-03-01

Advances in monitoring technology allow blood pressure waveforms to be collected at sampling frequencies of 250-1000 Hz for long time periods. However, much of the raw data are under-analysed. Heart rate variability (HRV) methods, in which beat-to-beat interval lengths are extracted and analysed, have been extensively studied. However, this approach discards the majority of the raw data. Our aim is to detect changes in the shape of the waveform in long streams of blood pressure data. Our approach involves extracting key features from large complex data sets by generating a reconstructed attractor in a three-dimensional phase space using delay coordinates from a window of the entire raw waveform data. The naturally occurring baseline variation is removed by projecting the attractor onto a plane from which new quantitative measures are obtained. The time window is moved through the data to give a collection of signals which relate to various aspects of the waveform shape. This approach enables visualisation and quantification of changes in the waveform shape and has been applied to blood pressure data collected from conscious unrestrained mice and to human blood pressure data. The interpretation of the attractor measures is aided by the analysis of simple artificial waveforms. We have developed and analysed a new method for analysing blood pressure data that uses all of the waveform data and hence can detect changes in the waveform shape that HRV methods cannot, which is confirmed with an example, and hence our method goes 'beyond HRV'.

Beyond HRV: attractor reconstruction using the entire cardiovascular waveform data for novel feature extraction

PubMed Central

Aston, Philip J; Christie, Mark I; Huang, Ying H; Nandi, Manasi

2018-01-01

Abstract Advances in monitoring technology allow blood pressure waveforms to be collected at sampling frequencies of 250–1000 Hz for long time periods. However, much of the raw data are under-analysed. Heart rate variability (HRV) methods, in which beat-to-beat interval lengths are extracted and analysed, have been extensively studied. However, this approach discards the majority of the raw data. Objective: Our aim is to detect changes in the shape of the waveform in long streams of blood pressure data. Approach: Our approach involves extracting key features from large complex data sets by generating a reconstructed attractor in a three-dimensional phase space using delay coordinates from a window of the entire raw waveform data. The naturally occurring baseline variation is removed by projecting the attractor onto a plane from which new quantitative measures are obtained. The time window is moved through the data to give a collection of signals which relate to various aspects of the waveform shape. Main results: This approach enables visualisation and quantification of changes in the waveform shape and has been applied to blood pressure data collected from conscious unrestrained mice and to human blood pressure data. The interpretation of the attractor measures is aided by the analysis of simple artificial waveforms. Significance: We have developed and analysed a new method for analysing blood pressure data that uses all of the waveform data and hence can detect changes in the waveform shape that HRV methods cannot, which is confirmed with an example, and hence our method goes ‘beyond HRV’. PMID:29350622

Effective diagnosis of Alzheimer's disease by means of large margin-based methodology.

PubMed

Chaves, Rosa; Ramírez, Javier; Górriz, Juan M; Illán, Ignacio A; Gómez-Río, Manuel; Carnero, Cristobal

2012-07-31

Functional brain images such as Single-Photon Emission Computed Tomography (SPECT) and Positron Emission Tomography (PET) have been widely used to guide the clinicians in the Alzheimer's Disease (AD) diagnosis. However, the subjectivity involved in their evaluation has favoured the development of Computer Aided Diagnosis (CAD) Systems. It is proposed a novel combination of feature extraction techniques to improve the diagnosis of AD. Firstly, Regions of Interest (ROIs) are selected by means of a t-test carried out on 3D Normalised Mean Square Error (NMSE) features restricted to be located within a predefined brain activation mask. In order to address the small sample-size problem, the dimension of the feature space was further reduced by: Large Margin Nearest Neighbours using a rectangular matrix (LMNN-RECT), Principal Component Analysis (PCA) or Partial Least Squares (PLS) (the two latter also analysed with a LMNN transformation). Regarding the classifiers, kernel Support Vector Machines (SVMs) and LMNN using Euclidean, Mahalanobis and Energy-based metrics were compared. Several experiments were conducted in order to evaluate the proposed LMNN-based feature extraction algorithms and its benefits as: i) linear transformation of the PLS or PCA reduced data, ii) feature reduction technique, and iii) classifier (with Euclidean, Mahalanobis or Energy-based methodology). The system was evaluated by means of k-fold cross-validation yielding accuracy, sensitivity and specificity values of 92.78%, 91.07% and 95.12% (for SPECT) and 90.67%, 88% and 93.33% (for PET), respectively, when a NMSE-PLS-LMNN feature extraction method was used in combination with a SVM classifier, thus outperforming recently reported baseline methods. All the proposed methods turned out to be a valid solution for the presented problem. One of the advances is the robustness of the LMNN algorithm that not only provides higher separation rate between the classes but it also makes (in combination with NMSE and PLS) this rate variation more stable. In addition, their generalization ability is another advance since several experiments were performed on two image modalities (SPECT and PET).

Advanced airway management in hoist and longline operations in mountain HEMS - considerations in austere environments: a narrative review This review is endorsed by the International Commission for Mountain Emergency Medicine (ICAR MEDCOM).

PubMed

Pietsch, Urs; Knapp, Jürgen; Kreuzer, Oliver; Ney, Ludwig; Strapazzon, Giacomo; Lischke, Volker; Albrecht, Roland; Phillips, Patrick; Rauch, Simon

2018-04-03

Providing sufficient oxygenation and ventilation is of paramount importance for the survival of emergency patients. Therefore, advanced airway management is one of the core tasks for every rescue team. Endotracheal intubation is the gold standard to secure the airway in the prehospital setting. This review aims to highlight special considerations for advanced airway management preceding human external cargo (HEC) evacuations. We systematically searched MEDLINE, EMBASE, and PubMed in August 2017 for articles on airway management and ventilation in patients before hoist or longline operation in HEMS. Relevant reference lists were hand-searched. Three articles with regard to advanced airway management and five articles concerning the epidemiology of advanced airway management in hoist or longline rescue missions were included. We found one case report regarding ventilation during hoist operations. The exact incidence of advanced airway management before evacuation of a patient by HEC is unknown but seems to be very low (< 5%). There are several hazards which can impede mechanical ventilation of patients during HEC extractions: loss of equipment, hyperventilation, inability to ventilate and consequent hypoxia, as well as inadequacy of monitoring. Advanced airway management prior to HEC operation is rarely performed. If intubation before helicopter hoist operations (HHO) and human cargo sling (HCS) extraction is considered by the rescue team, a risk/benefit analysis should be performed and a clear standard operating procedure (SOP) should be defined. Continuous and rigorous training including the whole crew is required. An international registry on airway management during HEC extraction would be desirable.

An Investigation of Aggregation in Synergistic Solvent Extraction Systems

NASA Astrophysics Data System (ADS)

Jackson, Andy Steven

With an increasing focus on anthropogenic climate change, nuclear reactors present an attractive option for base load power generation with regard to air pollution and carbon emissions, especially when compared with traditional fossil fuel based options. However, used nuclear fuel (UNF) is highly radiotoxic and contains minor actinides (americium and curium) which remain more radiotoxic than natural uranium ore for hundreds of thousands of years, presenting a challenge for long-term storage . Advanced nuclear fuel recycling can reduce this required storage time to thousands of years by removing the highly radiotoxic minor actinides. Many advanced separation schemes have been proposed to achieve this separation but none have been implemented to date. A key feature among many proposed schemes is the use of more than one extraction reagent in a single extraction phase, which can lead to the phenomenon known as "synergism" in which the extraction efficiency for a combination of the reagents is greater than that of the individual extractants alone. This feature is not well understood for many systems and a comprehensive picture of the mechanism behind synergism does not exist. There are several proposed mechanisms for synergism though none have been used to model multiple extraction systems. This work examines several proposed advanced extractant combinations which exhibit synergism: 2-bromodecanoic acid (BDA) with 2,2':6',2"-terpyridine (TERPY), tri-n-butylphosphine oxide (TPBO) with 2-thenoyltrifluoro acetone (HTTA), and dinonylnaphthalene sulfonic acid (HDNNS) with 5,8-diethyl-7-hydroxy-dodecan-6-oxime (LIX). We examine two proposed synergistic mechanisms involving and attempt to verify the ability of these mechanisms to predict the extraction behavior of the chosen systems. These are a reverse micellar catalyzed extraction model and a mixed complex formation model. Neither was able to effectively predict the synergistic behavior of the systems. We further examine these systems for the presence of large reverse micellar aggregates and thermodynamic signatures of aggregation. Behaviors differed widely from system to system, suggesting the possibility of more than one mechanism being responsible for similar observed extraction trends.

A fast and efficient method for device level layout analysis

NASA Astrophysics Data System (ADS)

Dong, YaoQi; Zou, Elaine; Pang, Jenny; Huang, Lucas; Yang, Legender; Zhang, Chunlei; Du, Chunshan; Hu, Xinyi; Wan, Qijian

2017-03-01

There is an increasing demand for device level layout analysis, especially as technology advances. The analysis is to study standard cells by extracting and classifying critical dimension parameters. There are couples of parameters to extract, like channel width, length, gate to active distance, and active to adjacent active distance, etc. for 14nm technology, there are some other parameters that are cared about. On the one hand, these parameters are very important for studying standard cell structures and spice model development with the goal of improving standard cell manufacturing yield and optimizing circuit performance; on the other hand, a full chip device statistics analysis can provide useful information to diagnose the yield issue. Device analysis is essential for standard cell customization and enhancements and manufacturability failure diagnosis. Traditional parasitic parameters extraction tool like Calibre xRC is powerful but it is not sufficient for this device level layout analysis application as engineers would like to review, classify and filter out the data more easily. This paper presents a fast and efficient method based on Calibre equation-based DRC (eqDRC). Equation-based DRC extends the traditional DRC technology to provide a flexible programmable modeling engine which allows the end user to define grouped multi-dimensional feature measurements using flexible mathematical expressions. This paper demonstrates how such an engine and its programming language can be used to implement critical device parameter extraction. The device parameters are extracted and stored in a DFM database which can be processed by Calibre YieldServer. YieldServer is data processing software that lets engineers query, manipulate, modify, and create data in a DFM database. These parameters, known as properties in eqDRC language, can be annotated back to the layout for easily review. Calibre DesignRev can create a HTML formatted report of the results displayed in Calibre RVE which makes it easy to share results among groups. This method has been proven and used in SMIC PDE team and SPICE team.

A New Method for Calculating Counts in Cells

NASA Astrophysics Data System (ADS)

Szapudi, István

1998-04-01

In the near future, a new generation of CCD-based galaxy surveys will enable high-precision determination of the N-point correlation functions. The resulting information will help to resolve the ambiguities associated with two-point correlation functions, thus constraining theories of structure formation, biasing, and Gaussianity of initial conditions independently of the value of Ω. As one of the most successful methods of extracting the amplitude of higher order correlations is based on measuring the distribution of counts in cells, this work presents an advanced way of measuring it with unprecedented accuracy. Szapudi & Colombi identified the main sources of theoretical errors in extracting counts in cells from galaxy catalogs. One of these sources, termed as measurement error, stems from the fact that conventional methods use a finite number of sampling cells to estimate counts in cells. This effect can be circumvented by using an infinite number of cells. This paper presents an algorithm, which in practice achieves this goal; that is, it is equivalent to throwing an infinite number of sampling cells in finite time. The errors associated with sampling cells are completely eliminated by this procedure, which will be essential for the accurate analysis of future surveys.

On-cartridge derivatisation using a calixarene solid-phase extraction sorbent for facile, sensitive and fast determination of formaldehyde in beer.

PubMed

Deng, Zhifen; Hu, Kai; Zhang, Yongming; Zhao, Wenjie; Wang, Fei; Guo, Ling; Zhang, Wenfen; He, Juan; Huang, Yanjie; Zhang, Shusheng

2016-11-15

This work demonstrates the successful application of an on-cartridge derivatisation procedure for facile, fast and sensitive determination of formaldehyde in beer by HPLC-UV. The derivatisation and solid-phase extraction (SPE) were integrated into a novel calixarene SPE sorbent: tetraazacalix[2]arene[2]triazine bonded silica gel. Specifically, 2,4-dinitrophenylhydrazine was adsorbed onto the sorbent in advance, based on the charge-transfer interaction between the macrocyclic molecule and nitrobenzenes. The method was optimised and validated: under the optimal conditions of derivatisation, SPE and HPLC separation, good linearity was obtained in the range of 0.080-3.2μgmL(-1) with a correlation coefficient of 0.9939, the limit of detection was 3.0ngmL(-1) (S/N=3), the limit of quantification was 10ngmL(-1) (S/N=10), and the recovery level using this method was desirable at 75-84%. The developed method was successfully applied to determine formaldehyde content in real beer samples; the results were in the range of 0.11-1.1μgmL(-1). Copyright © 2016. Published by Elsevier Ltd.

System identification methods for aircraft flight control development and validation

NASA Technical Reports Server (NTRS)

Tischler, Mark B.

1995-01-01

System-identification methods compose a mathematical model, or series of models, from measurements of inputs and outputs of dynamic systems. The extracted models allow the characterization of the response of the overall aircraft or component subsystem behavior, such as actuators and on-board signal processing algorithms. This paper discusses the use of frequency-domain system-identification methods for the development and integration of aircraft flight-control systems. The extraction and analysis of models of varying complexity from nonparametric frequency-responses to transfer-functions and high-order state-space representations is illustrated using the Comprehensive Identification from FrEquency Responses (CIFER) system-identification facility. Results are presented for test data of numerous flight and simulation programs at the Ames Research Center including rotorcraft, fixed-wing aircraft, advanced short takeoff and vertical landing (ASTOVL), vertical/short takeoff and landing (V/STOL), tiltrotor aircraft, and rotor experiments in the wind tunnel. Excellent system characterization and dynamic response prediction is achieved for this wide class of systems. Examples illustrate the role of system-identification technology in providing an integrated flow of dynamic response data around the entire life-cycle of aircraft development from initial specifications, through simulation and bench testing, and into flight-test optimization.

Multivariate data analysis and machine learning in Alzheimer's disease with a focus on structural magnetic resonance imaging.

PubMed

Falahati, Farshad; Westman, Eric; Simmons, Andrew

2014-01-01

Machine learning algorithms and multivariate data analysis methods have been widely utilized in the field of Alzheimer's disease (AD) research in recent years. Advances in medical imaging and medical image analysis have provided a means to generate and extract valuable neuroimaging information. Automatic classification techniques provide tools to analyze this information and observe inherent disease-related patterns in the data. In particular, these classifiers have been used to discriminate AD patients from healthy control subjects and to predict conversion from mild cognitive impairment to AD. In this paper, recent studies are reviewed that have used machine learning and multivariate analysis in the field of AD research. The main focus is on studies that used structural magnetic resonance imaging (MRI), but studies that included positron emission tomography and cerebrospinal fluid biomarkers in addition to MRI are also considered. A wide variety of materials and methods has been employed in different studies, resulting in a range of different outcomes. Influential factors such as classifiers, feature extraction algorithms, feature selection methods, validation approaches, and cohort properties are reviewed, as well as key MRI-based and multi-modal based studies. Current and future trends are discussed.

A Review of Classification Techniques of EMG Signals during Isotonic and Isometric Contractions

PubMed Central

Nazmi, Nurhazimah; Abdul Rahman, Mohd Azizi; Yamamoto, Shin-Ichiroh; Ahmad, Siti Anom; Zamzuri, Hairi; Mazlan, Saiful Amri

2016-01-01

In recent years, there has been major interest in the exposure to physical therapy during rehabilitation. Several publications have demonstrated its usefulness in clinical/medical and human machine interface (HMI) applications. An automated system will guide the user to perform the training during rehabilitation independently. Advances in engineering have extended electromyography (EMG) beyond the traditional diagnostic applications to also include applications in diverse areas such as movement analysis. This paper gives an overview of the numerous methods available to recognize motion patterns of EMG signals for both isotonic and isometric contractions. Various signal analysis methods are compared by illustrating their applicability in real-time settings. This paper will be of interest to researchers who would like to select the most appropriate methodology in classifying motion patterns, especially during different types of contractions. For feature extraction, the probability density function (PDF) of EMG signals will be the main interest of this study. Following that, a brief explanation of the different methods for pre-processing, feature extraction and classifying EMG signals will be compared in terms of their performance. The crux of this paper is to review the most recent developments and research studies related to the issues mentioned above. PMID:27548165

Health requirements for advanced coal extraction systems

NASA Technical Reports Server (NTRS)

Zimmerman, W. F.

1980-01-01

Health requirements were developed as long range goals for future advanced coal extraction systems which would be introduced into the market in the year 2000. The goal of the requirements is that underground coal miners work in an environment that is as close as possible to the working conditions of the general population, that they do not exceed mortality and morbidity rates resulting from lung diseases that are comparable to those of the general population, and that their working conditions comply as closely as possible to those of other industries as specified by OSHA regulations. A brief technique for evaluating whether proposed advanced systems meet these safety requirements is presented, as well as a discussion of the costs of respiratory disability compensation.

Gas Chromatic Mass Spectrometer

NASA Technical Reports Server (NTRS)

Wey, Chowen

1995-01-01

Gas chromatograph/mass spectrometer (GC/MS) used to measure and identify combustion species present in trace concentration. Advanced extractive diagnostic method measures to parts per billion (PPB), as well as differentiates between different types of hydrocarbons. Applicable for petrochemical, waste incinerator, diesel transporation, and electric utility companies in accurately monitoring types of hydrocarbon emissions generated by fuel combustion, in order to meet stricter environmental requirements. Other potential applications include manufacturing processes requiring precise detection of toxic gaseous chemicals, biomedical applications requiring precise identification of accumulative gaseous species, and gas utility operations requiring high-sensitivity leak detection.

Ion thruster design and analysis

NASA Technical Reports Server (NTRS)

Kami, S.; Schnelker, D. E.

1976-01-01

Questions concerning the mechanical design of a thruster are considered, taking into account differences in the design of an 8-cm and a 30-cm model. The components of a thruster include the thruster shell assembly, the ion extraction electrode assembly, the cathode isolator vaporizer assembly, the neutralizer isolator vaporizer assembly, ground screen and mask, and the main isolator vaporizer assembly. Attention is given to the materials used in thruster fabrication, the advanced manufacturing methods used, details of thruster performance, an evaluation of thruster life, structural and thermal design considerations, and questions of reliability and quality assurance.

Machine learning and computer vision approaches for phenotypic profiling.

PubMed

Grys, Ben T; Lo, Dara S; Sahin, Nil; Kraus, Oren Z; Morris, Quaid; Boone, Charles; Andrews, Brenda J

2017-01-02

With recent advances in high-throughput, automated microscopy, there has been an increased demand for effective computational strategies to analyze large-scale, image-based data. To this end, computer vision approaches have been applied to cell segmentation and feature extraction, whereas machine-learning approaches have been developed to aid in phenotypic classification and clustering of data acquired from biological images. Here, we provide an overview of the commonly used computer vision and machine-learning methods for generating and categorizing phenotypic profiles, highlighting the general biological utility of each approach. © 2017 Grys et al.

Olive Tree (Olea europeae L.) Leaves: Importance and Advances in the Analysis of Phenolic Compounds

PubMed Central

Abaza, Leila; Taamalli, Amani; Nsir, Houda; Zarrouk, Mokhtar

2015-01-01

Phenolic compounds are becoming increasingly popular because of their potential role in contributing to human health. Experimental evidence obtained from human and animal studies demonstrate that phenolic compounds from Olea europaea leaves have biological activities which may be important in the reduction in risk and severity of certain chronic diseases. Therefore, an accurate profiling of phenolics is a crucial issue. In this article, we present a review work on current treatment and analytical methods used to extract, identify, and/or quantify phenolic compounds in olive leaves. PMID:26783953

Machine learning and computer vision approaches for phenotypic profiling

PubMed Central

Morris, Quaid

2017-01-01

With recent advances in high-throughput, automated microscopy, there has been an increased demand for effective computational strategies to analyze large-scale, image-based data. To this end, computer vision approaches have been applied to cell segmentation and feature extraction, whereas machine-learning approaches have been developed to aid in phenotypic classification and clustering of data acquired from biological images. Here, we provide an overview of the commonly used computer vision and machine-learning methods for generating and categorizing phenotypic profiles, highlighting the general biological utility of each approach. PMID:27940887

Basic EMC (Electromagnetic Compatibility) Technology Advancement for C3 Systems, Macromodeling of Digital Circuits. Volume 2B.

DTIC Science & Technology

1984-04-01

dependent source to multiply a ramp by a unit sinusoid. Using this method, data could be extracted from a single run to show the magnitude of the...IHPUT VOLTAGE SOURCES VAC 1 0 0V VAl 2 0 0V VA2 3 0 0V VA3 4 0 PULSE(OV 3V ONSD 2NSR 2NSF 198NSPW) VB0 5 0 OV VB1 6 0 OV VB2 7 0 CV VB3 8 0 PULSE

HTP-NLP: A New NLP System for High Throughput Phenotyping.

PubMed

Schlegel, Daniel R; Crowner, Chris; Lehoullier, Frank; Elkin, Peter L

2017-01-01

Secondary use of clinical data for research requires a method to quickly process the data so that researchers can quickly extract cohorts. We present two advances in the High Throughput Phenotyping NLP system which support the aim of truly high throughput processing of clinical data, inspired by a characterization of the linguistic properties of such data. Semantic indexing to store and generalize partially-processed results and the use of compositional expressions for ungrammatical text are discussed, along with a set of initial timing results for the system.

Novel Binders and Methods for Agglomeration of Ore

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

S. K. Kawatra; T. C. Eisele; K. A. Lewandowski

2006-12-31

Many metal extraction operations, such as leaching of copper, leaching of precious metals, and reduction of metal oxides to metal in high-temperature furnaces, require agglomeration of ore to ensure that reactive liquids or gases are evenly distributed throughout the ore being processed. Agglomeration of ore into coarse, porous masses achieves this even distribution of fluids by preventing fine particles from migrating and clogging the spaces and channels between the larger ore particles. Binders are critically necessary to produce agglomerates that will not break down during processing. However, for many important metal extraction processes there are no binders known that willmore » work satisfactorily. Primary examples of this are copper heap leaching, where there are no binders that will work in the acidic environment encountered in this process, and advanced ironmaking processes, where binders must function satisfactorily over an extraordinarily large range of temperatures (from room temperature up to over 1200 C). As a result, operators of many facilities see a large loss of process efficiency due to their inability to take advantage of agglomeration. The large quantities of ore that must be handled in metal extraction processes also means that the binder must be inexpensive and useful at low dosages to be economical. The acid-resistant binders and agglomeration procedures developed in this project will also be adapted for use in improving the energy efficiency and performance of a broad range of mineral agglomeration applications, particularly heap leaching and advanced primary ironmaking. This project has identified several acid-resistant binders and agglomeration procedures that can be used for improving the energy efficiency of heap leaching, by preventing the ''ponding'' and ''channeling'' effects that currently cause reduced recovery and extended leaching cycle times. Methods have also been developed for iron ore processing which are intended to improve the performance of pellet binders, and have directly saved energy by increasing filtration rates of the pelletization feed by as much as 23%.« less

Layout-aware text extraction from full-text PDF of scientific articles.

PubMed

Ramakrishnan, Cartic; Patnia, Abhishek; Hovy, Eduard; Burns, Gully Apc

2012-05-28

The Portable Document Format (PDF) is the most commonly used file format for online scientific publications. The absence of effective means to extract text from these PDF files in a layout-aware manner presents a significant challenge for developers of biomedical text mining or biocuration informatics systems that use published literature as an information source. In this paper we introduce the 'Layout-Aware PDF Text Extraction' (LA-PDFText) system to facilitate accurate extraction of text from PDF files of research articles for use in text mining applications. Our paper describes the construction and performance of an open source system that extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles and is meant as a baseline for further experiments into more advanced extraction methods that handle multi-modal content, such as images and graphs. The system works in a three-stage process: (1) Detecting contiguous text blocks using spatial layout processing to locate and identify blocks of contiguous text, (2) Classifying text blocks into rhetorical categories using a rule-based method and (3) Stitching classified text blocks together in the correct order resulting in the extraction of text from section-wise grouped blocks. We show that our system can identify text blocks and classify them into rhetorical categories with Precision1 = 0.96% Recall = 0.89% and F1 = 0.91%. We also present an evaluation of the accuracy of the block detection algorithm used in step 2. Additionally, we have compared the accuracy of the text extracted by LA-PDFText to the text from the Open Access subset of PubMed Central. We then compared this accuracy with that of the text extracted by the PDF2Text system, 2commonly used to extract text from PDF. Finally, we discuss preliminary error analysis for our system and identify further areas of improvement. LA-PDFText is an open-source tool for accurately extracting text from full-text scientific articles. The release of the system is available at http://code.google.com/p/lapdftext/.

Classification of EEG Signals Based on Pattern Recognition Approach.

PubMed

Amin, Hafeez Ullah; Mumtaz, Wajid; Subhani, Ahmad Rauf; Saad, Mohamad Naufal Mohamad; Malik, Aamir Saeed

2017-01-01

Feature extraction is an important step in the process of electroencephalogram (EEG) signal classification. The authors propose a "pattern recognition" approach that discriminates EEG signals recorded during different cognitive conditions. Wavelet based feature extraction such as, multi-resolution decompositions into detailed and approximate coefficients as well as relative wavelet energy were computed. Extracted relative wavelet energy features were normalized to zero mean and unit variance and then optimized using Fisher's discriminant ratio (FDR) and principal component analysis (PCA). A high density EEG dataset validated the proposed method (128-channels) by identifying two classifications: (1) EEG signals recorded during complex cognitive tasks using Raven's Advance Progressive Metric (RAPM) test; (2) EEG signals recorded during a baseline task (eyes open). Classifiers such as, K-nearest neighbors (KNN), Support Vector Machine (SVM), Multi-layer Perceptron (MLP), and Naïve Bayes (NB) were then employed. Outcomes yielded 99.11% accuracy via SVM classifier for coefficient approximations (A5) of low frequencies ranging from 0 to 3.90 Hz. Accuracy rates for detailed coefficients were 98.57 and 98.39% for SVM and KNN, respectively; and for detailed coefficients (D5) deriving from the sub-band range (3.90-7.81 Hz). Accuracy rates for MLP and NB classifiers were comparable at 97.11-89.63% and 91.60-81.07% for A5 and D5 coefficients, respectively. In addition, the proposed approach was also applied on public dataset for classification of two cognitive tasks and achieved comparable classification results, i.e., 93.33% accuracy with KNN. The proposed scheme yielded significantly higher classification performances using machine learning classifiers compared to extant quantitative feature extraction. These results suggest the proposed feature extraction method reliably classifies EEG signals recorded during cognitive tasks with a higher degree of accuracy.

Classification of EEG Signals Based on Pattern Recognition Approach

PubMed Central

Amin, Hafeez Ullah; Mumtaz, Wajid; Subhani, Ahmad Rauf; Saad, Mohamad Naufal Mohamad; Malik, Aamir Saeed

2017-01-01

Feature extraction is an important step in the process of electroencephalogram (EEG) signal classification. The authors propose a “pattern recognition” approach that discriminates EEG signals recorded during different cognitive conditions. Wavelet based feature extraction such as, multi-resolution decompositions into detailed and approximate coefficients as well as relative wavelet energy were computed. Extracted relative wavelet energy features were normalized to zero mean and unit variance and then optimized using Fisher's discriminant ratio (FDR) and principal component analysis (PCA). A high density EEG dataset validated the proposed method (128-channels) by identifying two classifications: (1) EEG signals recorded during complex cognitive tasks using Raven's Advance Progressive Metric (RAPM) test; (2) EEG signals recorded during a baseline task (eyes open). Classifiers such as, K-nearest neighbors (KNN), Support Vector Machine (SVM), Multi-layer Perceptron (MLP), and Naïve Bayes (NB) were then employed. Outcomes yielded 99.11% accuracy via SVM classifier for coefficient approximations (A5) of low frequencies ranging from 0 to 3.90 Hz. Accuracy rates for detailed coefficients were 98.57 and 98.39% for SVM and KNN, respectively; and for detailed coefficients (D5) deriving from the sub-band range (3.90–7.81 Hz). Accuracy rates for MLP and NB classifiers were comparable at 97.11–89.63% and 91.60–81.07% for A5 and D5 coefficients, respectively. In addition, the proposed approach was also applied on public dataset for classification of two cognitive tasks and achieved comparable classification results, i.e., 93.33% accuracy with KNN. The proposed scheme yielded significantly higher classification performances using machine learning classifiers compared to extant quantitative feature extraction. These results suggest the proposed feature extraction method reliably classifies EEG signals recorded during cognitive tasks with a higher degree of accuracy. PMID:29209190

The effect of deodorization on volatile compositions of fucoidan extracted from brown seaweed (Sargassum sp.)

NASA Astrophysics Data System (ADS)

Khalafu, Sharifah Habibah Syed; Mustapha, Wan Aida Wan; Lim, Seng Joe; Maskat, Mohamad Yusof

2016-11-01

Fucoidan is a biologically active polysaccharide that were made up of complex mixture of fucose, sulfate and uronic acid. This study was conducted to identify the volatile compositions of crude fucoidan and deodorized fucoidans extracted from brown seaweed Sargassum sp. (Fsar). The volatile compositions was also compared with a standard commercial fucoidan (Fysk). Fucoidan was extracted from Sargassum sp. originated in coastal area of Indonesia, by using a low pH acid extraction method. Approximately 20 mL of 1% freshly extracted fucoidan was then subjected to deodorization process by using three different method i.e., by treating it with 10 g activated carbon (Fac), 0.4 g ion exchange resin, Amberlite 67 (Fresin) and 2 mL of 1% calcium carbonate (FCaCO3) and incubated for 12 hrs before further analysis. Forty-six volatile compounds were successfully identified in all of the five samples by using Headspace-Solid Phase Microextraction (HS-SPME) and analysed by using Gas Chromatography Mass Spectrometer (GCMS). In Fsar, 72% of the total volatile constituents were identified as aromatic hydrocarbons, 23% hydrocarbons and 5% alcohols. In Fysk, all compounds detected are in group hydrocarbons. In Fsar, all of the compounds identified were classified as odor active compounds which had a contribution to unpleasant odor in fucoidan. After deodorization, 72% of aromatic hydrocarbons detected in Fsar were reported to be absent in all deodorized fucoidans. Both Fresin and FCaCO3 showed a reduction in peak area percentages of phenol, 2,4-bis (1,1-dimethylethyl)- from Fsar (1.30%) to 0.79 and 1.07% respectively. Meanwhile in Fac, no presence of phenol, 2,4-bis (1,1-dimethylethyl) was reported. These findings are essential to propel the advancement of research in deodorization technologies of marine products, especially fucoidans.

Molecularly imprinted polymers for the detection of illegal drugs and additives: a review.

PubMed

Xiao, Deli; Jiang, Yue; Bi, Yanping

2018-04-04

This review (with 154 refs.) describes the current status of using molecularly imprinted polymers in the extraction and quantitation of illicit drugs and additives. The review starts with an introduction into some synthesis methods (lump MIPs, spherical MIPs, surface imprinting) of MIPs using illicit drugs and additives as templates. The next section covers applications, with subsections on the detection of illegal additives in food, of doping in sports, and of illicit addictive drugs. A particular focus is directed towards current limitations and challenges, on the optimization of methods for preparation of MIPs, their applicability to aqueous samples, the leakage of template molecules, and the identification of the best balance between adsorption capacity and selectivity factor. At last, the need for convincing characterization methods, the lack of uniform parameters for defining selectivity, and the merits and demerits of MIPs prepared using nanomaterials are addressed. Strategies are suggested to solve existing problems, and future developments are discussed with respect to a more widespread use in relevant fields. Graphical abstract This review gives a comprehensive overview of the advances made in molecularly imprinting of polymers for use in the extraction and quantitation of illicit drugs and additives. Methods for syntheses, highlighted applications, limitations and current challenges are specifically addressed.

Advances in Surface Plasmon Resonance Imaging allowing for quantitative measurement of laterally heterogeneous samples

NASA Astrophysics Data System (ADS)

Raegen, Adam; Reiter, Kyle; Clarke, Anthony; Lipkowski, Jacek; Dutcher, John

2012-02-01

The Surface Plasmon Resonance (SPR) phenomenon is routinely exploited to qualitatively probe changes to materials on metallic surfaces for use in probes and sensors. Unfortunately, extracting truly quantitative information is usually limited to a select few cases -- uniform absorption/desorption of small biomolecules and films, in which a continuous ``slab'' model is a good approximation. We present advancements in the SPR technique that expand the number of cases for which the technique can provide meaningful results. Use of a custom, angle-scanning SPR imaging system, together with a refined data analysis method, allow for quantitative kinetic measurements of laterally heterogeneous systems. The degradation of cellulose microfibrils and bundles of microfibrils due to the action of cellulolytic enzymes will be presented as an excellent example of the capabilities of the SPR imaging system.

Recent Applications of Neutron Imaging Methods

NASA Astrophysics Data System (ADS)

Lehmann, E.; Mannes, D.; Kaestner, A.; Grünzweig, C.

The methodical progress in the field of neutron imaging is visible in general but on different levels in the particular labs. Consequently, the access to most suitable beam ports, the usage of advanced imaging detector systems and the professional image processing made the technique competitive to other non-destructive tools like X-ray imaging. Based on this performance gain and by new methodical approaches several new application fields came up - in addition to the already established ones. Accordingly, new image data are now mostly in the third dimension available in the format of tomography volumes. The radiography mode is still the basis of neutron imaging, but the extracted information from superimposed image data (like for a grating interferometer) enables completely new insights. In the consequence, many new applications were created.

Volatile organic compounds: sampling methods and their worldwide profile in ambient air.

PubMed

Kumar, Anuj; Víden, Ivan

2007-08-01

The atmosphere is a particularly difficult analytical system because of the very low levels of substances to be analysed, sharp variations in pollutant levels with time and location, differences in wind, temperature and humidity. This makes the selection of an efficient sampling technique for air analysis a key step to reliable results. Generally, methods for volatile organic compounds sampling include collection of the whole air or preconcentration of samples on adsorbents. All the methods vary from each other according to the sampling technique, type of sorbent, method of extraction and identification technique. In this review paper we discuss various important aspects for sampling of volatile organic compounds by the widely used and advanced sampling methods. Characteristics of various adsorbents used for VOCs sampling are also described. Furthermore, this paper makes an effort to comprehensively review the concentration levels of volatile organic compounds along with the methodology used for analysis, in major cities of the world.

A layered modulation method for pixel matching in online phase measuring profilometry

NASA Astrophysics Data System (ADS)

Li, Hongru; Feng, Guoying; Bourgade, Thomas; Yang, Peng; Zhou, Shouhuan; Asundi, Anand

2016-10-01

An online phase measuring profilometry with new layered modulation method for pixel matching is presented. In this method and in contrast with previous modulation matching methods, the captured images are enhanced by Retinex theory for better modulation distribution, and all different layer modulation masks are fully used to determine the displacement of a rectilinear moving object. High, medium and low modulation masks are obtained by performing binary segmentation with iterative Otsu method. The final shifting pixels are calculated based on centroid concept, and after that the aligned fringe patterns can be extracted from each frame. After performing Stoilov algorithm and a series of subsequent operations, the object profile on a translation stage is reconstructed. All procedures are carried out automatically, without setting specific parameters in advance. Numerical simulations are detailed and experimental results verify the validity and feasibility of the proposed approach.

Advanced spectral methods for climatic time series

USGS Publications Warehouse

Ghil, M.; Allen, M.R.; Dettinger, M.D.; Ide, K.; Kondrashov, D.; Mann, M.E.; Robertson, A.W.; Saunders, A.; Tian, Y.; Varadi, F.; Yiou, P.

2002-01-01

The analysis of univariate or multivariate time series provides crucial information to describe, understand, and predict climatic variability. The discovery and implementation of a number of novel methods for extracting useful information from time series has recently revitalized this classical field of study. Considerable progress has also been made in interpreting the information so obtained in terms of dynamical systems theory. In this review we describe the connections between time series analysis and nonlinear dynamics, discuss signal- to-noise enhancement, and present some of the novel methods for spectral analysis. The various steps, as well as the advantages and disadvantages of these methods, are illustrated by their application to an important climatic time series, the Southern Oscillation Index. This index captures major features of interannual climate variability and is used extensively in its prediction. Regional and global sea surface temperature data sets are used to illustrate multivariate spectral methods. Open questions and further prospects conclude the review.

Implementation and Initial Testing of Advanced Processing and Analysis Algorithms for Correlated Neutron Counting

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

Santi, Peter Angelo; Cutler, Theresa Elizabeth; Favalli, Andrea

In order to improve the accuracy and capabilities of neutron multiplicity counting, additional quantifiable information is needed in order to address the assumptions that are present in the point model. Extracting and utilizing higher order moments (Quads and Pents) from the neutron pulse train represents the most direct way of extracting additional information from the measurement data to allow for an improved determination of the physical properties of the item of interest. The extraction of higher order moments from a neutron pulse train required the development of advanced dead time correction algorithms which could correct for dead time effects inmore » all of the measurement moments in a self-consistent manner. In addition, advanced analysis algorithms have been developed to address specific assumptions that are made within the current analysis model, namely that all neutrons are created at a single point within the item of interest, and that all neutrons that are produced within an item are created with the same energy distribution. This report will discuss the current status of implementation and initial testing of the advanced dead time correction and analysis algorithms that have been developed in an attempt to utilize higher order moments to improve the capabilities of correlated neutron measurement techniques.« less

CHOBS: Color Histogram of Block Statistics for Automatic Bleeding Detection in Wireless Capsule Endoscopy Video

PubMed Central

Ghosh, Tonmoy; Wahid, Khan A.

2018-01-01

Wireless capsule endoscopy (WCE) is the most advanced technology to visualize whole gastrointestinal (GI) tract in a non-invasive way. But the major disadvantage here, it takes long reviewing time, which is very laborious as continuous manual intervention is necessary. In order to reduce the burden of the clinician, in this paper, an automatic bleeding detection method for WCE video is proposed based on the color histogram of block statistics, namely CHOBS. A single pixel in WCE image may be distorted due to the capsule motion in the GI tract. Instead of considering individual pixel values, a block surrounding to that individual pixel is chosen for extracting local statistical features. By combining local block features of three different color planes of RGB color space, an index value is defined. A color histogram, which is extracted from those index values, provides distinguishable color texture feature. A feature reduction technique utilizing color histogram pattern and principal component analysis is proposed, which can drastically reduce the feature dimension. For bleeding zone detection, blocks are classified using extracted local features that do not incorporate any computational burden for feature extraction. From extensive experimentation on several WCE videos and 2300 images, which are collected from a publicly available database, a very satisfactory bleeding frame and zone detection performance is achieved in comparison to that obtained by some of the existing methods. In the case of bleeding frame detection, the accuracy, sensitivity, and specificity obtained from proposed method are 97.85%, 99.47%, and 99.15%, respectively, and in the case of bleeding zone detection, 95.75% of precision is achieved. The proposed method offers not only low feature dimension but also highly satisfactory bleeding detection performance, which even can effectively detect bleeding frame and zone in a continuous WCE video data. PMID:29468094

From Sour Grapes to Low-Hanging Fruit: A Case Study Demonstrating a Practical Strategy for Natural Language Processing Portability.

PubMed

Johnson, Stephen B; Adekkanattu, Prakash; Campion, Thomas R; Flory, James; Pathak, Jyotishman; Patterson, Olga V; DuVall, Scott L; Major, Vincent; Aphinyanaphongs, Yindalon

2018-01-01

Natural Language Processing (NLP) holds potential for patient care and clinical research, but a gap exists between promise and reality. While some studies have demonstrated portability of NLP systems across multiple sites, challenges remain. Strategies to mitigate these challenges can strive for complex NLP problems using advanced methods (hard-to-reach fruit), or focus on simple NLP problems using practical methods (low-hanging fruit). This paper investigates a practical strategy for NLP portability using extraction of left ventricular ejection fraction (LVEF) as a use case. We used a tool developed at the Department of Veterans Affair (VA) to extract the LVEF values from free-text echocardiograms in the MIMIC-III database. The approach showed an accuracy of 98.4%, sensitivity of 99.4%, a positive predictive value of 98.7%, and F-score of 99.0%. This experience, in which a simple NLP solution proved highly portable with excellent performance, illustrates the point that simple NLP applications may be easier to disseminate and adapt, and in the short term may prove more useful, than complex applications.

Method of underground mining by pillar extraction

DOEpatents

Bowen, Ray J.; Bowen, William R.

1980-08-12

A method of sublevel caving and pillar and top coal extraction for mining thick coal seams includes the advance mining of rooms and crosscuts along the bottom of a seam to a height of about eight feet, and the retreat mining of the top coal from the rooms, crosscuts and portions of the pillars remaining from formation of the rooms and cross-cuts. In the retreat mining, a pocket is formed in a pillar, the top coal above the pocket is drilled, charged and shot, and then the fallen coal is loaded by a continuous miner so that the operator remains under a roof which has not been shot. The top coal from that portion of the room adjacent the pocket is then mined, and another pocket is formed in the pillar. The top coal above the second pocket is mined followed by the mining of the top coal of that portion of the room adjacent the second pocket, all by use of a continuous miner which allows the operator to remain under a roof portion which has not been shot.

Black Hole Spectroscopy with Coherent Mode Stacking.

PubMed

Yang, Huan; Yagi, Kent; Blackman, Jonathan; Lehner, Luis; Paschalidis, Vasileios; Pretorius, Frans; Yunes, Nicolás

2017-04-21

The measurement of multiple ringdown modes in gravitational waves from binary black hole mergers will allow for testing the fundamental properties of black holes in general relativity and to constrain modified theories of gravity. To enhance the ability of Advanced LIGO/Virgo to perform such tasks, we propose a coherent mode stacking method to search for a chosen target mode within a collection of multiple merger events. We first rescale each signal so that the target mode in each of them has the same frequency and then sum the waveforms constructively. A crucial element to realize this coherent superposition is to make use of a priori information extracted from the inspiral-merger phase of each event. To illustrate the method, we perform a study with simulated events targeting the ℓ=m=3 ringdown mode of the remnant black holes. We show that this method can significantly boost the signal-to-noise ratio of the collective target mode compared to that of the single loudest event. Using current estimates of merger rates, we show that it is likely that advanced-era detectors can measure this collective ringdown mode with one year of coincident data gathered at design sensitivity.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Multiplexed Sequence Encoding: A Framework for DNA Communication.

PubMed

Zakeri, Bijan; Carr, Peter A; Lu, Timothy K

2016-01-01

Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication-data encoding, data transfer & data extraction-and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system-Multiplexed Sequence Encoding (MuSE)-that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA.

Multiple degree of freedom optical pattern recognition

NASA Technical Reports Server (NTRS)

Casasent, D.

1987-01-01

Three general optical approaches to multiple degree of freedom object pattern recognition (where no stable object rest position exists) are advanced. These techniques include: feature extraction, correlation, and artificial intelligence. The details of the various processors are advanced together with initial results.

Anti-Advanced Glycation End-product and Free Radical Scavenging Activity of Plants from the Yucatecan Flora.

PubMed

Dzib-Guerra, Wendy Del C; Escalante-Erosa, Fabiola; García-Sosa, Karlina; Derbré, Séverine; Blanchard, Patricia; Richomme, Pascal; Peña-Rodríguez, Luis M

2016-01-01

Formation and accumulation of advanced glycation end-products (AGE) is recognized as a major pathogenic process in diabetic complications, atherosclerosis and cardiovascular diseases. In addition, reactive oxygen species and free radicals have also been reported to participate in AGE formation and in cell damage. Natural products with antioxidant and antiAGE activity have great therapeutic potential in the treatment of diabetes, hypertension and related complications. Objective: to test ethanolic extracts and aqueous-traditional preparations of plants used to treat diabetes, hypertension and obesity in Yucatecan traditional medicine for their anti-AGE and free radical scavenging activities. ethanolic extracts of leaves, stems and roots of nine medicinal plants, together with their traditional preparations, were prepared and tested for their anti-AGE and antioxidant activities using the inhibition of advanced glycation end products and DPPH radical scavenging assays, respectively. the root extract of C. fistula (IC 50 = 0.1 mg/mL) and the leaf extract of P. auritum (IC 50 = 0.35 mg/mL) presented significant activity against vesperlysine and pentosidine-like AGE. Although none of the aqueous traditional preparations showed significant activity in the anti-AGE assay, both the traditional preparations and the ethanolic extracts of E. tinifolia, M. zapota, O. campechianum and P. auritum showed significant activity in the DPPH reduction assay. the results suggest that the metabolites responsible for the detected radical-scavenging activity are different to those involved in inhibiting AGE formation; however, the extracts with antioxidant activity may contain other metabolites which are able to prevent AGE formation through a different mechanism. Ethanolic extracts from nine plants used to treat diabetes, hypertension and obesity in Yucatecan traditional medicine were tested for their anti-AGE and free radical scavenging activities.Significant activity against vesperlysine and pentosidine-like AGE was detected in the root extract of Cassia fistula and the leaf extract of Piper auritum .Traditional preparations and the ethanolic extracts of Ehretia tinifolia, Manilkara zapota, Ocimum campechianum and Piper auritum showed significant activity in the DPPH reduction assay.Results suggest that the metabolites responsible for the detected radical-scavenging activity are different to those involved in inhibiting AGE formation. Abbreviations Used : AGE: Advanced glycation end-product; DPPH: 2,2-Diphenyl-1-picrylhydrazyl; DM: Diabetes mellitus; ROS: Reactive oxygen species; BSA: Bovine serum albumin; EtOH: Ethanol; EtOAc: Ethyl acetate; ANOVA: Analysis of variance; BA: Brosimum alicastrum ; BS: Bunchosia swartziana ; CF: Cassia fistula ; CN: Cocos nucifera ; ET: Ehretia tinifolia ; MZ: Manilkara zapota ; OC: Ocimum campechianum ; PA: Piper auritum ; RM: Rhizophora mangle ; L: Leaves; S: Stems; R: Roots; T: traditional preparation; I: Inflorescences; W: Water.

Advances in Spectral-Spatial Classification of Hyperspectral Images

NASA Technical Reports Server (NTRS)

Fauvel, Mathieu; Tarabalka, Yuliya; Benediktsson, Jon Atli; Chanussot, Jocelyn; Tilton, James C.

2012-01-01

Recent advances in spectral-spatial classification of hyperspectral images are presented in this paper. Several techniques are investigated for combining both spatial and spectral information. Spatial information is extracted at the object (set of pixels) level rather than at the conventional pixel level. Mathematical morphology is first used to derive the morphological profile of the image, which includes characteristics about the size, orientation, and contrast of the spatial structures present in the image. Then, the morphological neighborhood is defined and used to derive additional features for classification. Classification is performed with support vector machines (SVMs) using the available spectral information and the extracted spatial information. Spatial postprocessing is next investigated to build more homogeneous and spatially consistent thematic maps. To that end, three presegmentation techniques are applied to define regions that are used to regularize the preliminary pixel-wise thematic map. Finally, a multiple-classifier (MC) system is defined to produce relevant markers that are exploited to segment the hyperspectral image with the minimum spanning forest algorithm. Experimental results conducted on three real hyperspectral images with different spatial and spectral resolutions and corresponding to various contexts are presented. They highlight the importance of spectral–spatial strategies for the accurate classification of hyperspectral images and validate the proposed methods.

In Vitro Inhibitory Activity of Acca sellowiana Fruit Extract on End Products of Advanced Glycation.

PubMed

Muñiz, Alethia; Garcia, Abraham H; Pérez, Rosa M; García, Efren V; González, Daphne E

2018-02-01

Hyperglycemia plays an important role in the pathogenesis of diabetic complications, as it increases protein glycation, as well as the progressive accumulation of advanced glycation end products (AGEs), which are complex structures that produce fluorescence. The glycation reaction raises the levels of protein carbonyl, N ε -(carboxymethyl)lysine (CML), and fructosamine and decreases the level of thiol groups. In the present study, the antiglycation activity was determined by fluorescence intensity using the bovine serum albumin (BSA)/glucose, CML method, and the level of fructosamine. The oxidation of proteins was determined by the carbonyl protein content and thiol groups. The results show that the hexane extract of Acca sellowiana (FOH) at different concentrations (0.30-5 mg/ml) significantly inhibited the formation of AGEs in the BSA/glucose model during the 4 weeks of the study. FOH reduced the levels of fructosamine and CML. Our results showed a significant effect of FOH in the prevention of oxidative damage of proteins, as well as an effect on the oxidation of thiol groups and carbonyl proteins. The present study indicates that FOH is effective in inhibiting the glycation of proteins in vitro, so it can prevent or ameliorate the chronic conditions of diabetes associated with the formation of AGEs.

ON-SITE SOLID PHRASE EXTRACTION AND LABORATORY ...

EPA Pesticide Factsheets

Fragrance materials, such as synthetic musks in aqueous samples, are normally analyzed by GC/MS in the selected ion monitoring (SIM) mode to provide maximum sensitivity after liquid-liquid extraction of I -L samples. A I -L sample, however, usually provides too little analyte for full-scan data acquisition. An on-site extraction method for extracting synthetic musks from 60 L of wastewater effluent has been developed. Such a large sample volume permits high-quality, full-scan mass spectra to be obtained for various synthetic musk compounds. Quantification of these compounds was conveniently achieved from the full-scan data directly, without preparing SIM descriptors for each compound to acquire SIM data. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this Task and more in-depth coverage of each project. Briefly, each project's objective is stated below.Subtask 1: To integrate state-of-the-art technologies (polar organic chemical integrative samplers, advanced solid-phase extraction methodologies with liquid chromatography/electrospray/mass spectrometry) and apply them to studying the sources and fate of a select list of PPCPs. Application and improvement of analytical methodologies that can detect non-volatile, polar, water-sol

IN SITU SOLID-PHASE EXTRACTION AND ANALYSIS OF ...

EPA Pesticide Factsheets

Fragrance materials, such as synthetic musks in aqueous samples, are normally analyzed by GC/MS in the selected ion monitoring (SIM) mode to provide maximum sensitivity after liquid-liquid extraction of 1-L samples. A 1-L sample, however, usually provides too little analyte for full-scan data acquisition.We have developed an on-site extraction method for extracting synthetic musks from 60 L of wastewater effluent. Such a large sample volume permits high-quality, full-scan mass spectra to be obtained for various synthetic musk compounds. Quantification of these compounds was conveniently achieved from the full-scan data directly, without preparing SIM descriptors for each compound to acquire SIM data. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this Task and more in-depth coverage of each project. Briefly, each project's objective is stated below.Subtask 1: To integrate state-of-the-art technologies (polar organic chemical integrative samplers, advanced solid-phase extraction methodologies with liquid chromatography/electrospray/mass spectrometry) and apply them to studying the sources and fate of a select list of PPCPs. Application and improvement of analytical methodologies that can detect non-volatile, polar, water-s

Implementation of novel statistical procedures and other advanced approaches to improve analysis of CASA data.

PubMed

Ramón, M; Martínez-Pastor, F

2018-04-23

Computer-aided sperm analysis (CASA) produces a wealth of data that is frequently ignored. The use of multiparametric statistical methods can help explore these datasets, unveiling the subpopulation structure of sperm samples. In this review we analyse the significance of the internal heterogeneity of sperm samples and its relevance. We also provide a brief description of the statistical tools used for extracting sperm subpopulations from the datasets, namely unsupervised clustering (with non-hierarchical, hierarchical and two-step methods) and the most advanced supervised methods, based on machine learning. The former method has allowed exploration of subpopulation patterns in many species, whereas the latter offering further possibilities, especially considering functional studies and the practical use of subpopulation analysis. We also consider novel approaches, such as the use of geometric morphometrics or imaging flow cytometry. Finally, although the data provided by CASA systems provides valuable information on sperm samples by applying clustering analyses, there are several caveats. Protocols for capturing and analysing motility or morphometry should be standardised and adapted to each experiment, and the algorithms should be open in order to allow comparison of results between laboratories. Moreover, we must be aware of new technology that could change the paradigm for studying sperm motility and morphology.

Advance care planning for haemodialysis patients.

PubMed

Lim, Chi Eung Danforn; Ng, Rachel W C; Cheng, Nga Chong Lisa; Cigolini, Maria; Kwok, Cannas; Brennan, Frank

2016-07-26

End-stage kidney disease (ESKD) is a chronic, debilitative and progressive illness that may need interventions such as dialysis, transplantation, dietary and fluid restrictions. Most patients with ESKD will require renal replacement therapy, such as kidney transplantation or maintenance dialysis. Advance care planning traditionally encompass instructions via living wills, and concern patient preferences about interventions such as cardiopulmonary resuscitation and feeding tubes, or circumstances around assigning surrogate decision makers. Most people undergoing haemodialysis are not aware of advance care planning and few patients formalise their wishes as advance directives and of those who do, many do not discuss their decisions with a physician. Advance care planning involves planning for future healthcare decisions and preferences of the patient in advance while comprehension is intact. It is an essential part of good palliative care that likely improves the lives and deaths of haemodialysis patients. The objective of this review was to determine whether advance care planning in haemodialysis patients, compared with no or less structured forms of advance care planning, can result in fewer hospital admissions or less use of treatments with life-prolonging or curative intent, and if patient's wishes were followed at end-of-life. We searched the Cochrane Kidney and Transplant Specialised Register to 27 June 2016 through contact with the Information Specialist using search terms relevant to this review. We also searched the Cumulative Index of Nursing and Allied Health Literature (CINAHL), and Social Work Abstracts (OvidSP). All randomised controlled trials (RCTs) and quasi-RCTs (RCTs in which allocation to treatment was obtained by alternation, use of alternate medical records, date of birth or other predictable methods) looking at advance care planning versus no form of advance care planning in haemodialysis patients was considered for inclusion without language restriction. Data extraction was carried out independently by two authors using standard data extraction forms. Studies reported in non-English language journals were translated before assessment. Where more than one publication of one study exists, reports were grouped together and the publication with the most complete data was used in the analyses. Where relevant outcomes are only published in earlier versions these data were used. Any discrepancies between published versions were highlighted. Non-randomised controlled studies were excluded. We included two studies (three reports) that involved 337 participants which investigated advance care planning for people with ESKD. Neither of the included studies reported outcomes relevant to this review. Study quality was assessed as suboptimal. We found sparse data that were assessed at suboptimal quality and therefore we were unable to formulate conclusions about whether advance care planning can influence numbers of hospital admissions and treatment required by people with ESKD, or if patients' advance care directives were followed at end-of-life. Further well designed and adequately powered RCTs are needed to better inform patient and clinical decision-making about advance care planning and advance directives among people with ESKD who are undergoing dialysis.

Adaptive on-line calibration for around-view monitoring system using between-camera homography estimation

NASA Astrophysics Data System (ADS)

Lim, Sungsoo; Lee, Seohyung; Kim, Jun-geon; Lee, Daeho

2018-01-01

The around-view monitoring (AVM) system is one of the major applications of advanced driver assistance systems and intelligent transportation systems. We propose an on-line calibration method, which can compensate misalignments for AVM systems. Most AVM systems use fisheye undistortion, inverse perspective transformation, and geometrical registration methods. To perform these procedures, the parameters for each process must be known; the procedure by which the parameters are estimated is referred to as the initial calibration. However, when only using the initial calibration data, we cannot compensate misalignments, caused by changing equilibria of cars. Moreover, even small changes such as tire pressure levels, passenger weight, or road conditions can affect a car's equilibrium. Therefore, to compensate for this misalignment, additional techniques are necessary, specifically an on-line calibration method. On-line calibration can recalculate homographies, which can correct any degree of misalignment using the unique features of ordinary parking lanes. To extract features from the parking lanes, this method uses corner detection and a pattern matching algorithm. From the extracted features, homographies are estimated using random sample consensus and parameter estimation. Finally, the misaligned epipolar geographies are compensated via the estimated homographies. Thus, the proposed method can render image planes parallel to the ground. This method does not require any designated patterns and can be used whenever cars are placed in a parking lot. The experimental results show the robustness and efficiency of the method.

Layout-aware text extraction from full-text PDF of scientific articles

PubMed Central

2012-01-01

Background The Portable Document Format (PDF) is the most commonly used file format for online scientific publications. The absence of effective means to extract text from these PDF files in a layout-aware manner presents a significant challenge for developers of biomedical text mining or biocuration informatics systems that use published literature as an information source. In this paper we introduce the ‘Layout-Aware PDF Text Extraction’ (LA-PDFText) system to facilitate accurate extraction of text from PDF files of research articles for use in text mining applications. Results Our paper describes the construction and performance of an open source system that extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles and is meant as a baseline for further experiments into more advanced extraction methods that handle multi-modal content, such as images and graphs. The system works in a three-stage process: (1) Detecting contiguous text blocks using spatial layout processing to locate and identify blocks of contiguous text, (2) Classifying text blocks into rhetorical categories using a rule-based method and (3) Stitching classified text blocks together in the correct order resulting in the extraction of text from section-wise grouped blocks. We show that our system can identify text blocks and classify them into rhetorical categories with Precision1 = 0.96% Recall = 0.89% and F1 = 0.91%. We also present an evaluation of the accuracy of the block detection algorithm used in step 2. Additionally, we have compared the accuracy of the text extracted by LA-PDFText to the text from the Open Access subset of PubMed Central. We then compared this accuracy with that of the text extracted by the PDF2Text system, 2commonly used to extract text from PDF. Finally, we discuss preliminary error analysis for our system and identify further areas of improvement. Conclusions LA-PDFText is an open-source tool for accurately extracting text from full-text scientific articles. The release of the system is available at http://code.google.com/p/lapdftext/. PMID:22640904

How are patient populations characterized in studies investigating depression in advanced cancer? Results from a systematic literature review.

PubMed

Janberidze, Elene; Hjermstad, Marianne Jensen; Haugen, Dagny Faksvåg; Sigurdardottir, Katrin Ruth; Løhre, Erik Torbjørn; Lie, Hanne Cathrine; Loge, Jon Håvard; Kaasa, Stein; Knudsen, Anne Kari

2014-10-01

Prevalence rates of depression in patients with advanced cancer vary considerably. This may be because of heterogeneous samples and use of different assessment methods. Adequate sample descriptions and consistent use of measures are needed to be able to generalize research findings and apply them to clinical practice. Our objective was twofold: First, to investigate which clinically important variables were used to describe the samples in studies of depression in patients with advanced cancer; and second, to examine the methods used for assessing and classifying depression in these studies. PubMed, PsycINFO, Embase, and CINAHL were searched combining search term groups representing "depression," "palliative care," and "advanced cancer" covering 2007-2011. Titles and abstracts were screened, and relevant full-text articles were evaluated independently by two authors. Information on 32 predefined variables on cancer disease, treatment, sociodemographics, depression-related factors, and assessment methods was extracted from the articles. After removing duplicates, 916 citations were screened of which 59 articles were retained. Age, gender, and stage of the cancer disease were the most frequently reported variables. Depression-related variables were rarely reported, for example, antidepressant use (17%) and previous depressive episodes (12%). Only 25% of the studies assessed and classified depression according to a validated diagnostic system. Current practice for describing sample characteristics and assessing depression varies greatly between studies. A more standardized practice is recommended to enhance the generalizability and utility of findings. Stakeholders are encouraged to work toward a common standard for sample descriptions. Copyright © 2014 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

Recent Advances in Clinical Natural Language Processing in Support of Semantic Analysis

PubMed Central

Mowery, D.; South, B. R.; Kvist, M.; Dalianis, H.

2015-01-01

Summary Objectives We present a review of recent advances in clinical Natural Language Processing (NLP), with a focus on semantic analysis and key subtasks that support such analysis. Methods We conducted a literature review of clinical NLP research from 2008 to 2014, emphasizing recent publications (2012-2014), based on PubMed and ACL proceedings as well as relevant referenced publications from the included papers. Results Significant articles published within this time-span were included and are discussed from the perspective of semantic analysis. Three key clinical NLP subtasks that enable such analysis were identified: 1) developing more efficient methods for corpus creation (annotation and de-identification), 2) generating building blocks for extracting meaning (morphological, syntactic, and semantic subtasks), and 3) leveraging NLP for clinical utility (NLP applications and infrastructure for clinical use cases). Finally, we provide a reflection upon most recent developments and potential areas of future NLP development and applications. Conclusions There has been an increase of advances within key NLP subtasks that support semantic analysis. Performance of NLP semantic analysis is, in many cases, close to that of agreement between humans. The creation and release of corpora annotated with complex semantic information models has greatly supported the development of new tools and approaches. Research on non-English languages is continuously growing. NLP methods have sometimes been successfully employed in real-world clinical tasks. However, there is still a gap between the development of advanced resources and their utilization in clinical settings. A plethora of new clinical use cases are emerging due to established health care initiatives and additional patient-generated sources through the extensive use of social media and other devices. PMID:26293867

Recent Inventions and Trends in Algal Biofuels Research.

PubMed

Karemore, Ankush; Nayak, Manoranjan; Sen, Ramkrishna

2016-01-01

In recent times, when energy crisis compounded by global warming and climate change is receiving worldwide attention, the emergence of algae, as a better feedstock for third-generation biofuels than energy crops or plants, holds great promise. As compared to conventional biofuels feedstocks, algae offer several advantages and can alone produce a significant amount of biofuels sustainably in a shorter period to fulfill the rising demand for energy. Towards commercialisation, there have been numerous efforts put for- ward for the development of algae-derived biofuel. This article reviews and summarizes the recent inventions and the current trends that are reported and captured in relevant patents pertaining to the novel methods of algae biomass cultivation and processing for biofuels and value-added products. In addition, the recent advancement in techniques and technologies for microalgal biofuel production has been highlighted. Various steps involved in the production of algal biofuels have been considered in this article. Moreover, the work that advances to improve the efficiency and cost-effectiveness of the processes for the manufacture of biofuels has been presented. Our survey was conducted in the patent databases: WIPO, Spacenet and USPTO. There are still some technological bottlenecks that could be overcome by designing advanced photobioreactor and raceway ponds, developing new and low cost technologies for biomass cultivation, harvesting, drying and extraction. Recent advancement in algae biofuels methods is directed toward developing efficient and integrated systems to produce biofuels by overcoming the current challenges. However, further research effort is required to scale-up and improve the efficiency of these methods in the upstream and downstream technologies to make the cost of biofuels competitive with petroleum fuels.

Evaluation of inhibition of cancer cell proliferation in vitro with different berries and correlation with their antioxidant levels by advanced analytical methods.

PubMed

Flis, Sylwia; Jastrzebski, Zenon; Namiesnik, Jacek; Arancibia-Avila, Patricia; Toledo, Fernando; Leontowicz, Hanna; Leontowicz, Maria; Suhaj, Milan; Trakhtenberg, Simon; Gorinstein, Shela

2012-03-25

Dimethylsulfoxide extracts of Chilean berries [Myrteola nummularia, 'Murtilla-like'] vs. well known 'Murtilla', Chilean and Polish blueberries, and Chilean raspberries were investigated for their antioxidant, quenching and antiproliferative activities. The significantly highest levels of polyphenols, flavonoids, flavanols and their antioxidant activities were estimated in 'Murtilla' (MT) berries (P<0.05), than in other investigated samples. DPPH kinetic measurements were calculated to compare, distinguish and discriminate the antiradical activity among berry extracts by multivariate analysis. The lowest IC(50) values, 751 and 858 μg/ml, were obtained for MT extract on colon cancer cell lines HT-29 and SW48. HT-29 cells treated with MT extract showed a decrease in G1 phase cells from 77% to 56% (P<0.05). At the highest concentration of 2000 μg/ml MT extract caused 90-100% cell growth inhibition. Percentage of death cells treated with MT extract was 80.1% and 72.5% for SW48 and HT-29 cells, respectively. The inhibition of cancer cell proliferation highly correlated with the levels of polyphenols, flavonoids and their antioxidant activities. The interaction between drugs and serum albumin plays an important role in the distribution and metabolism of drugs, therefore the complexation reaction between flavonoids, and berries extracts, and bovine serum albumin (BSA) was investigated by 3-D fluorescence and FTIR spectroscopy. The results indicated that flavonoids and polyphenol extracts have strong ability to quench the intrinsic fluorescence of BSA by forming complexes. A shift in the maximum of amides FTIR-bands appeared. In conclusion, these findings suggest that the intake of a new kind of berry, as a source of natural antioxidants, may reduce colon cancer risk. Copyright © 2012 Elsevier B.V. All rights reserved.

Landscape consequences of natural gas extraction in Greene and Tioga Counties, Pennsylvania, 2004-2010

USGS Publications Warehouse

Slonecker, E.T.; Milheim, L.E.; Roig-Silva, C.M.; Fisher, G.B.

2012-01-01

Increased demands for cleaner burning energy, coupled with the relatively recent technological advances in accessing unconventional hydrocarbon-rich geologic formations, have led to an intense effort to find and extract natural gas from various underground sources around the country. One of these sources, the Marcellus Shale, located in the Allegheny Plateau, is currently undergoing extensive drilling and production. The technology used to extract gas in the Marcellus shale is known as hydraulic fracturing and has garnered much attention because of its use of large amounts of fresh water, its use of proprietary fluids for the hydraulic-fracturing process, its potential to release contaminants into the environment, and its potential effect on water resources. Nonetheless, development of natural gas extraction wells in the Marcellus Shale is only part of the overall natural gas story in the area of Pennsylvania. Coalbed methane, which is sometimes extracted using the same technique, is commonly located in the same general area as the Marcellus Shale and is frequently developed in clusters across the landscape. The combined effects of these two natural gas extraction methods create potentially serious patterns of disturbance on the landscape. This document quantifies the landscape changes and consequences of natural gas extraction for Greene County and Tioga County in Pennsylvania between 2004 and 2010. Patterns of landscape disturbance related to natural gas extraction activities were collected and digitized using National Agriculture Imagery Program (NAIP) imagery for 2004, 2005/2006, 2008, and 2010. The disturbance patterns were then used to measure changes in land cover and land use using the National Land Cover Database (NLCD) of 2001. A series of landscape metrics are also used to quantify these changes and are included in this publication.

Landscape consequences of natural gas extraction in Bradford and Washington Counties, Pennsylvania, 2004-2010

USGS Publications Warehouse

Slonecker, E.T.; Milheim, L.E.; Roig-Silva, C.M.; Malizia, A.R.; Marr, D.A.; Fisher, G.B.

2012-01-01

Increased demands for cleaner burning energy, coupled with the relatively recent technological advances in accessing unconventional hydrocarbon-rich geologic formations, led to an intense effort to find and extract natural gas from various underground sources around the country. One of these sources, the Marcellus Shale, located in the Allegheny Plateau, is undergoing extensive drilling and production. The technology used to extract gas in the Marcellus Shale is known as hydraulic fracturing and has garnered much attention because of its use of large amounts of fresh water, its use of proprietary fluids for the hydraulic-fracturing process, its potential to release contaminants into the environment, and its potential effect on water resources. Nonetheless, development of natural gas extraction wells in the Marcellus Shale is only part of the overall natural gas story in the area of Pennsylvania. Coalbed methane, which is sometimes extracted using the same technique, is often located in the same general area as the Marcellus Shale and is frequently developed in clusters across the landscape. The combined effects of these two natural gas extraction methods create potentially serious patterns of disturbance on the landscape. This document quantifies the landscape changes and consequences of natural gas extraction for Bradford County and Washington County, Pennsylvania, between 2004 and 2010. Patterns of landscape disturbance related to natural gas extraction activities were collected and digitized using National Agriculture Imagery Program (NAIP) imagery for 2004, 2005/2006, 2008, and 2010. The disturbance patterns were then used to measure changes in land cover and land use using the National Land Cover Database (NLCD) of 2001. A series of landscape metrics is used to quantify these changes and are included in this publication.

Landscape consequences of natural gas extraction in Allegheny and Susquehanna Counties, Pennsylvania, 2004--2010

USGS Publications Warehouse

Slonecker, E.T.; Milheim, L.E.; Roig-Silva, C.M.; Malizia, A.R.

2013-01-01

Increased demands for cleaner burning energy, coupled with the relatively recent technological advances in accessing unconventional hydrocarbon-rich geologic formations, have led to an intense effort to find and extract natural gas from various underground sources around the country. One of these sources, the Marcellus Shale, located in the Allegheny Plateau, is currently undergoing extensive drilling and production. The technology used to extract gas in the Marcellus Shale is known as hydraulic fracturing and has garnered much attention because of its use of large amounts of fresh water, its use of proprietary fluids for the hydraulic-fracturing process, its potential to release contaminants into the environment, and its potential effect on water resources. Nonetheless, development of natural gas extraction wells in the Marcellus Shale is only part of the overall natural gas story in this area of Pennsylvania. Coalbed methane, which is sometimes extracted using the same technique, is commonly located in the same general area as the Marcellus Shale and is frequently developed in clusters of wells across the landscape. The combined effects of these two natural gas extraction methods create potentially serious patterns of disturbance on the landscape. This document quantifies the landscape changes and consequences of natural gas extraction for Allegheny County and Susquehanna County in Pennsylvania between 2004 and 2010. Patterns of landscape disturbance related to natural gas extraction activities were collected and digitized using National Agriculture Imagery Program (NAIP) imagery for 2004, 2005/2006, 2008, and 2010. The disturbance patterns were then used to measure changes in land cover and land use using the National Land Cover Database (NLCD) of 2001. A series of landscape metrics is also used to quantify these changes and is included in this publication.

The Adverse Drug Reactions from Patient Reports in Social Media Project: Five Major Challenges to Overcome to Operationalize Analysis and Efficiently Support Pharmacovigilance Process

PubMed Central

Dahamna, Badisse; Guillemin-Lanne, Sylvie; Darmoni, Stefan J; Faviez, Carole; Huot, Charles; Katsahian, Sandrine; Leroux, Vincent; Pereira, Suzanne; Richard, Christophe; Schück, Stéphane; Souvignet, Julien; Lillo-Le Louët, Agnès; Texier, Nathalie

2017-01-01

Background Adverse drug reactions (ADRs) are an important cause of morbidity and mortality. Classical Pharmacovigilance process is limited by underreporting which justifies the current interest in new knowledge sources such as social media. The Adverse Drug Reactions from Patient Reports in Social Media (ADR-PRISM) project aims to extract ADRs reported by patients in these media. We identified 5 major challenges to overcome to operationalize the analysis of patient posts: (1) variable quality of information on social media, (2) guarantee of data privacy, (3) response to pharmacovigilance expert expectations, (4) identification of relevant information within Web pages, and (5) robust and evolutive architecture. Objective This article aims to describe the current state of advancement of the ADR-PRISM project by focusing on the solutions we have chosen to address these 5 major challenges. Methods In this article, we propose methods and describe the advancement of this project on several aspects: (1) a quality driven approach for selecting relevant social media for the extraction of knowledge on potential ADRs, (2) an assessment of ethical issues and French regulation for the analysis of data on social media, (3) an analysis of pharmacovigilance expert requirements when reviewing patient posts on the Internet, (4) an extraction method based on natural language processing, pattern based matching, and selection of relevant medical concepts in reference terminologies, and (5) specifications of a component-based architecture for the monitoring system. Results Considering the 5 major challenges, we (1) selected a set of 21 validated criteria for selecting social media to support the extraction of potential ADRs, (2) proposed solutions to guarantee data privacy of patients posting on Internet, (3) took into account pharmacovigilance expert requirements with use case diagrams and scenarios, (4) built domain-specific knowledge resources embeding a lexicon, morphological rules, context rules, semantic rules, syntactic rules, and post-analysis processing, and (5) proposed a component-based architecture that allows storage of big data and accessibility to third-party applications through Web services. Conclusions We demonstrated the feasibility of implementing a component-based architecture that allows collection of patient posts on the Internet, near real-time processing of those posts including annotation, and storage in big data structures. In the next steps, we will evaluate the posts identified by the system in social media to clarify the interest and relevance of such approach to improve conventional pharmacovigilance processes based on spontaneous reporting. PMID:28935617

[Investigation on Inhibitory Capacities of Seventeen Herbal Extracts on Oxidative Stress using Ultraviolet and Fluorescence Spectroscopy].

PubMed

Hou, Guang-yue; Zheng, Zhong; Song, Feng-rui; Liu, Zhi-qiang; Zhao, Bing

2015-03-01

Diabetic patients usually suffer from complications and the long-term secondary complications are the main cause of morbidity and mortality. The hyperglycemia-induced oxidative stress is one of the important pathogenesis of diabetic complications, while the oxidative stress is associated with the lipid peroxidation reaction and the formation of advanced glycation end products (AGEs). Our study was focus on the pathogenesis of diabetic complications and based on the oxidative stress reaction. In this research, the oxidative stress inhibiting effects of seventeen herbal extracts were studied based on spectroscopic methodology. The capacities of herbal extracts against the lipid peroxidation reaction of rat liver in vitro were investigated using spectrophotometric method. It showed that the inhibitory activity of Radix Scutellariae and Flos Sophorae Immaturus were better than other herbal extracts. Additionally, the herbal extracts rich in flavonoids, alkaloids and lignanoids showed good inhibitory activities on the lipid peroxidation reaction. On the contrary, the saponin-rich herbal extracts possessed weak inhibitory effects. We applied the BSA/glucose (fructose) system combined with fluorescent spectroscopy to determine the inhibitory activities of herbal extracts in glycation model reactions. The results showed that the AGEs formation inhibitory activity of Flos Sophorae Immaturus, Radix Scutellariae and Rhizoma Anemarrhenae were better than others in the BSA/glucose (fructose) system by fluorescene analysis. The results demonstrated that the herbal extracts rich in flavonoids were found to be more effective than that of those herbal extracts as alkaloids and terpenoids class in inhibiting oxidative stress, while the saponin-rich herbal extracts showed weak inhibitory activities against oxidative stress. The Flos Sophorae Immaturus and Radix Scutellariae extracts had better inhibitory activity to the oxidative stress, so their pharmacological activity could be explored in further investigations. These results demonstrated in this assay could provide a reference for the study of pharmacological activity, and thus lays the foundation for the further study of the application of natural products in the prevention and treatment of diabetic complications.

Recent Advances in Marine Algae Polysaccharides: Isolation, Structure, and Activities.

PubMed

Xu, Shu-Ying; Huang, Xuesong; Cheong, Kit-Leong

2017-12-13

Marine algae have attracted a great deal of interest as excellent sources of nutrients. Polysaccharides are the main components in marine algae, hence a great deal of attention has been directed at isolation and characterization of marine algae polysaccharides because of their numerous health benefits. In this review, extraction and purification approaches and chemico-physical properties of marine algae polysaccharides (MAPs) are summarized. The biological activities, which include immunomodulatory, antitumor, antiviral, antioxidant, and hypolipidemic, are also discussed. Additionally, structure-function relationships are analyzed and summarized. MAPs' biological activities are closely correlated with their monosaccharide composition, molecular weights, linkage types, and chain conformation. In order to promote further exploitation and utilization of polysaccharides from marine algae for functional food and pharmaceutical areas, high efficiency, and low-cost polysaccharide extraction and purification methods, quality control, structure-function activity relationships, and specific mechanisms of MAPs activation need to be extensively investigated.

DNA typing for the identification of old skeletal remains from Korean War victims.

PubMed

Lee, Hwan Young; Kim, Na Young; Park, Myung Jin; Sim, Jeong Eun; Yang, Woo Ick; Shin, Kyoung-Jin

2010-11-01

The identification of missing casualties of the Korean War (1950-1953) has been performed using mitochondrial DNA (mtDNA) profiles, but recent advances in DNA extraction techniques and approaches using smaller amplicons have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Therefore, 21 skeletal remains of Korean War victims and 24 samples from biological relatives of the supposed victims were selected based on circumstantial evidence and/or mtDNA-matching results and were analyzed to confirm the alleged relationship. Cumulative likelihood ratios were obtained from autosomal short tandem repeat, Y-chromosomal STR, and mtDNA-genotyping results, and mainly confirmed the alleged relationship with values over 10⁵. The present analysis emphasizes the value of mini- and Y-STR systems as well as an efficient DNA extraction method in DNA testing for the identification of old skeletal remains. © 2010 American Academy of Forensic Sciences.

Soil and leaf litter metaproteomics—a brief guideline from sampling to understanding

PubMed Central

Keiblinger, Katharina M.; Fuchs, Stephan; Zechmeister-Boltenstern, Sophie; Riedel, Katharina

2016-01-01

The increasing application of soil metaproteomics is providing unprecedented, in-depth characterization of the composition and functionality of in situ microbial communities. Despite recent advances in high-resolution mass spectrometry, soil metaproteomics still suffers from a lack of effective and reproducible protein extraction protocols and standardized data analyses. This review discusses the opportunities and limitations of selected techniques in soil-, and leaf litter metaproteomics, and presents a step-by-step guideline on their application, covering sampling, sample preparation, extraction and data evaluation strategies. In addition, we present recent applications of soil metaproteomics and discuss how such approaches, linking phylogenetics and functionality, can help gain deeper insights into terrestrial microbial ecology. Finally, we strongly recommend that to maximize the insights environmental metaproteomics may provide, such methods should be employed within a holistic experimental approach considering relevant aboveground and belowground ecosystem parameters. PMID:27549116

Algal biofuels: challenges and opportunities.

PubMed

Leite, Gustavo B; Abdelaziz, Ahmed E M; Hallenbeck, Patrick C

2013-10-01

Biodiesel production using microalgae is attractive in a number of respects. Here a number of pros and cons to using microalgae for biofuels production are reviewed. Algal cultivation can be carried out using non-arable land and non-potable water with simple nutrient supply. In addition, algal biomass productivities are much higher than those of vascular plants and the extractable content of lipids that can be usefully converted to biodiesel, triacylglycerols (TAGs) can be much higher than that of the oil seeds now used for first generation biodiesel. On the other hand, practical, cost-effective production of biofuels from microalgae requires that a number of obstacles be overcome. These include the development of low-cost, effective growth systems, efficient and energy saving harvesting techniques, and methods for oil extraction and conversion that are environmentally benign and cost-effective. Promising recent advances in these areas are highlighted. Copyright © 2013 Elsevier Ltd. All rights reserved.

Ultrasonic extraction of polysaccharides from Laminaria japonica and their antioxidative and glycosidase inhibitory activities

NASA Astrophysics Data System (ADS)

Wan, Peng; Yang, Xiaoman; Cai, Bingna; Chen, Hua; Sun, Huili; Chen, Deke; Pan, Jianyu

2015-08-01

In the present study, ultrasonic extraction technique (UET) is used to improve the yield of polysaccharides from Laminaria japonica (LJPs). And their antioxidative as well as glycosidase inhibitory activities are investigated. Box-Behnken design (BBD) combined with response surface methodology (RSM) is applied to optimize ultrasonic extraction for polysaccharides. The optimized conditions are obtained as extraction time at 54 min, ultrasonic power at 1050 W, extraction temperature at 80°C and ratio of material to solvent at 1:50 (g mL-1). Under these optimal ultrasonic extraction conditions, an actual experimental yield (5.75% ± 0.3%) is close to the predicted result (5.67%) with no significant difference ( P > 0.05). Vitro antioxidative and glycosidase inhibitory activities tests indicate that the crude polysaccharides (LJP) and two major ethanol precipitated fractions (LJP1 and LJP2) are in a concentration-dependent manner. LJP2 (30%-60% ethanol precipitated polysaccharides) possesses the strongest α-glucosidase inhibitory activity and moderate scavenging activity against hydroxyl radicals (66.09% ± 2.19%, 3.0 mg mL-1). Also, the inhibitory activity against α-glucosidase (59.08% ± 3.79%, 5.0 mg mL-1) is close to that of acarbose (63.99% ± 3.27%, 5.0 mg mL-1). LJP1 (30% ethanol precipitated polysaccharides) exhibits the strongest scavenging activity against hydroxyl radicals (99.80% ± 0.00%, 3.0 mg mL-1) and moderate α-glucosidase inhibitory activity (47.76% ± 1.92%, 5.0 mg mL-1). LJP shows the most remarkable DPPH scavenging activity (66.20% ± 0.11%, 5.0 mg mL-1) but weakest α-glucosidase inhibitory activity (37.77% ± 1.30%, 5.0 mg mL-1). However, all these LJPs exert weak inhibitory effects against α-amylase. These results show that UET is an effective method for extracting bioactive polysaccharides from seaweed materials. LJP1 and LJP2 can be developed as a potential ingredient in hypoglycemic agents or functional food for the management of diabetes. This study provides scientific evidence and advances in the preparation technology and a hypoglycemic activities evaluation method for seaweed polysaccharides, especially glycosidase inhibition in combination with an antioxidative activity evaluation method.

Separation of Zirconium and Hafnium: A Review

NASA Astrophysics Data System (ADS)

Xu, L.; Xiao, Y.; van Sandwijk, A.; Xu, Q.; Yang, Y.

Zirconium is an ideal material for nuclear reactors due to its low absorption cross-section for thermal neutrons, whereas the typically contained hafnium with strong neutron-absorption is very harmful for zirconium. This paper provides an overview of the processes for separating hafnium from zirconium. The separation processes are roughly classified into hydro- and pyrometallurgical routes. The current dominant zirconium production route involves pyrometallurgical ore cracking, multi-step hydrometallurgical liquid-liquid extraction for hafnium removal and the reduction of zirconium tetrachloride to the pure metal by the Kroll process. The lengthy hydrometallurgical Zr-Hf separation operations leads to high production cost, intensive labour and heavy environmental burden. Using a compact pyrometallurgical separation method can simplify the whole production flowsheet with a higher process efficiency. The known separation methods are discussed based on the following reaction features: redox characteristics, volatility, electrochemical properties and molten salt extraction. The commercially operating extractive distillation process is a significant advance in Zr-Hf separation technology but it suffers from high process maintenance cost. The recently developed new process based on molten salt-metal equilibrium for Zr-Hf separation shows a great potential for industrial application, which is compact for nuclear grade zirconium production starting from crude ore. In the present paper, the available separation technologies are compared. The advantages and disadvantages as well as future directions of research and development for nuclear grade zirconium production are discussed.

Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds.

PubMed

Chen, Lei; Zhang, Yu-Hang; Zheng, Mingyue; Huang, Tao; Cai, Yu-Dong

2016-12-01

Compound-protein interactions play important roles in every cell via the recognition and regulation of specific functional proteins. The correct identification of compound-protein interactions can lead to a good comprehension of this complicated system and provide useful input for the investigation of various attributes of compounds and proteins. In this study, we attempted to understand this system by extracting properties from both proteins and compounds, in which proteins were represented by gene ontology and KEGG pathway enrichment scores and compounds were represented by molecular fragments. Advanced feature selection methods, including minimum redundancy maximum relevance, incremental feature selection, and the basic machine learning algorithm random forest, were used to analyze these properties and extract core factors for the determination of actual compound-protein interactions. Compound-protein interactions reported in The Binding Databases were used as positive samples. To improve the reliability of the results, the analytic procedure was executed five times using different negative samples. Simultaneously, five optimal prediction methods based on a random forest and yielding maximum MCCs of approximately 77.55 % were constructed and may be useful tools for the prediction of compound-protein interactions. This work provides new clues to understanding the system of compound-protein interactions by analyzing extracted core features. Our results indicate that compound-protein interactions are related to biological processes involving immune, developmental and hormone-associated pathways.

An advanced study on the hydrometallurgical processing of waste computer printed circuit boards to extract their valuable content of metals.

PubMed

Birloaga, Ionela; Coman, Vasile; Kopacek, Bernd; Vegliò, Francesco

2014-12-01

This study refers to two chemical leaching systems for the base and precious metals extraction from waste printed circuit boards (WPCBs); sulfuric acid with hydrogen peroxide have been used for the first group of metals, meantime thiourea with the ferric ion in sulfuric acid medium were employed for the second one. The cementation process with zinc, copper and iron metal powders was attempted for solutions purification. The effects of hydrogen peroxide volume in rapport with sulfuric acid concentration and temperature were evaluated for oxidative leaching process. 2M H2SO4 (98% w/v), 5% H2O2, 25 °C, 1/10 S/L ratio and 200 rpm were founded as optimal conditions for Cu extraction. Thiourea acid leaching process, performed on the solid filtrate obtained after three oxidative leaching steps, was carried out with 20 g/L of CS(NH2)2, 6g/L of Fe(3+), 0.5M H2SO4, The cross-leaching method was applied by reusing of thiourea liquid suspension and immersing 5 g/L of this reagent for each other experiment material of leaching. This procedure has lead to the doubling and, respectively, tripling, of gold and silver concentrations into solution. These results reveal a very efficient, promising and environmental friendly method for WPCBs processing. Copyright © 2014 Elsevier Ltd. All rights reserved.

Tensor-driven extraction of developmental features from varying paediatric EEG datasets.

PubMed

Kinney-Lang, Eli; Spyrou, Loukianos; Ebied, Ahmed; Chin, Richard Fm; Escudero, Javier

2018-05-21

Constant changes in developing children's brains can pose a challenge in EEG dependant technologies. Advancing signal processing methods to identify developmental differences in paediatric populations could help improve function and usability of such technologies. Taking advantage of the multi-dimensional structure of EEG data through tensor analysis may offer a framework for extracting relevant developmental features of paediatric datasets. A proof of concept is demonstrated through identifying latent developmental features in resting-state EEG. Approach. Three paediatric datasets (n = 50, 17, 44) were analyzed using a two-step constrained parallel factor (PARAFAC) tensor decomposition. Subject age was used as a proxy measure of development. Classification used support vector machines (SVM) to test if PARAFAC identified features could predict subject age. The results were cross-validated within each dataset. Classification analysis was complemented by visualization of the high-dimensional feature structures using t-distributed Stochastic Neighbour Embedding (t-SNE) maps. Main Results. Development-related features were successfully identified for the developmental conditions of each dataset. SVM classification showed the identified features could accurately predict subject at a significant level above chance for both healthy and impaired populations. t-SNE maps revealed suitable tensor factorization was key in extracting the developmental features. Significance. The described methods are a promising tool for identifying latent developmental features occurring throughout childhood EEG. © 2018 IOP Publishing Ltd.

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

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Experimental validation of a numerical 3-D finite model applied to wind turbines design under vibration constraints: TREVISE platform

NASA Astrophysics Data System (ADS)

Sellami, Takwa; Jelassi, Sana; Darcherif, Abdel Moumen; Berriri, Hanen; Mimouni, Med Faouzi

2018-04-01

With the advancement of wind turbines towards complex structures, the requirement of trusty structural models has become more apparent. Hence, the vibration characteristics of the wind turbine components, like the blades and the tower, have to be extracted under vibration constraints. Although extracting the modal properties of blades is a simple task, calculating precise modal data for the whole wind turbine coupled to its tower/foundation is still a perplexing task. In this framework, this paper focuses on the investigation of the structural modeling approach of modern commercial micro-turbines. Thus, the structural model a complex designed wind turbine, which is Rutland 504, is established based on both experimental and numerical methods. A three-dimensional (3-D) numerical model of the structure was set up based on the finite volume method (FVM) using the academic finite element analysis software ANSYS. To validate the created model, experimental vibration tests were carried out using the vibration test system of TREVISE platform at ECAM-EPMI. The tests were based on the experimental modal analysis (EMA) technique, which is one of the most efficient techniques for identifying structures parameters. Indeed, the poles and residues of the frequency response functions (FRF), between input and output spectra, were calculated to extract the mode shapes and the natural frequencies of the structure. Based on the obtained modal parameters, the numerical designed model was up-dated.

The extraction of essential oil from patchouli leaves (Pogostemon cablin Benth) using microwave hydrodistillation and solvent-free microwave extraction methods

NASA Astrophysics Data System (ADS)

Putri, D. K. Y.; Kusuma, H. S.; Syahputra, M. E.; Parasandi, D.; Mahfud, M.

2017-12-01

Patchouli plant (Pogostemon cablin Benth) is one of the important essential oil-producing plant, contributes more than 50% of total exports of Indonesia’s essential oil. However, the extraction of patchouli oil that has been done in Indonesia is generally still used conventional methods that require enormous amount of energy, high solvent usage, and long time of extraction. Therefore, in this study, patchouli oil extraction was carried out by using microwave hydrodistillation and solvent-free microwave extraction methods. Based on this research, it is known that the extraction of patchouli oil using microwave hydrodistillation method with longer extraction time (240 min) only produced patchouli oil’s yield 1.2 times greater than solvent-free microwave extraction method which require faster extraction time (120 min). Otherwise the analysis of electric consumption and the environmental impact, the solvent-free microwave extraction method showed a smaller amount when compared with microwave hydrodistillation method. It is conclude that the use of solvent-free microwave extraction method for patchouli oil extraction is suitably method as a new green technique.

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

PubMed Central

Lorenzo, Rosa A.; Carro, Antonia M.; Alvarez-Lorenzo, Carmen; Concheiro, Angel

2011-01-01

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. PMID:21845081

To remove or not to remove? The challenge of extracting the template to make the cavities available in Molecularly Imprinted Polymers (MIPs).

PubMed

Lorenzo, Rosa A; Carro, Antonia M; Alvarez-Lorenzo, Carmen; Concheiro, Angel

2011-01-01

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.

Effectivity of advanced wastewater treatment: reduction of in vitro endocrine activity and mutagenicity but not of in vivo reproductive toxicity.

PubMed

Giebner, Sabrina; Ostermann, Sina; Straskraba, Susanne; Oetken, Matthias; Oehlmann, Jörg; Wagner, Martin

2018-02-01

Conventional wastewater treatment plants (WWTPs) have a limited capacity to eliminate micropollutants. One option to improve this is tertiary treatment. Accordingly, the WWTP Eriskirch at the German river Schussen has been upgraded with different combinations of ozonation, sand, and granulated activated carbon filtration. In this study, the removal of endocrine and genotoxic effects in vitro and reproductive toxicity in vivo was assessed in a 2-year long-term monitoring. All experiments were performed with aqueous and solid-phase extracted water samples. Untreated wastewater affected several endocrine endpoints in reporter gene assays. The conventional treatment removed the estrogenic and androgenic activity by 77 and 95 %, respectively. Nevertheless, high anti-estrogenic activities and reproductive toxicity persisted. All advanced treatment technologies further reduced the estrogenic activities by additional 69-86 % compared to conventional treatment, resulting in a complete removal of up to 97 %. In the Ames assay, we detected an ozone-induced mutagenicity, which was removed by subsequent filtration. This demonstrates that a post treatment to ozonation is needed to minimize toxic oxidative transformation products. In the reproduction test with the mudsnail Potamopyrgus antipodarum, a decreased number of embryos was observed for all wastewater samples. This indicates that reproductive toxicants were eliminated by neither the conventional nor the advanced treatment. Furthermore, aqueous samples showed higher anti-estrogenic and reproductive toxicity than extracted samples, indicating that the causative compounds are not extractable or were lost during extraction. This underlines the importance of the adequate handling of wastewater samples. Taken together, this study demonstrates that combinations of multiple advanced technologies reduce endocrine effects in vitro. However, they did not remove in vitro anti-estrogenicity and in vivo reproductive toxicity. This implies that a further optimization of advanced wastewater treatment is needed that goes beyond combining available technologies.

Evaluation of Asteraceae herbal extracts in the management of diabetes and obesity. Contribution of caffeoylquinic acids on the inhibition of digestive enzymes activity and formation of advanced glycation end-products (in vitro).

PubMed

Spínola, Vítor; Castilho, Paula C

2017-11-01

The study was performed to assess, for the first time, the in vitro anti-diabetic potential of ten Asteraceae plant extracts to inhibit the activity of digestive enzymes (α-amylase, α-, β-glucosidases and lipase) responsible for hydrolysis/digestion of sugar and lipids. Prevention of advanced glycation end-products (AGEs) formation was evaluated in bovine serum albumin/ribose glycation reaction model. The phytochemical profiles and caffeoylquinic acids (CQAs) contents were determined for the methanolic extract of each plant. Analyzed plant extracts exhibited significant inhibitory activity against key digestive enzymes linked to type II diabetes and obesity. A strong inhibition was observed for glucosidases and mild activity towards amylase and lipase (compared to reference compounds). Moreover, some extracts exhibited potent ability to prevent formation of AGEs, implicated in some diabetic complications. Caffeoylquinic acids were dominant in all plant extracts and findings demonstrate that these compounds are the most relevant hypoglycemic and anti-glycation agents. From the obtained results, Argyranthemum pinnatifidum, Helichrysum melaleucum, and Phagnalon lowei are good candidates for further development of phyto-pharmaceutical preparations as complementary therapy for diabetes and obesity control. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of Components in Water on the Extraction of Herbal Medicine
—Advanced Approach Using Multivariate Analysis—

NASA Astrophysics Data System (ADS)

Kanzaki, Yasushi

Many kinds of water products have been offered commercially suggesting some strange efficacy beyond our scientific knowledge even now at which various advanced scientific and technological research have been highly promoted. However, it seems quite obvious that such a strange efficacy must be nonexistent. If such efficacy were really existing, it must be solved by some suitable scientific procedure. In this study, the extraction of paeoniflorin from paeoniae radix was examined by varying the kind of extracting water. Then, the result was analyzed using multivariate analysis where the effect on the extraction was assumed to be ascribed to the ionic species dissolved in each water examined. The dissolved species were analyzed by chemical and instrumental analyses. According to the multivariate analysis, the amount of extracted paeoniflorin (Y) was presented by the following regression equation. The result shows that pH, [Ca2+], and [HCO3 -] were significant parameters and the combination of Ca2+ and HCO3 - affected negatively on the extraction of paeoniflorin.
Y=28.11-0.71 pH-0.0034[Ca2+]-0.93[HCO3 -]
where [Ca2+] is the concentration of calcium ion and [HCO3 -] is that of bicarbonate ion.

A 17-month time course study of human RNA and DNA degradation in body fluids under dry and humid environmental conditions.

PubMed

Sirker, Miriam; Schneider, Peter M; Gomes, Iva

2016-11-01

Blood, saliva, and semen are some of the forensically most relevant biological stains commonly found at crime scenes, which can often be of small size or challenging due to advanced decay. In this context, it is of great importance to possess reliable knowledge about the effects of degradation under different environmental conditions and to use appropriate methods for retrieving maximal information from limited sample amount. In the last decade, RNA analysis has been demonstrated to be a reliable approach identifying the cell or tissue type of an evidentiary body fluid trace. Hence, messenger RNA (mRNA) profiling is going to be implemented into forensic casework to supplement the routinely performed short tandem repeat (STR) analysis, and therefore, the ability to co-isolate RNA and DNA from the same sample is a prerequisite. The objective of this work was to monitor and compare the degradation process of both nucleic acids for human blood, saliva, and semen stains at three different concentrations, exposed to dry and humid conditions during a 17-month time period. This study also addressed the question whether there are relevant differences in the efficiency of automated, magnetic bead-based single DNA or RNA extraction methods compared to a manually performed co-extraction method using silica columns. Our data show that mRNA, especially from blood and semen, can be recovered over the entire time period surveyed without compromising the success of DNA profiling; mRNA analysis indicates to be a robust and reliable technique to identify the biological source of aged stain material. The co-extraction method appears to provide mRNA and DNA of sufficient quantity and quality for all different forensic investigation procedures. Humidity and accompanied mold formation are detrimental to both nucleic acids.

Detecting Inspection Objects of Power Line from Cable Inspection Robot LiDAR Data

PubMed Central

Qin, Xinyan; Wu, Gongping; Fan, Fei

2018-01-01

Power lines are extending to complex environments (e.g., lakes and forests), and the distribution of power lines in a tower is becoming complicated (e.g., multi-loop and multi-bundle). Additionally, power line inspection is becoming heavier and more difficult. Advanced LiDAR technology is increasingly being used to solve these difficulties. Based on precise cable inspection robot (CIR) LiDAR data and the distinctive position and orientation system (POS) data, we propose a novel methodology to detect inspection objects surrounding power lines. The proposed method mainly includes four steps: firstly, the original point cloud is divided into single-span data as a processing unit; secondly, the optimal elevation threshold is constructed to remove ground points without the existing filtering algorithm, improving data processing efficiency and extraction accuracy; thirdly, a single power line and its surrounding data can be respectively extracted by a structured partition based on a POS data (SPPD) algorithm from “layer” to “block” according to power line distribution; finally, a partition recognition method is proposed based on the distribution characteristics of inspection objects, highlighting the feature information and improving the recognition effect. The local neighborhood statistics and the 3D region growing method are used to recognize different inspection objects surrounding power lines in a partition. Three datasets were collected by two CIR LIDAR systems in our study. The experimental results demonstrate that an average 90.6% accuracy and average 98.2% precision at the point cloud level can be achieved. The successful extraction indicates that the proposed method is feasible and promising. Our study can be used to obtain precise dimensions of fittings for modeling, as well as automatic detection and location of security risks, so as to improve the intelligence level of power line inspection. PMID:29690560

Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks.

PubMed

Hale, Vanessa L; Tan, Chia L; Knight, Rob; Amato, Katherine R

2015-06-01

Studies of the gut microbiome have become increasingly common with recent technological advances. Gut microbes play an important role in human and animal health, and gut microbiome analysis holds great potential for evaluating health in wildlife, as microbiota can be assessed from non-invasively collected fecal samples. However, many common fecal preservation protocols (e.g. freezing at -80 °C) are not suitable for field conditions, or have not been tested for long-term (greater than 2 weeks) storage. In this study, we collected fresh fecal samples from captive spider monkeys (Ateles geoffroyi) at the Columbian Park Zoo (Lafayette, IN, USA). The samples were pooled, homogenized, and preserved for up to 8 weeks prior to DNA extraction and sequencing. Preservation methods included: freezing at -20 °C, freezing at -80 °C, immersion in 100% ethanol, application to FTA cards, and immersion in RNAlater. At 0 (fresh), 1, 2, 4, and 8 weeks from fecal collection, DNA was extracted and microbial DNA was amplified and sequenced. DNA concentration, purity, microbial diversity, and microbial composition were compared across all methods and time points. DNA concentration and purity did not correlate with microbial diversity or composition. Microbial composition of frozen and ethanol samples were most similar to fresh samples. FTA card and RNAlater-preserved samples had the least similar microbial composition and abundance compared to fresh samples. Microbial composition and diversity were relatively stable over time within each preservation method. Based on these results, if freezers are not available, we recommend preserving fecal samples in ethanol (for up to 8weeks) prior to microbial extraction and analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Method development for the analysis of ionophore antimicrobials in dairy manure to assess removal within a membrane-based treatment system.

PubMed

Hurst, Jerod J; Wallace, Josh S; Aga, Diana S

2018-04-01

Ionophore antimicrobials are heavily used in the livestock industries, both for preventing animal infection by coccidia protozoa and for increasing feed efficiency. Ionophores are excreted mostly unmetabolized and are released into the environment when manure is land-applied to fertilize croplands. Here, an analytical method was optimized to study the occurrences of five ionophore residues (monensin, lasalocid, maduramycin, salinomycin, and narasin) in dairy manure after solid-liquid separation and further treatment of the liquid manure by a membrane-based treatment system. Ionophore residues from the separated solid manure (dewatered manure) and suspended solids of manure slurry samples were extracted using ultrasonication with methanol, followed by sample clean-up using solid phase extraction (SPE) and subsequent analysis via liquid chromatography-tandem mass spectrometry (LC-MS/MS). The use of an ethyl acetate and methanol (1:1 v:v) mixture as an SPE eluent resulted in higher recoveries and lower method quantitation limits (MQL), when compared to using methanol. Overall recoveries from separated solid manure ranged from 73 to 134%. Liquid manure fractions were diluted with Nanopure™ water and cleaned up using SPE, where recoveries ranged from 51 to 100%. The developed extraction and LC-MS/MS methods were applied to analyze dairy manure samples subjected to an advanced manure treatment process involving a membrane-based filtration step (reverse osmosis). Monensin and lasalocid were detected at higher concentrations in the suspended solid fractions (4.40-420 ng/g for lasalocid and 85-1950 ng/g for monensin) compared to the liquid fractions (

Detecting Inspection Objects of Power Line from Cable Inspection Robot LiDAR Data.

PubMed

Qin, Xinyan; Wu, Gongping; Lei, Jin; Fan, Fei; Ye, Xuhui

2018-04-22

Power lines are extending to complex environments (e.g., lakes and forests), and the distribution of power lines in a tower is becoming complicated (e.g., multi-loop and multi-bundle). Additionally, power line inspection is becoming heavier and more difficult. Advanced LiDAR technology is increasingly being used to solve these difficulties. Based on precise cable inspection robot (CIR) LiDAR data and the distinctive position and orientation system (POS) data, we propose a novel methodology to detect inspection objects surrounding power lines. The proposed method mainly includes four steps: firstly, the original point cloud is divided into single-span data as a processing unit; secondly, the optimal elevation threshold is constructed to remove ground points without the existing filtering algorithm, improving data processing efficiency and extraction accuracy; thirdly, a single power line and its surrounding data can be respectively extracted by a structured partition based on a POS data (SPPD) algorithm from "layer" to "block" according to power line distribution; finally, a partition recognition method is proposed based on the distribution characteristics of inspection objects, highlighting the feature information and improving the recognition effect. The local neighborhood statistics and the 3D region growing method are used to recognize different inspection objects surrounding power lines in a partition. Three datasets were collected by two CIR LIDAR systems in our study. The experimental results demonstrate that an average 90.6% accuracy and average 98.2% precision at the point cloud level can be achieved. The successful extraction indicates that the proposed method is feasible and promising. Our study can be used to obtain precise dimensions of fittings for modeling, as well as automatic detection and location of security risks, so as to improve the intelligence level of power line inspection.

Positive lists of cosmetic ingredients: Analytical methodology for regulatory and safety controls - A review.

PubMed

Lores, Marta; Llompart, Maria; Alvarez-Rivera, Gerardo; Guerra, Eugenia; Vila, Marlene; Celeiro, Maria; Lamas, J Pablo; Garcia-Jares, Carmen

2016-04-07

Cosmetic products placed on the market and their ingredients, must be safe under reasonable conditions of use, in accordance to the current legislation. Therefore, regulated and allowed chemical substances must meet the regulatory criteria to be used as ingredients in cosmetics and personal care products, and adequate analytical methodology is needed to evaluate the degree of compliance. This article reviews the most recent methods (2005-2015) used for the extraction and the analytical determination of the ingredients included in the positive lists of the European Regulation of Cosmetic Products (EC 1223/2009): comprising colorants, preservatives and UV filters. It summarizes the analytical properties of the most relevant analytical methods along with the possibilities of fulfilment of the current regulatory issues. The cosmetic legislation is frequently being updated; consequently, the analytical methodology must be constantly revised and improved to meet safety requirements. The article highlights the most important advances in analytical methodology for cosmetics control, both in relation to the sample pretreatment and extraction and the different instrumental approaches developed to solve this challenge. Cosmetics are complex samples, and most of them require a sample pretreatment before analysis. In the last times, the research conducted covering this aspect, tended to the use of green extraction and microextraction techniques. Analytical methods were generally based on liquid chromatography with UV detection, and gas and liquid chromatographic techniques hyphenated with single or tandem mass spectrometry; but some interesting proposals based on electrophoresis have also been reported, together with some electroanalytical approaches. Regarding the number of ingredients considered for analytical control, single analyte methods have been proposed, although the most useful ones in the real life cosmetic analysis are the multianalyte approaches. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional Scanning Probe Imaging of Nanostructured Solar Energy Materials.

PubMed

Giridharagopal, Rajiv; Cox, Phillip A; Ginger, David S

2016-09-20

From hybrid perovskites to semiconducting polymer/fullerene blends for organic photovoltaics, many new materials being explored for energy harvesting and storage exhibit performance characteristics that depend sensitively on their nanoscale morphology. At the same time, rapid advances in the capability and accessibility of scanning probe microscopy methods over the past decade have made it possible to study processing/structure/function relationships ranging from photocurrent collection to photocarrier lifetimes with resolutions on the scale of tens of nanometers or better. Importantly, such scanning probe methods offer the potential to combine measurements of local structure with local function, and they can be implemented to study materials in situ or devices in operando to better understand how materials evolve in time in response to an external stimulus or environmental perturbation. This Account highlights recent advances in the development and application of scanning probe microscopy methods that can help address such questions while filling key gaps between the capabilities of conventional electron microscopy and newer super-resolution optical methods. Focusing on semiconductor materials for solar energy applications, we highlight a range of electrical and optoelectronic scanning probe microscopy methods that exploit the local dynamics of an atomic force microscope tip to probe key properties of the solar cell material or device structure. We discuss how it is possible to extract relevant device properties using noncontact scanning probe methods as well as how these properties guide materials development. Specifically, we discuss intensity-modulated scanning Kelvin probe microscopy (IM-SKPM), time-resolved electrostatic force microscopy (trEFM), frequency-modulated electrostatic force microscopy (FM-EFM), and cantilever ringdown imaging. We explain these developments in the context of classic atomic force microscopy (AFM) methods that exploit the physics of cantilever motion and photocarrier generation to provide robust, nanoscale measurements of materials physics that are correlated with device operation. We predict that the multidimensional data sets made possible by these types of methods will become increasingly important as advances in data science expand capabilities and opportunities for image correlation and discovery.

Human Pose Estimation from Monocular Images: A Comprehensive Survey

PubMed Central

Gong, Wenjuan; Zhang, Xuena; Gonzàlez, Jordi; Sobral, Andrews; Bouwmans, Thierry; Tu, Changhe; Zahzah, El-hadi

2016-01-01

Human pose estimation refers to the estimation of the location of body parts and how they are connected in an image. Human pose estimation from monocular images has wide applications (e.g., image indexing). Several surveys on human pose estimation can be found in the literature, but they focus on a certain category; for example, model-based approaches or human motion analysis, etc. As far as we know, an overall review of this problem domain has yet to be provided. Furthermore, recent advancements based on deep learning have brought novel algorithms for this problem. In this paper, a comprehensive survey of human pose estimation from monocular images is carried out including milestone works and recent advancements. Based on one standard pipeline for the solution of computer vision problems, this survey splits the problem into several modules: feature extraction and description, human body models, and modeling methods. Problem modeling methods are approached based on two means of categorization in this survey. One way to categorize includes top-down and bottom-up methods, and another way includes generative and discriminative methods. Considering the fact that one direct application of human pose estimation is to provide initialization for automatic video surveillance, there are additional sections for motion-related methods in all modules: motion features, motion models, and motion-based methods. Finally, the paper also collects 26 publicly available data sets for validation and provides error measurement methods that are frequently used. PMID:27898003

Application and sensitivity investigation of Fourier transforms for microwave radiometric inversions

NASA Technical Reports Server (NTRS)

Holmes, J. J.; Balanis, C. A.

1974-01-01

Existing microwave radiometer technology now provides a suitable method for remote determination of the ocean surface's absolute brightness temperature. To extract the brightness temperature of the water from the antenna temperature equation, an unstable Fredholm integral equation of the first kind was solved. Fast Fourier Transform techniques were used to invert the integral after it is placed into a cross-correlation form. Application and verification of the methods to a two-dimensional modeling of a laboratory wave tank system were included. The instability of the Fredholm equation was then demonstrated and a restoration procedure was included which smooths the resulting oscillations. With the recent availability and advances of Fast Fourier Transform techniques, the method presented becomes very attractive in the evaluation of large quantities of data. Actual radiometric measurements of sea water are inverted using the restoration method, incorporating the advantages of the Fast Fourier Transform algorithm for computations.

Determination of Diffusion Profiles in Altered Wellbore Cement Using X-ray Computed Tomography Methods

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

Mason, Harris E.; Walsh, Stuart D. C.; DuFrane, Wyatt L.

2014-06-17

The development of accurate, predictive models for use in determining wellbore integrity requires detailed information about the chemical and mechanical changes occurring in hardened Portland cements. X-ray computed tomography (XRCT) provides a method that can nondestructively probe these changes in three dimensions. Here, we describe a method for extracting subvoxel mineralogical and chemical information from synchrotron XRCT images by combining advanced image segmentation with geochemical models of cement alteration. The method relies on determining “effective linear activity coefficients” (ELAC) for the white light source to generate calibration curves that relate the image grayscales to material composition. The resulting data setmore » supports the modeling of cement alteration by CO 2-rich brine with discrete increases in calcium concentration at reaction boundaries. The results of these XRCT analyses can be used to further improve coupled geochemical and mechanical models of cement alteration in the wellbore environment.« less

Advanced spectrophotometric chemometric methods for resolving the binary mixture of doxylamine succinate and pyridoxine hydrochloride.

PubMed

Katsarov, Plamen; Gergov, Georgi; Alin, Aylin; Pilicheva, Bissera; Al-Degs, Yahya; Simeonov, Vasil; Kassarova, Margarita

2018-03-01

The prediction power of partial least squares (PLS) and multivariate curve resolution-alternating least squares (MCR-ALS) methods have been studied for simultaneous quantitative analysis of the binary drug combination - doxylamine succinate and pyridoxine hydrochloride. Analysis of first-order UV overlapped spectra was performed using different PLS models - classical PLS1 and PLS2 as well as partial robust M-regression (PRM). These linear models were compared to MCR-ALS with equality and correlation constraints (MCR-ALS-CC). All techniques operated within the full spectral region and extracted maximum information for the drugs analysed. The developed chemometric methods were validated on external sample sets and were applied to the analyses of pharmaceutical formulations. The obtained statistical parameters were satisfactory for calibration and validation sets. All developed methods can be successfully applied for simultaneous spectrophotometric determination of doxylamine and pyridoxine both in laboratory-prepared mixtures and commercial dosage forms.

Modeling Complex Biological Flows in Multi-Scale Systems using the APDEC Framework

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

Trebotich, D

We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA-laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscousmore » flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.« less

Modeling complex biological flows in multi-scale systems using the APDEC framework

NASA Astrophysics Data System (ADS)

Trebotich, David

2006-09-01

We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.

Extracting and Converting Quantitative Data into Human Error Probabilities

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

Tuan Q. Tran; Ronald L. Boring; Jeffrey C. Joe

2007-08-01

This paper discusses a proposed method using a combination of advanced statistical approaches (e.g., meta-analysis, regression, structural equation modeling) that will not only convert different empirical results into a common metric for scaling individual PSFs effects, but will also examine the complex interrelationships among PSFs. Furthermore, the paper discusses how the derived statistical estimates (i.e., effect sizes) can be mapped onto a HRA method (e.g. SPAR-H) to generate HEPs that can then be use in probabilistic risk assessment (PRA). The paper concludes with a discussion of the benefits of using academic literature in assisting HRA analysts in generating sound HEPsmore » and HRA developers in validating current HRA models and formulating new HRA models.« less

Deep Aquifer Remediation Tools (DARTs): A new technology for ground-water remediation

USGS Publications Warehouse

Naftz, David L.; Davis, James A.

1999-01-01

Potable ground-water supplies throughout the world are contaminated or threatened by advancing plumes containing radionuclides, metals, and organic compounds. Currently (1999), the most widely used method of ground-water remediation is a combination of extraction, ex-situ treatment, and discharge of the treated water, commonly known as pump and treat. Pump-and-treat methods are costly and often ineffective in meeting long-term protection standards (Travis and Doty, 1990; Gillham and Burris, 1992; National Research Council, 1994). This fact sheet describes a new and potentially cost-effective technology for removal of organic and inorganic contaminants from ground water. The U.S. Geological Survey (USGS) is currently exploring the possibilities of obtaining a U.S. Patent for this technology.

Extraction of polycyclic aromatic hydrocarbons and organochlorine pesticides from soils: a comparison between Soxhlet extraction, microwave-assisted extraction and accelerated solvent extraction techniques.

PubMed

Wang, Wentao; Meng, Bingjun; Lu, Xiaoxia; Liu, Yu; Tao, Shu

2007-10-29

The methods of simultaneous extraction of polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs) from soils using Soxhlet extraction, microwave-assisted extraction (MAE) and accelerated solvent extraction (ASE) were established, and the extraction efficiencies using the three methods were systemically compared from procedural blank, limits of detection and quantification, method recovery and reproducibility, method chromatogram and other factors. In addition, soils with different total organic carbon contents were used to test the extraction efficiencies of the three methods. The results showed that the values obtained in this study were comparable with the values reported by other studies. In some respects such as method recovery and reproducibility, there were no significant differences among the three methods for the extraction of PAHs and OCPs. In some respects such as procedural blank and limits of detection and quantification, there were significant differences among the three methods. Overall, ASE had the best extraction efficiency compared to MAE and Soxhlet extraction, and the extraction efficiencies of MAE and Soxhlet extraction were comparable to each other depending on the property such as TOC content of the studied soil. Considering other factors such as solvent consumption and extraction time, ASE and MAE are preferable to Soxhlet extraction.

ABSTRACTION FOR DATA INTEGRATION: FUSING MAMMALIAN MOLECULAR, CELLULAR AND PHENOTYPE BIG DATASETS FOR BETTER KNOWLEDGE EXTRACTION

PubMed Central

Rouillard, Andrew D.; Wang, Zichen; Ma’ayan, Avi

2015-01-01

With advances in genomics, transcriptomics, metabolomics and proteomics, and more expansive electronic clinical record monitoring, as well as advances in computation, we have entered the Big Data era in biomedical research. Data gathering is growing rapidly while only a small fraction of this data is converted to useful knowledge or reused in future studies. To improve this, an important concept that is often overlooked is data abstraction. To fuse and reuse biomedical datasets from diverse resources, data abstraction is frequently required. Here we summarize some of the major Big Data biomedical research resources for genomics, proteomics and phenotype data, collected from mammalian cells, tissues and organisms. We then suggest simple data abstraction methods for fusing this diverse but related data. Finally, we demonstrate examples of the potential utility of such data integration efforts, while warning about the inherit biases that exist within such data. PMID:26101093

Body to Scalp: Evolving Trends in Body Hair Transplantation

PubMed Central

Saxena, Kuldeep; Savant, Sandeep S.

2017-01-01

Follicular unit extraction (FUE) is becoming an increasingly popular method for hair restoration. As FUE leaves behind no linear scars, it is more suitable to harvest from various body areas including beard, chest, and extremities in hirsute individuals. Body hair characteristics such as thickness, length, and hair cycle may not completely match to that of the scalp hair. The techniques of harvesting body hairs are more time consuming, requiring higher degree of skill than regular scalp FUE. Body hair transplantation can be successfully used either alone or in combination with scalp hair in advanced grades of baldness, for improving the cosmetic appearance of hairlines and in scarring alopecia when there is paucity of donor scalp hair. Harvesting of body hairs opens up a new viable donor source for hair restoration surgeons, especially in cases of advanced Norwood grades five and above of androgenetic alopecia. PMID:28584752

Advanced Video Analysis Needs for Human Performance Evaluation

NASA Technical Reports Server (NTRS)

Campbell, Paul D.

1994-01-01

Evaluators of human task performance in space missions make use of video as a primary source of data. Extraction of relevant human performance information from video is often a labor-intensive process requiring a large amount of time on the part of the evaluator. Based on the experiences of several human performance evaluators, needs were defined for advanced tools which could aid in the analysis of video data from space missions. Such tools should increase the efficiency with which useful information is retrieved from large quantities of raw video. They should also provide the evaluator with new analytical functions which are not present in currently used methods. Video analysis tools based on the needs defined by this study would also have uses in U.S. industry and education. Evaluation of human performance from video data can be a valuable technique in many industrial and institutional settings where humans are involved in operational systems and processes.

The Coso geothermal area: A laboratory for advanced MEQ studies for geothermal monitoring

USGS Publications Warehouse

Julian, B.R.; Foulger, G.R.; Richards-Dinger, K.

2004-01-01

The permanent 16-station network of three-component digital seismometers at the Coso geothermal area, California, supplemented by 14 temporary instruments deployed in connection with the DOE Enhanced Geothermal Systems (EGS) Project, provides high-quality microearthquake (MEQ) recordings that are well suited to monitoring a producing geothermal area. We are currently using these data to investigate structure and active processes within the geothermal reservoir by applying three advanced methods: a) high-precision MEQ hypocenter location; b) time-dependent tomography; c) complete (moment tensor) MEQ source mechanism determination. Preliminary results to date resolve seismogenic structures in the producing field more clearly than is possible with conventional earthquake-location techniques. A shallow part of the producing field shows clear changes in the ratio of the seismic wave speeds, Vp/V s, between 1996 and 2002, which are probably related to physical changes in the reservoir caused by fluid extraction.

Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

PubMed

Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

2018-01-01

Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

Apparatus and methods for hydrocarbon extraction

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

Bohnert, George W.; Verhulst, Galen G.

Systems and methods for hydrocarbon extraction from hydrocarbon-containing material. Such systems and methods relate to extracting hydrocarbon from hydrocarbon-containing material employing a non-aqueous extractant. Additionally, such systems and methods relate to recovering and reusing non-aqueous extractant employed for extracting hydrocarbon from hydrocarbon-containing material.

Obtaining titanium dioxide nanoparticles with spherical shape and antimicrobial properties using M. citrifolia leaves extract by hydrothermal method.

PubMed

M, Sundrarajan; K, Bama; M, Bhavani; S, Jegatheeswaran; S, Ambika; A, Sangili; P, Nithya; R, Sumathi

2017-06-01

In this work, we synthesized titanium dioxide (TiO 2 ) nanoparticles using leaf extract of Morinda citrifolia (M. citrifolia) by the advanced hydrothermal method. The synthesized TiO 2 nanoparticles were characterized by X-ray diffraction (XRD), Fourier transmission infrared (FT-IR), Ultraviolet-visible diffuse reflectance (UV-Vis DRS), Ultraviolet-visible spectroscopy (UV-Vis), Raman spectroscopy, and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM with EDX) techniques. The XRD major peak at 27.3° corresponds to the (110) lattice plane of tetragonal rutile TiO 2 phase and average crystalline size of nanoparticles is 10nm. The FT-IR result confirmed that TiO 2 nanoparticles and the presences of very few amount of anthraquinone and phenolic compounds of the leaf extract. The obtained nanoparticles were also characterized by UV-Vis DRS absorption spectroscopy and an intense band at 423nm clearly reveals the formation of nanoparticles. SEM images with EDX spectra clearly reveal the size of the nanoparticles, between 15 and 19nm in excellent quasi-spherical shape, by virtue of stabilization (capping) agent. The presence of elements-titanium and oxygen was verified with EDX spectrum. Furthermore, the inhibitory activity of green synthesized TiO 2 nanoparticles was tested against human pathogens like Staphylococcus aureus, Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, Candida albicans, and Aspergillus niger by the agar well-diffusion method. The TiO 2 nanoparticles exhibited superior antimicrobial activity against Gram-positive bacteria, demonstrating their antimicrobial value against pathogenic diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

Automatic pole-like object modeling via 3D part-based analysis of point cloud

NASA Astrophysics Data System (ADS)

He, Liu; Yang, Haoxiang; Huang, Yuchun

2016-10-01

Pole-like objects, including trees, lampposts and traffic signs, are indispensable part of urban infrastructure. With the advance of vehicle-based laser scanning (VLS), massive point cloud of roadside urban areas becomes applied in 3D digital city modeling. Based on the property that different pole-like objects have various canopy parts and similar trunk parts, this paper proposed the 3D part-based shape analysis to robustly extract, identify and model the pole-like objects. The proposed method includes: 3D clustering and recognition of trunks, voxel growing and part-based 3D modeling. After preprocessing, the trunk center is identified as the point that has local density peak and the largest minimum inter-cluster distance. Starting from the trunk centers, the remaining points are iteratively clustered to the same centers of their nearest point with higher density. To eliminate the noisy points, cluster border is refined by trimming boundary outliers. Then, candidate trunks are extracted based on the clustering results in three orthogonal planes by shape analysis. Voxel growing obtains the completed pole-like objects regardless of overlaying. Finally, entire trunk, branch and crown part are analyzed to obtain seven feature parameters. These parameters are utilized to model three parts respectively and get signal part-assembled 3D model. The proposed method is tested using the VLS-based point cloud of Wuhan University, China. The point cloud includes many kinds of trees, lampposts and other pole-like posters under different occlusions and overlaying. Experimental results show that the proposed method can extract the exact attributes and model the roadside pole-like objects efficiently.

Signal processing techniques for damage detection with piezoelectric wafer active sensors and embedded ultrasonic structural radar

NASA Astrophysics Data System (ADS)

Yu, Lingyu; Bao, Jingjing; Giurgiutiu, Victor

2004-07-01

Embedded ultrasonic structural radar (EUSR) algorithm is developed for using piezoelectric wafer active sensor (PWAS) array to detect defects within a large area of a thin-plate specimen. Signal processing techniques are used to extract the time of flight of the wave packages, and thereby to determine the location of the defects with the EUSR algorithm. In our research, the transient tone-burst wave propagation signals are generated and collected by the embedded PWAS. Then, with signal processing, the frequency contents of the signals and the time of flight of individual frequencies are determined. This paper starts with an introduction of embedded ultrasonic structural radar algorithm. Then we will describe the signal processing methods used to extract the time of flight of the wave packages. The signal processing methods being used include the wavelet denoising, the cross correlation, and Hilbert transform. Though hardware device can provide averaging function to eliminate the noise coming from the signal collection process, wavelet denoising is included to ensure better signal quality for the application in real severe environment. For better recognition of time of flight, cross correlation method is used. Hilbert transform is applied to the signals after cross correlation in order to extract the envelope of the signals. Signal processing and EUSR are both implemented by developing a graphical user-friendly interface program in LabView. We conclude with a description of our vision for applying EUSR signal analysis to structural health monitoring and embedded nondestructive evaluation. To this end, we envisage an automatic damage detection application utilizing embedded PWAS, EUSR, and advanced signal processing.

Wavelet Filter Banks for Super-Resolution SAR Imaging

NASA Technical Reports Server (NTRS)

Sheybani, Ehsan O.; Deshpande, Manohar; Memarsadeghi, Nargess

2011-01-01

This paper discusses Innovative wavelet-based filter banks designed to enhance the analysis of super resolution Synthetic Aperture Radar (SAR) images using parametric spectral methods and signal classification algorithms, SAR finds applications In many of NASA's earth science fields such as deformation, ecosystem structure, and dynamics of Ice, snow and cold land processes, and surface water and ocean topography. Traditionally, standard methods such as Fast-Fourier Transform (FFT) and Inverse Fast-Fourier Transform (IFFT) have been used to extract Images from SAR radar data, Due to non-parametric features of these methods and their resolution limitations and observation time dependence, use of spectral estimation and signal pre- and post-processing techniques based on wavelets to process SAR radar data has been proposed. Multi-resolution wavelet transforms and advanced spectral estimation techniques have proven to offer efficient solutions to this problem.

Enhancing clinical concept extraction with distributional semantics

PubMed Central

Cohen, Trevor; Wu, Stephen; Gonzalez, Graciela

2011-01-01

Extracting concepts (such as drugs, symptoms, and diagnoses) from clinical narratives constitutes a basic enabling technology to unlock the knowledge within and support more advanced reasoning applications such as diagnosis explanation, disease progression modeling, and intelligent analysis of the effectiveness of treatment. The recent release of annotated training sets of de-identified clinical narratives has contributed to the development and refinement of concept extraction methods. However, as the annotation process is labor-intensive, training data are necessarily limited in the concepts and concept patterns covered, which impacts the performance of supervised machine learning applications trained with these data. This paper proposes an approach to minimize this limitation by combining supervised machine learning with empirical learning of semantic relatedness from the distribution of the relevant words in additional unannotated text. The approach uses a sequential discriminative classifier (Conditional Random Fields) to extract the mentions of medical problems, treatments and tests from clinical narratives. It takes advantage of all Medline abstracts indexed as being of the publication type “clinical trials” to estimate the relatedness between words in the i2b2/VA training and testing corpora. In addition to the traditional features such as dictionary matching, pattern matching and part-of-speech tags, we also used as a feature words that appear in similar contexts to the word in question (that is, words that have a similar vector representation measured with the commonly used cosine metric, where vector representations are derived using methods of distributional semantics). To the best of our knowledge, this is the first effort exploring the use of distributional semantics, the semantics derived empirically from unannotated text often using vector space models, for a sequence classification task such as concept extraction. Therefore, we first experimented with different sliding window models and found the model with parameters that led to best performance in a preliminary sequence labeling task. The evaluation of this approach, performed against the i2b2/VA concept extraction corpus, showed that incorporating features based on the distribution of words across a large unannotated corpus significantly aids concept extraction. Compared to a supervised-only approach as a baseline, the micro-averaged f-measure for exact match increased from 80.3% to 82.3% and the micro-averaged f-measure based on inexact match increased from 89.7% to 91.3%. These improvements are highly significant according to the bootstrap resampling method and also considering the performance of other systems. Thus, distributional semantic features significantly improve the performance of concept extraction from clinical narratives by taking advantage of word distribution information obtained from unannotated data. PMID:22085698

Applications of micellar enzymology to clean coal technology. [Laccase from Polyporus versicolor

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

Walsh, C.T.

1990-07-24

This project is designed to develop methods for pre-combustion coal remediation by implementing recent advances in enzyme biochemistry. The novel approach of this study is incorporation of hydrophilic oxidative enzymes in reverse micelles in an organic solvent. Enzymes from commercial sources or microbial extracts are being investigated for their capacity to remove organic sulfur from coal by oxidation of the sulfur groups, splitting of C-S bonds and loss of sulfur as sulfuric acid. Dibenzothiophen (DBT) and ethylphenylsulfide (EPS) are serving as models of organic sulfur-containing components of coal in initial studies.

Identifying explosives by dielectric properties obtained through wide-band millimeter-wave illumination

NASA Astrophysics Data System (ADS)

Weatherall, James C.; Barber, Jeffrey; Smith, Barry T.

2015-05-01

A method for extracting dielectric constant from free-space 18 - 40 GHz millimeter-wave reflection data is demonstrated. The reflection coefficient is a function of frequency because of propagation effects, and numerically fitting data to a theoretical model based on geometric optics gives a solution for the complex dielectric constant and target thickness. The discriminative value is illustrated with inert substances and military sheet explosive. In principle, the measurement of reflectivity across multiple frequencies can be incorporated into Advanced Imaging Technology (AIT) systems to automatically identify the composition of anomalies detected on persons at screening checkpoints.

Influencing of various phosphor parameters on the LED performance

NASA Astrophysics Data System (ADS)

Wu, Yi Ping; Zhang, Shu Qin; Jin, Shang-zhong; Shi, Chang Shou; Li, Liang; Yu, RenYong

2012-10-01

In this paper ,the advantages and disadvantages of the methods to achieve White LED are reviewed, and phosphor-converted white LEDs are discussed in detail. In the case of blue chip exciting YAG phosphor to get white LED, use Mie scattering theory to construct physical model, then analyze how the package, concentration, thickness and particle size of phosphor work on extraction efficiency, spatial Chroma uniformity and color temperature of white LED. The conclusion of this paper advances the application of LED solid-state light source. In the end, the paper puts forward the direction and focus of phosphor research.

Graph transformation method for calculating waiting times in Markov chains.

PubMed

Trygubenko, Semen A; Wales, David J

2006-06-21

We describe an exact approach for calculating transition probabilities and waiting times in finite-state discrete-time Markov processes. All the states and the rules for transitions between them must be known in advance. We can then calculate averages over a given ensemble of paths for both additive and multiplicative properties in a nonstochastic and noniterative fashion. In particular, we can calculate the mean first-passage time between arbitrary groups of stationary points for discrete path sampling databases, and hence extract phenomenological rate constants. We present a number of examples to demonstrate the efficiency and robustness of this approach.

[Advancements of computer chemistry in separation of Chinese medicine].

PubMed

Li, Lingjuan; Hong, Hong; Xu, Xuesong; Guo, Liwei

2011-12-01

Separating technique of Chinese medicine is not only a key technique in the field of Chinese medicine' s research and development, but also a significant step in the modernization of Chinese medicinal preparation. Computer chemistry can build model and look for the regulations from Chinese medicine system which is full of complicated data. This paper analyzed the applicability, key technology, basic mode and common algorithm of computer chemistry applied in the separation of Chinese medicine, introduced the mathematic mode and the setting methods of Extraction kinetics, investigated several problems which based on traditional Chinese medicine membrane procession, and forecasted the application prospect.

An improved strategy for skin lesion detection and classification using uniform segmentation and feature selection based approach.

PubMed

Nasir, Muhammad; Attique Khan, Muhammad; Sharif, Muhammad; Lali, Ikram Ullah; Saba, Tanzila; Iqbal, Tassawar

2018-02-21

Melanoma is the deadliest type of skin cancer with highest mortality rate. However, the annihilation in early stage implies a high survival rate therefore, it demands early diagnosis. The accustomed diagnosis methods are costly and cumbersome due to the involvement of experienced experts as well as the requirements for highly equipped environment. The recent advancements in computerized solutions for these diagnoses are highly promising with improved accuracy and efficiency. In this article, we proposed a method for the classification of melanoma and benign skin lesions. Our approach integrates preprocessing, lesion segmentation, features extraction, features selection, and classification. Preprocessing is executed in the context of hair removal by DullRazor, whereas lesion texture and color information are utilized to enhance the lesion contrast. In lesion segmentation, a hybrid technique has been implemented and results are fused using additive law of probability. Serial based method is applied subsequently that extracts and fuses the traits such as color, texture, and HOG (shape). The fused features are selected afterwards by implementing a novel Boltzman Entropy method. Finally, the selected features are classified by Support Vector Machine. The proposed method is evaluated on publically available data set PH2. Our approach has provided promising results of sensitivity 97.7%, specificity 96.7%, accuracy 97.5%, and F-score 97.5%, which are significantly better than the results of existing methods available on the same data set. The proposed method detects and classifies melanoma significantly good as compared to existing methods. © 2018 Wiley Periodicals, Inc.

[Progress of light extraction enhancement in organic light-emitting devices].

PubMed

Liu, Mo; Li, Tong; Wang, Yan; Zhang, Tian-Yu; Xie, Wen-Fa

2011-04-01

Organic light emitting devices (OLEDs) have been used in flat-panel displays and lighting with a near-30-year development. OLEDs possess many advantages, such as full solid device, fast response, flexible display, and so on. As the application of phosphorescence material, the internal quantum efficiency of OLED has almost reached 100%, but its external quantum efficiency is still not very high due to the low light extraction efficiency. In this review the authors summarizes recent advances in light extraction techniques that have been developed to enhance the light extraction efficiency of OLEDs.

Single-Grasp Object Classification and Feature Extraction with Simple Robot Hands and Tactile Sensors.

PubMed

Spiers, Adam J; Liarokapis, Minas V; Calli, Berk; Dollar, Aaron M

2016-01-01

Classical robotic approaches to tactile object identification often involve rigid mechanical grippers, dense sensor arrays, and exploratory procedures (EPs). Though EPs are a natural method for humans to acquire object information, evidence also exists for meaningful tactile property inference from brief, non-exploratory motions (a 'haptic glance'). In this work, we implement tactile object identification and feature extraction techniques on data acquired during a single, unplanned grasp with a simple, underactuated robot hand equipped with inexpensive barometric pressure sensors. Our methodology utilizes two cooperating schemes based on an advanced machine learning technique (random forests) and parametric methods that estimate object properties. The available data is limited to actuator positions (one per two link finger) and force sensors values (eight per finger). The schemes are able to work both independently and collaboratively, depending on the task scenario. When collaborating, the results of each method contribute to the other, improving the overall result in a synergistic fashion. Unlike prior work, the proposed approach does not require object exploration, re-grasping, grasp-release, or force modulation and works for arbitrary object start positions and orientations. Due to these factors, the technique may be integrated into practical robotic grasping scenarios without adding time or manipulation overheads.

Simultaneous determination of 76 micropollutants in water samples by headspace solid phase microextraction and gas chromatography-mass spectrometry.

PubMed

Martínez, C; Ramírez, N; Gómez, V; Pocurull, E; Borrull, F

2013-11-15

This study focuses on the development of an analytical method based on headspace solid phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) for the simultaneous determination of 76 micropollutants in water samples. The selected micropollutants include volatile organic compounds (VOCs) (e.g. chlorobenzenes, chloroalkanes), endocrine disrupting compounds (EDCs) (e.g. bisphenol A and tributyl phosphate), odour compounds (e.g. limonene, phenol), fragrance allergens (e.g. geraniol, eugenol) and some pesticides (e.g. heptachlor, terbutryn). The experimental conditions affecting their extraction, such as the type of fibre, temperature and time of extraction, sample volume and ionic strength of the samples were optimized using HS-SPME. The method showed good linear range, reproducibility between days, repeatability and low detection limits (at ng L(-1) levels). The validated method has been applied to determine the target organic micropollutants in aqueous samples from different experimental research units of surface water, sea water, waste water and those effluents of advance membrane treatments. The optimized method showed good performance in the different types of samples studied. The analysis revealed the presence of several micropollutants at concentrations between 20 and 5000 μg L(-1), such as ethylbenzene, o-xylene, p-isopropilbenzene, D-limonene, citral and isoeugenol, due to the fact that these species are commonly used in domestic and industrial applications. © 2013 Elsevier B.V. All rights reserved.

A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans.

PubMed

Mauchline, T H; Mohan, S; Davies, K G; Schaff, J E; Opperman, C H; Kerry, B R; Hirsch, P R

2010-05-01

To establish a reliable protocol to extract DNA from Pasteuria penetrans endospores for use as template in multiple strand amplification, thus providing sufficient material for genetic analyses. To develop a highly sensitive PCR-based diagnostic tool for P. penetrans. An optimized method to decontaminate endospores, release and purify DNA enabled multiple strand amplification. DNA purity was assessed by cloning and sequencing gyrB and 16S rRNA gene fragments obtained from PCR using generic primers. Samples indicated to be 100%P. penetrans by the gyrB assay were estimated at 46% using the 16S rRNA gene. No bias was detected on cloning and sequencing 12 housekeeping and sporulation gene fragments from amplified DNA. The detection limit by PCR with Pasteuria-specific 16S rRNA gene primers following multiple strand amplification of DNA extracted using the method was a single endospore. Generation of large quantities DNA will facilitate genomic sequencing of P. penetrans. Apparent differences in sample purity are explained by variations in 16S rRNA gene copy number in Eubacteria leading to exaggerated estimations of sample contamination. Detection of single endospores will facilitate investigations of P. penetrans molecular ecology. These methods will advance studies on P. penetrans and facilitate research on other obligate and fastidious micro-organisms where it is currently impractical to obtain DNA in sufficient quantity and quality.

Landscape consequences of natural gas extraction in Lackawanna and Wayne Counties, Pennsylvania, 2004-2010

USGS Publications Warehouse

Milheim, L.E.; Slonecker, E.T.; Roig-Silva, C.M.; Malizia, A.R.

2013-01-01

Increased demands for cleaner burning energy, coupled with the relatively recent technological advances in accessing unconventional hydrocarbon-rich geologic formations, have led to an intense effort to find and extract natural gas from various underground sources around the country. One of these sources, the Marcellus Shale, located in the Allegheny Plateau, is currently undergoing extensive drilling and production. The technology used to extract gas in the Marcellus Shale is known as hydraulic fracturing and has garnered much attention because of its use of large amounts of fresh water, its use of proprietary fluids for the hydraulic-fracturing process, its potential to release contaminants into the environment, and its potential effect on water resources. Nonetheless, development of natural gas extraction wells in the Marcellus Shale is only part of the overall natural gas story in this area of Pennsylvania. Conventional natural gas wells, which sometimes use the same technique, are commonly located in the same general area as the Marcellus Shale and are frequently developed in clusters across the landscape. The combined effects of these two natural gas extraction methods create potentially serious patterns of disturbance on the landscape. This document quantifies the landscape changes and consequences of natural gas extraction for Lackawanna County and Wayne County in Pennsylvania between 2004 and 2010. Patterns of landscape disturbance related to natural gas extraction activities were collected and digitized using National Agriculture Imagery Program (NAIP) imagery for 2004, 2005/2006, 2008, and 2010. The disturbance patterns were then used to measure changes in land cover and land use using the National Land Cover Database (NLCD) of 2001. A series of landscape metrics is also used to quantify these changes and is included in this publication.

Landscape consequences of natural gas extraction in Armstrong and Indiana Counties, Pennsylvania, 2004–2010

USGS Publications Warehouse

Slonecker, Terry E.; Milheim, Lesley E.; Roig-Silva, Coral M.; Malizia, Alexander R.

2013-01-01

Increased demands for cleaner burning energy, coupled with the relatively recent technological advances in accessing unconventional hydrocarbon-rich geologic formations, have led to an intense effort to find and extract natural gas from various underground sources around the country. One of these sources, the Marcellus Shale, located in the Allegheny Plateau, is currently undergoing extensive drilling and production. The technology used to extract gas in the Marcellus Shale is known as hydraulic fracturing and has garnered much attention because of its use of large amounts of fresh water, its use of proprietary fluids for the hydraulic-fracturing process, its potential to release contaminants into the environment, and its potential effect on water resources. Nonetheless, development of natural gas extraction wells in the Marcellus Shale is only part of the overall natural gas story in this area of Pennsylvania. Conventional natural gas wells are commonly located in the same general area as the Marcellus Shale and are frequently developed in clusters across the landscape. The combined effects of these two natural gas extraction methods create potentially serious patterns of disturbance on the landscape. This document quantifies the landscape changes and consequences of natural gas extraction for Armstrong County and Indiana County in Pennsylvania between 2004 and 2010. Patterns of landscape disturbance related to natural gas extraction activities were collected and digitized using National Agriculture Imagery Program (NAIP) imagery for 2004, 2005/2006, 2008, and 2010. The disturbance patterns were then used to measure changes in land cover and land use using the National Land Cover Database (NLCD) of 2001. A series of landscape metrics is also used to quantify these changes and is included in this publication.

Landscape consequences of natural gas extraction in Somerset and Westmoreland Counties, Pennsylvania,2004--2010

USGS Publications Warehouse

Milheim, L.E.; Slonecker, E.T.; Roig-Silva, C.M.; Malizia, A.R.

2013-01-01

Increased demands for cleaner burning energy, coupled with the relatively recent technological advances in accessing unconventional hydrocarbon-rich geologic formations, have led to an intense effort to find and extract natural gas from various underground sources around the country. One of these sources, the Marcellus Shale, located in the Allegheny Plateau, is currently undergoing extensive drilling and production. The technology used to extract gas in the Marcellus Shale is known as hydraulic fracturing and has garnered much attention because of its use of large amounts of fresh water, its use of proprietary fluids for the hydraulic-fracturing process, its potential to release contaminants into the environment, and its potential effect on water resources. Nonetheless, development of natural gas extraction wells in the Marcellus Shale is only part of the overall natural gas story in this area of Pennsylvania. Conventional natural gas wells, which sometimes use the same technique, are commonly located in the same general area as the Marcellus Shale and are frequently developed in clusters across the landscape. The combined effects of these two natural gas extraction methods create potentially serious patterns of disturbance on the landscape. This document quantifies the landscape changes and consequences of natural gas extraction for Somerset County and Westmoreland County in Pennsylvania between 2004 and 2010. Patterns of landscape disturbance related to natural gas extraction activities were collected and digitized using National Agriculture Imagery Program (NAIP) imagery for 2004, 2005/2006, 2008, and 2010. The disturbance patterns were then used to measure changes in land cover and land use using the National Land Cover Database (NLCD) of 2001. A series of landscape metrics is also used to quantify these changes and is included in this publication.

Landscape consequences of natural gas extraction in Sullivan and Wyoming Counties, Pennsylvania, 2004–2010

USGS Publications Warehouse

Slonecker, Terry E.; Milheim, Lesley E.; Roig-Silva, Coral M.; Malizia, Alexander R.

2013-01-01

Increased demands for cleaner burning energy, coupled with the relatively recent technological advances in accessing unconventional hydrocarbon-rich geologic formations, have led to an intense effort to find and extract natural gas from various underground sources around the country. One of these sources, the Marcellus Shale, located in the Allegheny Plateau, is currently undergoing extensive drilling and production. The technology used to extract gas in the Marcellus Shale is known as hydraulic fracturing and has garnered much attention because of its use of large amounts of fresh water, its use of proprietary fluids for the hydraulic-fracturing process, its potential to release contaminants into the environment, and its potential effect on water resources. Nonetheless, development of natural gas extraction wells in the Marcellus Shale is only part of the overall natural gas story in this area of Pennsylvania. Conventional natural gas wells, which sometimes use the same technique, are commonly located in the same general area as the Marcellus Shale and are frequently developed in clusters across the landscape. The combined effects of these two natural gas extraction methods create potentially serious patterns of disturbance on the landscape. This document quantifies the landscape changes and consequences of natural gas extraction for Sullivan County and Wyoming County in Pennsylvania between 2004 and 2010. Patterns of landscape disturbance related to natural gas extraction activities were collected and digitized using National Agriculture Imagery Program (NAIP) imagery for 2004, 2005/2006, 2008, and 2010. The disturbance patterns were then used to measure changes in land cover and land use using the National Land Cover Database (NLCD) of 2001. A series of landscape metrics is also used to quantify these changes and is included in this publication.

Landscape consequences of natural gas extraction in Fayette and Lycoming Counties, Pennsylvania, 2004–2010

USGS Publications Warehouse

Slonecker, E.T.; Milheim, L.E.; Roig-Silva, C.M.; Malizia, A.R.; Gillenwater, B.H.

2013-01-01

Increased demands for cleaner burning energy, coupled with the relatively recent technological advances in accessing unconventional hydrocarbon-rich geologic formations, have led to an intense effort to find and extract natural gas from various underground sources around the country. One of these sources, the Marcellus Shale, located in the Allegheny Plateau, is currently undergoing extensive drilling and production. The technology used to extract gas in the Marcellus Shale is known as hydraulic fracturing and has garnered much attention because of its use of large amounts of fresh water, its use of proprietary fluids for the hydraulic-fracturing process, its potential to release contaminants into the environment, and its potential effect on water resources. Nonetheless, development of natural gas extraction wells in the Marcellus Shale is only part of the overall natural gas story in this area of Pennsylvania. Conventional natural gas wells, which sometimes use the same technique, are commonly located in the same general area as the Marcellus Shale and are frequently developed in clusters across the landscape. The combined effects of these two natural gas extraction methods create potentially serious patterns of disturbance on the landscape. This document quantifies the landscape changes and consequences of natural gas extraction for Fayette County and Lycoming County in Pennsylvania between 2004 and 2010. Patterns of landscape disturbance related to natural gas extraction activities were collected and digitized using National Agriculture Imagery Program (NAIP) imagery for 2004, 2005/2006, 2008, and 2010. The disturbance patterns were then used to measure changes in land cover and land use using the National Land Cover Database (NLCD) of 2001. A series of landscape metrics is also used to quantify these changes and is included in this publication.

Landscape consequences of natural gas extraction in Beaver and Butler Counties, Pennsylvania, 2004-2010

USGS Publications Warehouse

Roig-Silva, Coral M.; Slonecker, E. Terry; Milheim, Lesley E.; Malizia, Alexander R.

2013-01-01

Increased demands for cleaner burning energy, coupled with the relatively recent technological advances in accessing unconventional hydrocarbon-rich geologic formations, have led to an intense effort to find and extract natural gas from various underground sources around the country. One of these sources, the Marcellus Shale, located in the Allegheny Plateau, is currently undergoing extensive drilling and production. The technology used to extract gas in the Marcellus Shale is known as hydraulic fracturing and has garnered much attention because of its use of large amounts of fresh water, its use of proprietary fluids for the hydraulic-fracturing process, its potential to release contaminants into the environment, and its potential effect on water resources. Nonetheless, development of natural gas extraction wells in the Marcellus Shale is only part of the overall natural gas story in this area of Pennsylvania. Conventional natural gas wells, which sometimes use the same technique, are commonly located in the same general area as the Marcellus Shale and are frequently developed in clusters across the landscape. The combined effects of these two natural gas extraction methods create potentially serious patterns of disturbance on the landscape. This document quantifies the landscape changes and consequences of natural gas extraction for Beaver County and Butler County in Pennsylvania between 2004 and 2010. Patterns of landscape disturbance related to natural gas extraction activities were collected and digitized using National Agriculture Imagery Program (NAIP) imagery for 2004, 2005/2006, 2008, and 2010. The disturbance patterns were then used to measure changes in land cover and land use using the National Land Cover Database (NLCD) of 2001. A series of landscape metrics is also used to quantify these changes and is included in this publication.

Crown-Level Tree Species Classification Using Integrated Airborne Hyperspectral and LIDAR Remote Sensing Data

NASA Astrophysics Data System (ADS)

Wang, Z.; Wu, J.; Wang, Y.; Kong, X.; Bao, H.; Ni, Y.; Ma, L.; Jin, J.

2018-05-01

Mapping tree species is essential for sustainable planning as well as to improve our understanding of the role of different trees as different ecological service. However, crown-level tree species automatic classification is a challenging task due to the spectral similarity among diversified tree species, fine-scale spatial variation, shadow, and underlying objects within a crown. Advanced remote sensing data such as airborne Light Detection and Ranging (LiDAR) and hyperspectral imagery offer a great potential opportunity to derive crown spectral, structure and canopy physiological information at the individual crown scale, which can be useful for mapping tree species. In this paper, an innovative approach was developed for tree species classification at the crown level. The method utilized LiDAR data for individual tree crown delineation and morphological structure extraction, and Compact Airborne Spectrographic Imager (CASI) hyperspectral imagery for pure crown-scale spectral extraction. Specifically, four steps were include: 1) A weighted mean filtering method was developed to improve the accuracy of the smoothed Canopy Height Model (CHM) derived from LiDAR data; 2) The marker-controlled watershed segmentation algorithm was, therefore, also employed to delineate the tree-level canopy from the CHM image in this study, and then individual tree height and tree crown were calculated according to the delineated crown; 3) Spectral features within 3 × 3 neighborhood regions centered on the treetops detected by the treetop detection algorithm were derived from the spectrally normalized CASI imagery; 4) The shape characteristics related to their crown diameters and heights were established, and different crown-level tree species were classified using the combination of spectral and shape characteristics. Analysis of results suggests that the developed classification strategy in this paper (OA = 85.12 %, Kc = 0.90) performed better than LiDAR-metrics method (OA = 79.86 %, Kc = 0.81) and spectral-metircs method (OA = 71.26, Kc = 0.69) in terms of classification accuracy, which indicated that the advanced method of data processing and sensitive feature selection are critical for improving the accuracy of crown-level tree species classification.

An improved independent component analysis model for 3D chromatogram separation and its solution by multi-areas genetic algorithm.

PubMed

Cui, Lizhi; Poon, Josiah; Poon, Simon K; Chen, Hao; Gao, Junbin; Kwan, Paul; Fan, Kei; Ling, Zhihao

2014-01-01

The 3D chromatogram generated by High Performance Liquid Chromatography-Diode Array Detector (HPLC-DAD) has been researched widely in the field of herbal medicine, grape wine, agriculture, petroleum and so on. Currently, most of the methods used for separating a 3D chromatogram need to know the compounds' number in advance, which could be impossible especially when the compounds are complex or white noise exist. New method which extracts compounds from 3D chromatogram directly is needed. In this paper, a new separation model named parallel Independent Component Analysis constrained by Reference Curve (pICARC) was proposed to transform the separation problem to a multi-parameter optimization issue. It was not necessary to know the number of compounds in the optimization. In order to find all the solutions, an algorithm named multi-areas Genetic Algorithm (mGA) was proposed, where multiple areas of candidate solutions were constructed according to the fitness and distances among the chromosomes. Simulations and experiments on a real life HPLC-DAD data set were used to demonstrate our method and its effectiveness. Through simulations, it can be seen that our method can separate 3D chromatogram to chromatogram peaks and spectra successfully even when they severely overlapped. It is also shown by the experiments that our method is effective to solve real HPLC-DAD data set. Our method can separate 3D chromatogram successfully without knowing the compounds' number in advance, which is fast and effective.

Advances in targeted proteomics and applications to biomedical research

PubMed Central

Shi, Tujin; Song, Ehwang; Nie, Song; Rodland, Karin D.; Liu, Tao; Qian, Wei-Jun; Smith, Richard D.

2016-01-01

Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed. PMID:27302376

Advances in targeted proteomics and applications to biomedical research

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

Shi, Tujin; Song, Ehwang; Nie, Song

Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074–1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications inmore » human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.« less

Information sciences experiment system

NASA Technical Reports Server (NTRS)

Katzberg, Stephen J.; Murray, Nicholas D.; Benz, Harry F.; Bowker, David E.; Hendricks, Herbert D.

1990-01-01

The rapid expansion of remote sensing capability over the last two decades will take another major leap forward with the advent of the Earth Observing System (Eos). An approach is presented that will permit experiments and demonstrations in onboard information extraction. The approach is a non-intrusive, eavesdropping mode in which a small amount of spacecraft real estate is allocated to an onboard computation resource. How such an approach allows the evaluation of advanced technology in the space environment, advanced techniques in information extraction for both Earth science and information science studies, direct to user data products, and real-time response to events, all without affecting other on-board instrumentation is discussed.

Glaucoma and cataract surgery: two roads merging into one.

PubMed

Shah, Manjool; Law, Geoffrey; Ahmed, Iqbal Ike K

2016-01-01

To discuss the increasing utilization of cataract extraction in the management of glaucoma and to highlight advances in surgical care that can promote synergistic treatment of these comorbid conditions. Recent years have demonstrated significant advances in the management of glaucoma through the use of novel microinvasive glaucoma devices. Furthermore, an increased understanding of the role of cataract surgery in the treatment of various glaucomas warrants review. Nevertheless, cataract surgery in the glaucoma patient warrants specific preoperative, intraoperative, and postoperative planning to optimize visual function and quality of life while mitigating potential risk factors for adverse events. Although the challenges of performing cataract extraction on glaucoma patients exist, the potential benefit to these patients is substantial. With attention to pre- and perioperative surgical planning and intraoperative technique, as well as with awareness and potential utilization of novel devices and treatment strategies, cataract extraction offers a unique platform for anatomical and functional improvement in this increasingly common cohort of patients.

Does radiography advanced practice improve patient outcomes and health service quality? A systematic review.

PubMed

Hardy, Maryann; Johnson, Louise; Sharples, Rachael; Boynes, Stephen; Irving, Donna

2016-06-01

To investigate the impact of radiographer advanced practice on patient outcomes and health service quality. Using the World Health Organization definition of quality, this review followed the Centre for Reviews and Dissemination guidance for undertaking reviews in healthcare. A range of databases were searched using a defined search strategy. Included studies were assessed for quality using a tool specifically developed for reviewing studies of diverse designs, and data were systematically extracted using electronic data extraction pro forma. 407 articles were identified and reviewed against the inclusion/exclusion criteria. Nine studies were included in the final review, the majority (n = 7) focusing on advanced radiography practice within the UK. Advanced practice activities considered were radiographer reporting, leading patient review clinics and barium enema examinations. The articles were generally considered to be of low-to-moderate quality, with most evaluating advanced practice within a single centre. With respect to specific quality dimensions, the included studies considered cost reduction, patient morbidity, time to treatment and patient satisfaction. No articles reported data relating to time to diagnosis, time to recovery or patient mortality. Radiographer advanced practice is an established activity both in the UK and internationally. However, evidence of the impact of advanced practice in terms of patient outcomes and service quality is limited. This systematic review is the first to examine the evidence base surrounding advanced radiography practice and its impact on patient outcomes and health service quality.

Uranium extraction from TRISO-coated fuel particles using supercritical CO2 containing tri-n-butyl phosphate.

PubMed

Zhu, Liyang; Duan, Wuhua; Xu, Jingming; Zhu, Yongjun

2012-11-30

High-temperature gas-cooled reactors (HTGRs) are advanced nuclear systems that will receive heavy use in the future. It is important to develop spent nuclear fuel reprocessing technologies for HTGR. A new method for recovering uranium from tristructural-isotropic (TRISO-) coated fuel particles with supercritical CO(2) containing tri-n-butyl phosphate (TBP) as a complexing agent was investigated. TRISO-coated fuel particles from HTGR fuel elements were first crushed to expose UO(2) pellet fuel kernels. The crushed TRISO-coated fuel particles were then treated under O(2) stream at 750°C, resulting in a mixture of U(3)O(8) powder and SiC shells. The conversion of U(3)O(8) into solid uranyl nitrate by its reaction with liquid N(2)O(4) in the presence of a small amount of water was carried out. Complete conversion was achieved after 60 min of reaction at 80°C, whereas the SiC shells were not converted by N(2)O(4). Uranyl nitrate in the converted mixture was extracted with supercritical CO(2) containing TBP. The cumulative extraction efficiency was above 98% after 20 min of online extraction at 50°C and 25 MPa, whereas the SiC shells were not extracted by TBP. The results suggest an attractive strategy for reprocessing spent nuclear fuel from HTGR to minimize the generation of secondary radioactive waste. Copyright © 2012 Elsevier B.V. All rights reserved.

Aqueous two-phase extraction of nickel dimethylglyoximato complex and its application to spectrophotometric determination of nickel in stainless steel.

PubMed

Yoshikuni, Nobutaka; Baba, Takayuki; Tsunoda, Natsuki; Oguma, Koichi

2005-03-31

A polyethylene glycol (PEG)-based aqueous two-phase system has been established for the extraction of Ni-dimethylglyoximato complex. Appropriate amounts of PEG solution and solid (NH(4))(2)SO(4) were added to the Ni-dimethylglyoximato complex which had been formed in the presence of sodium tartrate and K(2)S(2)O(8) at pH 12 in a separatory funnel and shaken vigorously for about 1min. The mixture was allowed to stand for 10min and then the absorbance of the extracted complex in the upper PEG-rich phase was measured at 470nm. Beer's law was obeyed over the range of 0.26-2.1ppm Ni. The proposed extraction method has been applied to the determination of Ni in steel. A steel sample was decomposed with an appropriate acid mixture. An aliquot of the sample solution was taken, treated with H(3)PO(4) and most of the iron and copper were removed by hydroxide precipitation using solid BaCO(3) to control the pH of the sample solution in advance of the extraction of Ni. The analytical results obtained for Ni in steel certified reference material JSS 650-10 (The Japan Iron and Steel Federation), BCS 323 (Bureau of Analysed Samples Ltd.) and NIST SRM 361 and 362 (National Institute of Standards and Technology) were in good agreement with certified values.

Signal extraction and wave field separation in tunnel seismic prediction by independent component analysis

NASA Astrophysics Data System (ADS)

Yue, Y.; Jiang, T.; Zhou, Q.

2017-12-01

In order to ensure the rationality and the safety of tunnel excavation, the advanced geological prediction has been become an indispensable step in tunneling. However, the extraction of signal and the separation of P and S waves directly influence the accuracy of geological prediction. Generally, the raw data collected in TSP system is low quality because of the numerous disturb factors in tunnel projects, such as the power interference and machine vibration interference. It's difficult for traditional method (band-pass filtering) to remove interference effectively as well as bring little loss to signal. The power interference, machine vibration interference and the signal are original variables and x, y, z component as observation signals, each component of the representation is a linear combination of the original variables, which satisfy applicable conditions of independent component analysis (ICA). We perform finite-difference simulations of elastic wave propagation to synthetic a tunnel seismic reflection record. The method of ICA was adopted to process the three-component data, and the results show that extract the estimates of signal and the signals are highly correlated (the coefficient correlation is up to more than 0.93). In addition, the estimates of interference that separated from ICA and the interference signals are also highly correlated, and the coefficient correlation is up to more than 0.99. Thus, simulation results showed that the ICA is an ideal method for extracting high quality data from mixed signals. For the separation of P and S waves, the conventional separation techniques are based on physical characteristics of wave propagation, which require knowledge of the near-surface P and S waves velocities and density. Whereas the ICA approach is entirely based on statistical differences between P and S waves, and the statistical technique does not require a priori information. The concrete results of the wave field separation will be presented in the meeting. In summary, we can safely draw the conclusion that ICA can not only extract high quality data from the mixed signals, but also can separate P and S waves effectively.

[DNA extraction from bones and teeth using AutoMate Express forensic DNA extraction system].

PubMed

Gao, Lin-Lin; Xu, Nian-Lai; Xie, Wei; Ding, Shao-Cheng; Wang, Dong-Jing; Ma, Li-Qin; Li, You-Ying

2013-04-01

To explore a new method in order to extract DNA from bones and teeth automatically. Samples of 33 bones and 15 teeth were acquired by freeze-mill method and manual method, respectively. DNA materials were extracted and quantified from the triturated samples by AutoMate Express forensic DNA extraction system. DNA extraction from bones and teeth were completed in 3 hours using the AutoMate Express forensic DNA extraction system. There was no statistical difference between the two methods in the DNA concentration of bones. Both bones and teeth got the good STR typing by freeze-mill method, and the DNA concentration of teeth was higher than those by manual method. AutoMate Express forensic DNA extraction system is a new method to extract DNA from bones and teeth, which can be applied in forensic practice.

Bridging semantics and syntax with graph algorithms—state-of-the-art of extracting biomedical relations

PubMed Central

Uzuner, Özlem; Szolovits, Peter

2017-01-01

Research on extracting biomedical relations has received growing attention recently, with numerous biological and clinical applications including those in pharmacogenomics, clinical trial screening and adverse drug reaction detection. The ability to accurately capture both semantic and syntactic structures in text expressing these relations becomes increasingly critical to enable deep understanding of scientific papers and clinical narratives. Shared task challenges have been organized by both bioinformatics and clinical informatics communities to assess and advance the state-of-the-art research. Significant progress has been made in algorithm development and resource construction. In particular, graph-based approaches bridge semantics and syntax, often achieving the best performance in shared tasks. However, a number of problems at the frontiers of biomedical relation extraction continue to pose interesting challenges and present opportunities for great improvement and fruitful research. In this article, we place biomedical relation extraction against the backdrop of its versatile applications, present a gentle introduction to its general pipeline and shared resources, review the current state-of-the-art in methodology advancement, discuss limitations and point out several promising future directions. PMID:26851224

Characterizing the Performance of the Princeton Advanced Test Stand Ion Source

NASA Astrophysics Data System (ADS)

Stepanov, A.; Gilson, E. P.; Grisham, L.; Kaganovich, I.; Davidson, R. C.

2012-10-01

The Princeton Advanced Test Stand (PATS) is a compact experimental facility for studying the physics of intense beam-plasma interactions relevant to the Neutralized Drift Compression Experiment - II (NDCX-II). The PATS facility consists of a multicusp RF ion source mounted on a 2 m-long vacuum chamber with numerous ports for diagnostic access. Ar+ beams are extracted from the source plasma with three-electrode (accel-decel) extraction optics. The RF power and extraction voltage (30 - 100 kV) are pulsed to produce 100 μsec duration beams at 0.5 Hz with excellent shot-to-shot repeatability. Diagnostics include Faraday cups, a double-slit emittance scanner, and scintillator imaging. This work reports measurements of beam parameters for a range of beam energies (30 - 50 keV) and currents to characterize the behavior of the ion source and extraction optics. Emittance scanner data is used to calculate the beam trace-space distribution and corresponding transverse emittance. If the plasma density is changing during a beam pulse, time-resolved emittance scanner data has been taken to study the corresponding evolution of the beam trace-space distribution.

Elastic-plastic models for multi-site damage

NASA Technical Reports Server (NTRS)

Actis, Ricardo L.; Szabo, Barna A.

1994-01-01

This paper presents recent developments in advanced analysis methods for the computation of stress site damage. The method of solution is based on the p-version of the finite element method. Its implementation was designed to permit extraction of linear stress intensity factors using a superconvergent extraction method (known as the contour integral method) and evaluation of the J-integral following an elastic-plastic analysis. Coarse meshes are adequate for obtaining accurate results supported by p-convergence data. The elastic-plastic analysis is based on the deformation theory of plasticity and the von Mises yield criterion. The model problem consists of an aluminum plate with six equally spaced holes and a crack emanating from each hole. The cracks are of different sizes. The panel is subjected to a remote tensile load. Experimental results are available for the panel. The plasticity analysis provided the same limit load as the experimentally determined load. The results of elastic-plastic analysis were compared with the results of linear elastic analysis in an effort to evaluate how plastic zone sizes influence the crack growth rates. The onset of net-section yielding was determined also. The results show that crack growth rate is accelerated by the presence of adjacent damage, and the critical crack size is shorter when the effects of plasticity are taken into consideration. This work also addresses the effects of alternative stress-strain laws: The elastic-ideally-plastic material model is compared against the Ramberg-Osgood model.

A simple, rapid and stability indicating validated method for quantification of lamotrigine in human plasma and dry plasma spot using LC-ESI-MS/MS: Application in clinical study.

PubMed

Namdev, Kuldeep Kumar; Dwivedi, Jaya; Chilkoti, Deepak Chandra; Sharma, Swapnil

2018-01-01

Lamotrigine (LTZ) is a phenyltriazine derivative which belongs to anti-epileptic drugs (AEDs) class and prescribed as mono- or adjunctive-therapy in treatment of epilepsy. Therapeutic drug monitoring (TDM) of AEDs provides a valid clinical tool in optimization of overall therapy. However, TDM is challenging due to the high biological samples (plasma/blood) storage/shipment costs and the limited availability of laboratories providing TDM services. Sampling in the form of dry plasma spot (DPS) or dry blood spot (DBS) are suitable alternative to overcome these issues. We developed and validated a new method for quantification of LTZ in human plasma and DPS. The extraction of LTZ from plasma and DPS was performed using liquid-liquid extraction with diethyl ether and an extraction solution composed of diethyl ether- methyl tert-butyl ether- acetone (50:30:20, v/v/v), respectively. Lamotrigine- 13C3, d3 was used as internal standard (ISTD) and the chromatographic separation was achieved on Hypurity Advance C18 column (150×4.6mm, 5μm). Quantitative estimation of LTZ and ISTD was performed on a liquid chromatography tandem mass spectrometer coupled with electrospray ionization interface operated under positive mode of ionization. Calibration curves were linear (r 2 >0.99) over the concentration range of 10-3020ng/mL for both plasma and DPS. Statistical analysis provides insignificant difference between LTZ concentration extracted from plasma and DPS samples. The method is found suitable for application in clinical study and in therapeutic monitoring of LTZ. To the best of our knowledge this is the first report which describing a validated stability indicating assay for quantification of LTZ in dry plasma spot. Copyright © 2017 Elsevier B.V. All rights reserved.

Changing perspectives on resource extraction.

NASA Astrophysics Data System (ADS)

Gibson, Hazel; Stewart, Iain; Pahl, Sabine; Stokes, Alison

2015-04-01

Over the last century, resource extraction in the UK has changed immeasurably; from relatively small-scale, manually-operated facilities to the larger technological advanced sites that exist today. The communities that live near these sites have also changed, from housing workers that were as much of a resource as the geological material, to local residents who are environmentally literate and strongly value their landscape. Nowadays great pressure is put on the extractive industry to work in both environmentally sustainable and socially ethical ways, but how does this impact upon the local population? How do communities perceive the resource extraction that neighbours them? And is this perception rooted in a general understanding of geology and the subsurface? To explore resident's perceptions of the geological environment, three villages in the southwest of England have been investigated, using a mixed-methods mental models approach. The villages were selected as each has a different geological setting, both commercially and culturally. The first village has a strong historical geological identity, but little current geological activity. The second village has a large tungsten mine in the process of beginning production. The third village has no obvious cultural or commercial relationships with geology and acts as the control site. A broad sample from each of the three villages was qualitatively interviewed, the results of which were analyzed using an emergent thematic coding scheme. These qualitative results were then modelled using Morgan et al's mental models method (2002) and tested using a quantitative questionnaire. The results of this mixed method approach reveals the principal perceptions (or mental models) of residents in these three villages. The villages each present a different general perception of resource exploitation, which appears to be culturally driven, with the first village having the most positive correlations. These mental models are important as they indicate the changing perceptions of local residents in relation to both their local geology and human exploitation of geological resources. The implications of this research for developing strategies of engagement with local communities will be discussed.

Anniversary Paper: Image processing and manipulation through the pages of Medical Physics

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

Armato, Samuel G. III; Ginneken, Bram van; Image Sciences Institute, University Medical Center Utrecht, Heidelberglaan 100, Room Q0S.459, 3584 CX Utrecht

The language of radiology has gradually evolved from ''the film'' (the foundation of radiology since Wilhelm Roentgen's 1895 discovery of x-rays) to ''the image,'' an electronic manifestation of a radiologic examination that exists within the bits and bytes of a computer. Rather than simply storing and displaying radiologic images in a static manner, the computational power of the computer may be used to enhance a radiologist's ability to visually extract information from the image through image processing and image manipulation algorithms. Image processing tools provide a broad spectrum of opportunities for image enhancement. Gray-level manipulations such as histogram equalization, spatialmore » alterations such as geometric distortion correction, preprocessing operations such as edge enhancement, and enhanced radiography techniques such as temporal subtraction provide powerful methods to improve the diagnostic quality of an image or to enhance structures of interest within an image. Furthermore, these image processing algorithms provide the building blocks of more advanced computer vision methods. The prominent role of medical physicists and the AAPM in the advancement of medical image processing methods, and in the establishment of the ''image'' as the fundamental entity in radiology and radiation oncology, has been captured in 35 volumes of Medical Physics.« less

Apparatus for hydrocarbon extraction

DOEpatents

Bohnert, George W.; Verhulst, Galen G.

2013-03-19

Systems and methods for hydrocarbon extraction from hydrocarbon-containing material. Such systems and methods relate to extracting hydrocarbon from hydrocarbon-containing material employing a non-aqueous extractant. Additionally, such systems and methods relate to recovering and reusing non-aqueous extractant employed for extracting hydrocarbon from hydrocarbon-containing material.

Bach2 repression mediates Th17 cell induced inflammation and associates with clinical features of advanced disease in chronic pancreatitis

PubMed Central

Sasikala, M; Ravikanth, VV; Murali Manohar, K; Deshpande, Neha; Singh, Sandhya; Pavan Kumar, P; Talukdar, R; Ghosh, Sudip; Aslam, Mohsin; Rao, GV; Pradeep, R; Reddy, D Nageshwar

2018-01-01

Objectives Altered immune homeostasis and involvement of T cells has been reported in chronic pancreatitis (CP). We evaluated the role of Bach2 (BTB and CNC homology basic leucine zipper transcription factor 2), a key regulator of immune homeostasis in the chronicity of CP. Methods Expression of Bach2 and T-cell transcription factors, enumeration of BACH2+/CD4+ T-lymphocytes were performed by qRT-PCR and flow cytometry respectively. Bach2silenced human CD4+ T-lymphocytes were exposed to CP tissue extract to assess T-cell lineage commitment. Aryl hydrocarbon receptor (Ahr) and Deubiquitinase enzyme A (DUBA/OTUD5gene) were evaluated as markers of persistent Th17 cell differentiation. Bach2 gene (exons) was sequenced to identify risk variants and functionally validated. Results Decrease in Bach2 (p < 0.0001) and increase (p < 0.001) in TBX21, RORC, Ahr, PRDM1, IL23R mRNA were noted in pancreatic tissues, while BACH2+/CD4+ T-lymphocytes were decreased (p < 0.01) in circulation and tissues. Exposure of Bach2 silenced CD4+ T-lymphocytes to CP tissue extract showed increased Ahr, decreased OTUD5, and enhanced Th17 cell differentiation. Sequencing of Bach2 gene revealed association of novel variant (rs9111 in 5′-UTR) with advanced disease and luciferase assay confirmed its role in Bach2 repression. Conclusion Bach2 repression mediates Th17 cell induced inflammation and rs9111-TT in individuals with primary genetic susceptibility to CP is associated with clinical features of advanced disease. PMID:29511557

Advanced Dispersed Fringe Sensing Algorithm for Coarse Phasing Segmented Mirror Telescopes

NASA Technical Reports Server (NTRS)

Spechler, Joshua A.; Hoppe, Daniel J.; Sigrist, Norbert; Shi, Fang; Seo, Byoung-Joon; Bikkannavar, Siddarayappa A.

2013-01-01

Segment mirror phasing, a critical step of segment mirror alignment, requires the ability to sense and correct the relative pistons between segments from up to a few hundred microns to a fraction of wavelength in order to bring the mirror system to its full diffraction capability. When sampling the aperture of a telescope, using auto-collimating flats (ACFs) is more economical. The performance of a telescope with a segmented primary mirror strongly depends on how well those primary mirror segments can be phased. One such process to phase primary mirror segments in the axial piston direction is dispersed fringe sensing (DFS). DFS technology can be used to co-phase the ACFs. DFS is essentially a signal fitting and processing operation. It is an elegant method of coarse phasing segmented mirrors. DFS performance accuracy is dependent upon careful calibration of the system as well as other factors such as internal optical alignment, system wavefront errors, and detector quality. Novel improvements to the algorithm have led to substantial enhancements in DFS performance. The Advanced Dispersed Fringe Sensing (ADFS) Algorithm is designed to reduce the sensitivity to calibration errors by determining the optimal fringe extraction line. Applying an angular extraction line dithering procedure and combining this dithering process with an error function while minimizing the phase term of the fitted signal, defines in essence the ADFS algorithm.

MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling

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

Burnum-Johnson, Kristin E.; Kyle, Jennifer E.; Eisfeld, Amie J.

The continued emergence and spread of infectious agents is of increasing concern due to increased population growth and the associated increased livestock production to meet food demands, increased urbanization and land-use changes, and greater travel. A systems biology approach to infectious disease research can significantly advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can only take place subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivationmore » and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis, Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis, Campylobacter jejuni, West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. Partial inactivation was observed for pathogens without exposed lipid membranes including 99.99% inactivation of community-associated methicillin-resistant Staphylococcus aureus, 99.6% and >99% inactivation of Clostridium difficile spores and vegetative cells, respectively, and 50% inactivation of adenovirus type 5. To demonstrate that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses, we highlight select proteomics, metabolomics and lipidomics data from human epithelial lung cells infected with wild-type and mutant forms of influenza H7N9. We believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics measurements from a single specimen.« less

MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling.

PubMed

Burnum-Johnson, Kristin E; Kyle, Jennifer E; Eisfeld, Amie J; Casey, Cameron P; Stratton, Kelly G; Gonzalez, Juan F; Habyarimana, Fabien; Negretti, Nicholas M; Sims, Amy C; Chauhan, Sadhana; Thackray, Larissa B; Halfmann, Peter J; Walters, Kevin B; Kim, Young-Mo; Zink, Erika M; Nicora, Carrie D; Weitz, Karl K; Webb-Robertson, Bobbie-Jo M; Nakayasu, Ernesto S; Ahmer, Brian; Konkel, Michael E; Motin, Vladimir; Baric, Ralph S; Diamond, Michael S; Kawaoka, Yoshihiro; Waters, Katrina M; Smith, Richard D; Metz, Thomas O

2017-01-26

The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This single-sample metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of clinically important bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis, Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis, Campylobacter jejuni, and West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. In addition, >99% inactivation, which increased with solvent exposure time, was also observed for pathogens without exposed lipid membranes including community-associated methicillin-resistant Staphylococcus aureus, Clostridium difficile spores and vegetative cells, and adenovirus type 5. The overall pipeline of inactivation and subsequent proteomic, metabolomic, and lipidomic analyses was evaluated using a human epithelial lung cell line infected with wild-type and mutant influenza H7N9 viruses, thereby demonstrating that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses. Based on these experimental results, we believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics measurements from a single specimen with high success for pathogens with exposed lipid membranes.

MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling

PubMed Central

Burnum-Johnson, Kristin E.; Kyle, Jennifer E.; Eisfeld, Amie J.; Casey, Cameron P.; Stratton, Kelly G.; Gonzalez, Juan F.; Habyarimana, Fabien; Negretti, Nicholas M.; Sims, Amy C.; Chauhan, Sadhana; Thackray, Larissa B.; Halfmann, Peter J.; Walters, Kevin B.; Kim, Young-Mo; Zink, Erika M.; Nicora, Carrie D.; Weitz, Karl K.; Webb-Robertson, Bobbie-Jo M.; Nakayasu, Ernesto S.; Ahmer, Brian; Konkel, Michael E.; Motin, Vladimir; Baric, Ralph S.; Diamond, Michael S.; Kawaoka, Yoshihiro; Waters, Katrina M.; Smith, Richard D.; Metz, Thomas O.

2017-01-01

The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This single-sample metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of clinically important bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis, Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis, Campylobacter jejuni, and West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. In addition, >99% inactivation, which increased with solvent exposure time, was also observed for pathogens without exposed lipid membranes including community-associated methicillin-resistant Staphylococcus aureus, Clostridium difficile spores and vegetative cells, and adenovirus type 5. The overall pipeline of inactivation and subsequent proteomic, metabolomic, and lipidomic analyses was evaluated using a human epithelial lung cell line infected with wild-type and mutant influenza H7N9 viruses, thereby demonstrating that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses. Based on these experimental results, we believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics measurements from a single specimen with high success for pathogens with exposed lipid membranes. PMID:28091625

NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures.

PubMed

Colen, Rivka; Foster, Ian; Gatenby, Robert; Giger, Mary Ellen; Gillies, Robert; Gutman, David; Heller, Matthew; Jain, Rajan; Madabhushi, Anant; Madhavan, Subha; Napel, Sandy; Rao, Arvind; Saltz, Joel; Tatum, James; Verhaak, Roeland; Whitman, Gary

2014-10-01

The National Cancer Institute (NCI) Cancer Imaging Program organized two related workshops on June 26-27, 2013, entitled "Correlating Imaging Phenotypes with Genomics Signatures Research" and "Scalable Computational Resources as Required for Imaging-Genomics Decision Support Systems." The first workshop focused on clinical and scientific requirements, exploring our knowledge of phenotypic characteristics of cancer biological properties to determine whether the field is sufficiently advanced to correlate with imaging phenotypes that underpin genomics and clinical outcomes, and exploring new scientific methods to extract phenotypic features from medical images and relate them to genomics analyses. The second workshop focused on computational methods that explore informatics and computational requirements to extract phenotypic features from medical images and relate them to genomics analyses and improve the accessibility and speed of dissemination of existing NIH resources. These workshops linked clinical and scientific requirements of currently known phenotypic and genotypic cancer biology characteristics with imaging phenotypes that underpin genomics and clinical outcomes. The group generated a set of recommendations to NCI leadership and the research community that encourage and support development of the emerging radiogenomics research field to address short-and longer-term goals in cancer research.

Defect detection and classification of galvanized stamping parts based on fully convolution neural network

NASA Astrophysics Data System (ADS)

Xiao, Zhitao; Leng, Yanyi; Geng, Lei; Xi, Jiangtao

2018-04-01

In this paper, a new convolution neural network method is proposed for the inspection and classification of galvanized stamping parts. Firstly, all workpieces are divided into normal and defective by image processing, and then the defective workpieces extracted from the region of interest (ROI) area are input to the trained fully convolutional networks (FCN). The network utilizes an end-to-end and pixel-to-pixel training convolution network that is currently the most advanced technology in semantic segmentation, predicts result of each pixel. Secondly, we mark the different pixel values of the workpiece, defect and background for the training image, and use the pixel value and the number of pixels to realize the recognition of the defects of the output picture. Finally, the defect area's threshold depended on the needs of the project is set to achieve the specific classification of the workpiece. The experiment results show that the proposed method can successfully achieve defect detection and classification of galvanized stamping parts under ordinary camera and illumination conditions, and its accuracy can reach 99.6%. Moreover, it overcomes the problem of complex image preprocessing and difficult feature extraction and performs better adaptability.

The pearls of using real-world evidence to discover social groups

NASA Astrophysics Data System (ADS)

Cardillo, Raymond A.; Salerno, John J.

2005-03-01

In previous work, we introduced a new paradigm called Uni-Party Data Community Generation (UDCG) and a new methodology to discover social groups (a.k.a., community models) called Link Discovery based on Correlation Analysis (LDCA). We further advanced this work by experimenting with a corpus of evidence obtained from a Ponzi scheme investigation. That work identified several UDCG algorithms, developed what we called "Importance Measures" to compare the accuracy of the algorithms based on ground truth, and presented a Concept of Operations (CONOPS) that criminal investigators could use to discover social groups. However, that work used a rather small random sample of manually edited documents because the evidence contained far too many OCR and other extraction errors. Deferring the evidence extraction errors allowed us to continue experimenting with UDCG algorithms, but only used a small fraction of the available evidence. In attempt to discover techniques that are more practical in the near-term, our most recent work focuses on being able to use an entire corpus of real-world evidence to discover social groups. This paper discusses the complications of extracting evidence, suggests a method of performing name resolution, presents a new UDCG algorithm, and discusses our future direction in this area.

Chemistry Perfumes Your Daily Life

NASA Astrophysics Data System (ADS)

Fortineau, Anne-Dominique

2004-01-01

The use of perfumes can be tracked back to many early civilizations. Historically, perfumes were composed exclusively of natural ingredients, mainly essential oils, and were reserved for the wealthiest people. The use of synthetic ingredients marked the beginning of modern perfumery at the end of the 19th century. Nowadays, perfumes are available to everyone and are present in a wide range of consumer goods. The methods used to extract perfume ingredients from their natural sources have changed over time as technology has advanced. Depending on the material, expression, distillation, and solvent extraction are the main techniques used to extract the odorant components from a natural source. Synthetic organic chemistry has provided perfumers with novel ingredients that are cheaper and more stable than many natural materials over the years. Today, more than 3000 fragrance ingredients are estimated to be available to perfumers to create a harmonious composition of head (for example, citrusy), heart (for example, fruity floral) and base notes (for example, musky). Future developments and uses of perfume are endless and as Ernest Beaux, the perfumer who created Chanel N85, once said, "In perfumery the future lies primarily in the hands of the chemists." Featured on the Cover See Featured Molecules .

Natural Language Processing in Radiology: A Systematic Review.

PubMed

Pons, Ewoud; Braun, Loes M M; Hunink, M G Myriam; Kors, Jan A

2016-05-01

Radiological reporting has generated large quantities of digital content within the electronic health record, which is potentially a valuable source of information for improving clinical care and supporting research. Although radiology reports are stored for communication and documentation of diagnostic imaging, harnessing their potential requires efficient and automated information extraction: they exist mainly as free-text clinical narrative, from which it is a major challenge to obtain structured data. Natural language processing (NLP) provides techniques that aid the conversion of text into a structured representation, and thus enables computers to derive meaning from human (ie, natural language) input. Used on radiology reports, NLP techniques enable automatic identification and extraction of information. By exploring the various purposes for their use, this review examines how radiology benefits from NLP. A systematic literature search identified 67 relevant publications describing NLP methods that support practical applications in radiology. This review takes a close look at the individual studies in terms of tasks (ie, the extracted information), the NLP methodology and tools used, and their application purpose and performance results. Additionally, limitations, future challenges, and requirements for advancing NLP in radiology will be discussed. (©) RSNA, 2016 Online supplemental material is available for this article.

A novel approach to mask defect inspection

NASA Astrophysics Data System (ADS)

Sagiv, Amir; Shirman, Yuri; Mangan, Shmoolik

2008-10-01

Memory chips, now constituting a major part of semiconductor market, posit a special challenge for inspection, as they are generally produced with the smallest half-pitch available with today's technology. This is true, in particular, to photomasks of advanced memory devices, which are at the forefront of the "low-k1" regime. In this paper we present a novel photomask inspection approach, that is particularly suitable for low-k1 layers of advanced memory chips, owing to their typical dense and periodic structure. The method we present can produce a very strong signal for small mask defects, by suppression of the modulation of the pattern's image. Unlike dark-field detection, however, here a single diffraction order associated with the pattern generates a constant "gray" background image, that is used for signal enhancement. We define the theoretical basis for the new detection technique, and show, both analytically and numerically, that it can easily achieve a detection line past the printability spec, and that in cases it is at least as sensitive as high-resolution based detection. We also demonstrate this claim experimentally on a customer mask, using the platform of Applied Material's newly released Aera2TM mask inspection tool. The high sensitivity demonstrates the important and often overlooked concept that resolution is not synonymous with sensitivity. The novel detection method is advantageous in several other aspects, such as the very simple implementation, the high throughput, and the relatively simple pre- and post-processing algorithms required for signal extraction. These features, and in particular the very high sensitivity, make this novel detection method an attractive inspection option for advanced memory devices.

Comparison of Spatiotemporal Mapping Techniques for Enormous Etl and Exploitation Patterns

NASA Astrophysics Data System (ADS)

Deiotte, R.; La Valley, R.

2017-10-01

The need to extract, transform, and exploit enormous volumes of spatiotemporal data has exploded with the rise of social media, advanced military sensors, wearables, automotive tracking, etc. However, current methods of spatiotemporal encoding and exploitation simultaneously limit the use of that information and increase computing complexity. Current spatiotemporal encoding methods from Niemeyer and Usher rely on a Z-order space filling curve, a relative of Peano's 1890 space filling curve, for spatial hashing and interleaving temporal hashes to generate a spatiotemporal encoding. However, there exist other space-filling curves, and that provide different manifold coverings that could promote better hashing techniques for spatial data and have the potential to map spatiotemporal data without interleaving. The concatenation of Niemeyer's and Usher's techniques provide a highly efficient space-time index. However, other methods have advantages and disadvantages regarding computational cost, efficiency, and utility. This paper explores the several methods using a range of sizes of data sets from 1K to 10M observations and provides a comparison of the methods.

Orthogonal analytical methods for botanical standardization: Determination of green tea catechins by qNMR and LC-MS/MS

PubMed Central

Napolitano, José G.; Gödecke, Tanja; Lankin, David C.; Jaki, Birgit U.; McAlpine, James B.; Chen, Shao-Nong; Pauli, Guido F.

2013-01-01

The development of analytical methods for parallel characterization of multiple phytoconstituents is essential to advance the quality control of herbal products. While chemical standardization is commonly carried out by targeted analysis using gas or liquid chromatography-based methods, more universal approaches based on quantitative 1H NMR (qHNMR) measurements are being used increasingly in the multi-targeted assessment of these complex mixtures. The present study describes the development of a 1D qHNMR-based method for simultaneous identification and quantification of green tea constituents. This approach utilizes computer-assisted 1H iterative Full Spin Analysis (HiFSA) and enables rapid profiling of seven catechins in commercial green tea extracts. The qHNMR results were cross-validated against quantitative profiles obtained with an orthogonal LC-MS/MS method. The relative strengths and weaknesses of both approaches are discussed, with special emphasis on the role of identical reference standards in qualitative and quantitative analyses. PMID:23870106

Getting to low-cost algal biofuels: A monograph on conventional and cutting-edge harvesting and extraction technologies

DOE PAGES

Coons, James E.; Kalb, Daniel M.; Dale, Taraka; ...

2014-08-31

Among the most formidable challenges to algal biofuels is the ability to harvest algae and extract intracellular lipids at low cost and with a positive energy balance. Here, we construct two paradigms that contrast energy requirements and costs of conventional and cutting-edge Harvesting and Extraction (H&E) technologies. By application of the parity criterion and the moderate condition reference state, an energy–cost paradigm is created that allows 1st stage harvesting technologies to be compared with easy reference to the National Alliance for Advanced Biofuels and Bioproducts (NAABB) target of $0.013/gallon of gasoline equivalent (GGE) and to the U.S. DOE's Bioenergy Technologiesmore » Office 2022 cost metrics. Drawing from the moderate condition reference state, a concentration-dependency paradigm is developed for extraction technologies, making easier comparison to the National Algal Biofuels Technology Roadmap (NABTR) target of less than 10% total energy. This monograph identifies cost-bearing factors for a variety of H&E technologies, describes a design basis for ultrasonic harvesters, and provides a framework to measure future technological advancements toward reducing H&E costs. Finally, we show that ultrasonic harvesters and extractors are uniquely capable of meeting both NAABB and NABTR targets. Ultrasonic technologies require further development and scale-up before they can achieve low-cost performance at industrially relevant scales. But, the advancement of this technology would greatly reduce H&E costs and accelerate the commercial viability of algae-based biofuels.« less

Extraction of GBH Film Medicine and Influence on Quality Evaluation of The Film

NASA Astrophysics Data System (ADS)

Ji, Y. B.; Lu, L.; Ru, X.; Guo, S. Z.; Qiao, A. N.; Wang, S. W.

2017-12-01

To know the extraction effects of GBH film medicine and the influence on film quality evaluation. Ultrasonic extraction and reflux extraction were used to extract the two methods with the traditional water decocting method to contrast. They were used to determining the content of total flavonoids. The same method was used to separate the root of the main medicinal herbs and the decoction of the water decoction of the other drug powder. They were used to determine the content of total flavonoids. The effect of extraction method on the preparation of membrane was investigated. The membrane preparation, evaluation and flexibility, respectively, film-forming property, smoothness and disintegration time are used to evaluating separately the effect of extraction method. The results showed that the extraction effect of 70% ethanol concentration of total flavonoids. The best extraction method had no effect on the film quality initial evaluation. This experiment provides a method for membrane extraction agent, has a certain practical significance.

Preliminary determination of geothermal working area based on Thermal Infrared and Synthetic Aperture Radar (SAR) remote sensing

NASA Astrophysics Data System (ADS)

Agoes Nugroho, Indra; Kurniawahidayati, Beta; Syahputra Mulyana, Reza; Saepuloh, Asep

2017-12-01

Remote sensing is one of the methods for geothermal exploration. This method can be used to map the geological structures, manifestations, and predict the geothermal potential area. The results from remote sensing were used as guidance for the next step exploration. Analysis of target in remote sensing is an efficient method to delineate geothermal surface manifestation without direct contact to the object. The study took a place in District Merangin, Jambi Province, Indonesia. The area was selected due to existing of Merangin volcanic complex composed by Mounts Sumbing and Hulunilo with surface geothermal manifestations presented by hot springs and hot pools. The location of surface manifestations could be related with local and regional structures of Great Sumatra Fault. The methods used in this study were included identification of volcanic products, lineament extraction, and lineament density quantification. The objective of this study is to delineate the potential zones for sitting the geothermal working site based on Thermal Infrared and Synthetic Aperture Radar (SAR) sensors. The lineament-related to geological structures, was aimed for high lineament density, is using ALOS - PALSAR (Advanced Land Observing Satellite - The Phased Array type L-band Synthetic Aperture Radar) level 1.1. The Normalized Difference Vegetation Index (NDVI) analysis was used to predict the vegetation condition using Landsat 8 OLI-TIRS (The Operational Land Imager - Thermal Infrared Sensor). The brightness temperature was extracted from TIR band to estimate the surface temperature. Geothermal working area identified based on index overlay method from extracted parameter of remote sensing data was located at the western part of study area (Graho Nyabu area). This location was identified because of the existence of high surface temperature about 30°C, high lineament density about 4 - 4.5 km/km2 and low NDVI values less than 0.3.

RESOLVE OVEN Field Demonstration Unit for Lunar Resource Extraction

NASA Technical Reports Server (NTRS)

Paz, Aaron; Oryshchyn, Lara; Jensen, Scott; Sanders, Gerald B.; Lee, Kris; Reddington, Mike

2013-01-01

The Oxygen and Volatile Extraction Node (OVEN) is a subsystem within the Regolith & Environment Science and Oxygen & Lunar Volatile Extraction (RESOLVE) project. The purpose of the OVEN subsystem is to release volatiles from lunar regolith and extract oxygen by means of a hydrogen reduction reaction. The complete process includes receiving, weighing, sealing, heating, and disposing of core sample segments while transferring all gaseous contents to the Lunar Advanced Volatile Analysis (LAVA) subsystem. This document will discuss the design and performance of the OVEN Field Demonstration Unit (FDU), which participated in the 2012 RESOLVE field demonstration.

Automatic Artifact Removal from Electroencephalogram Data Based on A Priori Artifact Information.

PubMed

Zhang, Chi; Tong, Li; Zeng, Ying; Jiang, Jingfang; Bu, Haibing; Yan, Bin; Li, Jianxin

2015-01-01

Electroencephalogram (EEG) is susceptible to various nonneural physiological artifacts. Automatic artifact removal from EEG data remains a key challenge for extracting relevant information from brain activities. To adapt to variable subjects and EEG acquisition environments, this paper presents an automatic online artifact removal method based on a priori artifact information. The combination of discrete wavelet transform and independent component analysis (ICA), wavelet-ICA, was utilized to separate artifact components. The artifact components were then automatically identified using a priori artifact information, which was acquired in advance. Subsequently, signal reconstruction without artifact components was performed to obtain artifact-free signals. The results showed that, using this automatic online artifact removal method, there were statistical significant improvements of the classification accuracies in both two experiments, namely, motor imagery and emotion recognition.

Automatic Artifact Removal from Electroencephalogram Data Based on A Priori Artifact Information

PubMed Central

Zhang, Chi; Tong, Li; Zeng, Ying; Jiang, Jingfang; Bu, Haibing; Li, Jianxin

2015-01-01

Electroencephalogram (EEG) is susceptible to various nonneural physiological artifacts. Automatic artifact removal from EEG data remains a key challenge for extracting relevant information from brain activities. To adapt to variable subjects and EEG acquisition environments, this paper presents an automatic online artifact removal method based on a priori artifact information. The combination of discrete wavelet transform and independent component analysis (ICA), wavelet-ICA, was utilized to separate artifact components. The artifact components were then automatically identified using a priori artifact information, which was acquired in advance. Subsequently, signal reconstruction without artifact components was performed to obtain artifact-free signals. The results showed that, using this automatic online artifact removal method, there were statistical significant improvements of the classification accuracies in both two experiments, namely, motor imagery and emotion recognition. PMID:26380294

An MRM-based workflow for absolute quantitation of lysine-acetylated metabolic enzymes in mouse liver.

PubMed

Xu, Leilei; Wang, Fang; Xu, Ying; Wang, Yi; Zhang, Cuiping; Qin, Xue; Yu, Hongxiu; Yang, Pengyuan

2015-12-07

As a key post-translational modification mechanism, protein acetylation plays critical roles in regulating and/or coordinating cell metabolism. Acetylation is a prevalent modification process in enzymes. Protein acetylation modification occurs in sub-stoichiometric amounts; therefore extracting biologically meaningful information from these acetylation sites requires an adaptable, sensitive, specific, and robust method for their quantification. In this work, we combine immunoassays and multiple reaction monitoring-mass spectrometry (MRM-MS) technology to develop an absolute quantification for acetylation modification. With this hybrid method, we quantified the acetylation level of metabolic enzymes, which could demonstrate the regulatory mechanisms of the studied enzymes. The development of this quantitative workflow is a pivotal step for advancing our knowledge and understanding of the regulatory effects of protein acetylation in physiology and pathophysiology.

Edge-Based Image Compression with Homogeneous Diffusion

NASA Astrophysics Data System (ADS)

Mainberger, Markus; Weickert, Joachim

It is well-known that edges contain semantically important image information. In this paper we present a lossy compression method for cartoon-like images that exploits information at image edges. These edges are extracted with the Marr-Hildreth operator followed by hysteresis thresholding. Their locations are stored in a lossless way using JBIG. Moreover, we encode the grey or colour values at both sides of each edge by applying quantisation, subsampling and PAQ coding. In the decoding step, information outside these encoded data is recovered by solving the Laplace equation, i.e. we inpaint with the steady state of a homogeneous diffusion process. Our experiments show that the suggested method outperforms the widely-used JPEG standard and can even beat the advanced JPEG2000 standard for cartoon-like images.

Investigation of remote sensing techniques as inputs to operational resource management models. [South Dakota

NASA Technical Reports Server (NTRS)

Schmer, F. A. (Principal Investigator); Isakson, R. E.; Eidenshink, J. C.

1977-01-01

The author has identified the following significant results. Successful operational applications of LANDSAT data were found for level 1 land use mapping, drainage network delineation, and aspen mapping. Visual LANDSAT interpretation using 1:125,000 color composite imagery was the least expensive method of obtaining timely level 1 land use data. With an average agricultural/rangeland interpretation accuracy in excess of 80%, such a data source was considered the most cost effective of those sources available to state agencies. Costs do not compare favorably with those incurred using the present method of extracting land use data from historical tabular summaries. The cost increase in advancing from the present procedure to a satellite-based data source was justified in terms of expanded data content.

Holistic Healing Through Herbs: Effectiveness of Aloe Vera on Post Extraction Socket Healing

PubMed Central

Talla, Harsha Vardhan; Bairi, Jaya Krishna; Gopaldas, Madhulatha; Bathula, Haritha; Vangdoth, Sandeep

2017-01-01

Introduction Advances in the field of alternative medicine has encouraged the use of various natural products for multiple uses in the field of dentistry for treatment of various oral diseases. A natural herbal product is Aloe vera, which has number of benefits with no reported side effects and gaining considerable importance in clinical research. Aim The aim of this cross-sectional randomized interventional study was to evaluate the effectiveness of Aloe vera in the healing of post extraction sockets. Materials and Methods A sample size of 40 patients undergoing atraumatic extraction was divided into two groups. Group A-patients were prescribed only analgesics and followed for seven consecutive days and socket healing assessment was done. Group B-Patients were given Aloe vera soaked gel foams, followed up to the third and seventh day by two observers and the socket healing was assessed using the standardized index by Landry, Turnbull and Howley. In addition to healing the common complaint associated with extraction wound, the pain was assessed using numerical rating scale. Data obtained was statistically analysed using Mann-whitney U test, Wilcoxon Signed ranks test and Spearman’s rank correlation method. Results Control group on the third and the seventh day showed healing of 60% and 70% respectively and the Aloe vera group showed a better result having a healing potential of 70% on the third day and 90% on the seventh day which was statistically significant with a (p-value<0.001). Aloe vera group showed a significant decrease in pain after two hours on the day of extraction followed by second, third and seventh day which was statistically significant (p-value<0.001) and better than the control group. Conclusion Aloe vera has been proved to have a unique property that is implicated in better healing than other group without any side effects. Aloe vera is economical, effective, powerful nutritional supplement and antioxidant that protects and promotes wound healing. PMID:28511517

Highly Effective DNA Extraction Method for Nuclear Short Tandem Repeat Testing of Skeletal Remains from Mass Graves

PubMed Central

Davoren, Jon; Vanek, Daniel; Konjhodzić, Rijad; Crews, John; Huffine, Edwin; Parsons, Thomas J.

2007-01-01

Aim To quantitatively compare a silica extraction method with a commonly used phenol/chloroform extraction method for DNA analysis of specimens exhumed from mass graves. Methods DNA was extracted from twenty randomly chosen femur samples, using the International Commission on Missing Persons (ICMP) silica method, based on Qiagen Blood Maxi Kit, and compared with the DNA extracted by the standard phenol/chloroform-based method. The efficacy of extraction methods was compared by real time polymerase chain reaction (PCR) to measure DNA quantity and the presence of inhibitors and by amplification with the PowerPlex 16 (PP16) multiplex nuclear short tandem repeat (STR) kit. Results DNA quantification results showed that the silica-based method extracted on average 1.94 ng of DNA per gram of bone (range 0.25-9.58 ng/g), compared with only 0.68 ng/g by the organic method extracted (range 0.0016-4.4880 ng/g). Inhibition tests showed that there were on average significantly lower levels of PCR inhibitors in DNA isolated by the organic method. When amplified with PP16, all samples extracted by silica-based method produced 16 full loci profiles, while only 75% of the DNA extracts obtained by organic technique amplified 16 loci profiles. Conclusions The silica-based extraction method showed better results in nuclear STR typing from degraded bone samples than a commonly used phenol/chloroform method. PMID:17696302

Effects of extraction methods on the antioxidant activities of polysaccharides from Agaricus blazei Murrill.

PubMed

Jia, Shaoyi; Li, Feng; Liu, Yong; Ren, Haitao; Gong, Guili; Wang, Yanyan; Wu, Songhai

2013-11-01

Five polysaccharides were obtained from Agaricus blazei Murrill (ABM) through different extraction methods including hot water extraction, single enzyme extraction (pectinase, cellulase or papain) and compound enzymes extraction (cellulase:pectinase:papain). Their characteristics such as the polysaccharide yield, polysaccharide content, protein content, infrared spectra were determined, and antioxidant activities were investigated on the basis of hydroxyl radical, DPPH free radical, ABTS free radical and reducing power. The results showed that five extracts exhibited antioxidant activities in a concentration-dependent manner. Compared with other methods, the compound enzymes extraction method was found to present the highest polysaccharides yield (17.44%). Moreover, compound enzymes extracts exhibited the strongest reducing power and highest scavenging rates on hydroxyl radicals, DPPH radicals and ABTS radicals. On the contrary, hot water extraction method had the lowest polysaccharides yield of 11.95%, whose extracts also exhibited the lowest antioxidant activities. Overall, the available data obtained in vitro models suggested that ABM extracts were natural antioxidants and compound enzymes extraction was an appropriate, mild and effective extracting method for obtaining the polysaccharide extracts from Agaricus blazei Murrill (ABM). Copyright © 2013 Elsevier B.V. All rights reserved.

Application of HPLC and ESI-MS techniques in the analysis of phenolic acids and flavonoids from green leafy vegetables (GLVs).

PubMed

Kumar, B Ramesh

2017-12-01

Diets containing high proportions of fruits and vegetables reduce the risk of onset of chronic diseases. The role of herbal medicines in improving human health is gaining popularity over the years, which also increases the need for safety and efficiency of these products. Green leafy vegetables (GLVs) are the richest source of phenolic compounds with excellent antioxidant properties. Increased consumption of diets containing phenolic compounds may give positive and better results to human health and significantly improves the immune system. Highly selective, susceptible and versatile analytical techniques are necessary for extraction, identification, and quantification of phenolic compounds from plant extracts, which helps to utilize their important biological properties. Recent advances in the pre-treatment procedures, separation techniques and spectrometry methods are used for qualitative and quantitative analysis of phenolic compounds. The online coupling of liquid chromatography with mass spectrometry (LC-MS) has become a useful tool in the metabolic profiling of plant samples. In this review, the separation and identification of phenolic acids and flavonoids from GLVs by LC-MS have been discussed along with the general extraction procedures and other sources of mass spectrometer used. The review is devoted to the understanding of the structural configuration, nature and accumulation pattern of phenolic acids and flavonoids in plants and to highlighting the recent developments in the chemical investigation of these compounds by chromatographic and spectroscopic techniques. It concludes with the advantages of the combination of these two methods and prospects.

Inhibitory action on the production of advanced glycation end products (AGEs) and suppression of free radicals in vitro by a Sri Lankan polyherbal formulation Nawarathne Kalka.

PubMed

Fernando, Chamira Dilanka; Karunaratne, Diyathi Tharindhi; Gunasinghe, Sachith Dilshan; Cooray, M C Dilusha; Kanchana, Prabuddhi; Udawatte, Chandani; Perera, Pathirage Kamal

2016-07-08

Advanced glycation end products (AGEs) and free radicals are inflammatory mediators and are implicated in many diseases such as diabetes, cancer, rheumatoid arthritis etc. Multi targeted poly herbal drug systems like Nawarathne Kalka (NK) are able to quench the overall effect of these mediators as they contain good combinations of phytochemicals that have least side effects in contrast to modern medicinal drugs. The objectives of this study were to evaluate phytochemical composition, free radical scavenging activity, cytotoxicity and the inhibitory action on the formation of AGEs by aqueous extract of NK. Total phenolic content (TPC) and total flavonoid content (TFC) were determined using Folin ciocalteu method and aluminium chloride assay respectively. Free radical scavenging activity was assessed by DPPH radical scavenging assay (DRSA), phosphomolybdenum reduction antioxidant assay (PRAA) and nitric oxide (NO) scavenging assay. Brine Shrimp Lethality (BSL) bioassay was performed as preliminary screening for cytotoxic activity. Inhibitory action on AGE formation was evaluated using fructose mediated glycation of bovine serum albumin using fluorescence spectroscopic method. The TPC and TFC were 75.1 ± 3.0 mg/g gallic acid equivalents and 68.7 ± 7.8 mg/g epigallocatechin gallate equivalents. The DRSA yielded EC50 of 19.15 ± 2.24 μg mL(-1) for NK. DRSA of NK extract was greater than butylated hydroxy toluene (EC50 = 96.50 ± 4.51 μg mL(-1)) but lesser than L-ascorbic acid (EC50 = 5.60 ± 0.51 μg mL(-1)). The total antioxidant capacity of NK as evidenced by PRAA was 106.4 ± 8.2 mg/g L-ascorbic acid equivalents. NK showed EC50 value of 99.3 ± 8.4 μg mL(-1) in the NO scavenging assay compared to the standard ascorbic acid (EC50 = 7.3 ± 0.3 μg mL(-1)). The extract indicated moderate cytotoxic activity in the BSL bioassay. The extract showed effective inhibitory action on the formation of AGEs with EC50 values of 116 ± 19 μg mL(-1), 125 ± 35 μg mL(-1) and 84 ± 28 μg mL(-1) in data obtained over three consecutive weeks respectively. Comparatively the reference standard, aminoguanidine at a concentration of 500 μg mL(-1) demonstrated 65 % inhibition on the formation of AGE after one week of sample incubation. The results proved the potential of NK as a free radical scavenger, moderate cytotoxic agent and an inhibitor on the formation of advanced glycation end-products.

Successful Treatment of Postpeak Stage Patients with Class II Division 1 Malocclusion Using Non-extraction and Multiloop Edgewise Archwire Therapy: A Report on 16 Cases

PubMed Central

Liu, Jun; Zou, Ling; Zhao, Zhi-he; Welburn, Neala; Yang, Pu; Tang, Tian; Li, Yu

2009-01-01

Aim To determine cephalometrically the mechanism of the treatment effects of non-extraction and multiloop edgewise archwire (MEAW) technique on postpeak Class II Division 1 patients. Methodology In this retrospective study, 16 postpeak Class II Division 1 patients successfully corrected using a non-extraction and MEAW technique were cephalometrically evaluated and compared with 16 matched control subjects treated using an extraction technique. Using CorelDRAW® software, standardized digital cephalograms pre- and post-active treatments were traced and a reference grid was set up. The superimpositions were based on the cranial base, the mandibular and the maxilla regions,and skeletal and dental changes were measured. Changes following treatment were evaluated using the paired-sample t-test. Student's t-test for unpaired samples was used to assess the differences in changes between the MEAW and the extraction control groups. Results The correction of the molar relationships comprised 54% skeletal change (mainly the advancement of the mandible) and 46% dental change. Correction of the anterior teeth relationships comprised 30% skeletal change and 70% dental change. Conclusion The MEAW technique can produce the desired vertical and sagittal movement of the tooth segment and then effectively stimulate mandibular advancement by utilizing the residual growth potential of the condyle. PMID:20690424

CNN based approach for activity recognition using a wrist-worn accelerometer.

PubMed

Panwar, Madhuri; Dyuthi, S Ram; Chandra Prakash, K; Biswas, Dwaipayan; Acharyya, Amit; Maharatna, Koushik; Gautam, Arvind; Naik, Ganesh R

2017-07-01

In recent years, significant advancements have taken place in human activity recognition using various machine learning approaches. However, feature engineering have dominated conventional methods involving the difficult process of optimal feature selection. This problem has been mitigated by using a novel methodology based on deep learning framework which automatically extracts the useful features and reduces the computational cost. As a proof of concept, we have attempted to design a generalized model for recognition of three fundamental movements of the human forearm performed in daily life where data is collected from four different subjects using a single wrist worn accelerometer sensor. The validation of the proposed model is done with different pre-processing and noisy data condition which is evaluated using three possible methods. The results show that our proposed methodology achieves an average recognition rate of 99.8% as opposed to conventional methods based on K-means clustering, linear discriminant analysis and support vector machine.

Four Different Methods Comparison for Extraction of Astaxanthin from Green Alga Haematococcus pluvialis

PubMed Central

Dong, Shengzhao; Huang, Yi; Zhang, Rui; Wang, Shihui; Liu, Yun

2014-01-01

Haematococcus pluvialis is one of the potent organisms for production of astaxanthin. Up to now, no efficient method has been achieved due to its thick cell wall hindering solvent extraction of astaxanthin. In this study, four different methods, hydrochloric acid pretreatment followed by acetone extraction (HCl-ACE), hexane/isopropanol (6 : 4, v/v) mixture solvents extraction (HEX-IPA), methanol extraction followed by acetone extraction (MET-ACE, 2-step extraction), and soy-oil extraction, were intensively evaluated for extraction of astaxanthin from H. pluvialis. Results showed that HCl-ACE method could obtain the highest oil yield (33.3 ± 1.1%) and astaxanthin content (19.8 ± 1.1%). Quantitative NMR analysis provided the fatty acid chain profiles of total lipid extracts. In all cases, oleyl chains were predominant, and high amounts of polyunsaturated fatty acid chains were observed and the major fatty acid components were oleic acid (13–35%), linoleic acid (37–43%), linolenic acid (20–31%), and total saturated acid (17–28%). DPPH radical scavenging activity of extract obtained by HCl-ACE was 73.2 ± 1.0%, which is the highest amongst the four methods. The reducing power of extract obtained by four extraction methods was also examined. It was concluded that the proposed extraction method of HCl-ACE in this work allowed efficient astaxanthin extractability with high antioxidant properties. PMID:24574909

Four different methods comparison for extraction of astaxanthin from green alga Haematococcus pluvialis.

PubMed

Dong, Shengzhao; Huang, Yi; Zhang, Rui; Wang, Shihui; Liu, Yun

2014-01-01

Haematococcus pluvialis is one of the potent organisms for production of astaxanthin. Up to now, no efficient method has been achieved due to its thick cell wall hindering solvent extraction of astaxanthin. In this study, four different methods, hydrochloric acid pretreatment followed by acetone extraction (HCl-ACE), hexane/isopropanol (6:4, v/v) mixture solvents extraction (HEX-IPA), methanol extraction followed by acetone extraction (MET-ACE, 2-step extraction), and soy-oil extraction, were intensively evaluated for extraction of astaxanthin from H. pluvialis. Results showed that HCl-ACE method could obtain the highest oil yield (33.3±1.1%) and astaxanthin content (19.8±1.1%). Quantitative NMR analysis provided the fatty acid chain profiles of total lipid extracts. In all cases, oleyl chains were predominant, and high amounts of polyunsaturated fatty acid chains were observed and the major fatty acid components were oleic acid (13-35%), linoleic acid (37-43%), linolenic acid (20-31%), and total saturated acid (17-28%). DPPH radical scavenging activity of extract obtained by HCl-ACE was 73.2±1.0%, which is the highest amongst the four methods. The reducing power of extract obtained by four extraction methods was also examined. It was concluded that the proposed extraction method of HCl-ACE in this work allowed efficient astaxanthin extractability with high antioxidant properties.

An improved independent component analysis model for 3D chromatogram separation and its solution by multi-areas genetic algorithm

PubMed Central

2014-01-01

Background The 3D chromatogram generated by High Performance Liquid Chromatography-Diode Array Detector (HPLC-DAD) has been researched widely in the field of herbal medicine, grape wine, agriculture, petroleum and so on. Currently, most of the methods used for separating a 3D chromatogram need to know the compounds' number in advance, which could be impossible especially when the compounds are complex or white noise exist. New method which extracts compounds from 3D chromatogram directly is needed. Methods In this paper, a new separation model named parallel Independent Component Analysis constrained by Reference Curve (pICARC) was proposed to transform the separation problem to a multi-parameter optimization issue. It was not necessary to know the number of compounds in the optimization. In order to find all the solutions, an algorithm named multi-areas Genetic Algorithm (mGA) was proposed, where multiple areas of candidate solutions were constructed according to the fitness and distances among the chromosomes. Results Simulations and experiments on a real life HPLC-DAD data set were used to demonstrate our method and its effectiveness. Through simulations, it can be seen that our method can separate 3D chromatogram to chromatogram peaks and spectra successfully even when they severely overlapped. It is also shown by the experiments that our method is effective to solve real HPLC-DAD data set. Conclusions Our method can separate 3D chromatogram successfully without knowing the compounds' number in advance, which is fast and effective. PMID:25474487

Fluorescence-based methods for detecting caries lesions: systematic review, meta-analysis and sources of heterogeneity.

PubMed

Gimenez, Thais; Braga, Mariana Minatel; Raggio, Daniela Procida; Deery, Chris; Ricketts, David N; Mendes, Fausto Medeiros

2013-01-01

Fluorescence-based methods have been proposed to aid caries lesion detection. Summarizing and analysing findings of studies about fluorescence-based methods could clarify their real benefits. We aimed to perform a comprehensive systematic review and meta-analysis to evaluate the accuracy of fluorescence-based methods in detecting caries lesions. Two independent reviewers searched PubMed, Embase and Scopus through June 2012 to identify papers/articles published. Other sources were checked to identify non-published literature. STUDY ELIGIBILITY CRITERIA, PARTICIPANTS AND DIAGNOSTIC METHODS: The eligibility criteria were studies that: (1) have assessed the accuracy of fluorescence-based methods of detecting caries lesions on occlusal, approximal or smooth surfaces, in both primary or permanent human teeth, in the laboratory or clinical setting; (2) have used a reference standard; and (3) have reported sufficient data relating to the sample size and the accuracy of methods. A diagnostic 2×2 table was extracted from included studies to calculate the pooled sensitivity, specificity and overall accuracy parameters (Diagnostic Odds Ratio and Summary Receiver-Operating curve). The analyses were performed separately for each method and different characteristics of the studies. The quality of the studies and heterogeneity were also evaluated. Seventy five studies met the inclusion criteria from the 434 articles initially identified. The search of the grey or non-published literature did not identify any further studies. In general, the analysis demonstrated that the fluorescence-based method tend to have similar accuracy for all types of teeth, dental surfaces or settings. There was a trend of better performance of fluorescence methods in detecting more advanced caries lesions. We also observed moderate to high heterogeneity and evidenced publication bias. Fluorescence-based devices have similar overall performance; however, better accuracy in detecting more advanced caries lesions has been observed.

Micelle-mediated extraction of elderberry blossom by whey protein and naturally derived surfactants.

PubMed

Śliwa, Karolina; Tomaszkiewicz-Potępa, Anna; Sikora, Elżbieta; Ogonowski, Jan

2013-01-01

Classical methods of the extraction of active ingredients from the plant material are expensive, complicated and often environmentally unfriendly. The micelle-mediated extraction method (MME) seems to be a good alternative. In this work, extractions of elderberry blossoms (Flos Sambuci) were performed using MME methods. Several popular surfactants and whey protein concentrate (WPC) was applied in the process. The obtained results were compared with those obtained in extraction by means of water. Antioxidant properties of the extracts were analyzed by using two different methods: reaction with di(phenyl)-(2,4,6-trinitrophenyl)iminoazanium (DPPH) reagent and Follin's method. Furthermore, the flavonoid content in the extracts was determined. The results confirmed that the MME method with using whey protein might be an alternative method for obtaining, rich in natural antioxidants, plant extracts.

Lead Contamination and Source Characterization in Soils Around a Lead-Zinc Smelting Plant in a Near-Urban Environment in Baoji, China.

PubMed

Deng, Wenbo; Li, Xuxiang; An, Zhisheng; Yang, Liu

2016-11-01

Economic reforms in China since 1978 have promoted nationwide socioeconomic advancement but led to a considerable amount of environmental pollution. The distribution and sources of Pb in a typical peri-urban industrial part of Baoji, China, were assessed by determining the Pb contents and isotopic compositions in 52 topsoil samples from the study area. The topsoil samples were polluted averagely with 40.88 mg Pb kg -1 , was 1.86 times higher than the Pb content of local background soil (22.04 mg kg -1 ). Pb isotopic compositions were determined by analyzing samples prepared using total digestion and acid extraction methods. Radiogenic isotopes contributed more to the Pb concentrations in the acid extracts than in the total digests. This was shown by the 207/206 Pb and 208/206 Pb ratios, which were 0.845-0.88 and 2.088-2.128, respectively, in the acid extracts and 0.841-0.875 and 2.086-2.125, respectively, in the total digests. This indicates that anthropogenic sources of Pb could be identified more sensitively in acid extracts than in total digests. The Pb isotope ratios showed that burning coal and smelting ore are the predominant anthropogenic sources of Pb in the study area, i.e., a lead-zinc smelter and a coking plant are major sources of Pb in the study area.

Accurate facade feature extraction method for buildings from three-dimensional point cloud data considering structural information

NASA Astrophysics Data System (ADS)

Wang, Yongzhi; Ma, Yuqing; Zhu, A.-xing; Zhao, Hui; Liao, Lixia

2018-05-01

Facade features represent segmentations of building surfaces and can serve as a building framework. Extracting facade features from three-dimensional (3D) point cloud data (3D PCD) is an efficient method for 3D building modeling. By combining the advantages of 3D PCD and two-dimensional optical images, this study describes the creation of a highly accurate building facade feature extraction method from 3D PCD with a focus on structural information. The new extraction method involves three major steps: image feature extraction, exploration of the mapping method between the image features and 3D PCD, and optimization of the initial 3D PCD facade features considering structural information. Results show that the new method can extract the 3D PCD facade features of buildings more accurately and continuously. The new method is validated using a case study. In addition, the effectiveness of the new method is demonstrated by comparing it with the range image-extraction method and the optical image-extraction method in the absence of structural information. The 3D PCD facade features extracted by the new method can be applied in many fields, such as 3D building modeling and building information modeling.

Antifungal activity of plant extracts against Aspergillus niger and Rhizopus stolonifer.

PubMed

Surapuram, Venkatasaichaitanya; Setzer, William N; McFeeters, Robert L; McFeeters, Hana

2014-11-01

Despite recent advances in antifungal development, fungi remain a devastating threat to human health and compromise viability of the food supply. Plant based antimicrobials represent a vast untapped source with tremendous potential. Herein we present the antifungal properties of more than 50 plant extracts against two important human and agricultural pathogens, Aspergillus niger and Rhizopus stolonifer. Multiple extracts exhibit promising MIC values of less than 100 μg/mL and are reported for both fungal species.

Inadequacy, Impurity and Infidelity; Modifying the Modified Brendel Alpha-Cellulose Extraction Method for Resinous Woods in Stable Isotope Dendroclimatology

NASA Astrophysics Data System (ADS)

Brookman, T. H.; Whittaker, T. E.; King, P. L.; Horton, T. W.

2011-12-01

Stable isotope dendroclimatology is a burgeoning field in palaeoclimate science due to its unique potential to contribute (sub)annually resolved climate records, over millennial timescales, to the terrestrial palaeoclimate record. Until recently the time intensive methods precluded long-term climate reconstructions. Advances in continuous-flow mass spectrometry and isolation methods for α-cellulose (ideal for palaeoclimate studies as, unlike other wood components, it retains its initial isotopic composition) have made long-term, calendar dated palaeoclimate reconstructions a viable proposition. The Modified Brendel (mBrendel) α-cellulose extraction method is a fast, cost-effective way of preparing whole-wood samples for stable oxygen and carbon isotope analysis. However, resinous woods often yield incompletely processed α-cellulose using the standard mBrendel approach. As climate signals may be recorded by small (<1%) isotopic shifts it is important to investigate if incomplete processing affects the accuracy and precision of tree-ring isotopic records. In an effort to address this methodological issue, we investigated three highly resinous woods: kauri (Agathis australis), ponderosa pine (Pinus ponderosa) and huon pine (Lagarastrobus franklinii). Samples of each species were treated with 16 iterations of the mBrendel, varying reaction temperature, time and reagent volumes. Products were investigated using microscopic and bulk transmission Fourier Transform infrared spectroscopy (FITR) to reveal variations in the level of processing; poorly-digested fibres display a peak at 1520cm-1 suggesting residual lignin and a peak at ~1600cm-1 in some samples suggests retained resin. Despite the different levels of purity, replicate analyses of samples processed by high temperature digestion yielded consistent δ18O within and between experiments. All α-cellulose samples were 5-7% enriched compared to the whole-wood, suggesting that even incomplete processing at high temperature can provide acceptable δ18O analytical external precision. For kauri, short, lower temperature extractions produced α-cellulose with δ18O consistently ~1% lower than longer, higher temperature kauri experiments. These findings suggest that temperature and time are significant variables that influence the analytical precision of α-cellulose stable isotope analysis and that resinous hardwoods (e.g. kauri) may require longer and/or hotter digestions than softwoods. The effects of mBrendel variants on the carbon isotope ratio precision of α-cellulose extracts will also be presented. Our findings indicate that the standard mBrendel α-cellulose extraction method may not fully remove lignins and resins depending on the type of wood being analysed. Residual impurities can decrease analytical precision and accuracy. Fortunately, FTIR analysis prior to isotopic analysis is a relatively fast and cost effective way to determine α-cellulose extract purity, ultimately improving the data quality, accuracy and utility of tree-ring based stable isotopic climate records.

Evaluation of DNA extraction methods for the analysis of microbial community in biological activated carbon.

PubMed

Zheng, Lu; Gao, Naiyun; Deng, Yang

2012-01-01

It is difficult to isolate DNA from biological activated carbon (BAC) samples used in water treatment plants, owing to the scarcity of microorganisms in BAC samples. The aim of this study was to identify DNA extraction methods suitable for a long-term, comprehensive ecological analysis of BAC microbial communities. To identify a procedure that can produce high molecular weight DNA, maximizes detectable diversity and is relatively free from contaminants, the microwave extraction method, the cetyltrimethylammonium bromide (CTAB) extraction method, a commercial DNA extraction kit, and the ultrasonic extraction method were used for the extraction of DNA from BAC samples. Spectrophotometry, agarose gel electrophoresis and polymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) analysis were conducted to compare the yield and quality of DNA obtained using these methods. The results showed that the CTAB method produce the highest yield and genetic diversity of DNA from BAC samples, but DNA purity was slightly less than that obtained with the DNA extraction-kit method. This study provides a theoretical basis for establishing and selecting DNA extraction methods for BAC samples.

Factors affecting skin tannin extractability in ripening grapes.

PubMed

Bindon, Keren A; Madani, S Hadi; Pendleton, Phillip; Smith, Paul A; Kennedy, James A

2014-02-05

The acetone-extractable (70% v/v) skin tannin content of Vitis vinifera L. cv. Cabernet Sauvignon grapes was found to increase during late-stage ripening. Conversely, skin tannin content determined following ethanol extraction (10, 20, and 50% v/v) did not consistently reflect this trend. The results indicated that a fraction of tannin became less extractable in aqueous ethanol during ripening. Skin cell walls were observed to become more porous during ripening, which may facilitate the sequestering of tannin as an adsorbed fraction within cell walls. For ethanol extracts, tannin molecular mass increased with advancing ripeness, even when extractable tannin content was constant, but this effect was negligible in acetone extracts. Reconstitution experiments with isolated skin tannin and cell wall material indicated that the selectivity of tannin adsorption by cell walls changed as tannin concentration increased. Tannin concentration, tannin molecular mass, and cell wall porosity are discussed as factors that may influence skin tannin extractability.

Natural colorants: Pigment stability and extraction yield enhancement via utilization of appropriate pretreatment and extraction methods.

PubMed

Ngamwonglumlert, Luxsika; Devahastin, Sakamon; Chiewchan, Naphaporn

2017-10-13

Natural colorants from plant-based materials have gained increasing popularity due to health consciousness of consumers. Among the many steps involved in the production of natural colorants, pigment extraction is one of the most important. Soxhlet extraction, maceration, and hydrodistillation are conventional methods that have been widely used in industry and laboratory for such a purpose. Recently, various non-conventional methods, such as supercritical fluid extraction, pressurized liquid extraction, microwave-assisted extraction, ultrasound-assisted extraction, pulsed-electric field extraction, and enzyme-assisted extraction have emerged as alternatives to conventional methods due to the advantages of the former in terms of smaller solvent consumption, shorter extraction time, and more environment-friendliness. Prior to the extraction step, pretreatment of plant materials to enhance the stability of natural pigments is another important step that must be carefully taken care of. In this paper, a comprehensive review of appropriate pretreatment and extraction methods for chlorophylls, carotenoids, betalains, and anthocyanins, which are major classes of plant pigments, is provided by using pigment stability and extraction yield as assessment criteria.

Simultaneous overlay and CD measurement for double patterning: scatterometry and RCWA approach

NASA Astrophysics Data System (ADS)

Li, Jie; Liu, Zhuan; Rabello, Silvio; Dasari, Prasad; Kritsun, Oleg; Volkman, Catherine; Park, Jungchul; Singh, Lovejeet

2009-03-01

As optical lithography advances to 32 nm technology node and beyond, double patterning technology (DPT) has emerged as an attractive solution to circumvent the fundamental optical limitations. DPT poses unique demands on critical dimension (CD) uniformity and overlay control, making the tolerance decrease much faster than the rate at which critical dimension shrinks. This, in turn, makes metrology even more challenging. In the past, multi-pad diffractionbased overlay (DBO) using empirical approach has been shown to be an effective approach to measure overlay error associated with double patterning [1]. In this method, registration errors for double patterning were extracted from specially designed diffraction targets (three or four pads for each direction); CD variation is assumed negligible within each group of adjacent pads and not addressed in the measurement. In another paper, encouraging results were reported with a first attempt at simultaneously extracting overlay and CD parameters using scatterometry [2]. In this work, we apply scatterometry with a rigorous coupled wave analysis (RCWA) approach to characterize two double-patterning processes: litho-etch-litho-etch (LELE) and litho-freeze-litho-etch (LFLE). The advantage of performing rigorous modeling is to reduce the number of pads within each measurement target, thus reducing space requirement and improving throughput, and simultaneously extract CD and overlay information. This method measures overlay errors and CDs by fitting the optical signals with spectra calculated from a model of the targets. Good correlation is obtained between the results from this method and that of several reference techniques, including empirical multi-pad DBO, CD-SEM, and IBO. We also perform total measurement uncertainty (TMU) analysis to evaluate the overall performance. We demonstrate that scatterometry provides a promising solution to meet the challenging overlay metrology requirement in DPT.

Screening antimicrobial activity of various extracts of Urtica dioica.

PubMed

Modarresi-Chahardehi, Amir; Ibrahim, Darah; Fariza-Sulaiman, Shaida; Mousavi, Leila

2012-12-01

Urtica dioica or stinging nettle is traditionally used as an herbal medicine in Western Asia. The current study represents the investigation of antimicrobial activity of U. dioica from nine crude extracts that were prepared using different organic solvents, obtained from two extraction methods: the Soxhlet extractor (Method I), which included the use of four solvents with ethyl acetate and hexane, or the sequential partitions (Method II) with a five solvent system (butanol). The antibacterial and antifungal activities of crude extracts were tested against 28 bacteria, three yeast strains and seven fungal isolates by the disc diffusion and broth dilution methods. Amoxicillin was used as positive control for bacteria strains, vancomycin for Streptococcus sp., miconazole nitrate (30 microg/mL) as positive control for fungi and yeast, and pure methanol (v/v) as negative control. The disc diffusion assay was used to determine the sensitivity of the samples, whilst the broth dilution method was used for the determination of the minimal inhibition concentration (MIC). The ethyl acetate and hexane extract from extraction method I (EA I and HE I) exhibited highest inhibition against some pathogenic bacteria such as Bacillus cereus, MRSA and Vibrio parahaemolyticus. A selection of extracts that showed some activity was further tested for the MIC and minimal bactericidal concentrations (MBC). MIC values of Bacillus subtilis and Methicillin-resistant Staphylococcus aureus (MRSA) using butanol extract of extraction method II (BE II) were 8.33 and 16.33mg/mL, respectively; while the MIC value using ethyl acetate extract of extraction method II (EAE II) for Vibrio parahaemolyticus was 0.13mg/mL. Our study showed that 47.06% of extracts inhibited Gram-negative (8 out of 17), and 63.63% of extracts also inhibited Gram-positive bacteria (7 out of 11); besides, statistically the frequency of antimicrobial activity was 13.45% (35 out of 342) which in this among 21.71% belongs to antimicrobial activity extracts from extraction method I (33 out of 152 of crude extracts) and 6.82% from extraction method II (13 out of 190 of crude extracts). However, crude extracts from method I exhibited better antimicrobial activity against the Gram-positive bacteria than the Gram-negative bacteria. The positive results on medicinal plants screening for antibacterial activity constitutes primary information for further phytochemical and pharmacological studies. Therefore, the extracts could be suitable as antimicrobial agents in pharmaceutical and food industry.

An ultrasensitive chemiluminescence immunoassay of chloramphenicol based on gold nanoparticles and magnetic beads.

PubMed

Tao, Xiaoqi; Jiang, Haiyang; Yu, Xuezhi; Zhu, Jinghui; Wang, Xia; Wang, Zhanhui; Niu, Lanlan; Wu, Xiaoping; Shen, Jianzhong

2013-05-01

A competitive, direct, chemiluminescent immunoassay based on a magnetic beads (MBs) separation and gold nanoparticles (AuNPs) labelling technique to detect chloramphenicol (CAP) has been developed. Horseradish peroxidase (HRP)-labelled anti-CAP monoclonal antibody conjugated with AuNPs and antigen-immobilized MBs were prepared. After optimization parameters of immunocomplex MBs, the IC50 values of chemiluminescence magnetic nanoparticles immunoassay (CL-MBs-nano-immunoassay) were 0.017 µg L(-1) for extract method I and 0.17 µg L(-1) for extract method II. The immunoassay with two extract methods was applied to detect CAP in milk. Comparison of these two extract methods showed that extract method I was advantageous in better sensitivity, in which the sensitivity was 10 times compared to that of extract method II, while extract method II was superior in simple operation, suitable for high throughout screen. The recoveries were 86.7-98.0% (extract method I) and 80.0-103.0% (extract method II), and the coefficients of variation (CVs) were all <15%. The satisfactory recovery with both extract methods and high correlation with traditional ELISA kit in milk system confirmed that the immunomagnetic assay based on AuNPs exhibited promising potential in rapid field screening for trace CAP analysis. Copyright © 2013 John Wiley & Sons, Ltd.

Decontamination of soil containing POPs by the combined action of solid Fenton-like reagents and microwaves.

PubMed

Cravotto, Giancarlo; Di Carlo, Stefano; Ondruschka, Bernd; Tumiatti, Vander; Roggero, Carlo Maria

2007-10-01

The effect on halogenated aromatics of solid, non-toxic oxidants such as sodium percarbonate and the urea/hydrogen peroxide complex (Fenton-like reagents) was investigated. A microwaves-assisted, solvent-free method for soil decontamination is presented. It marks a considerable advance in the search of more efficient, environment-friendly procedures for the degradative oxidation of persistent organic pollutants. Residual pollutants in treated soil samples were determined by GC/MS analysis after solvent extraction or direct thermal desorption. Results showed that 4-chloronaphthol, 2,4-dichlorophenoxyacetic acid and p-nonylphenol had been degraded completely, 2,4-dibromophenol to a large extent.

Current Strategies for the Detoxification of Jatropha curcas Seed Cake: A Review.

PubMed

Gomes, Taisa G; Hadi, Sámed I I A; Costa Alves, Gabriel S; Mendonça, Simone; De Siqueira, Felix G; Miller, Robert N G

2018-03-21

Jatropha curcas is an important oilseed plant, with considerable potential in the development of biodiesel. Although Jatropha seed cake, the byproduct of oil extraction, is a residue rich in nitrogen, phosphorus, potassium, and carbon, with high protein content suitable for application in animal feed, the presence of toxic phorbol esters limits its application in feed supplements and fertilizers. This review summarizes the current methods available for detoxification of this residue, based upon chemical, physical, biological, or combined processes. The advantages and disadvantages of each process are discussed, and future directions involving genomic and proteomic approaches for advancing our understanding of biodegradation processes involving microorganisms are highlighted.

Analytical Glycobiology at High Sensitivity: Current Approaches and Directions

PubMed Central

Novotny, Milos V.; Alley, William R.; Mann, Benjamin F.

2013-01-01

This review summarizes the analytical advances made during the last several years in the structural and quantitative determinations of glycoproteins in complex biological mixtures. The main analytical techniques used in the fields of glycomics and glycoproteomics involve different modes of mass spectrometry and their combinations with capillary separation methods such as microcolumn liquid chromatography and capillary electrophoresis. The needs for high-sensitivity measurements have been emphasized in the oligosaccharide profiling used in the field of biomarker discovery through MALDI mass spectrometry. High-sensitivity profiling of both glycans and glycopeptides from biological fluids and tissue extracts has been aided significantly through lectin preconcentration and the uses of affinity chromatography. PMID:22945852

A comparative study: the impact of different lipid extraction methods on current microalgal lipid research

PubMed Central

2014-01-01

Microalgae cells have the potential to rapidly accumulate lipids, such as triacylglycerides that contain fatty acids important for high value fatty acids (e.g., EPA and DHA) and/or biodiesel production. However, lipid extraction methods for microalgae cells are not well established, and there is currently no standard extraction method for the determination of the fatty acid content of microalgae. This has caused a few problems in microlagal biofuel research due to the bias derived from different extraction methods. Therefore, this study used several extraction methods for fatty acid analysis on marine microalga Tetraselmis sp. M8, aiming to assess the potential impact of different extractions on current microalgal lipid research. These methods included classical Bligh & Dyer lipid extraction, two other chemical extractions using different solvents and sonication, direct saponification and supercritical CO2 extraction. Soxhlet-based extraction was used to weigh out the importance of solvent polarity in the algal oil extraction. Coupled with GC/MS, a Thermogravimetric Analyser was used to improve the quantification of microalgal lipid extractions. Among these extractions, significant differences were observed in both, extract yield and fatty acid composition. The supercritical extraction technique stood out most for effective extraction of microalgal lipids, especially for long chain unsaturated fatty acids. The results highlight the necessity for comparative analyses of microalgae fatty acids and careful choice and validation of analytical methodology in microalgal lipid research. PMID:24456581

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

Parekh, V; Jacobs, MA

Purpose: Multiparametric radiological imaging is used for diagnosis in patients. Potentially extracting useful features specific to a patient’s pathology would be crucial step towards personalized medicine and assessing treatment options. In order to automatically extract features directly from multiparametric radiological imaging datasets, we developed an advanced unsupervised machine learning algorithm called the multidimensional imaging radiomics-geodesics(MIRaGe). Methods: Seventy-six breast tumor patients underwent 3T MRI breast imaging were used for this study. We tested the MIRaGe algorithm to extract features for classification of breast tumors into benign or malignant. The MRI parameters used were T1-weighted, T2-weighted, dynamic contrast enhanced MR imaging (DCE-MRI)more » and diffusion weighted imaging(DWI). The MIRaGe algorithm extracted the radiomics-geodesics features (RGFs) from multiparametric MRI datasets. This enable our method to learn the intrinsic manifold representations corresponding to the patients. To determine the informative RGF, a modified Isomap algorithm(t-Isomap) was created for a radiomics-geodesics feature space(tRGFS) to avoid overfitting. Final classification was performed using SVM. The predictive power of the RGFs was tested and validated using k-fold cross validation. Results: The RGFs extracted by the MIRaGe algorithm successfully classified malignant lesions from benign lesions with a sensitivity of 93% and a specificity of 91%. The top 50 RGFs identified as the most predictive by the t-Isomap procedure were consistent with the radiological parameters known to be associated with breast cancer diagnosis and were categorized as kinetic curve characterizing RGFs, wash-in rate characterizing RGFs, wash-out rate characterizing RGFs and morphology characterizing RGFs. Conclusion: In this paper, we developed a novel feature extraction algorithm for multiparametric radiological imaging. The results demonstrated the power of the MIRaGe algorithm at automatically discovering useful feature representations directly from the raw multiparametric MRI data. In conclusion, the MIRaGe informatics model provides a powerful tool with applicability in cancer diagnosis and a possibility of extension to other kinds of pathologies. NIH (P50CA103175, 5P30CA006973 (IRAT), R01CA190299, U01CA140204), Siemens Medical Systems (JHU-2012-MR-86-01) and Nivida Graphics Corporation.« less

Anti-inflammaging and antiglycation activity of a novel botanical ingredient from African biodiversity (Centevita™)

PubMed Central

Maramaldi, Giada; Togni, Stefano; Franceschi, Federico; Lati, Elian

2014-01-01

Purpose The aim of this study was to investigate the topical efficacy of a new purified extract from Madagascar, Gotu Kola (Centella asiatica [L.] Urban), both on human explants and on human volunteers, in relation to skin wrinkling and skin protection against ultraviolet light exposure. The extract, with a peculiar content of biologically active molecules, was investigated as a novel anti-inflammaging and antiglycation agent. Its typical terpenes, known as collagen synthesis promoters, represent at least 45% of the extract. It also contains a polyphenolic fraction cooperating to the observed properties. Methods C. asiatica purified extract was assayed on human skin explants maintained alive, and several parameters were evaluated. Among the most relevant, the thymine dimerization was evaluated by immunostaining. Malondialdehyde formation was evaluated as free-radical scavenging marker by enzyme-linked immunosorbent assay. The expression of interleukin-1α was observed by enzyme-linked immunosorbent assay as well. The product was further evaluated as an antiglycation agent, being glycation quantified by the advanced glycation product carboxymethyl lysine. C. asiatica purified extract was also evaluated as an antiwrinkling agent in a single-blind, placebo-controlled study. Formulated in a simple oil-in-water emulsion, the extent of wrinkling was assessed by skin replicas, skin firmness, skin elasticity, and collagen density measurements. Results C. asiatica purified extract could protect DNA from ultraviolet light-induced damage, decreasing the thymine photodimerization by over 28% (P<0.05). A reduced (26%, P<0.01) expression of interleukin-1α was also observed, supporting its anti-inflammatory potential. C. asiatica purified extract showed in vitro a total inhibition of carboxymethyl lysine formation induced by the glycating agent methylglyoxal. A clear epidermal densification of collagen network in the papillary dermis was observed. These in vitro data have been confirmed by clinical results. Conclusion These results qualify C. asiatica purified extract as an antiaging ingredient, addressing skin damage caused by inflammaging and glycation by relying on the synergy of triterpens and polyphenolics. PMID:24376360

Long-Term Oral Administration of Hop Flower Extracts Mitigates Alzheimer Phenotypes in Mice

PubMed Central

Sasaoka, Norio; Sakamoto, Megumi; Kanemori, Shoko; Kan, Michiru; Tsukano, Chihiro; Takemoto, Yoshiji; Kakizuka, Akira

2014-01-01

Coincident with the expanding population of aged people, the incidence of Alzheimer disease (AD) is rapidly increasing in most advanced countries. At present, no effective prophylactics are available. Among several pathological mechanisms proposed for AD, the “amyloid hypothesis” has been most widely accepted, in which accumulation or deposition of Aβ is considered to be the initial event. Thus, prevention of Aβ production would be an ideal strategy for the treatment or prevention of AD. Aβ is produced via the proteolytic cleavage of its precursor protein, APP (amyloid precursor protein), by two different enzymes, β and γ-secretases. Indeed, inhibitors against either or both enzymes have been developed and tested for clinical efficacy. Based on the “amyloid hypothesis”, we developed a luciferase-based screening method to monitor γ-secretase activity, screened more than 1,600 plant extracts, most of which have long been used in Chinese medicine, and observed that Hop extracts significantly inhibit Aβ production in cultured cells. A major component of the inhibitory activity was purified, and its chemical identity was determined by NMR to be Garcinielliptone HC. In vivo, oral administration of Hop extracts to AD model mice decreased Aβ depositions in the cerebral cortex of the parietal lobe, hippocampus, and artery walls (amyloid angiopathy) in the brains. In a Morris water maze test, AD model mice that had daily consumed Hop extracts in their drinking water showed significant mitigation of memory impairment at ages of 9 and 12 months. Moreover, in the open field test oral administration of Hop extracts also prevented an emotional disturbance that appeared in the AD mice at 18 months. Despite lifelong consumption of Hop extracts, no deleterious side effects were observed at any age. These results support the “amyloid hypothesis”, and indicate that Hop extract is a promising candidate for an effective prophylactic for AD. PMID:24489866

Antibacterial, antifungal and antioxidant activities of the ethanol extract of the stem bark of Clausena heptaphylla

PubMed Central

2012-01-01

Background There is wide spread interest in drugs derived from plants as green medicine is believed to be safe and dependable, compared with costly synthetic drugs that have adverse effects. Methods We have attempted to evaluate the antioxidant, In vitro thrombolytic, antibacterial, antifungal and cytotoxic effects of Clausena heptaphylla (Rutaceae) stem bark extract ethanol extract. Results Ethanolic stem bark extract of Clausena heptaphylla (CHET) contains flavonoids, alkaloids, saponins and steroids but it lacks tannins, anthraquinones and resins. Phenol content of the extract was 13.42 mg/g and flavonoid content was 68.9 mg/g. CHET exhibited significant DPPH free radical scavenging activity with IC50 value of 3.11 μg/ml. Reducing power of CHET was also moderately stronger. In the cytotoxicity assay, LC50 and Chi-square value of the ethanolic extract against brine shrimp nauplii were 144.1461 μg/ml and 0.8533 demonstrating potent cytotoxic effect of the extract. In vitro thrombolytic activity of CHET is significant with 45.38% clot lysis capability compared to that of Streptokinase (65.78%). In antibacterial screening, moderate zone of inhibition (6.5-9.0 mm in diameter) was observed against gram-positive Bacillus subtilis ATCC 11774, Bacillus cereus ATCC 10876, Staphylococcus aureus ATCC 25923, Bacillus polymyxa ATCC 842 and Bacillus megaterium ATCC 13578 and less promising zone of inhibition (3.0-4.5 mm in diameter) against gram-negative Salmonella typhi ATCC 65154, Shigella flexneri ATCC 12022, Proteus vulgaris ATCC 13315 and Escherichia coli ATCC 25922. Shigella sonnei ATCC 8992 did not show any sensitivity. The MIC values against these bacteria were ranged from 2,000 to 3,500 μg/ml. The extract showed significant zone of inhibition against Rhizopus oryzae DSM 2200, Aspergillus niger DSM 737 and Aspergillus ochraceus DSM 824 in antifungal assay. Conclusions Further advanced research is necessary to isolate and characterize the chemical components responsible for the therapeutic properties of the plant. PMID:23181593

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites.

PubMed

Covington, Brett C; McLean, John A; Bachmann, Brian O

2017-01-04

Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

PubMed Central

Liu, Xiaojing; Ser, Zheng; Cluntun, Ahmad A.; Mentch, Samantha J.; Locasale, Jason W.

2014-01-01

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. However, current platforms have different limiting factors, such as labor intensive sample preparations, low detection limits, slow scan speeds, intensive method optimization for each metabolite, and the inability to measure both positively and negatively charged ions in single experiments. Therefore, a novel metabolomics protocol could advance metabolomics studies. Amide-based hydrophilic chromatography enables polar metabolite analysis without any chemical derivatization. High resolution MS using the Q-Exactive (QE-MS) has improved ion optics, increased scan speeds (256 msec at resolution 70,000), and has the capability of carrying out positive/negative switching. Using a cold methanol extraction strategy, and coupling an amide column with QE-MS enables robust detection of 168 targeted polar metabolites and thousands of additional features simultaneously.  Data processing is carried out with commercially available software in a highly efficient way, and unknown features extracted from the mass spectra can be queried in databases. PMID:24894601

A spent coffee grounds based biorefinery for the production of biofuels, biopolymers, antioxidants and biocomposites.

PubMed

Karmee, Sanjib Kumar

2018-02-01

Spent coffee grounds are composed of lipid, carbohydrates, carbonaceous, and nitrogen containing compounds among others. Using n-hexane and n-hexane/isopropanol mixture highest oil yield was achived during soxhlet extraction of oil from spent coffee grounds. Alternatively, supercritical carbon dioxide can be employed as a green solvent for the extraction of oil. Using advanced chemical and biotechnological methods, spent coffee grounds are converted to various biofuels such as, biodiesel, renewable diesel, bioethanol, bioethers, bio-oil, biochar, and biogas. The in-situ transesterification of spent coffee grounds was carried out in a large scale (4 kg), which led to 80-83% biodiesel yield. In addition, a large number of value added and diversified products viz. polyhydroxyalkanoates, biosorbent, activated carbon, polyol, polyurethane foam, carotenoid, phenolic antioxidants, and green composite are obtained from spent coffee grounds. The principles of circular economy are applied to develop a sustanaible biorefinery based on valorisation of spent coffee grounds. Copyright © 2017 Elsevier Ltd. All rights reserved.

Searching the literature for proteins facilitates the identification of biological processes, if advanced methods of analysis are linked: a case study on microgravity-caused changes in cells.

PubMed

Bauer, Johann; Bussen, Markus; Wise, Petra; Wehland, Markus; Schneider, Sabine; Grimm, Daniela

2016-07-01

More than one hundred reports were published about the characterization of cells from malignant and healthy tissues, as well as of endothelial cells and stem cells exposed to microgravity conditions. We retrieved publications about microgravity related studies on each type of cells, extracted the proteins mentioned therein and analyzed them aiming to identify biological processes affected by microgravity culture conditions. The analysis revealed 66 different biological processes, 19 of them were always detected when papers about the four types of cells were analyzed. Since a response to the removal of gravity is common to the different cell types, some of the 19 biological processes could play a role in cellular adaption to microgravity. Applying computer programs, to extract and analyze proteins and genes mentioned in publications becomes essential for scientists interested to get an overview of the rapidly growing fields of gravitational biology and space medicine.

Robust parameter extraction for decision support using multimodal intensive care data

PubMed Central

Clifford, G.D.; Long, W.J.; Moody, G.B.; Szolovits, P.

2008-01-01

Digital information flow within the intensive care unit (ICU) continues to grow, with advances in technology and computational biology. Recent developments in the integration and archiving of these data have resulted in new opportunities for data analysis and clinical feedback. New problems associated with ICU databases have also arisen. ICU data are high-dimensional, often sparse, asynchronous and irregularly sampled, as well as being non-stationary, noisy and subject to frequent exogenous perturbations by clinical staff. Relationships between different physiological parameters are usually nonlinear (except within restricted ranges), and the equipment used to measure the observables is often inherently error-prone and biased. The prior probabilities associated with an individual's genetics, pre-existing conditions, lifestyle and ongoing medical treatment all affect prediction and classification accuracy. In this paper, we describe some of the key problems and associated methods that hold promise for robust parameter extraction and data fusion for use in clinical decision support in the ICU. PMID:18936019

Exploiting Small Leakages in Masks to Turn a Second-Order Attack into a First-Order Attack and Improved Rotating Substitution Box Masking with Linear Code Cosets.

PubMed

DeTrano, Alexander; Karimi, Naghmeh; Karri, Ramesh; Guo, Xiaofei; Carlet, Claude; Guilley, Sylvain

2015-01-01

Masking countermeasures, used to thwart side-channel attacks, have been shown to be vulnerable to mask-extraction attacks. State-of-the-art mask-extraction attacks on the Advanced Encryption Standard (AES) algorithm target S-Box recomputation schemes but have not been applied to scenarios where S-Boxes are precomputed offline. We propose an attack targeting precomputed S-Boxes stored in nonvolatile memory. Our attack targets AES implemented in software protected by a low entropy masking scheme and recovers the masks with 91% success rate. Recovering the secret key requires fewer power traces (in fact, by at least two orders of magnitude) compared to a classical second-order attack. Moreover, we show that this attack remains viable in a noisy environment or with a reduced number of leakage points. Eventually, we specify a method to enhance the countermeasure by selecting a suitable coset of the masks set.

Integration process of fermentation and liquid biphasic flotation for lipase separation from Burkholderia cepacia.

PubMed

Sankaran, Revathy; Show, Pau Loke; Lee, Sze Ying; Yap, Yee Jiun; Ling, Tau Chuan

2018-02-01

Liquid Biphasic Flotation (LBF) is an advanced recovery method that has been effectively applied for biomolecules extraction. The objective of this investigation is to incorporate the fermentation and extraction process of lipase from Burkholderia cepacia using flotation system. Initial study was conducted to compare the performance of bacteria growth and lipase production using flotation and shaker system. From the results obtained, bacteria shows quicker growth and high lipase yield via flotation system. Integration process for lipase separation was investigated and the result showed high efficiency reaching 92.29% and yield of 95.73%. Upscaling of the flotation system exhibited consistent result with the lab-scale which are 89.53% efficiency and 93.82% yield. The combination of upstream and downstream processes in a single system enables the acceleration of product formation, improves the product yield and facilitates downstream processing. This integration system demonstrated its potential for biomolecules fermentation and separation that possibly open new opportunities for industrial production. Copyright © 2017 Elsevier Ltd. All rights reserved.

Exploiting Small Leakages in Masks to Turn a Second-Order Attack into a First-Order Attack and Improved Rotating Substitution Box Masking with Linear Code Cosets

PubMed Central

DeTrano, Alexander; Karimi, Naghmeh; Karri, Ramesh; Guo, Xiaofei; Carlet, Claude; Guilley, Sylvain

2015-01-01

Masking countermeasures, used to thwart side-channel attacks, have been shown to be vulnerable to mask-extraction attacks. State-of-the-art mask-extraction attacks on the Advanced Encryption Standard (AES) algorithm target S-Box recomputation schemes but have not been applied to scenarios where S-Boxes are precomputed offline. We propose an attack targeting precomputed S-Boxes stored in nonvolatile memory. Our attack targets AES implemented in software protected by a low entropy masking scheme and recovers the masks with 91% success rate. Recovering the secret key requires fewer power traces (in fact, by at least two orders of magnitude) compared to a classical second-order attack. Moreover, we show that this attack remains viable in a noisy environment or with a reduced number of leakage points. Eventually, we specify a method to enhance the countermeasure by selecting a suitable coset of the masks set. PMID:26491717

Advanced Extraction of Spatial Information from High Resolution Satellite Data

NASA Astrophysics Data System (ADS)

Pour, T.; Burian, J.; Miřijovský, J.

2016-06-01

In this paper authors processed five satellite image of five different Middle-European cities taken by five different sensors. The aim of the paper was to find methods and approaches leading to evaluation and spatial data extraction from areas of interest. For this reason, data were firstly pre-processed using image fusion, mosaicking and segmentation processes. Results going into the next step were two polygon layers; first one representing single objects and the second one representing city blocks. In the second step, polygon layers were classified and exported into Esri shapefile format. Classification was partly hierarchical expert based and partly based on the tool SEaTH used for separability distinction and thresholding. Final results along with visual previews were attached to the original thesis. Results are evaluated visually and statistically in the last part of the paper. In the discussion author described difficulties of working with data of large size, taken by different sensors and different also thematically.

Unveiling the nucleon tensor charge at Jefferson Lab: A study of the SoLID case

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

Ye, Zhihong; Sato, Nobuo; Allada, Kalyan

2017-01-27

Here, future experiments at the Jefferson Lab 12 GeV upgrade, in particular, the Solenoidal Large Intensity Device (SoLID), aim at a very precise data set in the region where the partonic structure of the nucleon is dominated by the valence quarks. One of the main goals is to constrain the transversity quark distributions. We apply recent theoretical advances of the global QCD extraction of the transversity distributions to study the impact of future experimental data from the SoLID. Especially, we develop a model-independent method based on the hessian matrix analysis that allows to estimate the uncertainties of the transversity quarkmore » distributions and their tensor charge contributions extracted from the pseudo-data for the SoLID. Both u and d-quark transversity distributions are shown to be very well constrained in the kinematical region of the future experiments with the proton and the effective neutron targets.« less

Feature Extraction and Selection for Myoelectric Control Based on Wearable EMG Sensors.

PubMed

Phinyomark, Angkoon; N Khushaba, Rami; Scheme, Erik

2018-05-18

Specialized myoelectric sensors have been used in prosthetics for decades, but, with recent advancements in wearable sensors, wireless communication and embedded technologies, wearable electromyographic (EMG) armbands are now commercially available for the general public. Due to physical, processing, and cost constraints, however, these armbands typically sample EMG signals at a lower frequency (e.g., 200 Hz for the Myo armband) than their clinical counterparts. It remains unclear whether existing EMG feature extraction methods, which largely evolved based on EMG signals sampled at 1000 Hz or above, are still effective for use with these emerging lower-bandwidth systems. In this study, the effects of sampling rate (low: 200 Hz vs. high: 1000 Hz) on the classification of hand and finger movements were evaluated for twenty-six different individual features and eight sets of multiple features using a variety of datasets comprised of both able-bodied and amputee subjects. The results show that, on average, classification accuracies drop significantly ( p.

rEHR: An R package for manipulating and analysing Electronic Health Record data.

PubMed

Springate, David A; Parisi, Rosa; Olier, Ivan; Reeves, David; Kontopantelis, Evangelos

2017-01-01

Research with structured Electronic Health Records (EHRs) is expanding as data becomes more accessible; analytic methods advance; and the scientific validity of such studies is increasingly accepted. However, data science methodology to enable the rapid searching/extraction, cleaning and analysis of these large, often complex, datasets is less well developed. In addition, commonly used software is inadequate, resulting in bottlenecks in research workflows and in obstacles to increased transparency and reproducibility of the research. Preparing a research-ready dataset from EHRs is a complex and time consuming task requiring substantial data science skills, even for simple designs. In addition, certain aspects of the workflow are computationally intensive, for example extraction of longitudinal data and matching controls to a large cohort, which may take days or even weeks to run using standard software. The rEHR package simplifies and accelerates the process of extracting ready-for-analysis datasets from EHR databases. It has a simple import function to a database backend that greatly accelerates data access times. A set of generic query functions allow users to extract data efficiently without needing detailed knowledge of SQL queries. Longitudinal data extractions can also be made in a single command, making use of parallel processing. The package also contains functions for cutting data by time-varying covariates, matching controls to cases, unit conversion and construction of clinical code lists. There are also functions to synthesise dummy EHR. The package has been tested with one for the largest primary care EHRs, the Clinical Practice Research Datalink (CPRD), but allows for a common interface to other EHRs. This simplified and accelerated work flow for EHR data extraction results in simpler, cleaner scripts that are more easily debugged, shared and reproduced.

New method to enhance the extraction yield of rutin from Sophora japonica using a novel ultrasonic extraction system by determining optimum ultrasonic frequency.

PubMed

Liao, Jianqing; Qu, Baida; Liu, Da; Zheng, Naiqin

2015-11-01

A new method has been proposed for enhancing extraction yield of rutin from Sophora japonica, in which a novel ultrasonic extraction system has been developed to perform the determination of optimum ultrasonic frequency by a two-step procedure. This study has systematically investigated the influence of a continuous frequency range of 20-92 kHz on rutin yields. The effects of different operating conditions on rutin yields have also been studied in detail such as solvent concentration, solvent to solid ratio, ultrasound power, temperature and particle size. A higher extraction yield was obtained at the ultrasonic frequency of 60-62 kHz which was little affected under other extraction conditions. Comparative studies between existing methods and the present method were done to verify the effectiveness of this method. Results indicated that the new extraction method gave a higher extraction yield compared with existing ultrasound-assisted extraction (UAE) and soxhlet extraction (SE). Thus, the potential use of this method may be promising for extraction of natural materials on an industrial scale in the future. Copyright © 2015 Elsevier B.V. All rights reserved.

Steroid hormones in environmental matrices: extraction method comparison.

PubMed

Andaluri, Gangadhar; Suri, Rominder P S; Graham, Kendon

2017-11-09

The U.S. Environmental Protection Agency (EPA) has developed methods for the analysis of steroid hormones in water, soil, sediment, and municipal biosolids by HRGC/HRMS (EPA Method 1698). Following the guidelines provided in US-EPA Method 1698, the extraction methods were validated with reagent water and applied to municipal wastewater, surface water, and municipal biosolids using GC/MS/MS for the analysis of nine most commonly detected steroid hormones. This is the first reported comparison of the separatory funnel extraction (SFE), continuous liquid-liquid extraction (CLLE), and Soxhlet extraction methods developed by the U.S. EPA. Furthermore, a solid phase extraction (SPE) method was also developed in-house for the extraction of steroid hormones from aquatic environmental samples. This study provides valuable information regarding the robustness of the different extraction methods. Statistical analysis of the data showed that SPE-based methods provided better recovery efficiencies and lower variability of the steroid hormones followed by SFE. The analytical methods developed in-house for extraction of biosolids showed a wide recovery range; however, the variability was low (≤ 7% RSD). Soxhlet extraction and CLLE are lengthy procedures and have been shown to provide highly variably recovery efficiencies. The results of this study are guidance for better sample preparation strategies in analytical methods for steroid hormone analysis, and SPE adds to the choice in environmental sample analysis.

Frequency of data extraction errors and methods to increase data extraction quality: a methodological review.

PubMed

Mathes, Tim; Klaßen, Pauline; Pieper, Dawid

2017-11-28

Our objective was to assess the frequency of data extraction errors and its potential impact on results in systematic reviews. Furthermore, we evaluated the effect of different extraction methods, reviewer characteristics and reviewer training on error rates and results. We performed a systematic review of methodological literature in PubMed, Cochrane methodological registry, and by manual searches (12/2016). Studies were selected by two reviewers independently. Data were extracted in standardized tables by one reviewer and verified by a second. The analysis included six studies; four studies on extraction error frequency, one study comparing different reviewer extraction methods and two studies comparing different reviewer characteristics. We did not find a study on reviewer training. There was a high rate of extraction errors (up to 50%). Errors often had an influence on effect estimates. Different data extraction methods and reviewer characteristics had moderate effect on extraction error rates and effect estimates. The evidence base for established standards of data extraction seems weak despite the high prevalence of extraction errors. More comparative studies are needed to get deeper insights into the influence of different extraction methods.

Rapid method for the measurement of circulating thyroid hormones in low volumes of teleost fish plasma by LC-ESI/MS/MS

PubMed Central

Noyes, Pamela D.; Lema, Sean C.; Roberts, Simon C.; Cooper, Ellen M.

2014-01-01

Thyroid hormones are critical regulators of normal development and physiological functioning in all vertebrates. Radioimmunoassay (RIA) approaches have been the method of choice for measuring circulating levels of thyroid hormones in vertebrates. While sensitive, RIA-based approaches only allow for a single analyte measurement per assay, can lack concordance across platforms and laboratories, and can be prone to analytical interferences especially when used with fish plasma. Ongoing advances in liquid chromatography tandem mass spectrometry (LC/MS/MS) have led to substantial decreases in detection limits for thyroid hormones and other biomolecules in complex matrices, including human plasma. Despite these advances, current analytical approaches do not allow for the measurement of native thyroid hormone in teleost fish plasma by mass spectrometry and continue to rely on immunoassay. In this study, we developed a new method that allows for the rapid extraction and simultaneous measurement of total T4 (TT4) and total T3 (TT3) in low volumes (50 μL) of fish plasma by LC/MS/MS. Methods were optimized initially in plasma from rainbow trout (Oncorhynchus mykiss) and applied to plasma from other teleost fishes, including fathead minnows (Pimephales promelas), mummichogs (Fundulus heteroclitus), sockeye salmon (Oncorhynchus nerka), and coho salmon (Oncorhynchus kisutch). Validation of method performance with T4- and T3-spiked rainbow trout plasma at 2 and 4 ng/mL produced mean recoveries ranging from 82 to 95 % and 97 to 105 %, respectively. Recovery of 13C12-T4 internal standard in plasma extractions was: 99±1.8 % in rainbow trout, 85±11 % in fathead minnow, 73±5.0 % in mummichog, 73±1.7 % in sockeye salmon, and 80±8.4 % in coho salmon. While absolute levels of thyroid hormones measured in identical plasma samples by LC/MS/MS and RIA varied depending on the assay used, T4/T3 ratios were generally consistent across both techniques. Less variability was measured among samples subjected to LC/MS/MS suggesting a more precise estimate of thyroid hormone homeostasis in the species targeted. Overall, a sensitive and reproducible method was established that takes advantage of LC/MS/MS techniques to rapidly measure TT4 and TT3 with negligible interferences in low volumes of plasma across a variety of teleost fishes. PMID:24343452

Inhibitory effect of Clitoria ternatea flower petal extract on fructose-induced protein glycation and oxidation-dependent damages to albumin in vitro.

PubMed

Chayaratanasin, Poramin; Barbieri, Manuel Alejandro; Suanpairintr, Nipattra; Adisakwattana, Sirichai

2015-02-18

The accumulation of advanced glycation end products (AGEs) in body tissue has been implicated in the progression of age-related diseases. Inhibition of AGE formation is the imperative approach for alleviating diabetic complications. Clitoria ternatea extract (CTE) has been demonstrated to possess anti-diabetic activity. However, there is no scientific evidence supporting its anti-glycation activity. The objective of this study was to determine the inhibitory effect of CTE on fructose-induced formation of AGEs and protein oxidation. Antioxidant activity of CTE was also assessed by various methods. The aqueous extract of CTE (0.25-1.00 mg/ml) was measured for the content of total phenolic compounds, flavonoid, and anthocyanin by Folin-Ciocalteu assay, AlCl3 colorimetric method, and pH differential method, respectively. The various concentrations of CTE were incubated with BSA and fructose at 37°C for 28 days. The formation of fluorescent AGEs, the level of fructosamine, protein carbonyl content, and thiol group were measured. The in vitro antioxidant activity was measured by the 1,1-diphenyl 2-picrylhydrazyl (DPPH) scavenging activity, trolox equivalent antioxidant capacity (TEAC), ferric reducing antioxidant power (FRAP), hydroxyl radical scavenging activity (HRSA), superoxide radical scavenging activity (SRSA), and ferrous ion chelating power (FICP). The results demonstrated that the content of total phenolics, flavonoids and total anthocyanins in CTE was 53 ± 0.34 mg gallic acid equivalents/g dried extract, 11.2 ± 0.33 mg catechin equivalents/g dried extract, and 1.46 ± 0.04 mg cyanidin-3-glucoside equivalents/g dried extract, respectively. Moreover, CTE (0.25-1.00 mg/ml) significantly inhibited the formation of AGEs in a concentration-dependent manner. CTE also markedly reduced the levels of fructosamine and the oxidation of protein by decreasing protein carbonyl content and preventing free thiol depletion. In the DPPH radical scavenging activity and SRSA, CTE had the IC50 values of 0.47 ± 0.01 mg/ml and 0.58 ± 0.04 mg/ml. Furthermore, the FRAP and TEAC values of CTE were 0.38 ± 0.01 mmol FeSO4 equivalents/mg dried extract and 0.17 ± 0.01 mg trolox equivalents/mg dried extract. However, CTE showed weak scavenging activity on hydroxyl radical and a weak antioxidant iron chelator. The results showed that CTE has strong antiglycation and antioxidant properties and might have therapeutic potentials in the prevention of AGE-mediated diabetic complications.

Nondestructive Evaluation of Adhesive Bonds via Ultrasonic Phase Measurements

NASA Technical Reports Server (NTRS)

Haldren, Harold A.; Perey, Daniel F.; Yost, William T.; Cramer, K. Elliott; Gupta, Mool C.

2016-01-01

The use of advanced composites utilizing adhesively bonded structures offers advantages in weight and cost for both the aerospace and automotive industries. Conventional nondestructive evaluation (NDE) has proved unable to reliably detect weak bonds or bond deterioration during service life conditions. A new nondestructive technique for quantitatively measuring adhesive bond strength is demonstrated. In this paper, an ultrasonic technique employing constant frequency pulsed phased-locked loop (CFPPLL) circuitry to monitor the phase response of a bonded structure from change in thermal stress is discussed. Theoretical research suggests that the thermal response of a bonded interface relates well with the quality of the adhesive bond. In particular, the effective stiffness of the adhesive-adherent interface may be extracted from the thermal phase response of the structure. The sensitivity of the CFPPLL instrument allows detection of bond pathologies that have been previously difficult-to-detect. Theoretical results with this ultrasonic technique on single epoxy lap joint (SLJ) specimens are presented and discussed. This technique has the potential to advance the use of adhesive bonds - and by association, advanced composite structures - by providing a reliable method to measure adhesive bond strength, thus permitting more complex, lightweight, and safe designs.

LC-MS determination of steroidal glycosides from Dioscorea deltoidea Wall cell suspension culture: Optimization of pre-LC-MS procedure parameters by Latin Square design.

PubMed

Sarvin, Boris; Fedorova, Elizaveta; Shpigun, Oleg; Titova, Maria; Nikitin, Mikhail; Kochkin, Dmitry; Rodin, Igor; Stavrianidi, Andrey

2018-03-30

In this paper, the ultrasound assisted extraction method for isolation of steroidal glycosides from D. deltoidea plant cell suspension culture with a subsequent HPLC-MS determination was developed. After the organic solvent was selected via a two-factor experiment the optimization via Latin Square 4 × 4 experimental design was carried out for the following parameters: extraction time, organic solvent concentration in extraction solution and the ratio of solvent to sample. It was also shown that the ultrasound assisted extraction method is not suitable for isolation of steroidal glycosides from the D. deltoidea plant material. The results were double-checked using the multiple successive extraction method and refluxing extraction. Optimal conditions for the extraction of steroidal glycosides by the ultrasound assisted extraction method were: extraction time, 60 min; acetonitrile (water) concentration in extraction solution, 50%; the ratio of solvent to sample, 400 mL/g. Also, the developed method was tested on D. deltoidea cell suspension cultures of different terms and conditions of cultivation. The completeness of the extraction was confirmed using the multiple successive extraction method. Copyright © 2018 Elsevier B.V. All rights reserved.

Selection of an Appropriate Protein Extraction Method to Study the Phosphoproteome of Maize Photosynthetic Tissue

PubMed Central

Luís, Inês M.; Alexandre, Bruno M.; Oliveira, M. Margarida

2016-01-01

Often plant tissues are recalcitrant and, due to that, methods relying on protein precipitation, such as TCA/acetone precipitation and phenol extraction, are usually the methods of choice for protein extraction in plant proteomic studies. However, the addition of precipitation steps to protein extraction methods may negatively impact protein recovery, due to problems associated with protein re-solubilization. Moreover, we show that when working with non-recalcitrant plant tissues, such as young maize leaves, protein extraction methods with precipitation steps compromise the maintenance of some labile post-translational modifications (PTMs), such as phosphorylation. Therefore, a critical issue when studying PTMs in plant proteins is to ensure that the protein extraction method is the most appropriate, both at qualitative and quantitative levels. In this work, we compared five methods for protein extraction of the C4-photosynthesis related proteins, in the tip of fully expanded third-leaves. These included: TCA/Acetone Precipitation; Phenol Extraction; TCA/Acetone Precipitation followed by Phenol Extraction; direct extraction in Lysis Buffer (a urea-based buffer); and direct extraction in Lysis Buffer followed by Cleanup with a commercial kit. Protein extraction in Lysis Buffer performed better in comparison to the other methods. It gave one of the highest protein yields, good coverage of the extracted proteome and phosphoproteome, high reproducibility, and little protein degradation. This was also the easiest and fastest method, warranting minimal sample handling. We also show that this method is adequate for the successful extraction of key enzymes of the C4-photosynthetic metabolism, such as PEPC, PPDK, PEPCK, and NADP-ME. This was confirmed by MALDI-TOF/TOF MS analysis of excised spots of 2DE analyses of the extracted protein pools. Staining for phosphorylated proteins in 2DE revealed the presence of several phosphorylated isoforms of PEPC, PPDK, and PEPCK. PMID:27727304

Blast Testing Issues and TBI: Experimental Models That Lead to Wrong Conclusions.

PubMed

Needham, Charles E; Ritzel, David; Rule, Gregory T; Wiri, Suthee; Young, Leanne

2015-01-01

Over the past several years, we have noticed an increase in the number of blast injury studies published in peer-reviewed biomedical journals that have utilized improperly conceived experiments. Data from these studies will lead to false conclusions and more confusion than advancement in the understanding of blast injury, particularly blast neurotrauma. Computational methods to properly characterize the blast environment have been available for decades. These methods, combined with a basic understanding of blast wave phenomena, enable researchers to extract useful information from well-documented experiments. This basic understanding must include the differences and interrelationships of static pressure, dynamic pressure, reflected pressure, and total or stagnation pressure in transient shockwave flows, how they relate to loading of objects, and how they are properly measured. However, it is critical that the research community effectively overcomes the confusion that has been compounded by a misunderstanding of the differences between the loading produced by a free field explosive blast and loading produced by a conventional shock tube. The principles of blast scaling have been well established for decades and when properly applied will do much to repair these problems. This paper provides guidance regarding proper experimental methods and offers insights into the implications of improperly designed and executed tests. Through application of computational methods, useful data can be extracted from well-documented historical tests, and future work can be conducted in a way to maximize the effectiveness and use of valuable biological test data.

Semi Automated Land Cover Layer Updating Process Utilizing Spectral Analysis and GIS Data Fusion

NASA Astrophysics Data System (ADS)

Cohen, L.; Keinan, E.; Yaniv, M.; Tal, Y.; Felus, A.; Regev, R.

2018-04-01

Technological improvements made in recent years of mass data gathering and analyzing, influenced the traditional methods of updating and forming of the national topographic database. It has brought a significant increase in the number of use cases and detailed geo information demands. Processes which its purpose is to alternate traditional data collection methods developed in many National Mapping and Cadaster Agencies. There has been significant progress in semi-automated methodologies aiming to facilitate updating of a topographic national geodatabase. Implementation of those is expected to allow a considerable reduction of updating costs and operation times. Our previous activity has focused on building automatic extraction (Keinan, Zilberstein et al, 2015). Before semiautomatic updating method, it was common that interpreter identification has to be as detailed as possible to hold most reliable database eventually. When using semi-automatic updating methodologies, the ability to insert human insights based knowledge is limited. Therefore, our motivations were to reduce the created gap by allowing end-users to add their data inputs to the basic geometric database. In this article, we will present a simple Land cover database updating method which combines insights extracted from the analyzed image, and a given spatial data of vector layers. The main stages of the advanced practice are multispectral image segmentation and supervised classification together with given vector data geometric fusion while maintaining the principle of low shape editorial work to be done. All coding was done utilizing open source software components.

Feasibility of cytological specimens for ALK fusion detection in patients with advanced NSCLC using the method of RT-PCR.

PubMed

Wang, Yan; Liu, Yu; Zhao, Chao; Li, Xuefei; Wu, Chunyan; Hou, Likun; Zhang, Shijia; Jiang, Tao; Chen, Xiaoxia; Su, Chunxia; Gao, Guanghui; Li, Wei; Wu, Fengying; Li, Aiwu; Ren, Shengxiang; Zhou, Caicun; Zhang, Jun

2016-04-01

Histological tissues are preferred for anaplastic lymphoma kinase (ALK) fusion detection in non-small cell lung cancer (NSCLC). The aim of this study was to evaluate the feasibility of cytological sample as an alternative specimen for ALK fusion testing in patients with advanced NSCLC. Advanced NSCLC patients with cytological specimens or tumor tissue who had their ALK fusion status detected by the method of reverse transcriptase polymerase chain reaction (RT-PCR) in Shanghai Pulmonary Hospital, Tongji University were included into this study. The efficacy was evaluated in those with ALK fusion positive and received the therapy of crizotinib. 1274 patients were included in this study. Among them, 108 patients were ALK RT-PCR positive and 69 of them received crizotinib treatment. Among 1002 patients with cytological specimens, the average concentration of RNA extracted from cytological specimens was 60.99 ng/μl (95% confidence interval [CI], 55.56-66.60) and the incidence rate of ALK fusion was 8.3% (83/1002), which were similar to 63.16 ng/μl (95% CI, 51.88-76.34) (p=0.727) and 9.2% (25/272, p=0.624) in 272 patients with tumor tissue. Also, there were no statistically significant differences regarding to the objective response rate (ORR) (62.0% vs. 42.1%, p=0.177) and the median progression free survival (mPFS) [8.6 months (95% CI 7.30-9.84) vs. 7.0 months (95% CI 4.54-9.47), p=0.736] in patients of cytological group and tissue group after the treatment of crizotinib. Cytological specimens showed a high feasibility to detect ALK fusion status, which could be regarded as alternative samples for ALK fusion detection by the method of RT-PCR in patients with advanced NSCLC. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.